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1. oaoa aaa aaa 7 3 4 Speeding up the process ooa aaa nn nn 7 4 Exporting graphs in iia toa do a a e ea BR ORS A 7 5 Exporting Maps e s aaa dida as a Ge ae ee Gd 8 Curation and Administration 8 1 Laboratory workflow lt 2 4 0 aa cda o Be oe a oe lach 8 2 Barcode si a eon ee Baga ca A ta eke ra ete ae Rolph Bye 8 21 Sample labels E bea ote oe ea E 8 2 2 BoxlabDelstte pes A de ie GA 8 2 3 Series barcodes nics dur e RE a e o 8 3 Storage DOXES ret tran ic e o ne e A aw bine a a 8 3 1 Creating and editing boxes 0 a 8 3 2 Inventory e ee a ee a ee eed A ee a A 8 3 3 Checking boxes in and out 2 on 8 3 4 Locating samples r a e 2 2 04 sa ee ee re Be 9 Indexing 9 1 Types of index di sete eats kek ae en E Ba alee rs a 9 11 Exponential Index 2 2 as wee MR A ee ees a E E de 9 1 2 Polynomial Index ceci ir Sana are 9 13 Horizontal Line Index 2 2 o OA Floating index eii Oo he ra el Ae ee ae ae a 9 1 5 High Pass Filter Index 2 oo on 9 1 6 Cubic Spline Index ooa aaa 9 2 Indexing data een ne ns A fk ho o ce eek ee Dd alge ag 10 Crossdating and chronology building 10 1 Algorithms ica Werner Ph ia A ES ee A i Se ae LOT COE E AE cee Ae NND hE Bie a da de 101 2 rend 24 4 mina a fe OP ES lee Dan ey a ate ee Mk 10 1 3 Weiserjahre 4 tasa a Gok om BOs Reg heehee ee ere a amp TOLA IRV alue is a eee kk der a eh A de Go alee A oe 10 2 Crossdating Series Beh Lak GPE APO AR once el tly eters B
2. e C YMT 546 A A C 1001 1173 n 173 Raw 2 11 10 25 2010 12 55 y De File Edit Administration View Tools Graph Help Data Metadata A YMT as Metadata for Object amb Yenikapi Metro Change Y Object General a Object Title Istanbul Yenikapi Metro Element Comments X Type Site 7 Description Sample Files Creator Owner Radius Coverage v Location geometry Series 41 00576 28 95174 Location geometry GML representation of a location Can be either a point to represent a particular location or a polygon to represent an area or a geographical extent bounding box ls Click the lock to edit this Object Figure 4 2 Example of the metadata dialog The screen is showing the details of a TRiDaS object Note that the location geometry field is highlighted and so a description of what is expected in this field is given below revert to the previously chosen entry change the existing entry to a different one from the database or create a new record Please note that the content of these metadata screens is kept read only by default To edit the values you must first click the padlock icon to unlock the fields When you have finished making changes you need to press the save button to write the changes to the database before moving to another metadata screen Very few of the metadata fields in the TRiDaS data model are mandatory but a few are In this case these fiel
3. gt y Zag This index is not used for crossdataing because dividing each value by the same value doesn t change the shape of the curve only its magnitude A horizontal line index is however useful because every element in a sum must use the same units either raw or indexed Therefore if you want to include a raw sample with an indexed sample then a horizontal line index can be used to convert the raw sample without otherwise altering the shape of the curve 9 1 4 Floating Index This is a running average of the 11 surrounding years The adaptive index is generally used as a last resort when both exponential and a high degree polynomial have failed It is simply the average of the eleven surrounding years gt ind 1 11 data 1 5 data _4 ee eo dataj 4 data 5 This index was originally called floating average probably in reference to the fact that the index curve floats around not following any explicit y f x type formula But people tended to call it floating and then floating point which means something very different You might still hear people calling this index by these other names 9 15 High Pass Filter Index The high pass index is a more general case of the adaptive index Instead of simply taking the average of 11 values it takes a weighted average It s an example of a high pass filter because high frequency signals can pass through but low frequency signals are filtered out The default is
4. 506 916 619 968 637 519 191066 19 576 231116 241124 241154 24 24 24 782 889 889 241132 24 24 24 24 24 24 25 841 944 981 738 902 515 739 241046 241271 24 783 241261 241111 231106 231118 23 690 191146 191272 1 209 11611 21421 21042 21591 31479 31140 3 4 982 964 41097 5 5 847 962 51265 61007 8 940 101075 10 10 872 741 101049 10 843 101388 121181 12 12 13 681 861 846 141028 14 16 677 790 191252 20 979 231092 241225 241059 241221 24 24 955 999 241047 241209 24 24 24 24 24 25 871 709 785 885 670 750 241182 241123 241169 241146 241019 231123 231144 23 684 191362 191231 1 313 11369 21009 2 728 22178 3 990 31005 3 973 41003 4 5 5 973 961 970 51261 61097 8 10 10 10 936 952 959 812 101016 101057 101194 12 12 12 13 931 887 861 838 141051 16 710 161046 19 971 231148 231150 241135 241270 241424 241158 24 24 991 978 241053 24 24 24 24 24 25 24 989 949 742 841 855 963 701 241116 241096 24 24 920 916 231089 231268 23 901 191288 191083 1 883 11273 21089 2 781 21594 31063 31340 31147 41289 4 973 51295 51031 51019 61290 81131 10 897 101138 101126 10 970 101040 101260 12 992 12 708 12102
5. The remaining bytes in the file contain the actual data values stored as integer byte pairs All data are stored in multiples of 128 bytes If the number of data bytes given in the header at position 45 46 is not a multiple of 128 the file is padded with extra bytes accordingly Padded bytes should be ignored D 4 1 Ring widths Ring widths are stored in hundredths of a millimetre in the same order as the tree had been grown When working with archaeological or geological wood it might occur that a particular ring is damaged and therefore its width cannot be determined precisely To indicate that fact and to exclude this particular ring from further calculations its measured width is stored negative In the CATRAS program a negative ring width will be taken into account neither in the calculation of tree curves and chronologies nor in the statistics or in comparisons with other series D 4 2 Chronologies Chronology files are indicated at position 84 in the file header and contain additional data in respect to raw data files After the block of ring width data three additional data blocks follow Firstly the number of ring widths averaged at a particular position follows the sample depth Then the number of series with the same trend between subsequent ring widths at a particular position follows Then the number of series with the opposite trend between subsequent ring widths at a particular position follows All data blocks are stored in multiple
6. Z cd tmp Z wget http www tellervo org url of the updated package deb Z sudo dpkg install tellervo x x x deb Installation 11 The first line changes your current directory to the temporary folder The second command downloads the new package from the Tellervo server Make sure you enter the correct URL to the package you are upgrading to The final command installs the new package Again make sure you have the correct file name specified here If all goes well your webservice and database will be upgraded to the latest version and the server test routine will run to confirm all is correct If the server gives you any errors or warnings please contact the developers for further assistance 1 5 Uninstalling We understand that Tellervo will never suit the requirements of all users but as an open source product we would really appreciate feedback as to why it didn t work for you Without this feedback it is difficult to prioritize future development 1 5 1 Tellervo desktop application For Windows users Tellervo desktop can be uninstalled using the standard add remove programs feature in control panel or via the item in the Tellervo start menu Mac users should simply delete the application from their applications folder Linux users should use their prefered package management tool e g from the command line 4 sudo dpkg remove tellervo 1 5 2 Tellervo server A Please note that uninstalling the Tellervo server will delete
7. 1 2 4 2 1 meaning Indexing 47 gt ind 1 10 data _2 2 data _ 4 data 2 data 1 data 2 This comes from Cook and Peters 1981 who used it as a discrete filter before moving to a cubic spline Note that almost half 4 10 of the computed value is simply its old value The high pass index is nearly the same as the input so the x values are usually the lowest therefore do not choose this index solely on a low x value 9 1 6 Cubic Spline Index Cubic splines are a very specific type of high pass filter A cubic spline curve is created by combining a collection of cubic 3rd degree polynomial functions There are many methods for constructing cubic splines through a dataset The algorithm used by Tellervo has a parameter s which controls how tightly the spline fits the data A lower value fits the data more tightly a higher value fits the data more loosely Therefore s 0 fits the data exactly while s 1 is a simple line A good starting point for dendro data seems to be around s 171016 Cubic splines were first used for dendro by Cook and Peters 1981 using an algorithm from Reinsch 1967 You can change the s value used for the subic spline in the preferences You might use a cubic spline in the same cases you would use a high pass filter e g when the sample doesn t generally follow an exponential or polynomial curve very well perhaps due to a fire scar 9 2 Indexing data To index your data first you
8. If you are importing a file that contains entities that you don t already have stored in your database then you will need to clean them up and save them Select the most senior entity that needs to be imported in the TRiDaS hierarchy panel The metadata gleaned by Tellervo from the legacy file will be previewed in the metadata panel on the right Next click the lock icon at the bottom of the metadata panel and the metadata will become editable You will then need to spend some time filling out and cleaning up the metadata for this entity An important part of the import process is the standardization of the metadata Take for instance the example of the taxon Most legacy files have some method for indicating what species a file is about but most do so by allowing the user to type in a free text field The TRICYCLE libraries that Tellervo uses are able to read such fields but the red oak Quercus rubra may be represented in many ways oak red oak Oak Quercus Quercus sp Quercus rubra QUER etc not to mention the scientific synonyms for the species e g Quercus acerifolia Quercus ambigua Quercus angulizana to name but a few Many users would know that these represent the same species but if you were to query your database for Quercus rubra you would miss records stored under the other names It is therefore essential to standardize them to a single dictionary of terms In the case of species names Tellervo use the Catalogue of Life Bisb
9. MergeSamples As for MergeObjects but for samples MergeRadii As for MergeObjects but for radii 17 4 Complex database functions Beyond the standard database functions discussed in section 17 3 the Tellervo database uses PLJava perform more complex tasks PLJava means that we can leaverage the full power of Java to perform calculations and analyses on the database During the standard build process a small jar called tellervo pljava jar is created This contains classes from the packages org tellervo cpgdb and lorg tellervo indexing This jar is stored within the sqlj schema of the Tellervo database and the classes called as required by Postgres functions So unless you make changes to files within these packages you have no need to worry about PLJava If you do need to make changes then you will need to add the new jar to the database To do this you use the pljava functions within Postgres The main calls you need to make are Tellervo Database 97 Z SELECT sqlj replace_jar file usr share tellervo server tellervo pljava jar tellervo_jar false SELECT sqlj set_classpath cpgdb tellervo_jar The first replaces the existing jar with the one specified PLJava requires a name for the jar to use within the database and so we use tellervo_jar The second command sets the classpath for the specified schema the first argument to the contents of the specified jar the second argument Once you
10. lt c tellervo gt 15 4 Reading records The method for reading records from the Tellervo database is largely the same for any of the types of data the server handles The basic template for a read request is as follows lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmlins c http ww tellervo org schema 1 0 gt lt c request type read format gt lt E2entiny type 7 id gt lt c request gt lt c tellervo gt The entity type is one of project object element sample radius measurementSeries derivedSeries box securityUser or securityGroup The id attribute should be the database identifier for the entity you would like to read In Tellervo these are typically a UUID like this 339d8ea6 7448 11e1 ad85 9b6d022add7a The format attribute should be one of minimal summary standard or comprehensive depending on how much detail you require about the entity Keep in mind that a comprehensive request is likely to take much longer to fulfill than a minimal request so it s best for your user if you use the simplest request that fulfills your need 15 5 Deleting records The method for deleting records in Tellervo is very similar to reading records You simply use the request type delete and specify the entity type and id The basic template for a delete request looks like this lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmins c http w tellervo or
11. 144 130 126 99 196 137 75 87 122 122 745 351 263 217 185 139 118 56 117 114 111 130 204 129 117 69 109 114 182 HLO1 04 9002 1510 13 719 238 190 110 160 101 52 127 90 85 115 104 580 135 194 115 112 93 114 150 130 123 121 164 466 172 183 99 152 113 138 189 126 116 111 110 Appendix X WinDENDRO Format name WinDENDRO Other name s None known Type Text file Extension s txt Read write support Read only Reference implementation WinDENDRO Data metadata Data with some structured metadata Calendar type Gregorian Absolute dating support Yes Undated series support Yes Relative dating support No Multi series support Yes Original designer Regent Instruments X 1 Description WinDENDRO format is a dendro text file format designed by Regent Instruments for their WinDENDRO software Regent Instruments claims the format is proprietary Although it is unclear whether such a claim is legally binding for a plain text file the authors of DendroFilelOLib have decided to comply by not implementing a WinDENDRO format writer However in the interests of the dendro community and to ensure users can gain access to their data DendroFilelOLib does include support for reading WinDENDRO format files WinDENDRO files differ from most other formats in that they contain a great deal of information specific to the image used to measure the sample The WinDENDRO software
12. 2 21 2 16 2 0 1 0 1 0 1 0 1 0 2 0 2 2 0 2 0 91 1 46 1 64 1 100 1 62 2 44 2 21 2 27 1 65 1 57 1 129 1 67 2 29 2 63 2 27 2 20 1 1 0 0 1 1 0 0 1 0 2 0 2 0 2 1 1 0 1 0 1 0 1 1 0 2 0 2 0 1 1 1 0 NW tower 1AB DATING R UNMEAS PRE 1 1 0 1 0 1 0 0 1 0 2 2 0 2 0 0 1 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Appendix H DendroDB DendroDB None known Text file dat Read only DendroDB website Data and some structured metadata Astronomical Absolute dating support Yes Undated series support No Relative dating support No Multi series support Yes Original designer Simon Brewer H 1 Description The DendroDB format is an export file format produced by the DendroDB website database There is no known software that can natively read DendroDB files so a writer for this format has not been developed The format is self explanatory beginning with a copyright line followed by 7 metadata lines then the data itself There are eight possible data variables Total width Earlywood width Latewood width Min Density Max Density Earlywood density Latewood density Average density Ring width data is provided in microns but the units for density measurements are not document As of Feb 2011 the DendroDB
13. 2 Basic Permissions All rights granted under this License are granted for the term of copyright on the Program and are irrevocable provided the stated conditions are met This License explicitly affirms your unlimited permission to run the unmodified Program The output from running a covered work is covered by this License only if the output given its content constitutes a covered work This License acknowledges your rights of fair use or other equivalent as provided by copyright law You may make run and propagate covered works that you do not convey without conditions so long as your license otherwise remains in force You may convey covered works to others for the sole purpose of having them make modifications exclusively for you or provide you with facilities for running those works provided that you comply with the terms of this License in conveying all material for which you do not control copyright Those thus making or running the covered works for you must do so exclusively on your behalf under your direction and control on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you Conveying under any other circumstances is permitted solely under the conditions stated below Sublicensing is not allowed section 10 makes it unnecessary GNU General Public License 175 3 Protecting Users Legal Rights From Anti Circumvention Law No covered work shall be deemed part of
14. 69 55 57 43 55 68 97 98 43 54 47 75 77 70 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer Appendix N ODF Spreadsheet ODF Spreadsheet ODF ODS OpenDocument Spreadsheet OpenOffice org Spreadsheet XML file ods Read and write ISO IEC 26300 2006 Data only Gregorian Yes No No Yes OASIS consortium N 1 Description The OpenDocument Format ODF spreadsheet format is an XML based specification developed by the Or ganization for the Advancement of Structured Information Standards OASIS consortium It should not be confused with the similarly named Office Open XML format developed by Microsoft The ODF spreadsheet format is an open standard which can be read by most modern spreadsheet applications including MS Excel OpenOffice org and Google Docs Support for ODF spreadsheets in TRICYCLE is necessarily limited to a particular layout of spreadsheet Row 1 Header names for each column Column A Year values gt Column B One column for each series containing data values Cells are left empty if no data is available for a series because it does not extend to a particular year Data must be continuous for each series so missing unmeasured rings should be included as zero Please see the Excel sec
15. The style of a ATEX document is handled separated enabling the author to concentrate on content By removing the possibility for authors to tinker with font sizes etc ATEX forces you to create clear well structured documents For further details see http en wikibooks org wiki LaTeX The master document is Documentation tellervo manual tex and imports each chapter file To build the documentation you will need a editor to update and compile to PDF On Linux would suggest Kile on MacOSX TeXShop and on Windows WinEdt To add or edit bibliography entries you will also need a BIBTEX editor such as JabRef or BibDesk Images specific to the documentation should be stored in Documentation Images but you will also automat ically have access to the image and icon resources in the application itself This can be useful for instance when illustrating what icon a user needs to click for perform a task To reference a icon for instance you can use the path Icons 48x48 myicon png ATEX has fantastic cross referencing and citation functionality built in Please follow the lead of the existing documentation 13 15 Recording screencast tutorials One way we are trying to support users is by making clear video screencast tutorials of the major workflows in Tellervo will describe the steps require to use a combination of ffmpeg x11grab and Pitivi to do this in Linux but there are many other tools available so if you prefer to use them
16. There is therefore one less weiserjahre value in the final row than there are ring widths The final line of Corina data files contains the author s name preceded by a tilde 36 37 38 39 40 41 42 43 Corina Legacy 117 G 2 Example file Trebenna Byzantine Fortress NW tower ID 907010 NAME Trebenna UNMEAS_POST 1 FILENAME G DATA TRB TRBI1AB SUM TYPE S SPECIES Juniperus sp FORMAT R TERMINAL vv CONTINUOUS N QUALITY RECONCILED Y DATA 1001 125 219 207 139 1 1 1 4 1010 71 132 74 150 75 1 1 1 4 _ 1 1020 147 78 89 126 73 1 1 1 4 1 1030 149 155 122 126 53 1 1 1 1 1 1040 67 101 132 102 40 2 2 2 2 2 1050 30 44 46 40 34 2 2 2 2 2 1060 62 38 22 26 26 2 2 2 2 2 1070 17 18 50 21 33 2 2 2 2 2 1080 18 11 9 8 9990 ey ELEMENTS G DATA TRB TRB1A REC G DATA TRB TRB1B REC weiserjahre 1001 1 0 0 1 0 1 0 1 1010 1 0 0 1 1 0 0 1 1 0 1020 0 1 1 0 1 0 0 1 1 0 1030 1 0 0 1 1 0 0 1 1 1 1040 2 0 2 0 0 2 0 2 2 0 1050 2 0 1 1 0 2 0 2 1 1 1060 0 2 0 2 2 0 1 1 0 2 1070 1 1 2 0 0 2 2 0 0 1 1080 0 1 0 1 0 1 Unknown User Byzantine Fortress 1AB PITH 62 107 1 1 156 122 1 1 121 67 1 1 136 90 1 1 67 42 2 2 61 55 2 2 28 37 2 2 12 L 2 2 1 0 1 0 1 0 1 0 2 0 2 0 2 0 0 2 29 1 81 1 71 1 65 1 36 2 29
17. W 4 R made PB 22 6 2004 Zm gt ZzZzZzoon nnn x D 3 pal o YO S un v J 391 454 309 314 270 273 229 319 267 276 128 163 22 269 214 201 218 199 198 209 156 177 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer R 1 Description Appendix R Topham Topham Instrument format Text file txt Read and write Not known Data only n a No Yes No No John Topham The Topham format is probably the most simplistic of formats consisting of just a column of decimal data values and no metadata whatsoever Each data value is a decimal ring width in millimetres R 2 Example file 42 38 34 09 62 08 60 64 125 18 42 38 WWWWNHWWW www Format name Other name s Type TRiDaS Tree Ring Data Standard TRiDaS XML Text file Extension s xml Read write support Read and write Reference implementation TRICYCLE Data metadata Data and structured metadata Calendar type Gregorian Absolute dating support Yes Undated series support Yes Relative dating support Yes Multi series support Yes Appendix S TRiDaS Original designer Esther Jansma Peter Brewer and Ivo Zandhuis S 1 Description TRiDaS Tree Ring Data Standard see http www tridas org is a data fo
18. WaldKante gt TreeNo gt WoodMaterialType Unit WorkTraces gt UnmeasuredInnerRings The meaning of many of these keywords is fairly self explanatory but others are a little more obscure As there is no data typing or validation the format of the contents of these fields cannot be predicted This is particularly a problem when trying to compare fields such as Latitude Longitude and FirstMeasurementDate but is especially a problem when comparing files produced in different labs The header section is followed by a data section denoted by a line containing the keyword DATA followed by the type of data present which can be one of Tree HalfChrono Chrono Single Double Quad Tree HalfChrono and Chrono are the original keywords supported by early versions of TSAP but these are now deprecated in preferences of the more generic Single Double and Quad terms The terms Single Double and Quad are largely interchangeable with Tree HalfChrono and Chrono respectively but not completely Double can refer to both Tree and HalfChrono format data When the newer terms are used the header keyword DataFormat is used to record whether the data is equivalent to Tree HalfChrono or Chrono Single format data is typically used for storing raw measurement series Each data line contains 10 data values each being a left space padded integer taking up 6 characters Any spare data values in the final data line are filled with zeros Alternatively it app
19. full graphical interface Unlike Windows there are a number of different graphical interfaces or desktops to The Tellervo server 55 choose from in Linux the most popular being Gnome and KDE To install one of these you need to type one of the commands listed below The first line installs Gnome and the second KDE Windows users that are new to Linux may find KDE more familiar but Apple users may be more at home with Gnome Z sudo apt get install ubuntu desktop Z sudo apt get install kubuntu desktop 11 4 Security The basic installation of the Tellervo server includes the standard configuration for Apache PHP and Post greSQL Although these products are considered secure by default there are a number of measures that can be taken to make them more so If your server is only accessible within your local intranet e g behind a robust firewall then you may not feel it necessary to modify the standard setup Precautions may be deemed more important if you server is accessible from the internet In this case it would be wise to contact your local network administrator for further information 11 4 1 Usernames and passwords There are a number of default usernames and passwords setup on your server If your server is accessible for the internet we strongly advise you to change these defaults and anyone with knowledge of the Tellervo server could access and compromise your machine System user these are the credentials you use to log
20. not continuous QUALITY either one unmeasured ring more than one unmeasured ring FORMAT either R raw or indexed p gt INDEX_TYPE type of index used RECONCILED Y or N indicating whether the series has been reconciled against another series The data section comes next and this always starts with the line DATA and for reasons lost in time there are nine spaces afterwards Data lines come in pairs the first line containing the year and data values the second containing the sample depth count for each value For reasons unknown the first and last data line pair have a slightly different syntax to the others First data line begins with a space and an integer for the first year in the line There then follows 9 spaces followed by the integer data value for the first ring The remaining data values often less than a full decades worth on that line follow as integers left padded by spaces to take up 6 characters The sample depth line that pairs with this follows next starting with 16 spaces followed by the sample depth value enclosed in square brackets The remaining sample depth values follow in square brackets left padding with spaces to take up 6 characters Next comes the first normal data line This begins with a space followed by an integer year value The data values follow as integers left padded by spaces to take up 6 characters A data line has a decades worth of data values Next come
21. not your system or network credentials provided to you by your systems administrator If you are using your own Virtual Appliance server the default admin user details are provided in section 11 4 1 page 55 The dialog gives you the option for saving your username and or password if you prefer We recommend using this feature only on personal machines You may choose to cancel the login if you like and Tellervo will continue to load however you will not have access to the Tellervo database therefore very few functions will be available to you Once you have logged in you will be presented with the Tellervo home screen This contains the 9 Authentication JOE main menus for the program as well as three quick You must log in for access link icons for creating new records opening exist User name myusername N ing records and importing existing data files to the Pascword database Login to Y Remember my password 122 Mapping support Log in automatically Tellervo includes 3D mapping for visualization of sampling locations Although this is not necessary for most tasks to make use of the mapping func tions you will require a OpenGL 3D capable graphics card To check whether your computer already sup ports 3D mapping open Tellervo go to Admin then Site map Tellervo will warn you if your graphics card is not supported Figure 1 3 Tellervo server login dialog All MacOSX computers should automatically s
22. string is required it is provided using the I18n getText function which then retrieves the correct string for the current locale If no string is found then the default language English string is returned There is an Eclipse plugin to assist with this task called ResourceBundle Editor and it can be downloaded from http eclipse rbe sourceforge net Once installed it provides a GUI that allows you to simultaneously update all languages at once The 118n getText function can be passed variables for insertion into the translation next e g file name data value line number etc These can be passed either as a string array or as one or more strings The values are inserted into the translation string at the points marked 0 1 etc For instance the translation string File 0 exists Rename to 1 would accept two strings the first being the original filename and the second being To avoid confusing the original Tellervo class named Sample will be referred to as Tellervo Sample throughout this docu mentation Within the code all TRiDaS data model classes are prefixed with Tridas to help avoid confusion The Sample class is therefore not at all associated with the TridasSample class Developing Tellervo Desktop 67 the filename to rename to For obvious reasons only non translateable strings should be passed in this way as they will be inserted indentically in all languages The Resource Bundle also incl
23. with all words of the title equally prominent and visible You may add other material on the covers in addition Copying with changes limited to the covers as long as they preserve the title of the Document and satisfy these conditions can be treated as verbatim copying in other respects If the required texts for either cover are too voluminous to fit legibly you should put the first ones listed as many as fit reasonably on the actual cover and continue the rest onto adjacent pages If you publish or distribute Opaque copies of the Document numbering more than 100 you must either include a machine readable Transparent copy along with each Opaque copy or state in or with each Opaque copy a computer network location from which the general network using public has access to download using public standard network protocols a complete Transparent copy of the Document free of added material If you use the latter option you must take reasonably prudent steps when you begin distribution of Opaque copies in quantity to ensure that this Transparent copy will remain thus 180 Tellervo A guide for users and developers accessible at the stated location until at least one year after the last time you distribute an Opaque copy directly or through your agents or retailers of that edition to the public It is requested but not required that you contact the authors of the Document well before redistributing any large number of copies to give
24. y2 are the data of the moving sample in the overlap and N is the length of the overlap The first step is to make each dataset bivariate normal by replacing each value with the mean of the values around it and then taking its natural logarithm The preparation for the t score is therefore done as follows and is done to both the fixed and moving series Li 2 Lit Li HLi 2 5 gt x gt x Inle The student s T computation is then done as follows gt Sry Ey N i Tavo Yi Yang gt Srg Ex N 2 Lavg gt Syy Ly N yi e eg Sry gt r i vV Sea Syy 50 Tellervo A guide for users and developers The t score is an explorative statistic There is no univerally accepted threshold above which a t score is regarded as significant however Baillie and Pilcher 1973 suggest a value of 3 5 For more information see Wigley et al 1987 10 1 2 Trend Trend is another popular crossdate statistic It computes the percentage of years with the same trend going up or going down ness Scores greater than 60 70 are good Trend is also referred to as ufigkeitsko Gleichl effizient Gleichlaufigkeit and Eckstein s W The trend is the simplest crossdate For each sample it computes the trend of each 2 year interval 1001 1002 1002 1003 and so on The trend of a 2 year interval is simply whether the next ring is larger smaller or the same The trend score is the percent
25. 2 3 Real numbers au 4 28 ee eee a ee de D24 Categories iced oe et Ay BS a RA eG D 2 59 Dates wove ae an kak Pe EPA eee ee lees D 3 Metadata tdi U eds e sede de e ee NN e a BEN D 4 Datan titi La E a ho eee D 4 1 Ring widths oo non D 4 2 Chronologies 2 22 aaa E Cracow Binary Format E 1 Description A atda gen A Pe eed 99 101 101 102 103 103 104 105 105 106 106 107 107 107 108 108 108 108 108 108 109 109 109 111 CONTENTS vii Comma Separated Values F 1 Description an Aa a hy E ee Ree A R F 2 Example ta Se ac ha Be ed OR UA abe ee Corina Legacy G 1 Description aac de ds ls a A oe A G 2 Example til8a 2 2 sr A A oe th E a 2 DendroDB H 1 Description ei ae de NP do a le H 2 Example Anaa a E A re ee Heidelberg 111 Description 22 So 4 a e a 1 2 Example file raw series 2 2 1 3 Example file chronology 0 0 e e eee KINSYS KS J 1 Description e Kein diea ae a la a a ia T dd bo J 2 Example lea era E a Bera eher Microsoft Excel 97 2000 XP K 1 Description iaa ds A Be N a a a K 2 Examplestile co atadas Ba en BI A Microsoft Excel 2007 L 1 Description A A a to oa Nottingham M 1 Description ra E A M 2 ExXamplestile ro a Sich ach SAID ODF Spreadsheet N 1 Description u 2c a4ae 2eep SAF ek ebb da Oxford O1 Description u ee ee 0 2 Limitations a i etia a a A 0 3 Exampleifilex sasiore 8420 8 As Ka ho BES
26. 2008 normal Quercus normalld 49139 gt Quercus sp lt taxon gt lt dimensions gt lt unit normalTridas metres gt lt height gt 1 lt height gt lt width gt 1 lt width gt lt depth gt 1 lt depth gt lt dimensions gt lt authenticity gt Original lt authenticity gt lt sample gt lt title gt C TWI 65 A lt title gt lt identifier domain dendro cornell edu gt ff688357 b2d4 4394 a21a 90696cd4558c lt identifier gt lt createdTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt createdTimestamp gt lt lastModifiedTimestamp certainty exact 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 154 Tellervo A guide for users and developers gt 1997 02 01T 14 13 51 0Z lt lastModifiedTimestamp gt lt type normal Corina Dictionary normalld 1 normalStd Section gt Section lt type gt lt samplingDate certainty exact gt 1981 07 25 lt samplingDate gt lt state gt Dry lt state gt lt radius gt lt title gt C TWI 65 A B lt title gt lt identifier domain dendro cornell edu gt 5b7baa8b cd4e 4b3b 88fa 82939420e544 lt identifier gt lt createdTimestamp certainty exact gt 2006 05 04T 18 13 51 0Z lt createdTimestamp gt lt lastModifiedTimestamp certainty exact gt 2006 05 04T 18 13 51 0Z lt lastModifiedTi
27. 270 320 340 370 330 310 240 170 107012 1900 280 300 300 310 350 400 300 280 280 180 107012 1910 190 290 270 210 230 300 220 360 240 260 107012 1920 200 270 250 230 270 210 160 210 220 200 107012 1930 170 250 200 130 140 210 210 180 190 180 107012 1940 170 180 190 190 190 200 190 180 110 180 107012 1950 220 230 180 220 200 240 220 210 240 999 U 6 Example file chronology 107089 1 Antalya Elmali Isletmesi CDLI 107089 2 Turkey Cedar 1800M 3640 02955 1370 1988 107089 3 Peter I Kuniholm 1070001370 567 11115 1 798 11105 11407 1 398 1 436 1 543 1 490 1 225 1 1070001380 127 1 39 1 29 1 69 1 178 1 445 1 227 1 510 11020 11120 1 10700013901390 11310 1 979 11585 11111 1 444 1 214 1 520 1 275 1 224 1 1070001400 153 1 371 1 567 1 711 1 835 1 687 1 322 1 291 1 291 1218 1 1070001410 168 1 378 1 557 1 410 1 315 1 202 1 531 1 765 1 797 1840 1 1070001420 440 1 774 1 946 1 838 1 397 1 380 1 206 1510 1695 1521 1 1070001430 461 1 978 1 967 1 857 1 978 1 733 1 522 1 333 1577 1 477 1 1070001440 730 1 752 1 932 1 955 1 898 1 629 11170 1 738 1 920 1 363 1 160 Tellervo A guide for users and developers 1070001450 863 10700014601255 10700014701797 10700014801042 1070001490 800 10700015001629 10700015101026 10700015201225 10700015301086 1070001540 895 10700015501158 10700015601287 1070001570 990 1070001580 791 10700015901263 10700016001098 1070001610 915 10700016201173 10700016301123 10700016401093 10700016501030 1070001660 917 107000167
28. 3 to 1 2 4 1 2 3 gt prerm upgrade 1 2 4 FAILED 1 2 4 gt prerm failed upgrade 1 2 3 FAILE 1 2 3 gt postinst abort upgrade 1 2 4 FAILED OK OK OK 1 2 4 gt preinst upgrade 1 2 3 1 2 4 gt postrm abort upgrade 1 2 3 OK OK Half Installed Reinst required 1 2 3 gt postinst abort upgrade 1 2 4 FAILED Files are unpacked Installed 1 2 3 1 2 3 gt postrm upgrade 1 2 4 D 1 2 4 gt postrm failed upgrade 1 2 4 ALBO 1 2 3 gt preinst abort upgrade 1 2 4 FAILED OK Failed Config Installed 1 2 3 1 2 3 Reinst required a a FAL OK Old files are deleted 1 2 4 gt postrm abort upgrade 1 2 3 1 2 4 gt postinst configure 1 2 3 FAILED OK OK 1 2 3 gt postinst abort upgrade 1 2 4 OK Installed Failed Config 1 2 3 Installed 1 2 4 1 2 4 Unpacked Half Installed _ 1 2 3 Reinst required 1 2 3 Successful exit Exit with error message Figure 14 5 Flow chart showing how the prerm preinst postrm postinst scripts are run along with the parameters passed to them when installing and upgrading 80 Tellervo A guide for users and developers 14 3 Handling version dependencies In an ideal world the API for how clients talk to the Tellervo server would never change Unfortunately we don t live in an ideal world New features in Tellervo will require changes to the API as will changes to TRiDaS In anticipation of such changes the Tellervo server includes a me
29. 31217 31496 41454 4 835 41392 51012 51092 5 933 71151 81255 10 708 101146 101054 101159 101059 101165 12 12 13 14 14 16 638 886 936 900 642 721 181128 191145 231352 241023 24 964 241147 241281 24 24 24 758 870 957 241166 24 24 24 24 25 24 647 688 884 783 902 625 241162 24 952 241182 24 23 819 929 231130 231203 231069 191047 1 172 11364 11819 202 91 21387 31433 31500 31439 41209 4 800 41215 51195 51414 61144 71032 91136 10 627 10 928 101275 101060 101078 101325 12 624 12 878 13 939 141022 14 554 16 616 181144 191219 231397 24 971 241075 241141 241166 24 821 241037 24 958 24 850 24 689 24 723 24 792 24 697 251038 24 772 241118 241370 241282 241000 23 685 231244 231109 231084 19 968 1 126 11282 11807 2 982 21365 31406 31358 31603 41451 41182 41047 51409 51209 61022 8 968 91097 10 848 10 820 101052 101117 101170 101608 12 600 12 970 131003 14 781 14 589 16 576 181112 191162 231487 241071 24 820 241162 241580 24 914 241070 24 997 24 962 24 731 241046 24 594 24 768 251017 24 827 241007 241260 241527 24 763 23 894 231187 23 602 21 936 191089 1 69 11364 11464 21186 21574 31239 31171 31335 41292 4 952 51133 51107 51090 61001 8 592 101273 101010 10 935 101068 101314 101159 101161 12 12 13 14 14 16
30. 51 65 68 55 44 41 75 94 78 63 69 58 75 55 47 58 46 62 45 52 50 77 50 63 75 77 64 66 57 80 57 78 65 68 75 65 98 85 82119 89 85 87 83108 129123160117129121 88 69 97 77 96106 71 89 50 65133 89 88 50 60 95 95 91102158 83 55 98 70 45 46 40 36 64 58 52 58 56 94 51 48 47 60 49 48 Appendix W VFormat Format name VFormat Other name s OJ Format Type Text file Extension s Read write support Various depending on data type but commonly oj Read and write Reference implementation VFormat Data metadata Data with some structure metadata Calendar type Gregorian Absolute dating support Yes Undated series support No Relative dating support No Multi series support Yes Original designer Thomas Reimer and Hans Hubert Leuschner W 1 Description A relatively extensive format which includes highly encoded header lines for metadata VFormat files have an array of file extensions depending on the type of data the files contain VFormat files can contain mutliple data series Each series contains 2 4 header lines followed by a number of data lines The metadata fields are encoded into the header lines in specific character positions In line 1 the character positions are as follows 1 12 Series identifier The series identifier also determines the filename If there is just one series in the file then the series identifier will be the same as the filename For files with multiple series the filename will use characters 1 7 of the
31. Absolute dating support Yes Undated series support No Relative dating support No Multi series support Yes Original designer Bernhard Knibbe The PAST4 format Knibbe 2008 is the native file format for SCIEM s PAST4 software It is a hybrid XML file containing most metadata in structured XML but some metadata and all data as plain text It is unique amongst dendro data formats in that it contains not only data and metadata but also settings information for the PAST4 software such as details on what colours to use in graphs which series should be displayed on screen etc The general structure of a P4P file is as follows gt gt gt gt Project header required Settings optional Groups required repeatable Records required repeatable The root XML tag for the file is lt PAST_4_PROJECT_FILE gt Inside this is the lt PROJECT gt tag which contains the following attributes VVVVVVVVVVY ActiveGroup Zero based index specifying which group is active EditDate Date the file was last edited Groups Number of groups within this project Locked Either TRUE or FALSE indicating whether a password is required to open the file Name Name of the project Password Password used to lock the project PersID Abbreviation of the authors name Records Number of records in the project Reference Zero based index indicated which is the reference series 1 if none selected Sample Zero based index indicating which
32. Corresponding Source conveyed under this section must be accompanied by the Installation Information But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product for example the work has been installed in ROM The requirement to provide Installation Information does not include a requirement to continue to provide support service warranty or updates for a work that has been modified or installed by the recipient or for the User Product in which it has been modified or installed Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network Corresponding Source conveyed and Installation Information provided in accord with this section must be in a format that is publicly documented and with an implementation available to the public in source code form and must require no special password or key for unpacking reading or copying Additional Terms Additional permissions are terms that supplement the terms of this License by making exceptions from one or more of its conditions Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License to the extent that they are valid under applicable law If additional permissions apply only to part of the Program that
33. Created August 24 2010 10 23 AM Measured by Leann Canady Last Modified August 24 2010 10 23 AM Supervised by Charlotte Pearson Ring widths ES Single Pinned Double Pinned Wood Completeness Pith is incomplete A total of 54 rings were measured Heartwood is incomplete Sapwood is absent Bark is absent Interpretation The first ring of this series begins in relative year 1001 The pith of this radius was laid down in exactly relative year 1001 and died after relative year 1055 Element and sample details Taxon Quercus Element type Post Sample type Cross section Figure 8 3 An example of a report showing barcode and basic metadata about a series Curation and Administration 43 8 3 3 Checking boxes in and out Tellervo includes function for checking boxes in and out of a store much like when a book is borrowed from a library The Administration gt Curation gt Check out box from store and Administration gt Curation gt Return box to store menus do just this You can either scan the box barcode or select the box from the drop down menu These options record when a box is checked out in and by whom These details can be seen by users in the box details dialog 8 3 4 Locating samples As you might expect Tellervo also includes a function for locating your physical samples This is available in the Administration gt Curation gt Find
34. Dendro for Windows Data and some structured metadata Calendar type Gregorian Absolute dating support Yes Undated series support No Relative dating support Yes Multi series support No Original designer lan Tyers Appendix Q Sheffield Q 1 Description Sheffield format Tyers 1999 is a dendro specific text file designed by lan Tyers for his Dendro for Windows application It is probably most widely used in the UK but is also used in continental Europe as well as New Zealand The format contains both data and some structured metadata with each field value stored one per line The order of fields is fixed so missing data must be indicated by the use of a question mark The data present on each line is as follows rom Site name sample number Free form text not including up to 64 characters Number of rings Whole positive number Date type Single character A absolute date R relative date Start date Whole number can be negative If absolute year then add 10000 to value so LAD 10001 Raw data type or Mean data type Single character R annual raw ring width data NB earlier versions used some other codes here for species e g ABEFPSU these are all interpreted as equivalent to R Single character W timber mean with signatures X chron mean with signatures T timber mean C chron mean M un weighted master sequence Raw sapwood number or mean number of timbers chronologies Whole positiv
35. IEEE 754 Standard for Floating Point Arithmetic D 2 4 Categories Categories are typically recorded as single bytes as most categories have just a few possible values They can therefore be conceptualized as being integers where O first option 1 second option etc The exception to this is for species because there are more than 256 species In this case a byte pair is used in exactly the same way as described for integers above The only problem for species is that the codes are unique to each laboratory and refer to values enumerated in a separate wnm file Without this dictionary the species code is of little use D 2 5 Dates The date of the creation of the series and the date of the last amendment to the series are stored as three single bytes each one for day one for month and one for year The year is stored with an offset of 1900 Therefore numbers from 1 to 100 belong to the 20th century calendar year 1901 to 2000 and numbers from 101 to 200 belong to the 21th century calendar year 2001 to 2100 D 3 Metadata The first 128 bytes contain the file header information and the remainder of the file contains the ring width data and sample depth data if series is a chronology If a series is only partly suitable for further analysis CATRAS 109 then this indicated in bytes 49 52 The quality code at position 58 is an overall rating for the series This helps to exclude poor series from analyses other than dating D 4 Data
36. Integer indicating the quality of the record The record tag then contains a lt HEADER gt tag with a lt CDATA section which includes additional free text header information There are no requirements as to how information should be laid out in this field however many users seem to adopt the Heidelberg style of keyword value Next comes the lt DATA gt tag which is empty except another lt CDATA section This is where the actual ring width data is stored Each data value is recorded on a separate line using CR LR line breaks Each line contains the following six tab delimited fields gt gt gt gt gt v Ring width as a floating point number Sample depth Number of sample increasing Latewood percentage as a floating point value 0 1 0 if not known Duplicate backup ring width value to store the original ring width value If an index is applied the ring width value in column 1 is altered Comment string about this particular ring P 1 Dating PAST4 contains an option for enabling disabling the year 0 but it does not record within the data file whether the option was set when the file was created By default the year O is disabled therefore the library treats PASTA files as if they use the Gregorian calendar but it is possible that files were in fact created with the Astronomical calendar in mind 30 144 Tellervo A guide for users and developers P 2 Example file lt xml version 1 0 gt lt P
37. Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer Appendix L Microsoft Excel 2007 Microsoft Excel 2007 Office Open XML Spreadsheet OOXML OpenXML XML file xlsx Read and write ISO 29500 Data only Gregorian Yes No No Yes Microsoft L 1 Description This is the new XML file format introduced by Microsoft with Excel 2007 Unlike the binary format used by the previous version of Excel this format is an open standard However it should not be confused with the OpenDocument Format standard that was developed by the OASIS consortium The layout of the data sheet should be just as for the Excel 97 2000 XP format Row 1 Header names for each column Column A Year values Column B One column for each series containing data values Cells are left empty if no data is available for a series because it does not extend to a particular year Data must be continuous for each series so missing unmeasured rings should be included as zero See the screenshot in the Microsoft Excel 97 2000 XP format to see how an example of how the spreadsheet should look Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Orig
38. Reading byte code Reading byte code is more complicated than reading text files Each byte is 8 bits and therefore can represent up to 256 values Depending on the type of information each byte contains the bytes are interpreted in one of four ways 108 Tellervo A guide for users and developers D 2 1 Strings Some of the bytes in CATRAS files contain character information In this case each byte represents a letter In java an array of bytes can be directly decoded into a string D 2 2 Integers As a byte can only represent 256 values whenever an integer is required it is stored as a byte pair Each byte pair consists of a least significant byte LSB and a most significant byte MSB The order that they appear in files typically varies between platforms and is known as endianness As CATRAS solely runs on Microsoft x86 processors we can safely assume that all CATRAS files will be using little endian i e LSB MSB The counting in a byte pair therefore works as follows Value LSB MSB 1 1 0 2 2 0 3 3 0 256 0 1 257 1 1 258 2 1 A byte pair can therefore store 256x256 65536 values more than enough for most number fields D 2 3 Real numbers Statistical values such as arithmetic mean standard deviation first order autocorrelation and mean sensitivity are given for all the ring widths and optionally for the ring widths in a restricted part of the series The real numbers are given in standard format defined by the
39. Tellervo development means that we have been unable to produce native installers for platforms other that Ubuntu The VirtualBox method can be used on all modern operating systems so we strongly suggest you stick with this method However if you are an experience systems administrator and are feeling brave it is possible to set up the Tellervo server manually The Tellervo server is essentially a PostgreSQL database accessed via a PHP webservice running on Apache 2 The following dependencies are therefore required postgresql 9 1 postgis postgresql contrib 9 1 postgresql 9 1 pljava sun java6 jre apache2 php5 php5 pgsql php5 curl php5 mhash The basic procedure for installation is as follows Install all dependencies Create PostgreSQL database from Tellervo template SQL file Set up a database user and provide access to the server in the pg_hba conf file Give this user read and write permissions to the database Copy the webservice code into a web accessible folder Set up Apache to see this folder by creating an entry in the sites enabled folder Restart PostgreSQL and Apache and check you can access the webservice from a web browser vvvvvvy 1 2 Installing the desktop application Installation packages for the Tellervo desktop application are available for Windows MacOSX and Ubuntu Linux Tellervo can also be run on other operating systems as long as they support Java 6 or later To install Tellervo download the installatio
40. The GNU General Public License is a free copyleft license for software and other kinds of works The licenses for most software and other practical works are designed to take away your freedom to share and change the works By contrast the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program to make sure it remains free software for all its users We the Free Software Foundation use the GNU General Public License for most of our software it applies also to any other work released this way by its authors You can apply it to your programs too When we speak of free software we are referring to freedom not price Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software and charge for them if you wish that you receive source code or can get it if you want it that you can change the software or use pieces of it in new free programs and that you know you can do these things To protect your rights we need to prevent others from denying you these rights or asking you to surrender the rights Therefore you have certain responsibilities if you distribute copies of the software or if you modify it responsibilities to respect the freedom of others For example if you distribute copies of such a program whether gratis or for a fee you must pass on to the recipients the same freedoms that you received You must make sure that t
41. The Maven osxappbundle plugin is able to produce both app and dmg files Unfortunately the libraries for producing dmg files are proprietary to Apple When Maven is run on Windows or Linux it is therefore only able to produce a zipped app file and not dmg We therefore recommend producing the Mac release on OSX either natively or under a virtual machine Note that the osxappbundle plugin does not support the inclusion of additional files such as native libraries within the app file This task is therefore handled separately by the AntRun plugin that inserts the libraries directly to the app file 13 9 3 Linux Deb package A Linux Debian package is produced using the JDeb Maven plugin If Maven does its job properly it should all just work as part of the standard maven package phase In addition to the configuration in the pom xml there are three files that are used to configure the final deb file In src deb control there is a control file which describes the runtime dependencies maintainer of the package description etc In Native BuildResources Lin Build are two files one a simple bash script that is used to launch Tellervo on the users computer and the other a desktop file for configuring how it appears in the users menus All three of these files are automatically updated with the current version number so hopefully you shouldn t need to change anything 13 9 4 Linux RPM package 13 9 5 Native libraries Although Teller
42. a sample menu There are three methods for locating a sample via barcode via lab code and manually by object element sample If you have the sample in your hand and you simply want to know which box it should be returned to you can scan the barcode If you are looking for a sample and you know its lab code then you can enter this instead Alternatively you can use the drop down menus to search for one or more samples at once For instance you can locate all the samples for a particular object and element Chapter 9 Indexing Trees tend to put on big rings when they re young and smaller rings when they get older Some trees put on very large rings while others put on very small rings These variations in growth can make it difficult to crossdate samples Some dendrochronologists therefore prefer to index or normalize their ring width data before combining into chronologies Indexing is a manipulation you can perform on your data to make it easier to crossdate The procedure for indexing is as follows 1 You open a series raw data You ask Tellervo to index it Tellervo shows you some possible curves You pick a curve based on its graph statistical scores and your expectation of how the tree is growing Tellervo converts each year s ring width to a ratio of actual growth to expected growth for that year You save the series indexed data 591 Reh Indexing changes the units of a dataset A raw sample has units of hundredths of a m
43. a standard webpage If you add the following HTML code to a webpage it will give you a simple form If you type your XML request document into the form and click submit the Tellervo server will respond with an XML document containing the answer to your query lt form method post action http name of your server tellervo gt lt textarea name xmlrequest gt lt input type submit value submit gt lt form gt A page with just such a form is available in the root of your Tellervo server installation as the page post php When the response is viewed in a web browser it will be rendered using a style sheet but if you view the source code you ll see the underlying XML document A simple HTML form like this can be handy for helping you send some rough requests to the server to help you understand how things work The Tellervo client or any other client that wants to talk to the Tellervo server does exactly this It sends XML formatted request documents to the server as POST requests and the server returns an XML document containing the reply The client then reads the XML reply and displays the result to the user in any way it sees fit wona w 00 Jo 9 84 Tellervo A guide for users and developers 15 2 Standard request response The request XML document you send the server needs to validate against the Tellervo XML schema available in the schema folder of your Tellervo server or in the src main
44. allows users to measure ring widths from scans or photographs of samples rather than by using a traditional measuring platform WinDENDRO files are really just tab delimited text files with data in columns in a specific order with a few additional header lines Line 1 should contain 8 tab delimited fields Field 1 WINDENDRO Field 2 WinDENDRO file format version number either 3 or 4 Field 3 Orientation of the data R in rows C in columns All WinDENDRO files are in rows Field 4 The column number where the data values begin For version 3 files this is 13 and version 4 files this is 36 Field 5 The direction the data is recording in P pith to bark B bark to pith Field 6 Whether the data is recorded incrementally 1 or cumulatively C WinDENDRO files are always incremental Field 7 Whether the bark width has been measured Y or N If yes then there will be one more data value than there are rings vv 168 Tellervo A guide for users and developers gt Field 8 RING Line 2 contains the field names For version 3 files these are VVVVVVYV vvvyv TreeName The name of the tree being measured Path identification ID of the path along which the series is measured Site identification Name of the site from which the tree was taken YearLastRing Year of the last ring in the series Sapwood Distance in mm from the start of the sample to the start of the sapwood Tree he
45. an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996 or similar laws prohibiting or restricting circumvention of such measures When you convey a covered work you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work and you disclaim any intention to limit operation or modification of the work as a means of enforcing against the work s users your or third parties legal rights to forbid circumvention of technological measures 4 Conveying Verbatim Copies You may convey verbatim copies of the Program s source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice keep intact all notices stating that this License and any non permissive terms added in accord with section 7 apply to the code keep intact all notices of the absence of any warranty and give all recipients a copy of this License along with the Program You may charge any price or no price for each copy that you convey and you may offer support or warranty protection for a fee 5 Conveying Modified Source Versions You may convey a work based on the Program or the modifications to produce it from the Program in the form of source code under the terms of
46. and you may not initiate litigation including a cross claim or counterclaim in a lawsuit alleging that any patent claim is infringed by making using selling offering for sale or importing the Program or any portion of it Patents A contributor is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based The work thus licensed is called the contributor s contributor version A contributor s essential patent claims are all patent claims owned or controlled by the contributor whether already acquired or hereafter acquired that would be infringed by some manner permitted by this License of making using or selling its contributor version but do not include claims that would be infringed only as a consequence of further modification of the contributor version For purposes of this definition control includes the right to grant patent sublicenses in a manner consistent with the requirements of this License Each contributor grants you a non exclusive worldwide royalty free patent license under the contributor s essential patent claims to make use sell offer for sale import and otherwise run modify and propagate the contents of its contributor version In the following three paragraphs a patent license is any express agreement or commitment however denominated not to enforce a patent such as an express permission to practice a patent or covenant not
47. database does not contain data prior to 441AD so handling of BC AD transition has not been tested The DendroDB web interface suggests that BC dates should be entered as negative integers but it also allows request for data from year 0 This suggests the database uses an Astronomical calendar and this is how the DendrolOLib treats it 120 Tellervo A guide for users and developers H 2 Example file Data downloaded from DendroDB Site Example site Contact A N Other Species Larix sibirica Parameter Latewood width Latitude 53 25 Longitude 57 35 Elevation 1670 Tree Core Year 1 1 1648 16 1649 21 1650 8 1651 10 1652 6 1653 8 1654 11 1655 13 1656 9 1657 10 1658 10 1659 4 1660 1661 1662 1663 Latewood width PRR RP RP RPP RPP PRP PPP PRP RP RPP EPP RPP PRP AR 0 YO Please acknowledge authors Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer 1 1 Description Appendix Heidelberg Heidelberg TSAP FH Text file fh Read and write TSAP Win Data and extensible metadata Gregorian Yes Yes Yes Yes Frank Rinn The Heidelberg format Rinn 2008 is the native file format for Rinntech s TSAP Win software It supports metadata in the form of keyword value pairs There are more than 140 standa
48. each step of the wedge determined during the light intensity calibration DensStepsWoodDens Equivalent wood density of each step of the wedge determined during light intensity calibration DiskArea Area of the sample DiskPerim Perimeter of the sample DiskAvgDiam Average diameter of the sample DiskFormCoef Sample area form coefficient CompWoodArea Total area occupied by the compression areas WinDENDRO 169 VoidArea Total area occupied by the void areas PathLength Length of radius measured Lines 3 contain the actual data and metadata one line for each series Following the 13 or 36 columns of metadata depending on file version there are x number of columns containing ring values The values are recorded as floating point data The units for these data values are mm for widths for percentages g cm for densities radians for angles Appendix Y XML Error Codes Table Y 1 The Corina webservice provides error feedback by means of an error code and description Section Code Description General 001 Error connecting to database 002 Generic SQL error Authentication 101 Authentication failed 102 Login required 103 Permission denied 104 Unsupported request 105 Invalid server nonce 106 User unknown 107 Unsupported client 108 Unsupported client version 109 Password needs to be updated 110 Password upgrade required Miscellaneous 666 Unknown Error 667 Program bug Internal 701 Internal SQL err
49. edited by the system administrator these should be handled in the systemconfig php file The systemconfig php file is automatically generated during installation upgrade of the server from entries in the database table tblconfig This means that any changes to the system configuration can be handled as part of the database upgrade simply by adding new rows or editing existing rows in tblconfig Each entry in this table is made available to the webservice as a global variable once the tellervo server script has been run For instance the row containing key wsversion and value 1 0 0 is available as the variable wsversion within the webservice 14 5 Making a new release As mentioned in section 14 2 the server package is created at the same time as the desktop binaries as part of the Maven package procedure There are however a number of steps you need to undertake to make sure this goes smoothly Make sure this documentation is up to date Increment the lt serverversion gt tag in the pom xml file gt Make sure that any upgrades that need to be made to the database are included in a new and unique SQL file stored in Databases db upgrade patches Each file from this folder is run by the installer unless it has previously been run gt If this version of the server needs a particular version of the client then you ll need to set this value in the tblsupportedclient table by including a relevant SQL statement in your db update patches scri
50. for the same cover previously added by you or by arrangement made by the same entity you are acting on behalf of you may not add another but you may replace the old one on explicit permission from the previous publisher that added the old one The author s and publisher s of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version Combining documents You may combine the Document with other documents released under this License under the terms defined in section 4 above for modified versions provided that you include in the combination all of the Invariant Sections of all of the original documents unmodified and list them all as Invariant Sections of your combined work in its license notice and that you preserve all their Warranty Disclaimers The combined work need only contain one copy of this License and multiple identical Invariant Sections may be replaced with a single copy If there are multiple Invariant Sections with the same name but different contents make the title of each such section unique by adding at the end of it in parentheses the name of the original author or publisher of that section if known or else a unique number Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work In the combination you must combine any sections Entitled History in the various
51. from the Neolithic to the present lt description gt lt laboratory gt 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 TRiDaS 153 lt name gt Malcolm and Carolyn Weiner Laboratory for Aegean and Near Eastern Dendrochronology lt name gt lt address gt lt addressLinel gt B48 Goldwin Smith Hall lt addressLinel gt lt addressLine2 gt Cornell University lt addressLine2 gt lt cityOrTown gt Ithaca lt cityOrTown gt lt stateProvinceRegion gt NY lt stateProvinceRegion gt lt postalCode gt 14853 lt postalCode gt lt country gt USA lt country gt lt address gt lt laboratory gt lt category gt Archaeology lt category gt lt investigator gt Peter Kuniholm lt investigator gt lt period gt 1976 present lt period gt lt reference gt referencel lt reference gt lt object gt lt title gt White Tower Thessaloniki lt title gt lt identifier domain dendro cornell edu gt 28acb483 f337 412f a063 59d911c37594 lt identifier gt lt createdTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt createdTimestamp gt lt lastModifiedTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt lastModified Timestamp gt lt type normalStd C
52. going to Run gt Run configurations then create a new Maven Build with the required goal The main goals are as follows clean This deletes any previously compiled classes and packages in the target folder It should only be necessary to run this occassionally if Maven has got a bit confused If this is the case you may also need to force Eclipse to clean too by going to Project gt Clean generate sources Runs JAXB to generated classes representing the entities within the Tellervo schema see section 13 10 for further details The classes are also generated for TRiDaS entities but these are deleted in favour of using those provided by the TridasJLib library package This compiles Tellervo and builds a single executable JAR containing all dependencies thanks to the maven shade plugin along with native Windows MacOSX and Linux packages These are all placed in structured folders within target Binaries ready for deploying on a website install This installs the compiled jar in your local Maven repository This is normally used when you are building a library that is being used by another program It is therefore not necessary for Tellervo deploy This uploads the compiled jar into the maven tridas org repository Note that you will need to either run this phase from the command line or by setting up a customer run configuration in Eclipse have had some issues with the m2e plugin getting a little stuck If you find you
53. icons are accessed via the static Builder class This has various accessor functions which take the filename and the size required and return the icon itself or a URI of the icon from within the Jar 13 5 1 Ring remarks There are two types of ring remarks in Tellervo TRiDaS controlled remarks and Tellervo controlled remarks The end user does not know the difference between the two the only difference between them is how they are handled behind the scenes TRiDaS remarks are those designated in the TRiDaS schema whereas Tellervo remarks are those defined specifically for Tellervo They are represented differently in TRiDaS files like this lt tridas remark normalTridas double pinned gt lt tridas remark normal Tellervo normalStd insect damage normalld 165 gt To add a new remark type to Tellervo you will need to first enter it in the database table tlkpreadingnote specifying the vocabulary as 2 Tellervo To display a custom icon for this remark in the software you will need to add a 16x16 and a 48 x 48 version to the resources an then add an entry to the TellervoRemarklconMap in org tellervo desktop remarks Remarks java The 16x 16 icon is used in the editor interface and the 48 x 48 in PDFs 13 6 Translations There is internationalization infrastructure in place to enable Tellervo to be offered in multiple languages This is done through the use of Resource Bundles one for each language Within the code whenever a
54. in to the command prompt in your Tellervo Virtual Appliance By default the user is tellervo and the password is dendrochronology To change this log in to the command prompt and type passwd and follow the instructions There is no easy way to recover this password if you loose it PostgreSQL database user these are the credentials used by the webservice to read and write to the database and are set by the database administrator during the initial configuration of the Tellervo server You are only ever likely to need this again if you want to directly access the database from a third party tool like PGAdminlll You can reset this password from the Tellervo Virtual Appliance command prompt by typing tellervo server reconfigure Tellervo admin user these are the admin credentials that you use to log in with in your Tellervo desktop application Be default the user is admin and the password is qu3rcu5 You should change these the first time you open the Tellervo desktop application by going to Admin gt Change password 11 4 2 Authentication and encryption Tellervo uses a relatively sophisticated method to ensure that unauthorised users cannot access the Tellervo database through the webservice It is loosely based around http digest authentication and uses a challenge and response scheme This makes use of cryptographic hashes a relatively short digital fingerprint of some data but which cannot be decompiled to retrieve the
55. interface A webservice is an interface designed to be accessed by programs that send requests and receive responses Tellervo uses a style of HTTP POX Plain Old XML to send and receive requests via an HTTP POST In simple terms the Tellervo client sends an XML document that describes the request via POST to the Tellervo server The server then reads the XML request performs the request and then compiles the information that has been requested finally returning the information to the client as another XML document The syntax of the XML document containing the request and response is determined by the Tellervo XML schema and makes heavy use of the TRiDaS XML schema for describing dendrochronological entities The Tellervo schema is the final authority on what is allowed in a request or response so if you find a conflict between this documentation and the schema then it is most likely because the documentation is out of date or it s simply incorrect As you become familiar with the schema you ll probably find it easier to refer to it rather than this documentation to understand what is expected n One of the best ways of understanding the structure of requests and reponses is to use the XML monitor in the Tellervo Help menu to view the documents being sent and received by the Tellervo client 15 1 Basics of sending requests The webservice accepts requests via the POST mechanism of HTTP The simplest way to understand this is to think of this as
56. is the selected sample 1 if none selected Version Version number for this PAST4 format At the time of writing only one version exists 400 Of these fields only Name Groups and Records are mandatory The project tag can also contain a lt CDATA tag which allows the storing of a project description in plain text 142 Next comes the lt SETTINGS gt tag This is one very large XML tag with many attributes controlling the what PAST4 should display the data The contents of this tag are optional and are therefore irrelevant for the transfer of dendro data Next comes one or more lt GROUPS gt tags A group is an arbitrary collection of series perhaps representing a number of measurements of a single object or perhaps an administrative collection of series Groups can be nested in a hierarchy but rather than use the hierarchical nature of XML files the format instead lists all groups side by side and maintains the relationships through the use of an owner attribute containing the index of the parent group This arrangement means than any changes to the hierarchy or the deletion of a group requires all indices to be carefully updated to avoid corrupting the file The group tag has the following attributes p gt Name Name of the group Visible Either TRUE or FALSE indicating whether the group should be shown in graphs Fixed Either TRUE or FALSE indicating whether the group can be moved Locked Either TRUE or F
57. it A patent license is discriminatory if it does not include within the scope of its coverage prohibits the exercise of or is conditioned on the non exercise of one or more of the rights that are specifically granted under this License You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software under which you make payment to the third party based on the extent of your activity of conveying the work and under which the third party grants to any of the parties who would receive the covered work from you a discriminatory patent license a in connection with copies of the covered work conveyed by you or copies made from those copies or b primarily for and in connection with specific products or compilations that contain the covered work unless you entered into that arrangement or that patent license was granted prior to 28 March 2007 Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law No Surrender of Others Freedom If conditions are imposed on you whether by court order agreement or otherwise that contradict the conditions of this License they do not excuse you from the conditions of this License If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other p
58. mouse is on the screen This means you don t need to lift your eyes from your microscope to ensure you are clicking the button correctly When you re finished measuring press escape to exit this mode Certain devices e g Boekler Microcode boxes do not listen for requests to reset to zero In this case to measure each ring individually you would need to manually reset the reading to zero following each measurement This would of course be extremely tedious In this situation Tellervo measures cumulatively from the beginning of the first ring and calculates the ring width based on the previous ring boundary position With this method you must be careful not to knock your sample and you must also take special care when altering radii to navigate around problem structures If you do knock your sample the best way to recover is to reset your platform to zero and press the measure button Next press the stop measuring button manually fix the values in the data table then begin measuring again from where you left off If you are in Early and latewood widths measuring mode the measurements are made and sent to the data table in pairs The first measurement should be of the earlywood of the ring and the next value the latewood measurement Whether you are currently measuring early or latewood is indicated as a message at the bottom of the measuring panel Getting started 15 While you measure your sample you can flag features in a ring
59. or more elements and can also refer to another sub object For instance a single file may contain three objects an archaeological site object within which there is a building object within which there is a beam object The list of possible object types is extensible and is thus flexible enough to incorporate the diversity of data required by the dendro community Only information that is essential for dendrochronological research is recorded here Other related data may be provided in the form of a link to an external database such as a museum catalogue oono e 152 Tellervo A guide for users and developers An element is a piece of wood originating from a single tree Examples include one plank of a water well a single wooden panel in a painting the left hand back plate of a violin one beam in a roof a tree trunk preserved in the soil a living tree The element is a specific part of exactly one object or sub object An object will often consist of more than one element e g when dealing with the staves elements of a barrel object One or more samples can be taken from an element and an element may be dated using one or more derivedSeries A sample is a physical specimen or non physical representation of an element Examples include core from a living tree core from a rafter in a church roof piece of charcoal from an archaeological trench slice from a pile used in a pile foundation wax imprint of the outer end of a plank photo
60. original documents forming one section Entitled History likewise combine any sections Entitled Acknowledgements and any sections Entitled Dedications You must delete all sections Entitled Endorsements GNU General Public License 181 10 Ts Collections of documents You may make a collection consisting of the Document and other documents released under this License and replace the individual copies of this License in the various documents with a single copy that is included in the collection provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects You may extract a single document from such a collection and distribute it individually under this License provided you insert a copy of this License into the extracted document and follow this License in all other respects regarding verbatim copying of that document Aggregation with independent works A compilation of the Document or its derivatives with other separate and independent documents or works in or on a volume of a storage or distribution medium is called an aggregate if the copyright resulting from the compilation is not used to limit the legal rights of the compilation s users beyond what the individual works permit When the Document is included in an aggregate this License does not apply to the other works in the aggregate which are not themselves derivative works of the Docu
61. part may be used separately under those permissions but the entire Program remains governed by this License without regard to the additional permissions When you convey a copy of a covered work you may at your option remove any additional permissions from that copy or from any part of it Additional permissions may be written to require their own removal in certain cases when you modify the work You may place additional permissions on material added by you to a covered work for which you have or can give appropriate copyright permission Notwithstanding any other provision of this License for material you add to a covered work you may if authorized by the copyright holders of that material supplement the terms of this License with terms a Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License or b Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it or c Prohibiting misrepresentation of the origin of that material or requiring that modified versions of such material be marked in reasonable ways as different from the original version or d Limiting the use for publicity purposes of names of licensors or authors of the material or e Declining to grant rights under trademark law for use of some trade names trademarks or service marks or f Requiring in
62. please be my guest will however note that making the tutorials high resolution is extremely important as lower quality video codecs make it very difficult to read screens So far I ve been unable to use the simple wrapper tools like recordMyDesktop to record at high resolution The highest resolution video accepted by Youtube and Vimeo at the time of writing is HD720 1280x720 We will therefore work towards recording our tutorials to this level By natively recording a section of our desktop of this size we remove the need for shrinking and distoring our video so it is best to ensure all the action goes on within a rectangle of this size I ve created a desktop wallpaper with these dimensions marked from the upper left hand corner To do the recording we need to install the following Z sudo apt get install ffmpeg pitivi x264 Developing Tellervo Desktop 73 13 16 Making a new release Making a new release should be a relatively quick and simply process but there are still a few things to remember gt gt gt vY vV VvV Yy v vV vV Y v Make sure this documentation is up to date Update the logging appenders to an appropriate level so that the user is not swamped by debug messages If this release relies upon a certain version of the Tellervo server make sure you set this correctly in src main java org tellervo desktop core App java This is important to ensure that users aren t working against an old ver
63. projectTitle object Title elementTitle sampleTitle If the file contains several series from different samples of the same object then the file would be projectTitle objectTitle If multiple output files end up with the same name then like the numerical convention described above the files will have an incremental number appended to the end Unfortunately most input data files do not contain rich name information so files end up being called unnamedProject unnamedObject unnamedElement etc This convention is therefore more appropriate when converting from TRiDaS to other formats Series code This convention is only applicable to formats that contain just one series The file is named according to the series code Series code 8 characters Same as Series code however the file name is truncated to 8 characters if the series code is longer Keycode Similar to Series code but preferentially uses a keycode supplied by some file formats if available If a keycode is not provided then it falls back to using the series code Note that some formats e g CATRAS require the file name to be the same as a field within the file In this case the naming convention is overidden so no matter what convention you specify the filename will be the same If you manually rename a CATRAS file you will come across errors when loading it in the CATRAS application Importing and exporting 35 7 1 2 Character sets Character sets are th
64. public permission to use the Modified Version under the terms of this License in the form shown in the Addendum below D Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document s license notice H Include an unaltered copy of this License l Preserve the section Entitled History Preserve its Title and add to it an item stating at least the title year new authors and publisher of the Modified Version as given on the Title Page If there is no section Entitled History in the Document create one stating the title year authors and publisher of the Document as given on its Title Page then add an item describing the Modified Version as stated in the previous sentence J Preserve the network location if any given in the Document for public access to a Transparent copy of the Document and likewise the network locations given in the Document for previous versions it was based on These may be placed in the History section You may omit a network location for a work that was published at least four years before the Document itself or if the original publisher of the version it refers to gives permission K For any section Entitled Acknowledgements or Dedications Preserve the Title of the section and preserve in the section all the substance and tone of each of the contributor acknowledgements and or dedications given therein L Preserve all the
65. region Figure 5 4 shows an example overlay of sea surfaces temperatures loaded dynamically from the NASA EO server 1000 Km eae Figure 5 4 Map screenshot with a NASA sea surface temperature overlay dynamically loaded from the NASA WMS server 5 4 Exporting maps You can export maps by going to File gt Export map as image For best results maximize your map window first You may also like to turn off various map widgets by going to the View menu The exported image will include everything you can see on your map screen Chapter 6 Graphing The graphing component is reused in many places throughout the Tellervo desktop application The following description although based on the main graphing screen in Tellervo is largely applicable to all dialogs that include graphs e g crossdating indexing and reconciliation The main method for graphing your tree ring data is by choosing an option from the Graph menu Depending on the type of series you have open the options available to you will be different For raw measurement series you will just have the option to Graph active series This will give you a simple graph of the current series that you have open If you have a derived series open then you may also choose Graph component series which will plot all the series that go to create this series or Graph all series which graphs all the component series as well as the current series 6 1 Controlling graphs Wh
66. section 4 provided that you also meet all of these conditions a The work must carry prominent notices stating that you modified it and giving a relevant date b The work must carry prominent notices stating that it is released under this License and any conditions added under section 7 This requirement modifies the requirement in section 4 to keep intact all notices c You must license the entire work as a whole under this License to anyone who comes into possession of a copy This License will therefore apply along with any applicable section 7 additional terms to the whole of the work and all its parts regardless of how they are packaged This License gives no permission to license the work in any other way but it does not invalidate such permission if you have separately received it d If the work has interactive user interfaces each must display Appropriate Legal Notices however if the Program has interactive interfaces that do not display Appropriate Legal Notices your work need not make them do so A compilation of a covered work with other separate and independent works which are not by their nature extensions of the covered work and which are not combined with it such as to form a larger program in or on a volume of a storage or distribution medium is called an aggregate if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation s users beyond what
67. separate unknown objects Rather that manually specifying the correct object repeatedly you can use the merge objects button to do this for you You need then only pick the correct object from the database once Another method for improving your efficiency is to use the 7 4 Exporting graphs 7 5 Exporting maps Chapter 8 Curation and Administration 8 1 Laboratory workflow Tellervo includes a number of functions to assist you with the curation of your physical sample collection To understand how these are designed to assist users we must first consider the workflow within a laboratory In research laboratories samples generally come to the lab in large batches following field collection In this case the typical workflow may be as follows Collect samples and record field notes as accurately as possible On returning to the lab enter field notes as soon as possible into the bulk data entry interface Print sample barcode labels Prepare physical samples and label with barcodes Assign samples to storage boxes Measure samples using barcodes to recall metadata from database Crossdate samples build chronologies When all samples from a box are completed register box as archived and then store Oo AON OT e N For commercial labs offering dendrochronological dating as a service samples more likely to arrive in smaller batches In this case the bulk data entry interface may not be the most efficient method for ent
68. series identifiers that are the same throughout the file with the remaining different characters replaced by an underscore The 8th character of the filename would contain a running number for files that would otherwise be named the same The series identifier is made up of the following characters 1 Code representing the project or country 2 Code representing the region of ecological area 3 4 Code number for sample site optionally encoded using hexadecimal or hexatresimal to enable values greater than 99 5 6 Series tree number optionally encoded using hexadecimal or hexatresimal to enable values greater than 99 7 Height code encoded as follows 1 1m 2 2m 9 9m A 10m B 11m S Lumber height 30cm T breast height 130cm 8 Running number if several series have the same values in columns 1 7 9 Fixed as a dot character 10 Either single partial mean curves or chronologies 164 Tellervo A guide for users and developers 11 Code for statistical treatment One of F frequency filtered series index M mean O original P pointer year stat Q cluster pointer year stat R residual S moving deviation or variance T trend fitted curve model W wuchswert X series with standardized running mean and variance Z central moment deviation or variance between several series 12 Code for the measured parameter One of D mean density F earlywo
69. some programs use tabs instead When reading Tucson files COFECHA and ARSTAN ignore all lines that do not match the standard data line format As such some users have used this to enable them to include multiple comment lines in their files The ITRDB documentation says they should be recorded as DDMM or DDDMM but this along with sign N S E W or would require 11 characters when the Tucson specification only allows for 10 Perhaps this was due to an assumption that all places would be in the northern hemisphere This has resulted in a large amount of variation in the way that coordinates are recorded making it extremely difficult to parse them without error Here are some examples including some that use 11 chars not 10 4652N01101E 4652 01101 4652 01101 465201101 N4652E01101 4652 01101 U 5 Example file raw series 107 1 OBERGURGL 107 2 AUSTRIA NORWAY SPRUCE 6726 4652N01101E 1911 1959 107 3 GIERTZ 08 76 107011 1911 78 93 43 100 93 110 135 115 102 107011 1920 92 125 110 135 98 80 75 125 102 110 107011 1930 105 105 95 120 135 140 110 120 130 135 107011 1940 120 130 130 165 135 145 155 160 88 135 107011 1950 140 150 140 130 115 130 130 110 110 135 107011 1960 125 120 135 160 15 102 105 135 105 140 107011 1970 120 115 100 110 110 999 107012 1862 450 580 550 480 620 420 390 420 107012 1870 360 370 300 360 470 460 410 430 510 500 107012 1880 500 510 500 410 380 430 340 380 350 400 107012 1890 290 260
70. specification e g TRiDaS must be UTF 8 In this case your choice will be ignored The final complication with regards character sets is the line feed character s For historical reasons different operating systems use different characters to represent a new line Depending on the software that is used to read a file this can cause problems Tellervo itself will automatically adapt to files with any type of line feed characters so reading files in Tellervo will never be a problem When writing out files Tellervo will use the default line feed for the operating system you are running unless you choose a platform specific character set For instance if you run Tellervo on Windows and choose a MacRoman writing charset Tellervo will use Mac style line feeds 7 2 Importing data The first and simplest method for importing existing data into Tellervo is using the simple File gt Import data menu This allows you to read in the raw ring width data values from existing files without taking any notice of associated metadata This option is suitable if the format you are importing is a data only format or if the file doesn t contain a meaningful amount of metadata A The Tellervo system is currently limited to reading in raw data files It does not allow for reading in of chronology files as these contain a more complex level of metadata Support for chronology files will be included in a later release Import the data by going to File gt Import da
71. the Tellervo jar file to your hard disk You can run Tellervo from the command line by typing java jar tellervo jar Note that several native libraries are required to enable Java to interface with your serial port and 3D graphics hardware If you want to take advantage of these features in Tellervo you will need to manually install these libraries Please contact the Tellervo developers for more information Once you have installed your Tellervo Desktop application and you have access to a Tellervo server you are now ready to launch Tellervo for the first time 1 2 1 First time launch When you launch Tellervo for the first time you will be presented with a setup wizard figure 1 2 Following the wizard to configure the main settings required before you can begin to use Tellervo If you want to re run this wizard at any time you can do so from the entry in the Help menu You can also manually edit all these settings from the Tellervo preferences dialog which can be found in Edit gt Preferences e Setup wizard ES Welcome to the Corina setup wizard This wizard will take you through the steps that are necessary to configure Corina The wizard will automatically use settings that you have previously configured Cancel Figure 1 2 The Tellervo setup wizard will launch the first time you start Tellervo The pages of the wizard include Network connection this configures how your computer accesses the internet Most
72. to sue for patent infringement To grant such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party If you convey a covered work knowingly relying on a patent license and the Corresponding Source of the work is not available for anyone to copy free of charge and under the terms of this License through a publicly available network server or other readily accessible means then you must either 1 cause the Corresponding Source to be so available or 2 arrange to deprive yourself of the benefit of the patent license for this particular work or 3 arrange in a manner consistent with the requirements of this License to extend the patent license to downstream recipients Knowingly relying means you have actual knowledge that but for the patent license your conveying the covered work in a country or your recipient s use of the covered work in a country would infringe one or more identifiable patents in that country that you have reason to believe are valid If pursuant to or in connection with a single transaction or arrangement you convey or propagate by procuring conveyance of a covered work and grant a patent license to some of the parties receiving the covered work authorizing them to use propagate modify or convey a specific copy of the covered work then the patent license you grant is automatically extended to all recipients of the covered work and works based on
73. toothed graph using the radio buttons The remaining buttons are as follows g P Zoom in on the horizontal axis jo Zoom out on the horizontal axis ja Zoom in on the vertical axis ja Zoom out on the vertical axis Toggle show hide the grid lines 4 Toggle show hide the series labels ja Toggle show hide the vertical axis Vias A Spread the series evening up the vertical axis Set the baselines of all the series to zero Resize graph to fit horizontally mir ke Toggle show hide the legend There are also a number of keyboard shortcuts that you might find useful Tab Cycles through each graph component Ctrl W Increase vertical scale Ctri S Decrease vertical scale Ctri A Increase horizontal scale Ctrl D Decrease horizontal scale Up arrow Moves selected graph up by 10 units Down arrow Moves selected graph down by 10 units Moves selected graph up by 1 unit Moves selected graph down by 1 unit HOME Scroll to first year of series END Scroll to last year of series PAGE UP Scroll left by one page width PAGE DOWN Scroll right by one page width SPACE Sets horizontal origin of all graphs to the same value 6 2 Exporting graphs To export your graphs for use in reports you can go to File gt Export plot as PDF file or File gt Export plot as PNG file This presents you with a dialog for setting the colors labels and size of the exported image This functionality is due for an ov
74. which takes an ob ject code rather than ID FindObjectsAndDescendantsWhere Returns the objects and that match a given WHERE clause and their descendants Does not return duplicates FindElementObjectAncestors Returns the ancestry tree of objects given an element id Really just a helper function for FindObjectAncestors GetGroupMembership This function returns a unique list of all the groups the specified user is a member of GetGroupMembershipArray This function returns an integer array of all the securityGrouplDs the specified user is a member of GetUserPermissions Returns an array of the permissions the specified user has for a particular object ID The function backtracks tree gt site gt default and site gt default if no explicit permissions are found If No permission is returned it is the only member of the array If a user is a member of group 1 admin they automatically get all permissions MergeObjects This function merges two objects together The first object is taken as the basis with all its fields maintained unchanged Any fields that are different in the second object are noted in the comments field for checking later If a field is null in the first object but present in the second then this value is used The function cascades through the entity hierarchy merge subordinate entities where required using the other merge functions MergeElements As for MergeObjects but for elements
75. whole number in mm O if unrecorded or mean Unmeasured inner rings single character whole number use pith codes number of rings or H heartwood N none Unmeasured outer rings single character whole number use edges code number of rings except that S sapwood with no edge and V is the spring felling equivalent other codes are H heartwood with no edge N none Group Phase free form text not including up to 14 characters Short title free form text not including up to 8 characters Period single character C modern P post medieval M medieval S Saxon R Roman A pre Roman 2 duplicate e g repeat measure B multiperiod e g long master unknown ITRDB species code 4 character code refer to ITRDB species codes Interpretation and anatomical notes no interpretation notes The interpretation and the anatomical notes can be in any order but each must consist of three parts a single character A or for anatomy or interpretation a separator for interpretations the date of the start for anatomy the ringno a separator for anatomy the anatomical code for interpretations P for plus O for felled and a number for the length of the range where more than one record is present these are separated by there must not be a terminal separator and each record must consist of the tree parts The anatomical codings can be anything of a single character but supported usage is based on Hans Hubert Leusc
76. your rights under this License including any patent licenses granted under the third paragraph of section 11 However if you cease all violation of this License then your license from a particular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means this is the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License If your rights have been terminated and not permanently reinstated you do not qualify to receive new licenses for the same material under section 10 Acceptance Not Required for Having Copies You are not required to accept this License in order to receive or run a copy of the Program Ancillary propagation of a covered work occurring solely as a consequence of using peer to peer transmission to receive a copy likewise does not require acceptance However nothing other th
77. 0 750 1070001680 797 1070001690 928 1070001700 717 1070001710 980 1070001720 930 10700017301047 10700017401284 10700017501119 10700017601118 10700017701072 10700017801098 1070001790 974 1070001800 949 10700018101068 1070001820 839 1070001830 920 1070001840 697 1070001850 619 1070001860 842 1070001870 822 10700018801021 1070001890 798 1070001900 977 10700019101167 10700019201387 10700019301235 10700019401537 10700019501384 10700019601547 1070001970 963 10700019801034 1 896 11220 12035 21040 21040 31282 31035 31164 31146 4 951 41370 51082 51028 5 995 6 902 81128 10 991 101122 10 781 101159 101268 101222 12 675 12 940 13 961 13 699 14 817 16 931 171141 191242 231255 241240 241171 24 903 241265 24 990 241184 241063 241103 24 973 24 345 241015 24 710 25 932 24 871 241237 24 827 241484 241335 241387 231172 231015 231095 19 870 1 965 11364 11821 21404 2 503 31126 31175 31283 41403 4 745 41245 5 899 51206 5 956 71002 81334 10 735 101191 101111 101023 10 971 101052 12 12 614 955 131043 14 14 16 746 718 718 181080 191001 231267 241258 24 853 241038 241256 24 24 813 852 241045 241151 24 24 24 24 25 24 779 545 888 838 799 870 241249 24 482 241293 24 799 231217 231151 231208 231368 191186 1 390 11035 11927 2 2 955 869 31409
78. 1 13 822 141341 16 877 161067 191076 231062 23 938 241114 241022 241208 241101 241163 24 852 241013 24 906 24 580 24 815 24 770 24 793 251149 24 704 241045 241108 24 859 241252 23 896 231245 23 968 191572 189990 ou mm PrPwwwwoNDpNDHr Format name Other name s Type Extension s Read write support Reference implementation Data metadata Tucson Tucson Compact Compact Text file rwm Read and write Various DPL programs including FMT Data only Appendix V Compact Calendar type Astronomical Absolute dating support Yes Undated series support No Relative dating support No Multi series support Yes Original designer Richard Holmes V 1 Description The Tucson Compact format was design by Richard Holmes for use with a number of the applications in the Dendro Program Library DPL Holmes designed it as a space saving alternative to the standard Tucson format at a time when disk space was expensive The format never really caught on perhaps due to the complexity and variability of the format The key feature of Tucson Compact format is the inclusion of a code that describes the layout of the data within the series This code means that only the required amount of space is allocated to each data value in the text file with little wastage No space is provided for metadata Tucson Compact files can contain one or more series of data so the description of a data series below can be repeate
79. 1 134 Cook E Peters K 1981 The smoothing spline A new approach to standardizing forest interior tree ring width series for dendroclimatic studies Tree Ring Bulletin 41 45 53 Cormen T Leiserson C RL R C S 2001 Intro duction to Algorithms The MIT Press Huber B Fletcher J 1970 Dendrochronology in Europe Jansma E Brewer P Zandhuis l 2010 TRiDaS 1 1 The tree ring data standard Dendrochronolo gia 28 99 130 Knibbe B 2008 PAST4 Personal Analysis System for Treering Research software version 4 5 SCIEM Reinsch C 1967 Smoothing by spline functions Nu merische Mathematik 10 177 183 Rinn F 2008 TSAP Win software Rinntech Hei delberg Tyers l 1999 Dendro For Windows program guide ARCUS Report 500 Van Loan C 1999 Introduction to Scientific Com puting A Matrix Vector Approach Using MATLAB Prentice Hall Wigley T Jones P Briffa K 1987 Cross dating methods in dendrochronology Journal of Archaeo logical Science 14 51 64 For Tellervo versions 1 1 x server and 1 0 x desktop Compiled May 10 2013
80. 1 5 2 Tellervo servet ni e A ee AA a a 2 Getting started 2 1 Measuring a new sample 2 2 2 on 2 2 Opening existing data ma Kr Us ke A ee ea er N 2 3 Reconciling datas arg s son 3 8 2 5 Kr Ela dg oa ee le ae ea eh 3 Measuring platforms 4 Metadata 4 1 Tree Ring Data Standard TRiDaS 2 CC Common 4 2 Entering sample metadata 2 2 2 Cm nn nn 4 3 Entering bulk metadata on 4 4 Metadata browser ee 4 5 Laboratory codes caia 2 20 50 A a a a ee 5 Mapping 5 1 Navigation ae or A A A A A es 5 1 1 Mouse with scroll wheel 0 0 0 o 51 2 Single b tton MOUSE s e pb She Ps Berner nn A 5 2 Inter cting with d ta s io msi ad a ra be ee ti 5 3 Map layers 2 4 2 E Aca A A BR toe AO 4d 53d Data layers disie etea ke hak ee eh 2G de 5 3 2 Web Map Service WMS 2 222 Coon 5 4 Exporting maps th 4 2S act dol Ade O A E ose Bete A 6 Graphing 6 1 Controllinggraphs cidad A ee Ba ee we 9 CONTENTS 6 2 Exporting graphs a a zn E EAS AAA ae 7 Importing and exporting 7 1 Exp rting data u o a ee a a e A rt e 7 1 1 Naming conventions sorsas s d cdte animi a a Boe a 7 12 Charactersets nn 028 See WE ee E a 7 2 Importing data a ae alter ee NEG 7 3 Importing data and metadata 2 2 2 Hu non nn 7 3 1 The import dialog 2 00 00 2 7 3 2 Importing when entities are already in the database 7 3 3 Importing when entities are not in the database
81. 10 115 113 120 130 110 120 150 120 120 110 115 160 160 145 135 145 125 115 145 149 120 150 160 99 110 75 70 82 96 90 120 151 155 130 132 133 149 110 130 120 128 118 125 115 95 90 110 98 80 85 97 88 70 100 90 70 80 90 85 78 95 84 70 90 80 75 70 0 0 0 0 0 0 0 1 3 Example file chronology HEADER KeyCode ABCK0530 DataFormat HalfChrono SeriesT ype Mean curve Length 60 DateBegin 987 DateEnd 1046 Dated Dated Location Example site S pecies QUSP GlobalMathCommentCount 0 ImageCount 0 CommentCount 0 BibliographyCount 0 DATA Double 125 1 125 2 264 2 206 2 115 2 111 2 188 2 308 2 197 2 419 2 238 2 227 2 279 2 293 2 271 2 309 2 170 2 204 2 163 2 175 2 164 2 211 2 134 2 141 2 107 2 72 2 74 2 91 2 110 2 47 2 87 2 87 2 35 2 47 2 80 2 66 2 38 2 82 2 78 2 65 2 63 2 76 2 67 2 91 2 73 3 39 3 41 3 78 3 57 3 54 3 41 3 39 3 52 3 53 3 43 3 48 3 32 3 32 3 48 3 59 3 J 1 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer Description Appendix J KINSYS KS KINSYS KS KINSYS KINSYS KS Sauvala MIT Text file MIT Read KINSYS KS Data and structured metadata Gregorian Yes No No Yes Unknown The KINSYS KS format was designed for use with the application of the same name at the Finnish Forest Research Institute M
82. 123 125 1 1 0 125 1 gt lt DATA gt lt RECORD gt lt RECORD Keycode title6 Length 4 Owner 0 Chrono FALSE Locked FALSE Filter FALSE Filterlndex 1 FilterS1 100 FilterS2 100 FilterB1 FALSE FilterWeight Offset 0 Color 0 Checked FALSE VShift 0 IsMeanValue 0 Pith FALSE SapWood 0 Location locationCommentl1 Species QUSP Waldkante FirstValidRing 0 LastValidRing 0 UseValidRingsOnly FALSE gt lt HEADER gt lt CDATA Unit 1 100th millimetres gt lt HEADER gt lt DATA gt lt CDATA 123 1 1 0 123 123 1 1 0 123 123 1 1 0 123 125 1 1 0 125 gt lt DATA gt lt RECORD gt lt RECORD Keycode Unnamed series Length 2 Owner 1 Chrono FALSE Locked FALSE Filter FALSE Filterlndex 1 FilterS1 100 FilterS2 100 FilterB1 FALSE FilterWeight Offset 0 Color 0 Checked FALSE VShift 0 IsMeanValue 0 Pith FALSE SapWood 0 Location Species Waldkante FirstValidRing 0 LastValidRing 0 UseValidRingsOnly FALSE gt lt HEADER gt lt CDATA Unit Wierd units gt lt HEADER gt lt DATA gt lt CDATA 96 1 1 0 96 fire_damage fire_damage 34 1 1 0 34 fire_damage fire_damage 1 gt lt DATA gt lt RECORD gt lt PAST_4_PROJECT_FILE gt Format name Sheffield Other name s D Format Type Text file Extension s d Read write support Reference implementation Data metadata Read and write
83. 51 51 x C YMT 1212 A B 2 Sarah Simpson Raw Quercus 2010 04 16 1001 1052 52 x ly EMMTIDIDADA Katharina Contar Da ISHED An nna e 11001108955 se IT conca ox Figure 2 4 Screenshot of the database browser dialog The browse tab shows a heirarchical tree view of the contents of your Tellervo database based upon the TRiDaS data model The panel will be pre populated with all the objects in your database but it is possible to drill down by right clicking on an object and choosing Expand branch Expanding an object for instance will show all the elements associated with that object and expanding an element will show all the samples associated with the specified element To better understand the TRiDaS terminology please read chapter 4 page 19 By double clicking or right clicking and choosing Search for associated series on an item in the browse panel Tellervo will search the database for all series that are associated with the specified entity The results of the search will be shown in the series table on the right of the screen This table shows basic metadata about each search and is sortable by click on any of the column headers To open a series simply select one of these series and click OK If the database browser is open in multiple series mode then you can use the arrow buttons to select multiple series to open in one go There is also a Show options button on the database browser dialog This adds addition
84. 95 R Standard deviation 96 100 R First order autocorrelation 101 104 R Mean sensitivity 105 106 l Number of rings for mean 107 108 l Number of rings for autocorrelation Statistics for restricted part of series 109 112 R Arithmetic mean 113 116 R Standard deviation 117 120 R First order autocorrelation 121 124 R Mean sensitivity 125 126 l Number of rings for mean 127 128 l Number of rings for autocorrelation Table D 1 Summary of the metadata portion of CATRAS files Data types are strings C integers I real numbers R binary categories B and dates D Bytes 89 128 contain descriptive statistics for the file Bytes 89 108 concern the entire series and bytes 109 128 a subset of the series where some poor quality data defined in bytes 49 52 have been excluded Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer E 1 Description Appendix E Cracow Binary Format Cracow Binary Format Cracow Binary file AVR and AVS Read Unknown Data only n a No Yes No No Unknown This is a binary format used primarily in Polish labs e g AGH UST in Cracow Universities in Szczecin Torun and Katowice It is a simple data only format with no support for calendars or dating There are two types of file AVR and AVS but the format for them is i
85. ALSE If locked the group can be used in the calculation of further mean values Changed Internal TRUE or FALSE value for keeping track of changes Expanded TRUE or FALSE value indicating whether the group should be expanding in the project navigator window UseColor TRUE or FALSE value for is content should be displayed in color HasMeanValue TRUE or FALSE indicating if the group has a dynamic mean value IsChrono TRUE or FALSE indicating if the group mean is calculated with sample depth information Checked TRUE or FALSE indicating if the group is locked and checked Selected TRUE or FALSE indicated in the group is selected in the project navigation window Color 24bit integer indicating the RGB volor value for the group using Borland format Quality Integer value describing the quality of the group mean MVKeycode String code for the group If empty the Name field is used Owner Integer pointing containing the index of the parent group if this group is in a hierarchy If its a top level group it should be 1 vv vvvvvvvvy As with the project tag the group tag can also contain a lt CDATA section for storing a plain text description of the group The final tag type in the file is the lt RECORDS gt tag These contain the actual data series and most of the metadata Like group tags records tags are placed side by side in the file and are placed into the group hierarchy by the use of the owner attribute In addi
86. AST_4_PROJECT_FILE gt lt PROJECT Name title0 Version 400 Locked FALSE Password CreationDate 04 05 2006 2 13 51 PM EditDate 09 01 2010 13 02 ActiveGroup 0 Reference 1 Sample 1 PersID investigator0 Groups 2 Records 3 gt lt CDATA descriptionO 1 gt lt PROJECT gt lt SETTINGS gt lt GROUP Name titlel Visible TRUE Fixed FALSE Locked FALSE Changed FALSE Expanded TRUE UseColor TRUE HasMeanValue FALSE IsChrono FALSE Checked FALSE Selected FALSE Color 0 MVKeycode Owner 1 gt lt CDATA gt lt GROUP gt lt GROUP Name Unnamed Group Visible TRUE Fixed FALSE Locked FALSE Changed FALSE Expanded TRUE UseColor TRUE HasMeanValue FALSE IsChrono FALSE Checked FALSE Selected FALSE Color 0 MVKeycode Owner 1 gt lt CDATA gt lt GROUP gt lt RECORD Keycode title6 Length 4 Owner 0 Chrono FALSE Locked FALSE Filter FALSE FilterIndex 1 FilterS1 100 FilterS2 100 FilterB1 FALSE FilterWeight Offset 0 Color 0 Checked FALSE VShift 0 IsMeanValue 0 Pith FALSE SapWood 0 Location locationComment1 Species Quercus Waldkante FirstValidRing 0 LastValidRing 0 UseValidRingsOnly FALSE gt lt HEADER gt lt CDATA Unit 1 100th millimetres gt lt HEADER gt lt DATA gt lt CDATA 123 1 1 0 123 123 1 1 0 123 123 1 T 0
87. AllowKnownClients is set to TRUE 14 3 1 Client requiring a recent server In the event that changes are made to the client that means it needs a particular version of the server to run then this information is specified in the static string App earliestServerVersionSupported This value should be a three part version number e g 1 1 1 No other changes are required When the user tries to connect to a server with a version prior to the minimum version specified they will be shown an error message explaining that they need to get the Tellervo administrator to upgrade the server 14 3 2 Server requires a recent client In the event that changes are made to the server which mean that a recent version of the client is required then this information is stored in the database in the tblsupportedclient table The client field should contain a unique portion of the HTTP_USER_AGENT header provided by the client The version number field should be a 2 or 3 part number e g 1 1 or 1 1 1 In the event that a user tried to connect to a Tellervo server using a client that is too old then they will be given a clear error message informing them that they need to upgrade 14 4 Handling server configuration The Tellervo server is configured using two main PHP files config php and systemconfig php The configuration is split into two primarily because the config php values are considered to be editable by the server administrator whereas those in system
88. Invariant Sections of the Document unaltered in their text and in their titles Section numbers or the equivalent are not considered part of the section titles M Delete any section Entitled Endorsements Such a section may not be included in the Modified Version N Do not retitle any existing section to be Entitled Endorsements or to conflict in title with any Invariant Section O Preserve any Warranty Disclaimers If the Modified Version includes new front matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document you may at your option designate some or all of these sections as invariant To do this add their titles to the list of Invariant Sections in the Modified Version s license notice These titles must be distinct from any other section titles You may add a section Entitled Endorsements provided it contains nothing but endorsements of your Modified Version by various parties for example statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard You may add a passage of up to five words as a Front Cover Text and a passage of up to 25 words as a Back Cover Text to the end of the list of Cover Texts in the Modified Version Only one passage of Front Cover Text and one of Back Cover Text may be added by or through arrangements made by any one entity If the Document already includes a cover text
89. Mean EffectiveMeanSensitivity EffectiveNORFAC Key EffectiveNORFM EffectiveStandardDeviation Eigenvalue Elevation Estimated TimePeriod Exposition FieldNo FilmNo FirstMeasurementDate FirstMeasurementPersID FromSeed ToDateBegin GlobalMathComment n GlobalMathCommentCount GraphParam Group HouseName HouseNo ImageCellRow ImageComment n ImageFile n ImageCount ImageFile Interpretation InvalidRingsAfter InvalidRingsBefore JuvenileWood KeyCode KeyNo LabotaryCode LastRevisionDate LastRevisionPersID Latitude VVVVVVVVVVVVVVVVVVVVVVV VV VV VV VV VV VV VV VV VV VV VV VV VY VV VV VVVY LeaveLoss Length Location LocationCharacteristics Longitude MajorDimension MathComment MathComment n MathCommentCount MeanSensitivity MinorDimension MissingRingsAfter MissingRingsBefore NumberOfSamplesInChrono NumberOfTreesInChrono Persld Pith Project ProtectionCode Province QualityCode Radius RadiusNo RelGroundWaterLevel RingsFromSeedToPith SampleType SamplingHeight SamplingPoint SapWoodRings Sequence SeriesEnd SeriesStart Series Type ShapeOfSample Site SiteCode SocialStand Soil Type Species SpeciesName StandardDeviation State StemDiskNo Street Timber TimberHeight TimberType TimberWidth TotalAutoCorrelation TotalMean TotalMeanSensitivity TotalNORFAC TotalNORFM TotalStandardDeviation Town TownZipCode Heidelberg 123 gt Tree p gt UnmeasuredOuterRings TreeHeight gt
90. Measurements This is most useful when given the ID of a direct VMeasurement to find any sums redates or others based upon it FindVMParents This function traverses the database and gives a list of parents VMeasurements This is most useful when given the ID of a Sum Redate or Index to find which VMeasurements it was based on FindChildrenOf This function returns a list of all VMeasurements derived from something Given tree and 16 for instance it will find all VMeasurements derived from Tree ID 16 e g 96 Tellervo A guide for users and developers Z select from cpgdb findchildrenof specimen 1 A Does not traverse through object relationships Will only return children of a single particular object See FindChildrenOfObjectAncestor FindChildrenOfObjectAncestor This function returns a list of all VMeasurements derived from a particular object and its descendants The output is the same format as FindChildrenOf FindObjectTopLevelAncestor Returns the toplevel ancestor object of a given object Will return the given object if it has no toplevel ancestor FindObjectAncestors Returns the ancestor objects of a given object guaranteed from bottom to top Can return an empty set FindObjectDescendants Returns the descendant objects of a given object using a depth first traversal Can return an empty set FindObjectDescendantsByCode Convenience wrapper around FindObjectDescendants
91. O Heed de 10 3 Managing chronologies nn nn 11 The Tellervo server 11 1 Backing up and restoring your database 0 nn 11 1 1 Backup whole Virtual Appliance 2 22 22 Corn 11 1 2 Restoring a Virtual Appliance backup 2 2222 2 En nn nn 11 1 3 Backup PostgreSQL database 2 2 En e 11 1 4 Restoring a PostgreSQL database 2 22 CE nn nn 11 2 Upgrading the sefver oa lee 4 4 Be SE rer Re A 11 3 Graphical Interface to the Virtual Appliance 2 o o a A A lie LE as aa in ge ee ee 11 4 1 Usernames and passwords 2 02 0000 ee 11 4 2 Authentication and encryption 2 2 0 00 0000 eee eee CONTENTS 11 5 Directly accessing the database 2 2 Connie 11 51 PGAdminlI 2 2 2428 Paar Heer e e 11 5 2 ODBC 2 hc na EEE ae Guan A more dase a 11553 PSQU un dd et BS oe Ae aa a ok ee 11 6 Tellervo server configuration aooaa ee 11 6 1 Standard server configuration 11 6 2 Advanced server configuration 0 11 7 Managing map services 2 2 2 on on 12 Help and support 12 1 Gettingihelp Stine amp 2 tl Bee Dun Ped a A u 12 2 Support for future development 2 2 2 2 2 2 n m nn Il Developers guide 13 Developing Tellervo Desktop 13 1 Soure CO E u is A E u EE dea 13 2 Development environment 22 2 CE a 13 3 Dependencia tr na 13 4 Code layout at a ee a et 13 5 Multimedia resources o a 13 5 1 Ring remarks v o e eoe a e 13 6 T
92. Preamble K acura acu ate ak BALA ete AS BBs ak ee eed Z 4 Terms and conditions 2 2 2 2 0 0 0 0000000000034 References Index 157 157 157 158 158 159 159 161 161 162 163 163 164 167 167 171 173 173 174 178 178 183 185 Preface The Tellervo application is primarily designed for the measurement of tree ring widths and the organization and curation of the data metadata and physical samples for dendrochronological research It is cross platform running on all Java 6 and later enabled operating systems including Windows MacOSX and Linux and open source lt includes support for standard measuring platforms including Velmex Lintab and Henson Tellervo is a substantial rewrite of the original dendro application Corina developed at Cornell University since 2000 Corina itself following an earlier DOS based version programmed in C which in turn was derived from a collection of FORTRAN and C utilities While Corina was built around a standard file based data management system Tellervo uses an object relational database management system ORDBMS and server client webser vice infrastructure based on the Tree Ring Data Standard TRiDaS The application was renamed Tellervo to reflect the substantial changes made from the original Corina code base This manual is divided into two main sections the first for users the second for developers Tellervo is open source software see the details of the license on
93. RL http maven geomajas org maven iscpif fr Identifier maven iscpif fr URL http maven iscpif fr snapshots thirdparty maven iscpif fr Identifier thirdparty maven iscpif fr URL http maven iscpif fr thirdparty 6 Add proxy connectors for the above repositories 7 Run the MavenDeployCommands sh script to deploy the handful of repositories that we need that are in no repositories 8 You will need to run a similar file to deploy dependencies for TRiDaSJLib See the tridas source code for details The remote repositories contain libraries maintained by others that are not at the time of writing in the central Maven repositories We include them here to ensure they are cached in our repository and so are available to our developers even if these external repositories go down Our new repository will be populated with these external artefacts when a developer first requests them They are retrieved from the external repositories and cached in ours It is possible to manually deploy artifacts to the repository using the web interface but this is slow and tedious We normally deploy direct from Eclipse using the maven deploy goal RON Chapter 15 Webservice specifications This chapter outlines the basic syntax required for talking to the Tellero webservice and is largely aimed at developers who want to create new clients to interact with the Tellervo server The Tellervo database is accessed solely through the webservice
94. S entities At the bottom of the screen is a table containing any warnings associated with the conversion In this case there are no warnings Once you have picked the file you d like to import an import dialog screen similar to that shown in figure 7 2 is displayed The dialog is divided into three main sections TRiDaS hierarchy top left Data viewer top right and Warnings panel bottom The TRiDaS hierarchy panel contains a representation of the file being imported according to the TRiDaS data model This table also contains a status column to indicate whether input is required from the user The two main status options are Stored in database to indicate that the entity is already stored in the Tellervo database and Attention required to indicate the entity needs to be cleaned up by the user The data viewer panel on the top right of the dialog contains three tabs The first gives a standard text editor representation of the file being imported Note that when errors are detected in the file Tellervo will highlight where possible the portion of the file that is causing the problem The second tab contains a metadata editor for the current TRiDaS entity The third tab contains a viewer for ring width values if the entity selected is a measurment series Importing and exporting 37 The warnings panel at the bottom of the screen contains a list of any warnings that have occurred during the conversion process There can be many i
95. TED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES 17 Interpretation of Sections 15 and 16 If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee This manual is released inder the GNU Free Documentation License FDL v1 3 Copyright 2011 Peter W Brewer Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 3 or any later version published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts Z 3 Preamble Copyright 2000 2001 2002 2007 2008 Free Software Foundation Inc http fsf org Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Th
96. Tele VO A guide for users and developers By Peter W Brewer For Tellervo versions 1 1 x server GRAN A and 1 0 x desktop GPL Free as in Freedom 2013 Peter W Brewer Laboratory of Tree Ring Research 1215 E Lowell Street Tucson Arizona 85721 USA 1 520 621 0753 BI p brewer ltrr arizona edu Compiled May 10 2013 Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 3 or any later version published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts A copy of the license is included in the appendix entitled GNU Free Documentation License pages 178 181 TELLERVO A guide for users and developers By Peter W Brewer Compiled May 10 2013 Contents User Guide 1 Installation 1 1 Server installation iii a Ba a ee ee le ee 3 1 1 1 Install as Virtual Appliance 2 2222 oo oo on nn 1 1 2 Ubuntu native installation 2 2222 o nn 1 1 3 Advanced install on other operating systems 2 22 0 1 2 Installing the desktop application o o 12d cRifststime launch ire A A E DA A 122 Mapping SUPPO 2 4 4 3 Wis ae el eb 1 3 Upgrading Tellervo desktop 22 2 2 on n nn 1 4 Upgrading Tellervo Server 2 22 E CC on e 1 5 Uninstalling taa BR RER a oe ele p Ba ie Ren 1 5 1 Tellervo desktop application 2 2 2222 Enno 200000002 pees
97. age of intervals in the overlap which are the same For example a 75 trend a very good score by the way means that for 75 of the intervals in the overlap both samples went up in the same years and down in the same years If one sample stays the same and the other increases or decreases Tellervo considers that to be halfway between a same trend and different trend and gives it half a point Trend is a non parametric algorithm because it only takes into account if a given ring is bigger or smaller than the previous one not by how much To the trend a drop of 100 1 looks exactly the same as a drop of 100 99 Two completely random samples will have a trend of 50 on average So you d expect a trend must be greater than 50 to be significant According to Huber and Fletcher 1970 a trend is significant if 1 tr gt 50 IR For example a pair of samples with a 50 year overlap needs a 50 50450 57 1 trend to be significant but at a 400 year overlap need only a 50 50 400 52 5 trend In practice however this doesn t tend to work terribly well Using this scheme there are typically about three times as many significant trend scores as t scores and users want this narrowed down a bit more So take o 3 and use 2 tr gt 50 aa This gives about the same number of significant trend scores as t scores Trends are also used in reconciliation After they ve been reconciled both readings of a sam
98. al advanced methods for filtering the series table to help you find the data you are interested in 2 3 Reconciling data Tellervo has been developed not only for experience dendrochronologists but as a tool for teaching students It therefore includes a comprehensive reconciling tool for supervisors to check the quality of measurements made by students The reconcile dialog does a comparison of a measurement series made by a student with a references series of the same radius measured by the supervisor The same dialog can also prove useful for comparing measurements from two experienced dendrochronologists when handling particularly difficult samples Chapter 3 Measuring platforms Although it is possible to manually enter the ring widths of your samples into Tellervo it is normal to automate this process using a measuring platform Tellervo supports the most common measuring platforms including Velmex and Lintab However please note that standard Lintab platforms use a proprietary communications protocol Rinntech the manufacturers of Lintab platforms claim intellectual property rights over this protocol During discussions between the Tellervo development team and Rinntech an agreement was reached whereby the Tellervo developers agreed not to release details of the protocol In turn Rinntech has agreed to produce an adapter that can be attached to Lintab platforms so that they communicate with an open ASCII protocol Users wishing to u
99. allow access to the specified database user Configure Apache to access the webservice Verify setup by checking Apache and PostgreSQL are running that the webservice is accessible the database is accessible and that various configuration files can be read Print test report to screen vvv 14 2 1 Tellervo server script At the heart of most of the configuration and control of the Tellervo server is the tellervo server script This is a command line PHP script that is launched after installation and can be re run by the user to make changes to the configuration Although such a script would normally be written in Bash or similar we decided to go with PHP because of the requirement to interact with the Tellervo PostgreSQL database The script isolates the common tasks performed into functions It uses the getopt function to read both long e g blah and short e g b arguments from the command line These depending on the arguments given the script then calls the relevant functions To comply with standard protocols the script uses the exit function to return whether the requested task was successful or not Returning zero means the script was successful and returning any other integer means the script failed This is important so that the package management system knows when things have gone wrong and can then attempt to roll back if possible The script includes a number of helper functions and classes that you may find useful w
100. ally designed for use with the MS DOS version of Corina but was also used as the native file format in the later Java versions up to and including v1 1 A Corina file contains yearly data ring width and number of samples for that year some fixed metadata and optionally weiserjahre data and a listing of element samples for summed samples The title comes first on a line by itself followed by a blank line The title is repeated later so this is only to make it easier for people or external programs to read the title The metadata section comes next The syntax is TAG value Tags are all uppercase Their order is fixed Some values are terminated by a newline others by the next semicolon Valid tags and their internal names are VVVVVVVVVVYV ID 8 character ID used when exporting to Tucson format NAME Name of the series DATING Either R relative or A absolute UNMEAS_PRE Number of unmeasured rings towards the pith UNMEAS_POST Number of unmeasured rings towards the bark FILENAME COMMENTS COMMENTS2 etc Free text comments TYPE either C core H charcoal or S section SPECIES SAPWOOD Count of sapwood rings PITH either P present present but undateable or N absent 116 Tellervo A guide for users and developers gt TERMINAL either B bark W waney edge v near edge vv unknown CONTINUOUS referring to the outer ring either C continuous R partially continuous or N
101. an based system Install using your favorite package management system or from the command line like this e g sudo dpkg install tellervo xx xx_all deb On Ubuntu and similar distributions the package should add a Tellervo shortcut to your applications menu Alternatively you can start Tellervo from the command line by typing tellervo For other Linux distributions you are probably better off using the standard Java executable described below Note though that you will need to manually install serial port and 3D graphics libraries to use these features Tellervo was initially developed against Sun Java 6 JRE however now OpenJDK6 is routinely used See section 13 11 page 70 for more information The Snow Leopard requirement for Mac computers means that Tellervo cannot be run on older PowerPC based MacOSX computers However if you have old PowerPC iMacs you could consider replacing the operating system with a modern Linux distribution like Ubuntu Linux continues to support PowerPC architecture even in the most recent releases You will of course not be able to run any of your other exisiting MacOSX software Installation 9 in Tellervo If there is demand for a package for other Linux distributions we may make these available in the future For instance basic RPMs have been produced but we do not have the time or resources to test these at the moment Other operating systems Make sure you have Java 6 installed then download
102. an this License grants you permission to propagate or modify any covered work These actions infringe copyright if you do not accept this License Therefore by modifying or propagating a covered work you indicate your acceptance of this License to do so GNU General Public License 177 10 11 12 13 14 Automatic Licensing of Downstream Recipients Each time you convey a covered work the recipient automatically receives a license from the original licensors to run modify and propagate that work subject to this License You are not responsible for enforcing compliance by third parties with this License An entity transaction is a transaction transferring control of an organization or substantially all assets of one or subdividing an organization or merging organizations If propagation of a covered work results from an entity transaction each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party s predecessor in interest had or could give under the previous paragraph plus a right to possession of the Corresponding Source of the work from the predecessor in interest if the predecessor has it or can get it with reasonable efforts You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License For example you may not impose a license fee royalty or other charge for exercise of rights granted under this License
103. and write Reference implementation CATRAS Data metadata Data and some structured metadata Calendar type Gregorian Absolute dating support Yes Undated series support Yes Relative dating support No Multi series support No Original designer Roland Aniol Appendix D CATRAS D 1 Background The CATRAS format Aniol 1983 is the only known binary dendro data format As such it can t be read by a simple text editor and can t be imported by spreadsheet or database programs The format was designed by Roland Aniol for use in his program of the same name The binary nature of the format means the files are typically much smaller than text files containing similar data The closed nature of the format originally meant that users were tied to the application The fact that users can t manually edit the file means that the validity of files is not a problem like it is with most other dendro formats The format was originally decoded in the early 1990 s and permission was granted by Aniol for a converter to be included in Henri Grissino Mayer s CONVERT5 application Subsequently others have independently released application and code that can read CATRAS files to a greater or lesser extent Following its original release in 1983 CATRAS was updated several times the most recent version v4 42 was released in 2010 The code in DendroFilelOLib is based in part on Matlab Fortran and C code of Ronald Visser Henri Grissino Mayer and lan Tyers D 2
104. antae 2010 08 16 1001 1035 35 x dis YAR Yarak n DATA ONLY Christia C YMT 1340 A A 1 Leann Canady Raw Plantae 2010 08 16 1001 1047 47 x dis YAS Mu la Yass ada Byzantine Shi C YMT 1335 A B 1 Leann Canady Raw Plantae 2010 08 16 1001 1033 33 x dis YAY Samsun ar amba Yayc lar M C YMT 1335 A A 1 Leann Canady Raw Plantae 2010 08 16 1001 1029 29 x 3 5 C YMT 1330 A B 2 Katie Griggs Raw Plantae 2010 08 18 1001 1031 31 x b YBY Afyon ay Yusuf bin Yakub Mel C YMT 1330 A B 1 Leann Canady Raw Plantae 2010 08 17 1001 1031 31 x YIL Bursa Yildirim Darussifasi C YMT 1330 A A 2 Katie Griggs Raw Plantae 2010 08 18 1001 1041 41 x dls YMK Istanbul Yenikapi Marmaray Ka C YMT 1330 A A 1 Leann Canady Raw Plantae 2010 08 17 1001 1042 42 x Istanbul Yenikapi Metro C YMT 1316 A B 1 Leann Canady Raw Plantae 2010 08 16 1001 1056 56 x C YMT 1316 A A 1 Leann Canady Raw Plantae 2010 08 16 1001 1060 60 x OR Forget finca aletas C YMT 1315 A B 1 Leann Canady Raw Plantae 2010 08 17 1001 1041 41 x di YOT Yass ada Ottoman Shipwreck C YMT 1315 A A 1 Leann Canady Raw Plantae 2010 08 17 1001 1046 46 x i YOZ Yozgat aml Milli Parki Orman C YMT 1314 A B 1 Leann Canady Raw Plantae 2010 08 16 1001 1054 54 x db yrdy yrdy56 C YMT 1314 A A 1 Leann Canady Raw Plantae 2010 08 16 1001 1060 60 x dis YRM Malatya Eski Malatya Yar mt C YMT 1216 A B 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1072 72 x dls YU CSG CSG Former Yugosla
105. are all open source there are no license fees to pay 1 Open VirtualBox and go to File gt Import Appliance E W A RAM if you have powerful machine Press the choose button and locate the virtual appliance file that you downloaded from the website Rename the server if you choose then press the finish import button Once the server is installed highlight it in the virtual machine list and press the settings button Go to Network and choose Attached to Bridged Adapter You may also like to give the system more 6 Click ok then back on the main page press the run button 7 Read and accept the information about how to gain and release control of the keyboard in VirtualBox 8 The server will boot and eventually present you with a command line login screen Log in with the following temporary details Username tellervo Password dendrochronology 9 Once you are logged in the server will automatically ask you a series of questions 10 Answer the questions and the configuration will finish by testing your new server see figure 1 1 11 Note down the URL of your new Tellervo webservice as you will need to enter this when you start your Tellervo desktop client If you need to know the URL at a later date you can run the tests again by typing 22 tellervo server test 12 You can now install and run the Tellervo Desktop application see section 1 2 To save on download size and disk space only the esse
106. are getting Maven build errors you may like to try running Maven from the command line Navigate to the base of your Tellervo folder and type mvn clean mvn package mvn install or mvn deploy depending on what you are trying to do Developing Tellervo Desktop 69 13 9 1 Windows installer Maven generates the Windows executable for the Tellervo application through the launch4j plugin Windows users however expect an installer that will create menu entries and add uninstall options to the control panel An installer is also required to install the user manual and the native libraries required for the serial port and 3D graphics features in Tellervo The best open source tool for creating Windows installer scripts is NSIS see http nsis sourceforge net This is an extremely flexible scripting system that does all we need If you have NSIS installed the Maven package goal should create both Windows 32 and 64 bit installers automatically We use the Maven antrun plugin to run the makensis executable twice once on a script for build the 32bit executable and a second for creating the 64 bit executable These scripts are stored in Native BuildResources WinBuild and are indentical they import the major of the script from the same file with the exception of the location of the native libraries folder The Maven resource plugin moves them into the target folder and replaces the version numbering for use in filenames etc 13 9 2 Mac package
107. ata files or measuring new samples you can access your data through the database browser This is accessed through the File gt Open or File gt Open multiple menus and an example of the dialog is shown in figure 2 4 The same database browser dialog is used in multiple places throughout Tellervo e g when adding addition series to graphs and when choosing chronologies to crossdate against The database browser is divided into two main parts On the left is the browse and search tabs and on the right is the series table Selecting options in the browse or search tab populates the series table on the right with all the series that match the specified criteria A The search tab is currently a work in progress so we recommend you use the browse tab until further notice This doesn t mean you don t have to backup your data though Whoever is in charge of maintaining your Tellervo database should make sure regular backups are made preferably offsite 16 Tellervo A guide for users and developers o Database browser DEORE gt o o Ta Browse Name Y Version User Type Taxon Modified Begin End n Rec Ja l C YMT 1349 A B 1 Leann Canady Raw Plantae 2010 08 16 1001 1048 48 x la i YAL Yale University Ben Foster Hoya C YMT 1349 A A 1 Leann Canady Raw Plantae 2010 08 13 1001 1062 62 x a YAP Corum Eskiyapar r C YMT 1340 A B 1 Leann Canady Raw Pl
108. ately as values A derivedSeries is a calculated series of values and is a minor modification of the v series concept proposed by Brewer et al 2010 Examples include index average of a collection of measurementSeries such as a chronology A derivedSeries is derived from one or more measurementSeries and has multiple values associated with it A value is the result of a single ring measurement Examples include total ring width earlywood width latewood width The values are related to a measurementSeries or a derivedSeries In case of a measurementSeries the variable and its measurement unit e g microns 1 100th mm etc are recorded as well Tellervo supports both total ring width and early latewood values Support for other variables is planned for a future version Working top to bottom the TRiDaS entities are nested within each other For instance a project contains one or more objects which in turn contains one or more elements and so on The benefit of this is that you record data once and once only In standard file based dendrochronological software when creating measurement series you are typically required to type the name of the site the species of tree etc over and over again This is not only time consuming but very error prone Keeping data consistent is also difficult For instance if it was determined that a tree species was identified incorrectly in existing file based software the user would need to locat
109. available to the public and in some countries other activities as well To convey a work means any kind of propagation that enables other parties to make or receive copies Mere interaction with a user through a computer network with no transfer of a copy is not conveying An interactive user interface displays Appropriate Legal Notices to the extent that it includes a convenient and prominently visible feature that 1 displays an appropriate copyright notice and 2 tells the user that there is no warranty for the work except to the extent that warranties are provided that licensees may convey the work under this License and how to view a copy of this License If the interface presents a list of user commands or options such as a menu a prominent item in the list meets this criterion 1 Source Code The source code for a work means the preferred form of the work for making modifications to it Object code means any non source form of a work A Standard Interface means an interface that either is an official standard defined by a recognized standards body or in the case of interfaces specified for a particular programming language one that is widely used among developers working in that language The System Libraries of an executable work include anything other than the work as a whole that a is included in the normal form of packaging a Major Component but which is not part of that Major Comp
110. ave used a barcode nearly all of this metadata will be filled in for you otherwise you will need to fill this out yourself Details about metadata can be found in chapter 4 page 19 Once you have populated the metadata tab you can then switch to the data tab figure 2 1 Ki P ABC 1 A A 1 1001 1000 n 0 DEORE File Edit Administration View Tools Graph Help 2 i Z Oks zta amp a gt Year po 1 2 3 4 5 6 7 18 9 Rel Yr 1001 Ef a P gt b r calendar Relative Variable Ring width Units um Mean sensitivity n a Data Metadata i Figure 2 1 An empty data window ready to receive measurements Note the status bar at the bottom includes buttons for changing the measurement variable display units and cumulative statistics The data table stores ring width values in decadal rows following the standard convention which derives from data entry via punch cards Undated sequences begin in the relative year 1001 for the same reason 14 Tellervo A guide for users and developers Before you begin measuring you need to tell Tellervo what sort of measurements you are making whole ring widths or early latewood widths the default is whole ring widths To specify early latewood widths you need to go to Edit gt Measuring mode gt Early and latewood widths If you use this menu after you have already measured some rings you will be warned that Tellervo will delete the data you have already
111. brandt paintings in a museum What is considered a project is up to the laboratory performing the research It could be the dating of a group of objects but the laboratory can also decide to define a separate project for each object Therefore a project can have one or more objects associated with it Due to historical reasons TRiDaS projects are not currently supported within Tellervo although future plans include adding project support a An object is the item to be investigated Examples include violin excavation site painting on a wooden panel water well church carving ship forest An object could also be more specific for example mast of a ship roof of a church Depending on the object type various descriptions are made possible An object can have one or more elements and can also refer to another sub object For instance a single file may contain three objects an archaeological site object within which there is a building object within which there is a beam object The list of possible object types is extensible and is thus flexible enough to incorporate the diversity of data required by the dendro community Only information that is essential for dendrochronological research is recorded here Other related data may be provided in the form of a link to an external database such as a museum catalogue Y An element is a piece of wood originating from a single tree Examples include one plank of a water well a single w
112. business in San Francisco California as well as future copyleft versions of that license published by that same organization Incorporate means to publish or republish a Document in whole or in part as part of another Document An MMC is eligible for relicensing if it is licensed under this License and if all works that were first published under this License somewhere other than this MMC and subsequently incorporated in whole or in part into the MMC 1 had no cover texts or invariant sections and 2 were thus incorporated prior to November 1 2008 The operator of an MMC Site may republish an MMC contained in the site under CC BY SA on the same site at any time before August 1 2009 provided the MMC is eligible for relicensing References Aniol R 1983 Tree ring analysis using CATRAS Dendrochronologia 1 45 53 Baillie M Pilcher J 1973 A simple crossdating program for tree ring research Tree Ring Bulletin 33 7 14 Bisby F A Roskov Y R Ruggiero M A Orrell T M Paglinawan L E Brewer P W Bailly N van Hertum J 2007 Species 2000 and ITIS Cat alogue of Life 2007 Annual Checklist CD ROM Species 2000 Reading Brewer P Murphy D Jansma E 2011 TRiCY CLE a universal conversion tool for digital tree ring data Tree Ring Research 67 135 144 Brewer P Sturgeon K Madar L Manning S 2010 A new approach to dendrochronological data management Dendrochronologia 28 13
113. by right clicking on any cell in the table and selecting one or more of the standard notes see figure 2 3 Tellervo supports all standard TRiDaS remarks including fire damage frost damage crack false ring s compression wood tension wood traumatic ducts single pinned double pinned triple pinned and many others Rings that include remarks are indicated by the relevant icon in the data screen Depending on your method of work this can be useful for keeping track of sample pin holes For instance if a missing or false ring is discovered after a sample has been pinholed the offset in pinholes can be easily seen without resurfacing the sample In addition to the right click menu you can also ac cess ring remarks by opening the remarks panel using New series 1001 1001 n 1 Raw 2 the button on the toolbar This panel gives the the Data Metadata ability to add free text remarks to individual rings Year 0 1 2 3 4 5 6 n a aps 1001 am One final method for adding remarks is specific to E Insert year Insert fire history researchers Standard FHX style remarks El Insert missing ring Insert can be added to rings by pressing the equivalent FHX Delete year L character code key in the relevant ring cells For in A i E Fire damage stance pressing a lower case a in a cell will add the K Frost damage fire injury in latewood remark 4 Crack False ring s The data screen also contains a status bar at th
114. chanism for detecting when a client is too old to handle the API that it is using In this case the server will refuse to handle the request A similar complementary mechanism is in place in the client for instances when a client is attempting to talk to an older server that it no longer supports At the moment the Tellervo desktop client is the only known software that talks to the Tellervo server but in the future we may have other 3rd party clients making requests For example it would be possible to develop a central data repository much like the ITRDB or perhaps as an extension to the existing ITRDB that harvests data from multiple labs each running the Tellervo server Alternatively existing 3rd party desktop applications e g TSAP Win PAST4 etc may be extended to enable them to obtain data directly from servers running the Tellervo server software Either way it is important to include the ability to specify the oldest versions of clients that are able to connect and also to be able to specify different versions for different types of clients It is also necessary to include the ability to allow or disallow access to the server by unknown client applications If a new program is written by other developers and it attempts to access the server it could contain bugs or even malicious code that interferes with the server For a production instance of the server this is obviously undesirable therefore the systems configuration option only
115. codes are used throughout Tellervo to describe TRiDaS entities They can also be used in many places to specify entities that the user would like to choose For instance in the database browser you can type the lab code for an object element sample radius or series to search the system for all the series that match the specified entity For instance entering ABC 5 would search for all series associated with element 5 from object ABC Metadata Example ABC 1 A A 1 Element Code _ ABC 1 This tree grew at a site called ABC lt was the first tree sampled at the site and received the element code of 1 Element 1 Sample Code ABC 1 A Two samples were taken from tree 1 Sample Sample These were labeled A and B If there A B were more than two samples tends to happen with charcoal the third and fourth would be labeled C and D and so on The lab code we are constructing is for the first sample A Radius Code HO ABC 1 A A i i A sample may have many radii the Rad Rad el a first radius receives the letter A and the second B and so on For cores there is usually only one radius A to measure Series Series Series Code ABC 1 A A 1 A radii will have at least 2 readings The final letter in the lab code relates to the first or
116. collected Once in early and latewood widths measuring mode you will be able to choose which data is displayed in the table by clicking the variable box on the status line and choose between Ring width Earlywood width Latewood width Early Latewood width To begin measuring your sample you can now go to Edit gt Start measuring press the start measuring button on the toolbar or you can press F5 While measuring you should be provided with audible feedback for each ring measured with a more pronounced sound made every 10th ring If there is a problem communicating with your measuring hardware check your settings in the preferences dialog If you still have problems contact the Tellervo developers by going to Help gt Report bug on last transaction making sure you include your email address and any further information If your sample is already dated and or you already know how many rings your sample has then you can initialise your data matrix using the button on the toolbar This gives you a dialog requesting date and ring number information which can be useful for those of you that use the skeleton plotting method prior to measuring Note by default Tellervo labels rings as relative years beginning in 1001 If your sample is dated you should explicity tell Tellervo either using the initialise grid function prior to measuring or by going to Tools gt Redate once you ve finished Depending on the measuring platform hardware you have yo
117. config php should normally only be edited by Tellervo developers If you want to make configuration options editable by the administrator of the Tellervo server then these should be implemented within the config php file There is a config php template file which is used to construct the config php file on the users system Simply adding hardcoded entries to this file is the simplest way when a default value is appropriate If the value of your field needs to be generated either by asking the administrator a question e g name of lab or dynamically at the time of installation e g IP address of the server then this template file should contain placeholder values which can then be replaced by the tellervo server configuration script For instance the config php template file contains a placeholder for the hostname of the server like this hostname 1P The value is set by the tellervo server script using the function Keep in mind though that a user with the necessary privileges would need to provide this new program with their credentials for it to make changes to data Developing Tellervo Server 81 setConfigVariable var value Keep in mind though that during an upgrade the config php is maintained and not replaced If you make additions to the config php template you will also need to make provision for handling changes to the end users existing config php If you want to add new configuration fields that don t need to be
118. ction comes from Van Loan 1999 Sometimes the exponential index does a lousy job If a tree is living in a crowded area and the trees around it get cut down suddenly it has much better growing conditions so it might grow faster as it gets older instead of slower If you tried to use an exponential curve on a tree like this it would exaggerate this growth and useful data would get flattened out The result is you re looking at the growing conditions of this one tree so it s not going to crossdate as well Alternatively imagine you are working on a tree with a fire scar that has a few very large rings An exponential index wouldn t take much notice of this because most of the sample is still shaped like an exponential curve but when you applied it they would be grossly out of proportion For these types of samples there are other indexing algorithms available 9 1 2 Polynomial Index When you ask Tellervo to perform a Polynomical Index it tries to fit a polynomial curve to your data using the following equation gt yY ant ap 1271 4 a9 aiz ao You decide what degree polynomial n to use and Tellervo automatically finds the best values of ao a an to fit your data 9 1 3 Horizontal Line Index This only changes the magnitude not shape of the curve and is used when you would link to combine raw and indexed data together It is a special case of polynomial where the horizontal line is equal to the average value
119. ctured metadata however standardisa tion of metadata is very poor resulting in metadata often being little more than free text comments Calendar type Astronomical Absolute dating support Yes Undated series support No Relative dating support No Multi series support Yes Original designer Richard Holmes U 1 Description The Tucson format is perhaps the most widely used dendro data format Unfortunately it seems there was never definitive documentation Support for the format has been incorporated into a number of dendro applications but without format documentation there are variations in these implementations resulting in quite a lot of subtle differences in files The often tight association between the Dendro Program Library DPL and the ITRDB means that perhaps the most definitive documentation for the format is the ITRDB website The Tucson format is best considered as covering two different sub formats which are often referred to by their file extensions RWL and CRN RWL files are used for storing ring width data whereas CRN files are used for storing chronologies The ITRDB website includes detailed information on how to include structured metadata in Tucson format files Unfortunately there are no tools for creating and or validating Tucson files so the vast majority of files circulating in the community today including those in the ITRDB do not adhere to these standards U 2 RWL files Tucson RWL files begin with three li
120. d multiple times in a single file All lines should be 80 characters long and the first line of a series is denoted by a tilde in the final column This meta line contains four fields Chars 0 9 number of data values terminated with N Chars 11 19 start year terminated with l Chars 21 68 series title Chars 69 79 fortran format descriptor Char 80 Tilde marker The Fortran format descriptor in the example below is 2 26F3 0 The constituent parts are as follows p gt 2 this is the scaling factor for the data values In this case 2 10 2 0 01 Please note that in the Convert5 program this scaling factor is only read once in the first header line so files with multiple series each with different scaling factors will read incorrectly 26F means there are 26 values in each line 3 0 means that each data value should be read as 3 integer values 162 Tellervo A guide for users and developers The example below therefore means there are 26 data values per line each consisting of 3 digits which should be interpreted by multiplying by 0 01 i e values are in 1 10ths mm V 2 Example file on on Fk WH eH 176 N 1277 1 ABCDO1 2 26F3 0 142338334409362308360264325318134151219268290222278258173198294202170176172121 87130114108170135131126 87100 86104103127112 94 96120168149119124 79 67 88 90 93 77 49 42 53 38 57 43 50 41 56 66 62 55 55 45 47 63 58 60 44 45 49 50 62 61 43 54 91 60 56 43 52
121. data block begins with the marker line VAL like metadata keys subsequent characters are ignored so sometimes the rest of this line is used for comments Subsequent lines contain integer values delimited by a space or line feed Missing rings are marked with a comma character and the end of the data is marked with a semicolon C 2 Additional information There is nothing in the specification to say what precision the data values should be in Following conversations with users it appears that Besancon files are mostly 1 100th mm but this is not always the case Some files include a Pr cision field but this is not documented or standardised There are a number of additional fields that are commonly used but which do not appear in the format specification These are also supported by the DendroFilelOLib ESP Species ECO Bark present C 3 Example file abc22 43 Lon 129 Esp quercus sp Nat lambris Precision 1 100 Moelle non presente Aub 0 valeurs 149 119 156 146 170 187 197 146 191 177 137 108 160 108 120 177 136 174 190 109 189 176 170 162 114 126 133 152 146 127 119 131 146 133 147 82 57 77 77 82 96 49 97 76 88 82 72 83 81 90 85 87 78 104 111 132 141 105 104 120 1 0 I Ba aS 89 94 88 90 115 111 106 107 120 80 92 98 84 97 82 100 86 99 65 85 113 90 82 57 57 99 94 9 105 120 110 93 96 131 133 123 122 113 119 95 127 88 104 Format name CATRAS Other name s None known Type Binary Extension s cat Read write support Read
122. de columns button on the top right of the screen The bulk entry interface also includes support for reading GPS units By pressing the satellite button on the toolbar the user can provide a GPS Exchange GPX format file containing the waypoint locations recorded in the field Tellervo will add a waypoint column to the spreadsheet with a drop down menu which will automatically populate the latitude and longitude fields for the record It is common for many of the metadata fields to be the same in a single field collection For instance when coring trees in a forest they are often of the same species Rather than requiring the user to repeatedly type the same data over and over the copy row button can be used to duplicate a record and then the user can change the few fields that are different Another time saving feature is the ability to cut and paste back and forth between Tellervo and spreadsheet programs like Microsoft Excel This can be particularly helpful if you already have large amounts of metadata entered into a spreadsheet The best way to do this is to populate a row in Tellervo then copy this into Excel This will show then show you the order of columns and the format that Tellervo expects data to be in When you have entered all the data you want you can press the Import selected button to write the records to the database Start on the objects tab then move to elements then samples The samples page has the additio
123. delete lt c request Type gt lt c status gt Error lt c status gt lt c message code 907 gt Foreign key violation You must delete all entities associated with an object before deleting the object tself lt c message gt lt c header gt lt c tellervo gt 15 3 Authentication requests There are two methods for authenticating yourself against the Tellervo server plain and secure We strongly recommend you use the secure method as the user name and password are sent in plain text over the internet when using the plain method This goes against so much of the hard work we ve put in to making the system our w 86 Tellervo A guide for users and developers secure It is quite likely that we will disable the plain authentication method by default in the future For now it will be left in place as it makes testing new clients much easier For further details and discussion about the authentication design please see section 16 1 page 91 15 3 1 Plain authentication If you still want to go ahead and use plain authentication despite all the risks then this is how you do it lt xml version 1 0 encoding UTF 8 gt lt tellervo xmIns http www tellervo org schema 1 0 xmlns tridas http ww tridas org ie gt lt request type plainlogin gt lt authenticate username yourusername password yourpassword gt lt request gt lt tellervo gt 15 3 2 Secure authentication Although this is
124. demnification of licensors and authors of that material by anyone who conveys the material or modified versions of it with contractual assumptions of liability to the recipient for any liability that these contractual assumptions directly impose on those licensors and authors All other non permissive additional terms are considered further restrictions within the meaning of section 10 If the Program as you received it or any part of it contains a notice stating that it is governed by this License along with a term that is a further restriction you may remove that term If a license document contains a further restriction but permits relicensing or conveying under this License you may add to a covered work material governed by the terms of that license document provided that the further restriction does not survive such relicensing or conveying If you add terms to a covered work in accord with this section you must place in the relevant source files a statement of the additional terms that apply to those files or a notice indicating where to find the applicable terms Additional terms permissive or non permissive may be stated in the form of a separately written license or stated as exceptions the above requirements apply either way Termination You may not propagate or modify a covered work except as expressly provided under this License Any attempt otherwise to propagate or modify it is void and will automatically terminate
125. dentical the only difference being that the AVR extension indicates the file is a measurement series file and AVS extension indicates a chronology file The file begins with a six character header ale Ring number where sapwood begins Zero Ring number where sapwood ends also length of sample Zero 6 a AUN Zero Zero If there is no sapwood recorded then bytes 2 and 4 will both be zero The zero bytes at positions 1 3 5 and 6 can be used as a signature to check the file is in Cracow format Following the six header bytes there comes the ring width values Each ring value is stored in two bytes the second containing the values from 0 to 99 and the first contains the values 100 For instance the ring value 345 would be stored in two values 3 and 45 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer F 1 Description Appendix F Comma Separated Values Comma Separated Values CSV Text file Various typically txt or csv Read and write n a Data only Gregorian Yes No No No n a Comma separated values format is a simple text format for representing tabular data It is not specific to dendrochronology data and is supported by most spreadsheet and database applications Data is delimited into columns using a c
126. di a a i 15 2 2 Errors and warnings 2 2 2 22mm nn 15 3 Authentication requests 2 22 22 2 nn rn 15 3 1 Plain authentication 2 22 22 rn nn 15 3 2 Secure authentication 2 22 22 0 o o 15 3 3 Cookies and sessions 222 0 0 rn 15 354 1 Logout ccoo pa ehr ser a o A Gg een 15 4 Reading records AA KK e at aa la 15 5 Deleting records 22 2 2 2 onen 15 6 Creating records aoaaa aaa 15 7 Updating records 4 2 0 G08 e a e a li 15 8 Reading and setting permissions 2 2 2 2 2m 16 Systems architecture 16 1 Authentication design 2 2 Cm nn 16 2 Database permissions design 2 22 2 Cum nn 16 3 Universally Unique Identifiers 2 22 Cu oo n nn 16 4 Barcode specifications 2 2 2 17 Tellervo Database 17 1 Database structure 2 2 ae A a a a E a 17 2 Spatial eXtension su data aa 17 3 CPGDB functions e aras A et le 17 4 Complex database functions 00 2 020004 Ill Appendices A Belfast Apple A 1 Description ar sn Ager BP 2208 2 A Pa A 2 Example filen 2600 ata di ee ee B Belfast Archive B 1 Des e he ee N B 2 Exa mpe fileres oi panes teh Be en hoe eta C Besancon C 1 Description 4 2 45 0a el a TR ORG EN ES C 2 Additional information 2 2222 a Emm C 3 Example files 2 24 0 id deg Goan na oh ho D CATRAS D 1 Backgrounds 2 Hr ta Sh Ale ASS GN ot an a e TAs ht a D 2 Reading bytecode oaoa o DL Strings feeb a koe nee ea A RR a PR Integers a u vor ag ae lee MM a ee D
127. ding UTF 8 gt lt tridas xmIns xsi http ww w3 org 2001 XMLSchema instance xsi schemaLocation http www tridas org 1 2 1 dev sourceforge tridas XMLSchema 1 2 1 tridas 1 2 1 xsd xmIns http www tridas org 1 2 1 xmins xlink http ww w3 org 1999 xlink gt lt project gt lt title gt Aegean Dendrochronology Project lt title gt lt identifier domain dendro cornell edu gt C lt identifier gt lt createdTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt createdTimestamp gt lt lastModifiedTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt lastModifiedTimestamp gt lt type gt Dating lt type gt lt description gt Our key long range goal is to build long multi millennial scale tree ring chronologies in the Aegean and Near East that will extend from the present to the early Holocene to cover broadly speaking the last 10 000 years of human and environmental history Our raison d etre is to provide a dating method for the study of history and prehistory in the Aegean that is accurate to the year This kind of precision has up to now been lacking in ancient studies of this area Indeed few archaeological problems stimulate as much rancor as chronology especially that of the Eastern Mediterranean The work of the Aegean and Near Eastern Dendrochronology Project aims to help to bring some kind of rational and neutral order to Aegean and Near Eastern chronology
128. dled by the installer for the respective platforms 13 10 Java Architecture for XML Binding JAXB Java Architecture for XML Binding JAXB is a technology that automatically maps Java classes to XML schemas and vice versa It includes the ability to marshall data from Java classes to XML files and unmarshall data from XML files into Java class representations JAXB is used by TridasJLib to create Java class representations of the TRiDaS data model It is also used directly in Tellervo to create classes for the Tellervo web service Although the Tellervo webservice is based heavily on TRiDaS the two were developed in parallel the Tellervo schema extends TRiDaS by including classes such as dictionaries and the box concept which are required for a lab data management application The Tellervo JAXB classes are automatically built by Maven using the maven jaxb2 plugin and placed within the src main generated folder Please note that any manual changes to these classes will automatically be overriden the next time Maven is run If you feel that changes are necessary to these classes then it is likely that one or more of the following needs modification gt The Tellervo schema located in src main resources schemas gt The Tellervo JAXB bindings located in src main resources binding The specification for how JAXB is run located in the pom xml file Please note that JAXB supports plugins and extensions for enhancin
129. drag up and down Tilt Hold Shift on the keyboard and Left mouse button click and drag up and down or use Page Up and Page Down on the keyboard Rotate Hold Shift on the keyboard and Left mouse button click and drag left and right Stop Spacebar Reset Heading N Reset all R Another method of navigating around the map is by using the built in gazetteer You can enter and place name or coordinate information into the box at the bottom of the screen and you will fly to the requested location 5 2 Interacting with data Each marker on the map represents either a TRiDaS object or element in your Tellervo database By clicking on these pins you can get more information from the database see figure 5 3 The example above shows the ring marker is of a site in Napoli called Poggiomarino code name POG You can see the option for searching for all series in the database associated with this site and also the option for viewing all the metadata Mapping 29 POG Napoli Poggiomarino Site Search for L 3 View associated series metadata Figure 5 3 Screenshot of a map with information pin expanded 5 3 Map layers Tellervo comes ready configured with basic map layers including high resolution satellite imagery and basic political features You can turn background layers on and off by going to View gt Layers or using the layer panel at the left of the screen when using Site map Map layers are down
130. ds are highlighted with a red star Note that whether a field is mandatory or not can depend on the other fields that have been filled in For instance the dimensions of an element are not required but if dimensions are given then the units for these measurements must also be provided A number of the metadata fields are restricted with regards the values that you can enter These are known as controlled vocabularies in TRiDaS terms Controlled vocabulary fields are represented by drop down menus Similarly fields that expect numerical values such as element dimensions will only allow numbers The final method data entry method is through custom dialogs for example there is a custom dialog for entering location information This accepts coordinates in either decimal degrees or degrees minutes and seconds Alternatively you can use data from a GPS handset by providing a GPS Exchange GPX format file containing the waypoints The GPX format is the most common interchange format for GPS data You can pick the relevant waypoint from the drop down menu You can also preview the defined coordinates on a map using the view on map button A popular open source GPS communication tool is GPS Babel It is an easy to use application which can download data from the majority of GPS handsets See http www gpsbabel org for more information 4 3 Entering bulk metadata Entering metadata on a sample by sample basis works perfectly well but does not n
131. e or distribute the Document except as expressly provided under this License Any attempt otherwise to copy modify sublicense or distribute it is void and will automatically terminate your rights under this License However if you cease all violation of this License then your license from a particular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means this is the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License If your rights have been terminated and not permanently reinstated receipt of a copy of some or all of the same material does not give you any rights to use it Future revisions of this license The Free Software Foundation may publish new revised versions of the GNU Free Documentation License from time to time Such new versions will be similar in spirit to the pres
132. e all data series from this tree and manally update the metdata This is not the case in Tellervo A tree is represented just once in Tellervo and samples of this tree and the subsequent measurement series reference this one entry If metadata for this tree needs to be changed the tree record is updated in just this one place Because the measurement series obtain this information by reference then all associated series are automatically kept up to date 4 2 Entering sample metadata The metadata for a series is viewed and edited on the Metadata tab of the main window such as that shown in figure 4 2 You can see the interface is organized according to the TRiDaS data model with separate tabs for object through to series When creating a new series the metadata screens must be populated in order This is necessary because of the nesting of entities described above For instance an element is associated with an object so an object must be chosen before an element can be defined Likewise an element must be chosen before any samples of this element can be defined Much of the time the entities that you need will already be stored within the database Instead of re entering data you simply need to select the existing entry from the database saving a great deal of time Depending on the situation buttons will appear at the top of the dialog to let you choose an entry from the database 22 Tellervo A guide for users and developers
133. e bot Compression wood tom By clicking on the units section you can switch between micron and 1 100th mm units Tellervo un derstands the units being supplied by the measuring platform therefore changes here are purely for dis play purposes only If you have a platform that measures in microns but prefer to see the values in 1 100th mm then you can use this feature There are also options on the status bar that enable you to choose one of a variety of summary statistics about your series Figure 2 3 Right click context menu showing some of the options for adding remarks to rings Once you have finished measuring your sample you should then go to File gt Save to save your series to the database 2 2 Opening existing data If you have used traditional dendrochronology software you are probably used to opening existing dendro data files from your computer Tellervo works in a different way All data accessed by Tellervo is stored within the central Tellervo database rather than in files The database provides many benefits over file based storage most importantly it means there is a high degree of security and integrity in your data To use data that you have stored in existing data files you must first import your data into the Tellervo database This gives you the opportunity to clean up your data For details of how to import your data see chapter 7 page 33 Once you have data in your database either by importing existing d
134. e complications arising from the virtual measurement concept creating new series in Tellervo is necessarily more complicated than any other of the TRiDaS entities The workflow required to create a new series is illustrated in figure 14 3 14 2 Server package The Ubuntu server package is built by Maven at the same time as the desktop package see section 13 9 during the package goal The server packaging is done as a secondary execution of the JDeb plugin JDeb is configured in the pom xml by including all the files that need to be copied along with where in the target file system they should be placed The database files are installed to usr share tellervo server and the webservices files to var www tellervo The metadata for the deb file is included in the control file located in Native BuildResources LinBuild Server Control JDeb makes use of Ubuntu s excellent package management system to handle the dependencies Adding or editing dependencies is simply a matter of changing the depends attribute control file The ServerControl folder also contains scripts called preinst postinst prerm and postrm which are launched before and after installation and before uninstalling These files are called with different parameters depending on whether this is part of a fresh install an upgrade or an aborted install There are a number of rules that the resulting deb package should follow e g if a program is configured twice then t
135. e integer values in the file are measured in 0 01mm 1 100th mm units whereas if a 9999 stop marker is used the units are 0 001mm microns The stop marker is therefore used to indicate the end of the data series and the units the data are stored in There appears to be no official specification as to how missing rings should be encoded but the standard notation seems to be to use 999 or 0 U 3 CRN files Tucson CRN files are used to store chronology data In addition to each data values they also have space for a sample depth or count value to record how many values were combined to give each data value CRN files should strictly begin with the same 3 header lines that are described above for RWL Like RWL files the specification is often partially adhered to and at times ignored completely The data lines for CRN files are quite different to RWL Chars 1 6 Series ID Next 4 chars Year of first value in this row Ten data value blocks consisting of four integer characters for the data value then a space then two integer characters for sample depth The stop marker in a CRN file should be 9990 U 4 Workarounds and quirks No information was given as to how to handle the non existent year OAD BC For data files with years all in the AD period this is not a problem Most dendro software seem to treat year numbers in Tucson files as using the Astronomical Calendar whereby 1 1AD 0 1BC 1 2BC etc This goes agai
136. e mechanism for pairing computer character codes with the character glyphs that we read The widely used standard was originally ASCII but this does not include diacritic characters and characters specific to certain languages There have since been many character encodings proposed e g ISO 8859 1 for Western Europe and ISO 8859 7 for Greece as well as some that are specific to Windows and Mac operating systems e g Windows 1252 and MacRoman The character set that is becoming most widely used today is Unicode UTF 8 This is capable of representing the vast majority of characters 107 000 while remaining backwards compatible for the 128 characters that ASCII is able to represent If an incorrect character encoding is used to interpret a file normally the majority of characters will display correctly where the character sets share the same encodings but more unusual characters will be displayed incorrectly typically square boxes or question marks The character encoding is set to the default for the operating system you are running For instance on MacOSX this will be MacRoman and for Windows it will be Windows 1250 If you know your input file is in a different encoding you should set it in the input charset box If your output file needs to be read on an operating system other than the one you are currently running then you may like to override the writer charset Please note that for certain writers the character set used is part of the file
137. e number or 0 gt Whole positive number Raw edges inf or Mean chronology type Single character Y has bark has bark W terminal ring probably complete i e possibly Winter Felled S terminal ring probably incomplete i e possibly Summer Felled B has h s 146 Tellervo A guide for users and developers oo Ko 10 11 12 13 14 15 16 17 18 19 20 21 22 boundary has h s boundary N has no specific edge NB but may have sap U sap bark unknown C charred outer edge P possibly charred outer edge Single character R raw unfiltered data 5 5 year running mean indexed data U unknown mean type Author and comment Free form text not including up to 64 characters UK National grid reference 2 characters even no of digits up to 14 characters in all not known e g TQ67848675 Latitude and longitude Either decimal format e g 53 382457 1 513623 or previously N51730 W1 20 Pith single character C centre of tree V within 5 years of centre F 5 10 years of centre G greater than 10 unknown Cross section code Two character code first character A whole roundwood B half round C quartered D radial split plank E tangential sawn plank second character 1 untrimmed 2 trimmed X irregularly trimmed or X core unclassifiable unknown unrecorded Major dimension whole number in mm 0 if unrecorded or mean Minor dimension
138. e purpose of this License is to make a manual textbook or other functional and useful document free in the sense of freedom to assure everyone the effective freedom to copy and redistribute it with or without modifying it either commercially or noncommercially Secondarily this License preserves for the author and publisher a way to get credit for their work while not being considered responsible for modifications made by others This License is a kind of copyleft which means that derivative works of the document must themselves be free in the same sense lt complements the GNU General Public License which is a copyleft license designed for free software We have designed this License in order to use it for manuals for free software because free software needs free documentation a free program should come with manuals providing the same freedoms that the software does But this License is not limited to software manuals it can be used for any textual work regardless of subject matter or whether it is published as a printed book We recommend this License principally for works whose purpose is instruction or reference Z 4 Terms and conditions 1 Applicability and definitions This License applies to any manual or other work in any medium that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License Such a notice grants a world wide royalty free license unlimited GNU G
139. e the standard PostgreSQL command line tool psql to populate an empty database Z createdb tellervo_new Z psql tellervo new lt tmp backup sql 11 2 Upgrading the server Upgrading the server requires you to type a few commands into the Linux command line First of all please ensure that you back up your Virtual Appliance and or database before continuing We will always endeavour to make sure that nothing happens to your database even if the upgrade fails for some reason in which case the system should roll back to your previous version again but things don t always go to plan 1 Log in to your Tellervo server console 2 Type the following commands Z cd tmp Z wget http url of new server file Z dpkg install tellervo server X X X deb The URL of the new file can be obtained from the Tellervo website It would be possible for us to set up an mechanism which server administrators could opt in to to upgrade Tellervo servers automatically We may deploy this in the future but we d rather keep the process of upgrading as a conscious decision for the foreseeable future but especially until we are confident that the upgrade process will not compromise your database 11 3 Graphical Interface to the Virtual Appliance For those of you that are unfamiliar with Linux the basic command line prompt is not likely to be very comfortable If you are interesting in looking at the server in more detail you may therefore prefer to install a
140. e yourself For instance you may like to write complicated SQL queries to probe your database in ways not currently supported by the Tellervo desktop client A Any changes made to the database may have drastic consequences We strongly recommend that you never write changes directly to the database as this can cause loss of data and corrupt future upgrades to Tellervo 11 5 1 PGAdminl One of the easiest ways to access the PostgreSQL database is through the application PGAdminlll This is a cross platform open source application for communicating with PostgreSQL databases You can install PGAdminlll on your desktop computer and access the remotely running database using your database user credentials For security reasons by default the Tellervo database cannot be accessed from computers outside of the Tellervo server The may sound peculiar because the webservice can be accessed from computers anywhere on the web but the database is actually accessed by the webservice which is essentially a user running on the same computer as the database To access the database directly from a remote computer you must therefore open access first This is done by adding an entry to the file etc postgresql 9 1 main pg_hba conf My personal command line text editor of choice is vim but it is a little confusing to the uninitiated If you are unfamiliar with command line text editing you are probably best to use pico Z sudo pico etc postgresql 9 1 main
141. ears that TSAP Win also accepts this data section as single integer values one per line Double format data is for storing data with sample depth information typically chronologies Like the single format section data is stored as 10 integer values each taking up 6 characters and left padded with spaces The values are in pairs of ring widths and sample depths therefore five rings are stored per line Quad format data is for storing chronologies with sample depth as well as data on how many of the constituent series increase and decrease This format therefore requires four numbers for each data point ring width sample depth increasing series decreasing series Numbers are stored as integers left space padded as before but this time only using 5 characters not 6 Four data points are included on each line therefore this means there are 16 numbers per row and each row is 80 characters long 124 Tellervo A guide for users and developers 1 2 Example file raw series HEADER DateEnd 66 KeyNo 27 Project Growth studies Length 103 Location Example site Species PISY SapWoodRings 14 WaldKanteWKF State Colorado Persld FR KeyCode 271017 Country USA DateOfSampling 19950506 TreeNo 5 CoreNo 1 Exposition North West CreationDate 19970526 SoilType Sand DATA Tree 125 130 99 120 115 145 151 130 135 151 200 190 151 170 170 174 170 200 210 130 180 197 210 160 180 155 180 199 140 150 146 140 145 150 155 1
142. ecessarily fit best with the typical workflow of a laboratory Samples do not typically arrive in a lab in ones and twos rather in large quantities following a field excursion In this case it is most efficient to enter all the metadata for the samples Metadata 23 bd Bulk data entry JOG objectstis elements Y samples 44 Es Add row eed Delete row s Il fio Copy row s x R Selected Object Co Title Type Description Waypoint Latitude Lor Visible Column w ABC Test site Site y Object C Y Title U Comme W Type y Descript Y Latitude Y Longtitu Y Waypoint kJ Parent LOK J Import selected Figure 4 3 The bulk metadata entry screen The show hide columns button has been pressed showing how the user can turn on and off particular columns as they arrive This is often best in terms of data accuracy as the metadata can be entered while the field notes are still fresh in the mind To enable the efficient entry of lots of metadata Tellervo includes the bulk data entry interface This can be accessed from the file menu and is illustrated in figure 4 3 There are three pages one each for objects elements and samples The interface is designed like a spreadsheet so as to be as familiar to users as possible Each row of the table represents a new entry in the Tellervo database Which columns are shown to the user is determined by the show hi
143. ee PAST4 P 1 Dating ic ak Bee ey a a Mite P 2 Example ilens ao leo Fhe a Bhar ote ene are Sheffield Q 1 Description u ru ii e ee en ae Q 2 Dating aa en AOU oath a a ee ety Q 3 Example tiles fr A u A Be Topham R 1 Description Lec Luto dote de Ne td de lata do de te ani lo dl ne R 2 Example files anana ua Dunn 2k E ar een sr here nenne TRiDaS S 1 Description 4 ia a ar A e oS S 2 Example file coco ida Agos TRIMS T 1 Examplestiles Fern a a std 113 113 114 115 115 117 119 119 120 121 121 124 124 125 125 126 129 129 130 131 131 133 133 134 135 135 137 137 138 139 141 143 144 145 145 146 147 149 149 149 151 151 152 155 viii CONTENTS U Tucson U 1 Description cart a Dr o ds U 2 MS ICAA eae oe Gr A a OB GA A U 3 ERN HIES pete et pee et als te th ee ack Ete a eich U 4 Workarounds and quirks 2 2 2 20 pe ee U 5 Example file raw series 2 2 oo nommen U 6 Example file chronology 0 0 200005 V Tucson Compact v 1 Description au u a RA a V 2 Example files ii Goes 22 8 2 22 ee ee a a W VFormat W 1 Deseription u 2 2 aos nenn A ken W 2 Example filess cc 2 oy She Ge a he a YS ROR ASN X WinDENDRO X 1 Description sisis e oe et amp Boe ee eee Ba aa Y XML Error Codes Z GNU General Public License Z 1 Preambl x 24 le 2 ua dk e a eth aha i a i ae a A Z 2 Terms and Conditions 0 0 0 0 0 0000000000004 Z 3
144. elect SVN gt Project from SVN There are two methods of accessing the Tellervo repository anonymously in which case you will have read only access or with a username provided by the Tellervo development team Anonymous users will need to add a repository in the form svn svn code sf net p tellervo code 0 trunk and full users will need to use svntssh svn code sf net p tellervo code 0 trunk Once the project has downloaded to your workspace you may need to set the compliance level This can be done by going to Project gt Properties gt Java compiler and choosing compliance level of 6 0 Tellervo uses a handful of Java 6 specific functions particularly with regards JAXB so will not run successfully with Java 5 To launch Tellervo you will need to Run gt Run Java application Create a new run configuration with the main class set to org tellervo desktop gui Startup 13 3 Dependencies As of June 2011 Maven is used to build Tellervo rather than the original Ant One of the main benefits of Maven is that it handles dependencies much more dynamically than Ant This has become more of an issue as the Tellervo project as grown as it is now dependent on over 80 different open source libraries In an ideal world any libraries that your code is dependent on should be available in central Maven repositories and downloaded and installed seamlessly as part of the build process Maven should also handle transient dependencies i e depende
145. en newly created graphs are plotted according to the scale on the axes A feature of Tellervo graphs though is that they can be manipulated directly on the screen Both dendrochronology was computerized dendrochronologists would plot rings manually on to graph paper These paper graphs were then placed on lightboxes and moved around to enable comparisons The graph function in Tellervo emulates this behaviour allowing users to click and drag graphs around to test for visual matches Figure 8 1 shows an example graph dialog The mouse is hovering of the blue measurement series at relative year 1040 illustrating Tellervo s highlighting and guide line capabilities A feature not shown in this screenshot is the illustration of sapwood rings When sapwood rings are present the corresponding years on the chart are denoted via a heavier line e File Edit View Help TE Standard Semilog Toothed AR EBK JA JR A A Components C SMK 94 A B 2 1001 1063 n 63 C SMK 94 A B 1 1001 1063 n 63 Selected color HN Blue y add Remove Figure 6 1 An example graph window con taining two undated series of the same sample on a semi log graph Note the legend is visible _ with the options for adding or removing series 32 Tellervo A guide for users and developers The layout of graphs can be changed using both the toolbar buttons and menu options The type of graph can be changed between a standard line graph a semi log graph and a
146. eneral Public License 179 in duration to use that work under the conditions stated herein The Document below refers to any such manual or work Any member of the public is a licensee and is addressed as you You accept the license if you copy modify or distribute the work in a way requiring permission under copyright law A Modified Version of the Document means any work containing the Document or a portion of it either copied verbatim or with modifications and or translated into another language A Secondary Section is a named appendix or a front matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document s overall subject or to related matters and contains nothing that could fall directly within that overall subject Thus if the Document is in part a textbook of mathematics a Secondary Section may not explain any mathematics The relationship could be a matter of historical connection with the subject or with related matters or of legal commercial philosophical ethical or political position regarding them The Invariant Sections are certain Secondary Sections whose titles are designated as being those of Invariant Sections in the notice that says that the Document is released under this License If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant The Document may co
147. enerate the class it will create placeholders for all the relevant methods The toString method enables you to return the name for the device you are implementing whereas all the is methods enable Tellervo to understand the capabilities of the device For instance some devices will accept requests to zero the current measurement and or request the current measurement value while others will not instead they rely on hardware buttons on the device itself Some devices can have the port settings such as baud parity stopbits etc altered and the corresponding is Editable functions indicate whether this is possible All user interfaces in Tellervo are modified in accordance with these methods and show the user only relevant buttons The guts of the work in the class are performed in the following methods setDefaultPortParams this method sets all the default port communications parameters The abstract class already sets typical values so you only need to override this if they need to change dolnitialize this method is run when the platform is initialized If your platform needs to do any sort of handshaking then this is where this should be done serialEvent this method handles any events that are detected from the serial port All new data received from the platform is decoded here Values and errors are passed on via the fireSerialSampleEvent method Remember that all values should be sent as measurements in micro
148. ent nonce is a random string of your choosing that is used in the hash The snonce server nonce is the nonce you ve just obtained from the server The seq sequence is the value also obtained from the server Finally the hash is an MD5 hash of user name md5hashofpassword snonce cnonce If all is well the server will respond with the details of the person that is logging in 15 3 3 Cookies and sessions The webservice uses a session cookie so that the user doesn t need to authenticate with each request The cookie lasts for up to 30 minutes of inactivity after which point the server will request the user to re authenticate before it will serve a request Any client attempting to access the Tellervo server will therefore need to handle cookies and be ready to respond to requests to re authenticate Bowne au Fwne au FwnNe Webservice specifications 87 If a session does time out a request to the server will result in an response with the header containing an error status with code 102 see section 15 2 2 and appendix Y and the nonce tag ready for the client to re authenticate 15 3 4 Logout The session cookie will ensure that a user is logged out after a period of inactivity but if you want to force a logout you can simply use the following type of request lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmlins c http ww tellervo org schema 1 0 gt lt c request type logout gt
149. ent version but may differ in detail to address new problems or concerns See http www gnu org copyleft Each version of the License is given a distinguishing version number If the Document specifies that a particular numbered version of this License or any later version applies to it you have the option of following the terms and conditions either of that specified version or of any later version that has been published not as a draft by the Free Software Foundation If the Document does not specify a version number of this License you may choose any version ever published not as a draft by the Free Software Foundation If the Document specifies that a proxy can decide which future versions of this License can be used that proxy s public statement of acceptance of a version permanently authorizes you to choose that version for the Document Relicensing Massive Multiauthor Collaboration Site or MMC Site means any World Wide Web server that publishes copyrightable works and also provides prominent facilities for anybody to edit those works A public wiki that anybody can edit is an example of such a server A Massive Multiauthor Collaboration or MMC contained in the site means any set of copyrightable works thus published on the MMC site CC BY SA means the Creative Commons Attribution Share Alike 3 0 license published by Creative Commons Corporation a not for profit corporation with a principal place of
150. entification code stored in the Tellervo database for each of these entities Due to Tellervo s use of universally unique identifiers UUIDs these codes are guaranteed to be unique opening the opportunity of labs to loan samples much like libraries do with books There are many styles or symbologies of barcodes 40 Tellervo A guide for users and developers in use today but Tellervo uses one of the most common Code 128 which is supported by the vast majority of barcode readers For a detailed discussion on the specifications of the Tellervo barcode see section 16 4 Basic barcode readers are now cheap and widely available with basic devices retailing for a few tens of dollars Most are characterized as keyboard interface devices and work like an automated keyboard typing in a string of characters when a label is scanned Within the Tellervo application whenever the user is required to specify a box sample or series they have the option of typing the human readable lab code or scanning the barcode By using the barcode the user can be sure they are not entering typographic errors so we recommend using barcodes whenever possible The most important barcode is the label for the physical wood sample These are easily generated through the Administration gt Labels gt Sample labels menu entry Currently the layout of these labels is fixed but in the future we aim to provide different styles 8 2 1 Sample labels Before label
151. equipment you are using Note that this refers to the equipment that the computer is attached to and not necessarily the measuring platform itself For instance Velmex platforms are typically connected through a Metronics digital readout device Included in this list is the EvelO device which is an open source device designed for the Cornell Tree Ring Laboratory Circuit drawings for this device can be obtained from the Cornell lab to enable Hensen measuring platforms to be used with 18 Tellervo and other software If you measuring platform is not included in the list it should be relatively easy for us to add support so please get in touch and we ll see what we can do Alternatively you could implement support yourself either personally or by employing an independent developer Technical details on how to do this are included in section 13 13 page 71 Next you must choose the port that your platform is connected to from the pull down menu In Windows this will be a COM port in Linux and Mac this will be a dev xxx port Depending on the type of platform you choose you may also need to set various communication parameters If these boxes are enabled please check the documentation that came with your measuring platform to ensure these values are set correctly To check whether your platform is working click the Test connection button see figure 3 2 and attempt to measure a few rings Different measuring platforms have different capabi
152. erhaul in the future to provide more flexible support for publication quality graphics Chapter 7 Importing and exporting Importing and exporting of dendro data in Tellervo is provided through the TRICYCLE libraries TRICYCLE is a universal dendro data conversion application for converting back and forth between 24 supported data formats Brewer et al 2011 The open source libraries that provide the functionality to TRICYCLE are incorporated directly into Tellervo providing support for all these formats Belfast Apple Nottingham Belfast Archive ODF Spreadsheet Besancon including SYLPHE variants Oxford CATRAS PAST4 Cracow Binary Format Sheffield D Format Dendro for Windows Comma delimited text files CSV Topham Corina Legacy TRiDaS DendroDB TRIMS Heidelberg TSAP Win Tucson RWL and CRN KINSYS KS Tucson Compact Microsoft Excel 97 2000 XP VFormat Microsoft Excel 2007 WinDENDRO Table 7 1 List of the twenty four formats supported by Tellervo See appendices A X pages 101 169 for full descriptions 7 1 Exporting data Exporting data is initiated by the File gt Export data menu If this is called from the main Tellervo data window it will export the current series If it is called from the Tellervo home screen then it will present you with the database browser and allow you to pick one or more series to export If you use the menu from within the main data editor then it will export The export dialog contains two tab
153. ering metadata In this case the user may simply prefer to use the File gt New method for each sample Either way the concept behind the curation of a collection in Tellervo revolves around the accurately recording as much metadata about a sample as possible then labeling the physical sample with a label containing a barcode for Tellervo and sample code for the user By entering a sample into the database as soon as it enters the lab it can be traced throughout the workflow When a chronology is built it is easily to quickly and efficient locate all samples that have been used By assigning samples to boxes groups of similar samples e g from the same site can also be easily stored together and located quickly and efficiently 8 2 Barcodes Barcodes allow you to keep track of what samples you have and where they are stored Although it is not essential to use the barcode functions we strongly suggest you do because they save time and money but most importantly they greatly reduce the scope for erroneous data entry For instance when measuring a sample a user simply scans its barcode and all the relevant metadata is retrieved from the database rather than relying on them to enter data manually Barcodes have been routinely used in the retail industry since the 1980s They can be equally as useful in dendrochronology laboratories Tellervo creates and reads barcodes for samples measurement series and boxes Each barcode encodes the unique id
154. ertinent obligations then as a consequence you may not convey it at all For example if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program Use with the GNU Affero General Public License Notwithstanding any other provision of this License you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work and to convey the resulting work The terms of this License will continue to apply to the part which is the covered work but the special requirements of the GNU Affero General Public License section 13 concerning interaction through a network will apply to the combination as such Revised Versions of this License The Free Software Foundation may publish revised and or new versions of the GNU General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns 178 Tellervo A guide for users and developers Each version is given a distinguishing version number If the Program specifies that a certain numbered version of the GNU General Public License or any later version applies to it you have the option of following the terms and conditions eithe
155. etla The format is for raw measurement series and contains both data and structured metadata The primary focus of the metadata fields included are for forestry sampling The format allows for multiple data series within a single file with each series beginning with a 14 line header followed by multiple data lines and finishing with the line DATA END x The first line of the header contains the date and time the file was created All subsequent header lines are numbered 0 1 2 etc and contain one or more metadata fields delimited with a backslash as shown below VVVVVVVVVVVVVYV Measurement timestamp 0 Project code Project name Responsible person 1 Sampling date 2 Ycoord Xcoord Elevation 3 Experiment Period of measurement Location 4 Plot Subplot 5 Measurement series code ID Code 6 Tree species code 7 Last measurement year Subsample code 8 Incomplete growth estimated age increase Last ring type 9 Sampling azimuth measurement direction Sample height Sample height code 10 User defined parameters 11 Number of tree rings in sample Data type Columns Number of decimals 12 Number of tree rings measured 126 Tellervo A guide for users and developers The meanings and formats of these fields are as follows Measurement timestamp This is the date and time that the file was created It is in the format dd mm yy hh mm ss Project code Adm
156. ext file This is a little more involved so it is only recommended if you are familiar with command line 54 Tellervo A guide for users and developers and or Linux You can create the file with a command like the one below but you should read up on pg dump so that you understand the possible options that you can use Z pg dump Fc folder and file to make mybackup sql database_name For example the following line will backup the database called tellervo the standard name for your database into a file called backup sql in the tmp folder Keep in mind that the tmp folder is cleaned each time the server is booted Z pg dump Fc tmp backup sql tellervo It then makes sense to transfer this backup off the virtual machine onto a separate computer as per nor mal backup procedures If you are familiar with Linux you could do this by using SFTP or similar transfer protocols If you just want a quick and dirty method you could save the backup sql file to var www tellervo server and then you can access the file from any web browser at the address http your server ip tellervo server backup sql Keep in mind though that anyone could potential download the file as long as it is left there so you will want to delete it as soon as you have transferred it You can do this from the server command line by typing sudo rm var www tellervo org backup sql 11 1 4 Restoring a PostgreSQL database To restore your database from a backup file you can us
157. f less than 4 characters Char 16 hyphen Chars 17 20 Last year in sequence when series is securely dated Year should be left padded with spaces if less than 4 characters Char 21 space Char 22 Description typically name of site building etc Final char optional apostrophe 2 contains Integer number of years 138 Tellervo A guide for users and developers gt Comma Integer start year The start year on line 2 and the first year on line 1 will be the same for securely dated series When the series is tentatively or relatively dated the first year and or the last year on line 1 will be left blank For undated series the start year is set to 1001 The data lines follow the two header lines These typically contain 10 data values per line but there can be more if rings have been added or less e g last line The values are in 1 100th mm integers and can only contain three digits e g max 999 1 100th mm Data values are space delimited Some example files contain values that are left padded with zeros if the value is on 1 or 2 characters wide e g 025 rather than 25 Following the data values there should be an empty line followed by an optional sample count depth block The count block is formatted in largely the same way as the data values block The values are stored in columns 2 characters rather than 3 characters wide Like the data values the count values are space delimited integers typically b
158. g schema 1 0 gt lt c request type delete gt A E gt lt c request gt lt c tellervo gt Cascading deletes are not permitted in Tellervom therefore only entities that are not used by other entities in the database can be deleted For example you cannot delete an object which has elements associated you would need to delete in the elements first Attempts to delete an entity which still has associated records will cause the webservice to return a 907 Foreign key violation error 15 6 Creating records New records are are typically created by passing a TRiDaS representation of the entity you d like to create inside a create request The basic template of a create request looks like this onone w Ao A ou WHR 88 Tellervo A guide for users and developers lt xml version 1 0 encoding UTF 8 gt lt tellervo xmIns http www tellervo org schema 1 0 xmiIns tridas http www tridas org Pa lt request type create lt tridas sample gt parentEntityID gt lt tridas sample gt lt request gt lt tellervo gt The request tag should include the parentEntitylD attribute with the ID of the parent entity in the database e g the TRiDaS element to which a sample belongs for instance Please note that there are a number of mandatory fields for each TRiDaS entity These must be populated otherwise the webservice will return a 902 Missing user parameter error I
159. g the classes that it produces One thing to note in the Maven pom xml is a nasty workaround when running JAXB As the Tellervo schema depends on the GML and TRiDaS schemas these classes are also built by JAXB These classes however are already provided by the DendroFilelO library It should be possible to use a feature called episodes to handle this but this seems buggy and causes issues For now we use an antrun task to delete the duplicate classes immediately after they are produced 13 11 Java version Although we would like Tellervo to run on older versions of Java specifically Java 5 there are a number of features of Java 6 such as JAXB that we really need This isn t really a problem on Linux and Windows as Java 6 has been around for a long time now but it is a bit problematic for MacOSX users For internal reasons Apple was extremely slow bringing Java 6 to MacOSX only releasing it with 10 6 Snow Leopard several years after Windows and Linux Tellervo will therefore not run on older Mac machines This will gradually become less of an issue as machines age and Snow Leopard or later becomes less difficult for users to fulfill Tellervo was originally developed against the Sun JDK Although Sun re released much of its JDK under the GPL license there are still portions that are only available under proprietary licenses due to various plugins being the copyright of third parties Although it is still distributed at no cost it is no
160. have done this you should be able to call your Java functions from within Postgres Please note that if you add dependencies to your classes that are not provided by the standard Java virtual machine these must also be added to the tellervo pljava jar You can get rather cryptic java lang NoClassDefFoundE errors which do not necessarily name the additional dependency but the class from which it is called Part Ill Appendices Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer A 1 Description Appendix A Belfast Apple Belfast Apple None known Text file Various typically txt and dat Read and write No original software is known to exist so TRICYCLE is pro posed as the reference implementation Data only with comment n a No Yes No No John Pilcher Belfast Apple is a simple text file format see also Belfast Archive originating from the Queens University Belfast lab and originally designed for use on an Apple II computer This format is not known to be actively used but a large amount of data especially at Belfast is archived in this format gt gt gt gt gt Line 1 name of the site or object the data refers to Line 2 identifier for the sample the data refers to Line 3 number of data values in the f
161. he Tree Ring Data Standard TRiDaS Before you use Tellervo you may find it useful to read Jansma et al 2010 so that you get a better understanding of the principles of TRiDaS but a summary is also provided here 4 1 Tree Ring Data Standard TRiDaS TRiDaS is an XML based data standard for recording dendrochronological data and metadata More than 80 dendrochronologists computer scientists and specialists from research disciplines that rely on dendrochronology have so far contributed to its development including dendroarchaeologists art and architecture historians ecologists geologists and climatologists The standard is therefore capable of recording the wide variety of metadata required by these different fields TRiDaS builds upon other established standards such as GML for the recording of locality information The extensible nature of XML also means that TRiDaS can evolve to accommodate the changing needs of dendrochronologists over time TRiDaS includes a total of eight data entities project object element sample radius measurementSeries derivedSeries and value Detailed descriptions of each of these entities are given below and their relationships are illustrated in figure 4 1 A project is defined by a laboratory and encompasses dendrochronological research of a particular object or group of objects Examples include the dating of a building the research of forest dynamics in a stand of living trees the dating of all Rem
162. he sample the data refers to Line 3 number of data values in the file Lines 4 line feed delimited data values as integers in 1 100th mm The lines ARCHIVE and END OF TEXT denote the start and finish of the metadata section The metadata section contains the following lines gt gt gt vvvvvyv Line 1 start year as an integer Line 2 unknown Line 3 Double representing the resolution of data values e g 1 1 10ths mm 01 1 100th mm 001 microns etc Line 4 unknown Line 5 unknown Line 6 unknown Line 7 title of the data series Line 8 unknown Line 9 unknown 104 Tellervo A guide for users and developers B 2 Example file EXAMPLE SITE 1 176 342 338 334 409 362 308 360 264 325 318 51 48 47 60 49 48 ARCHIVE 1277 9177 01 1 035795 0 212144 BOB 25 03 95 EXAMPLE SITE 01 Pith F Sap 32 mu END OF TEXT Appendix C Besancon Format name Besancon Other name s SYLPHE Type Text file Extension s txt Read write support Read and write Reference implementation Not known Data metadata Data and some structured metadata Calendar type Gregorian Absolute dating support Yes Undated series support Yes Relative dating support No Multi series support Yes Original designer Georges Lambert C 1 Description The Besancon format is most commonly used in a number of French laborator
163. he second run should know and understand about previously provided details the details of which can be found in the Debian Policy Manual along with information how and when each of the pre and post scripts is run Hopefully this side of Debian Policy Manual http www debian org doc debian policy but a more accessible description is found at http wiki debian org MaintainerScripts 76 Tellervo A guide for users and developers Insert row into tblmeasurement Update tbimeasurement Webservice step Lastmodified timestamp El Insert multiple rows into tblreading DB trigger Create vmeasurement row using createnewvmeasurement vmeasurementmodified trigger Add new notes using gt ees VmeasurementRelYear NoteTrigger does error checking on notes Figure 14 1 Illustration of the steps that happen during the creation of a new measurement series The stages are presented top to bottom in the approximate order in which they are executed The majority of the processing is done as a result of the database function createnewvmeasurement being called by the webservice Figure 14 2 Illustration of the steps that happen during the alteration of an existing measurement series The stages are presented top to bottom in the approximate order in which they are executed Developing Telle
164. hen modifying the script echoTruncatedString str Slength echos a string to the console but truncates it to length if necessary If the string is shorter than length then it is padded with spaces This is useful to ensure the following text is displayed aligned e g test results requireRoot check whether the user running the script has root privileges checkServicelsRunning service checks whether the named service is running on the system This is performed by checking whether the provided string is present in the response from the shell command ps ax setConfigVariable Svar value does a search and replace for a placeholder variable in the config php file replacing with value Placeholders should be stored in the config php template as VARIABLENAME promptForPwd isCreating TRUE is an interactive script for getting a password from the user It checks that the password is strong and asks for it twice to check for typos class Colors can be used to display coloured text on the console Useful for highlighting errors and test results Developing Tellervo Server 79 Standard installation procedure FAILED FAILED preinst install postrm abort install OK Files are unpacked postinst configure OK Installed Successful exit Failed Config Not Installed Half Installed Reinst required Exit with error message Upgrade from version 1 2
165. hey too receive or can get the source code And you must show them these terms so they know their rights Developers that use the GNU GPL protect your rights with two steps 1 assert copyright on the software and 2 offer you this License giving you legal permission to copy distribute and or modify it For the developers and authors protection the GPL clearly explains that there is no warranty for this free software For both users and authors sake the GPL requires that modified versions be marked as changed so that their problems will not be attributed erroneously to authors of previous versions Some devices are designed to deny users access to install or run modified versions of the software inside them although the manufacturer can do so This is fundamentally incompatible with the aim of protecting users freedom to change the software The systematic pattern of such abuse occurs in the area of products for individuals to use which is precisely where it is most unacceptable Therefore we have designed this version of the GPL to prohibit the practice for those products If such problems arise substantially in other domains we stand ready to extend this provision to those domains in future versions of the GPL as needed to protect the freedom of users 174 Tellervo A guide for users and developers Finally every program is threatened constantly by software patents States should not allow patents to restrict development and
166. hners anatomical codes D Density Band R Reaction Wood L Light Latewood H Dense Latewood F Frost Ring K Small Earlywood Vessels oak G Great Latewood Vessels oak T Wound Tissue N Narrow Latewood A Light Latewood End P Narrow and Light Latewood Q Narrow and Dense Latewood Data type single character D ring widths E early wood widths only L late wood widths only R late early wood widths i e reverse of normal rings minimum density A maximum density S early late i e sequentially and separately M mixed means of others The remaining lines contain the data gt vv vvvyv For each width equivalent to the value of length the individual increments etc if a C X T or W type mean No negatives or zeros Check field Single character H For each width the individual weightings of the mean sequences If an X or W type mean No negatives or zeros Check field Single character R For each width the number of individual series with rising values No negatives or zeros Check field Single character F For each width the number of individual series with falling values No negatives Q 2 Dating The format copes with the problem of the non existent year OAD BC by adding 10000 to all year values Therefore Sheffield 147 Year Value in file 1AD 1BC 9999BC 10000BC Q 3 Example file 10001 10000 2 1 Ship wreck 4 timber mean 170 A 10784
167. icular group the permissions for the tree will be derived from the site from which the tree was found If however permissions are assigned to the tree then these will override those of the site In this way it will be possible to allow a group to read the data from one particular tree from a site in which there otherwise do not have permission to access Privileges are cumulative This means that if a user is a member of multiple groups then they will gain all the privileges assigned to those groups If one of the groups that the user is a member of has no privileges set on an object it will however override all other privileges Therefore if a user is a member of groups A and B and group A has read privilege and group B has no privilege then the user will not be able to access the record A special admin group has been created into which only the most trusted users are placed Members of the admin group automatically gain full privileges on all data within the database They also have permission to perform a number of administrative tasks that standard users are insulated from 16 3 Universally Unique Identifiers All entities in the Tellervo database have a primary key based on the Universally Unique Identifier UUID con cept This is a randomly created 128 bit number which due to the astronomically large number of possibilities 3 x 1038 means that it is guaranteed to be unique across all installations of Tellervo This code i
168. ies The format allows for multiple series in the same file Each series or element block in Lambert s notation is made up of a header line optional metadata and a data block each of which are delimited by a line feed The header line begins with a dot character then one or more spaces then an element name without spaces followed by a space and any number of ignored characters The metadata fields are space or line feed delimited Each field is recorded using a key of three letters The format allows for the full spelling out of the field if preferred but it is the first three letters that are read by software so LON is the same as LONGEUR Some fields are unimodal in that their presence is all that is required e g CAM means that cambium was observed Other fields are bimodal which means they require a value to be associated with them In this case the field key is followed by a space and then an integer or string value e g POS 1950 The accepted metadata fields are as follows LON Number of data values POS The temporary first ring date given relatively to a group ORI The year for the first ring TER The year for the last ring Should be the same as ORI LON MOE Pith present CAM Cambium present AUB Number of the first sapwood ring 106 Tellervo A guide for users and developers All other information in the metadata block should be ignored This feature is often used to allow the inclusion of multi line comments The
169. ight Height of tree in metres Tree age Age of the tree If unknown this should be 0 then it is assumed to be equal to the number of rings SectionHeight Height up the tree in metres at which the sample was taken User variable User defined variable must be numerical RingCount Number of rings the series contains Data Type Keyword indicating the type of data measured This can be RINGWIDTH EARLYWIDTH LATEWIDTH EARLYWIDTH LATEWIDTH DENSITY EARLYDENSITY LATEDENSITY MAX DENSITY MINDENSITY RINGANGLE OffsetToNext The number of lines to skip to go to the next data line of the same type For instance a file can contain earlywood and latewood data for multiple samples If this is the case then each sample will have two rows one for each variable and the Offset ToNext field will be 1 In additional to these fields version 4 files also include the following gt gt vvv vvv vv v vvvvyv ImageName The filename for the image used to do this analysis If the image was taken directly from the scanner or camera then this field will be SCANNER Analysis Date Time Date and time the measurements were initially saved to disk in format dd m m YYYY HH mm Acquisition Date Time Date and time the image file was acquired in format dd mm YYYY HH mm Modified Date Time Date and time the file was last modified in format dd mm YYYY HH mm ImageSize H V NBits Channel The image size in pixels followed by bits per pi
170. ile Lines 4 line feed delimited data values as integers in 1 100th mm Final line contains a comment typically starting with COMMENT 102 A 2 Example file EXAMPLE SITE A1805 106 188 165 184 112 103 111 239 226 132 143 146 140 100 176 139 124 115 78 80 156 75 110 80 130 83 157 99 115 102 110 108 87 135 107 96 70 128 119 86 101 106 129 88 101 151 106 97 110 97 91 93 100 124 99 134 125 105 96 107 142 100 COMMENT PB 15 NOV 99 Tellervo A guide for users and developers Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer B 1 Description Appendix B Belfast Archive Belfast Archive None known Text file Various typically arx txt and dat Read only No original software is known to exist so TRICYCLE is pro posed as the reference implementation Data with limited metadata Gregorian Yes No No Yes Martin Munro Belfast Archive is a simple text file format based on the original Belfast Apple format at the Queens University Belfast lab It shares the same features as Belfast Apple but with the addition of a number of metadata fields at the end of the file Line 1 name of the site or object the data refers to Line 2 identifier for t
171. ile we develop we would likely show all messages up to and including trace but when we deploy we might only want to show messages up to and including warn Log4J also enables us to log to several places known as appenders e g console log file or a component within our application It is also possible to change the level of logging depending on the log type so minimal messages can be sent to the console but verbose messages to the log file Tellervo has the following four appenders configured Standard log file tellervo log that rolls over up to 2mb of messages Submission log file tellervo submission log that contains the last 100kb of verbose messages and is used by the bug submission tool to enable users to notify developers of problems Console standard messages to the console when launched from command line Swing GUI a swing component for displaying basic logs to the users in the application To alter the way these appenders are configured you need to edit the log4j xml file See the Log4J documen tation for further information Using the logging framework is very simple Just define a Logger as a static variable in your class like this private final static Logger log LoggerFactory getLogger MyClassName class where MyClassName is the name of the current class Then you can log messages simply by calling log warn My message log debug My message etc Before managed logging wa
172. illimeter 0 01 mm or microns An indexed sample has units of parts per thousand 0 1 or o This doesn t cause a problem with crossdating The t score normalizes all samples as part of its test and the trend only cares if the values are increasing or decreasing For more information on crossdating and chronology building see chapter 10 lt does however cause a problem with summing since summing needs to take the average what s the average of Imm and 75 Therefore the samples in a sum must be either all raw or all indexed 9 1 Types of index There are a total of six different indexing methods available in Tellervo 9 1 1 Exponential Index This is the most commonly used index as it matches the way trees typically grow Quickly when young and then gradually slower An exponential index is therefore by far the most common index you ll use as 9 times out of 10 this will be the best choice This index tries to fit an equation of the following form to your data searching for the best values of a b and D gt y a be px Y This is sometimes called a negative exponential index because the exponent is negative Tellervo doesn t require that the exponent is negative but if it s not using this index probably isn t such a good idea it means the tree is generally getting bigger not smaller 46 Tellervo A guide for users and developers The least squares algorithm used comes from Cormen et al 2001 the matrix solving fun
173. inal designer M 1 Description Nottingham Nottingham Laboratory format Text file txt Read and write Unknown Data only n a No Yes No Yes Cliff Litton Appendix M Nottingham The Nottingham format was designed by Cliff Litton It is a simple text format with no support for metadata Line 1 contains a series name and an integer indicating how many data values there are in the file Subsequent lines contain the data represented as 1 100th mm integers in twenty columns seemingly in either 4 characters or 3 characters 1 space There is no known reference implementation for this format and few known examples of data so little is known about how it should handle unusual situations such as negative values values 999 etc MN ADR WKH 134 Tellervo A guide for users and developers M 2 Example file ABCDO1 176 342 338 334 409 294 202 170 176 112 94 96 120 50 41 56 66 91 60 56 43 58 46 62 45 65 98 85 82 96 106 71 89 45 46 40 36 362 308 172 121 168 149 62 55 52 51 52 50 119 89 50 65 64 58 360 264 325 87 130 114 119 124 79 55 45 47 65 68 55 77 50 63 85 87 83 133 89 88 52 58 56 318 134 151 219 268 290 108 170 135 131 126 87 67 88 90 93 77 49 63 58 60 44 45 49 44 41 75 94 78 63 75 77 64 66 57 80 108 129 123 160 117 129 5060 95 95 91 102 94 51 48 47 60 49 222 278 258 173 198 86 104 103 127 100 42 50 69 57 121 158 48 53 62 58 78 88 83 38 61 75 65
174. incorporation into a dwelling In determining whether a product is a consumer product doubtful cases shall be resolved in favor of coverage For a particular product received by a particular user normally used refers to a typical or common use of that class of product regardless of the status of the particular user or of the way in which the particular user actually uses or expects or is expected to use the product A product is a consumer product regardless of whether the product has substantial commercial industrial or non consumer uses unless such uses represent the only significant mode of use of the product Installation Information for a User Product means any methods procedures authorization keys or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its 176 Tellervo A guide for users and developers Corresponding Source The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made If you convey an object code work under this section in or with or specifically for use in a User Product and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term regardless of how the transaction is characterized the
175. inistrative code for the project Project name Administrative name for the project Responsible person Person responsible for the project Sampling date Date the sample was taken formated dd mm yy Ycoord Y coordinate of the location of the site in Finnish KKJ Uniform Grid coordinates Xcoord X coordinate of the location of the site in Finnish KKJ Uniform Grid coordinates Elevation Elevation of the site in metres Experiment Period of measurement Location Name of site Plot Code number for the plot being sampled Subplot Code number of the sub plot being sampled Measurement series code Code for the measurement series ID Code Tree species code Species code using either the ITRDB or VMI Finnish National Forest Inventory schemes Last measurement year Calendar year for the last measurement Subsample code Code for if the sample is broken into pieces marked a b c etc x marks a problematic samples where there are difficulties in analysis Incomplete growth If the last incomplete growth ring is measured that this is set to 1 otherwise it is 0 Estimated age increase Estimate for the number of tree rings between the birth of the tree and the pith at the sample height Taken from VMI correction tables produced on a site and regional basis Last ring type If the last incomplete ring is earlywood then this is marked as 1 otherwise it is marked as 9 Sampling azimuth Either a letter code for
176. is shown in figure 8 2 Y Until dynamic label styles have been implemented box labels will print one per page To make use of the second label on the page the same sheet should be fed through the printer a second time 8 2 3 Series barcodes Series barcodes are printed at the top of a standard series report see figure 8 3 These are produced through the File gt Print or File gt Print preview menus 8 3 Storage boxes Tellervo uses the term box to refer to the collection of samples you archive Many labs including Cornell use cardboard bankers boxes to store samples once they are completed but the same box concept could refer to draws or shelves in your collection Curation and Administration 41 Created October 23 2009 10 23 AM Label updated July 12 2011 9 40 AM Object Elements Samples KRR 1 1 KSR 1 12 14 KSY 1 14 14 KTM 1 13 13 KYP 1 1 Grand Total 43 Comments No comments recorded Figure 8 2 An example of a box label from the Cornell collection The label provides a human readable name for the box GR38 a barcode for accessing the box details within Tellervo and a summary of the samples contained within the box 8 3 1 Creating and editing boxes Records for boxes in the system are created and edited through the Administration gt Curation gt Box details menu To editing an existing box you can scan the barcode label on the box or select from the list To create a new b
177. lab The second drawback is that it makes a copy of your entire server including the whole operating system therefore each backup takes a lot more space 1 Open VirtualBox 2 If you server is running you will need to do a full shutdown From the server console type sudo halt then once it has halted you can close the console window and select Power off the machine 3 Select your virtual machine in the list on the left and go to File gt Export Appliance 4 Follow the wizard specifying a file where you d like to back the server up to Keep in mind that this will contain a complete copy of the server including operating system so could be 1Gb or more 11 1 2 Restoring a Virtual Appliance backup If you have followed the instructions in section 11 1 1 to backup your Virtual Appliance the steps to restoring your server are very similar to how your initially installed it Simply open VirtualBox then go to File gt Import Appliance and select the backup file that you made Follow the wizard and it should restore your server You can restore onto the same computer that was originally running the virtual machine remember to give it a new name though if this is the case or alternatively to any other computer with VirtualBox installed This method can therefore be used to share entire databases 11 13 Backup PostgreSQL database The more standard way of backing up your database is to do a dump of the PostgreSQL database itself into a large t
178. lities For instance some include a physical switch for firing measurement events others also include switches for resetting measurements to zero Some platforms e g Lintab also continuously report the measurement values to the computer So depending on the hardware you use Tellervo will present the you with slightly different options The test dialog includes information about the capa bilities of your platform as well as a log window to 9 Form Conneckion 3008 show the raw information being received by Tellervo If you are having trouble interfacing with your plat Success Data recieved from platform form you should send the communications log to the developers along with as much information about Data Received Capabilities Communications Log your hardware as possible 380um sp j 480m Once you are satisfied that you are getting the correct y results from the measuring platform click close on the test window and then close the preferences dialog to return to the Tellervo home screen Oze emo PO Restart Test Figure 3 2 Testing the connection to a hardware measuring platform Chapter 4 Metadata Metadata is data about data In Tellervo this means all the information associated with your physical samples and measurement series e g species location who measured it dimensions slope soil type etc The metadata in Tellervo and in fact the entire Tellervo data model is based on t
179. llervo org schema 1 0 xmlIns gml http www opengis net gml xmlns xlink http www w3 org 1999 xlink xmins tridas http www tridas org 1 2 2 gt gt lt tellervo xmIns http www tellervo org schema 1 0 xmIns g http www opengis net gml xmins x http www w3 org 1999 xlink xmIns t http www tridas org 1 2 2 gt 15 2 2 Errors and warnings The webservice uses two tags within the header section of the return document to inform about errors and warnings These tags are the status and message tags The status tag can be set to OK Notice Warning or Error When there is an error the message tag includes a code attribute along with the actual error message The list of possible error codes is provided in appendix Y An example of a typical error response is shown below lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmIns c http www tellervo org schema 1 0 gt lt c header gt lt c securityUser id 1 username admin firstName Admin lastName user gt lt c webserviceVersion gt 1 1 0 lt c webserviceVersion gt lt c clientVersion gt Tellervo WSI null httpcore 4 1 HttpClient 4 1 1 ts null revisionnum lt c clientVersion gt lt c requestDate gt 2012 04 02T15 01 59 04 00 lt c requestDate gt lt c queryTime unit seconds gt 0 07 lt c queryTime gt lt c requestUrl gt tellervo lt c requestUrl gt lt c request T ype gt
180. lly and only if you received the object code with such an offer in accord with subsection 6b d Convey the object code by offering access from a designated place gratis or for a charge and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge You need not require recipients to copy the Corresponding Source along with the object code If the place to copy the object code is a network server the Corresponding Source may be on a different server operated by you or a third party that supports equivalent copying facilities provided you maintain clear directions next to the object code saying where to find the Corresponding Source Regardless of what server hosts the Corresponding Source you remain obligated to ensure that it is available for as long as needed to satisfy these requirements e Convey the object code using peer to peer transmission provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d A separable portion of the object code whose source code is excluded from the Corresponding Source as a System Library need not be included in conveying the object code work A User Product is either 1 a consumer product which means any tangible personal property which is normally used for personal family or household purposes or 2 anything designed or sold for
181. lly made changes If changes are made to the files outside of Netbeans then the Netbeans form designer can no longer edit these files so please make sure you are certain this is how you want to proceed The classes generated by Netbeans are typically used by a subclass via inheritance so that any changes can be external to the form designer generated files More recently the Google WindowBuilder Pro tool has been used for interface design This has the benefit of usually being able to parse existing code enabling the modification of existing dialogs WindowsBuilder does have its quirks though so make sure you keep up to date with new releases 13 13 Supporting measuring platforms The support for hardware measuring platforms has been designed to be as modular and extensible as possible Adding support for additional measuring platform types should therefore be quick and painless To begin you need to extend the abstract class org tellervo desktop hardware AbstractSerialMeasuringDevice You can of course also extend the class implementation of another platform if you only need to modify a few settings This is the case for both the QC10 and QC1100 devices which extend the GenericASCl Device class The implementation code is identical for all three but the derived classes set the port settings to the default values for the two QuadraChek boxes There are a number of methods that you will need to override from the base class If you use Eclipse to g
182. loaded on the fly so there is likely to be a delay when you initially visit to a new region However up to 2Gb of map data can be cache locally to your hard disk so on future visits maps should load quickly 5 3 1 Data layers Data map layers i e site and sample locations are controlled with the layer list on the left of the screen When viewing series you will have the option of adding layers containing points for all the other series at the current site and showing all the sites in the database In the Site map you can use the Add layer button to add data layers of the following types All Tellervo objects this adds a single layer containing all the objects within the Tellervo database Tellervo entity from database this adds a layer containing the location of one record from the Tellervo database This is specified by labcode e g ABC would add a pin for the site ABC whereas ABC 1 would add a pin for the element ABC 1 Elements from an object this adds a layer containing all the elements for a specified object The object is specified by labcode All ITRDB sites this downloads the location of all sites currently available in the ITRDB database and adds them as a single layer ESRI Shapefile this enables you to load an ESRI shapefile stored locally on your computer Tellervo supports polygon polyline and point files although currently it does not enable you to style this data Data for a layer is presented
183. ment If the Cover Text requirement of section 3 is applicable to these copies of the Document then if the Document is less than one half of the entire aggregate the Document s Cover Texts may be placed on covers that bracket the Document within the aggregate or the electronic equivalent of covers if the Document is in electronic form Otherwise they must appear on printed covers that bracket the whole aggregate Translation Translation is considered a kind of modification so you may distribute translations of the Document under the terms of section 4 Replacing Invariant Sections with translations requires special permission from their copyright holders but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections You may include a translation of this License and all the license notices in the Document and any Warranty Disclaimers provided that you also include the original English version of this License and the original versions of those notices and disclaimers In case of a disagreement between the translation and the original version of this License or a notice or disclaimer the original version will prevail If a section in the Document is Entitled Acknowledgements Dedications or History the requirement section 4 to Preserve its Title section 1 will typically require changing the actual title Termination You may not copy modify sublicens
184. mestamp gt lt woodCompleteness gt lt pith presence absent gt lt heartwood presence incomplete gt lt sapwood presence complete gt lt bark presence present gt lt woodCompleteness gt lt measurementSeries gt lt title gt C TWT 65 A B A lt title gt lt identifier domain dendro cornell edu gt 8c50234e 8eda 41bb b578 01cc881dleal lt identifier gt lt createdTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt createdTimestamp gt lt lastModifiedTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt lastModifiedTimestamp gt lt analyst gt Laura Steele lt analyst gt lt dendrochronologist gt Peter Kuniholm lt dendrochronologist gt lt measuringMethod normalStd Corina Dictionary normalld 1 gt Measuring platform lt measuringMethod gt lt interpretation gt lt firstYear suffix AD gt 1254 lt firstYear gt lt statFoundation gt lt statValue gt 8 3 lt statValue gt lt type gt t score lt type gt lt usedSoftware gt Corina 2 10 lt usedSoftware gt lt statFoundation gt lt deathYear suffix AD gt 1535 lt deathYear gt lt provenance gt Possibly from the region of Serres lt provenance gt lt interpretation gt lt values gt lt variable normalTridas Ring width gt lt unit normalTridas 1 100th millimetres gt lt value value 54 gt lt value value 111 gt lt value value 71 gt lt value value 40 g
185. mple derived from 1 derivedSeries documentation a calculated series of values hierarchical relationship a project has one or more objects an element has one or more samples Metadata 21 sub object An object will often consist of more than one element e g when dealing with the staves elements of a barrel object One or more samples can be taken from an element and an element may be dated using one or more derivedSeries An sample is a physical specimen or non physical representation of an element Examples include core from a living tree core from a rafter in a church roof piece of charcoal from an archaeological trench slice from a pile used in a pile foundation wax imprint of the outer end of a plank photo of a back plate of a string instrument Note that a sample always exists and that it can either be physical e g a core or representative e g a picture A sample is taken from exactly one element and can be represented by one or more radii y A radius is a line from pith to bark along which the measurements are taken A radius is derived from exactly one sample It can be measured more than once resulting in multiple measurementSeries r 3 r A measurementSeries is a series of direct raw measurements along a radius A single measure mentSeries can be standardised or a collection of measurementSeries can be combined into a derived Series The measurements themselves are stored separ
186. much more secure it is also somewhat more complicated because it involves a challenge and response scheme using cryptographic nonces and hashes The first step is for the client to request a nonce from the server This is done as follows lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmIns c http www tellervo org schema 1 0 xmins gml http ww opengis net gml xmins xlink http www w3 org 1999 xlink xmlns tridas http www tridas org m2 gt lt c request type nonce gt lt c tellervo gt The returned document will include a nonce header tag like this lt c nonce seq 176378 gt 97566d4d2e8b8c5696b6667fef8429f5 lt c nonce gt Armed with your nonce you can then send a request to log in securely as follows lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmins c http www tellervo org schema 1 0 xmins gml http ww opengis net gml xmins xlink http ww w w3 org 1999 xlink xmlns tridas http www tridas org 1 2 2 gt lt c request type securelogin gt lt c authenticate username admin cnonce 3f975c569f978731e570 snonce 97566 d4d2e8b8c5696b6667fef8429f5 hash d315ec50f7f1809492d5ef132ad4aa06 seq 176378 gt lt c request gt lt c tellervo gt The authenticate attributes are filled as follows The username is simply the username for a user with permission to access the Tellervo server The cnonce cli
187. n addition to handling the standard TRiDaS project object element sample radius measurementSeries derivedSeries entities the Tellervo webservice can also create some Tellervo specific records These are securi tyUser securityGroup box and permission How to create and alter permissions records is described in more detail in section 15 8 as they are more complicated but securityUser securityGroup and boxes are handled in the same way as TRiDaS entities 15 7 Updating records Updating existing records in Tellervo is done in much the same way as creating records The basic template is as follows lt xml version 1 0 encoding UTF 8 gt lt c tellervo xmIns c http www tellervo org schema 1 0 xmiIns tridas http ww tridas ore 1 2 2 gt lt c request type update gt lt tridas element gt lt tridas element gt lt ce request gt lt c tellervo gt The main difference is that you must specify the TRiDaS lt identifier gt tag containing the ID of the record you are trying to update 15 8 Reading and setting permissions lt request type create gt lt permission gt lt permissionToCreate gt true lt permissionToCreate gt lt permissionToRead gt true lt permissionToRead gt lt permissionToUpdate gt true lt permissionToUpdate gt lt permissionToDelete gt true lt permissionToDelete gt lt entity type object id 760a19e2 229c 1lel 8756 03 b2aff2fe33 gt lt securityGrou
188. n file for your operating system from http www tellervo org download The website should provide you with a link to the installer for your current operating system 7 Windows Run the setup exe and follow the instructions If you do not have Java installed the installer will direct you to the Java website where you can get the latest version Once installed Tellervo can be launched via the Start menu Please note that that the 64 bit version of Tellervo should only be used if you have the 64 bit version of Java The vast majority of Windows users will have 32 bit version of Java regardless of the type of processor or operating system they are using If you install the incorrect version you ll be warned and the 3D mapping will be disabled amp Mac OS X As mentioned above Tellervo requires Java 6 Although MacOSX ships with Java installed unfortunately Apple have been very slow to provide Java 6 Although it was released in 2006 it was not until August 2009 that Apple made Java 6 available as part of v10 6 Snow Leopard Tellervo can therefore only be run on Snow Leopard or later To install Tellervo download then open the zip file and drag the Tellervo app into your applications folder To use the 3D mapping or measuring platform hardware in Tellervo you will also need to install the Tellervo Drivers package Ubuntu Linux A deb file is available which was designed for use on Ubuntu distributions but should work on any Debi
189. nal feature of creating barcode labels Once you ve finished importing your metadata simply press the barcode button and a PDF file will be generated 4 4 Metadata browser The metadata browser interface provides a convenient way to view all the metadata within your Tellervo database It can be accessed through the Administration menu of from the home screen The metadata browser contains two parts a hierarchical representation of all TRiDaS entities in your database on the left and a metadata viewer for the selected entry on the right This interface is also the best method for fixing mistakes in your database 24 Tellervo A guide for users and developers Although Tellervo s database architecture maintains integrity within your data it does come at the price of being a little more complicated to fix mislabelled series For instance what if you were to measure a series B and assign it to sample ABC 138 A only later to realize you misread the label and it was in fact ABC 188 A In a traditional file based system you would probably just need to rename the file you d just created In Tellervo however you need to redefine the relationship of the series within the database and reassign it to the correct sample This is best understood when looking at the hierarchical tree in the metadata browser Hopefully you will see that you what you need to do is to move the series from its current position in the database to the correct one The
190. nced with Linux and running servers The second option is to intall the native Ubuntu package on an Ubuntu Linux server The source code for the server is also available so it is perfectly possible for more experienced users to set up the Tellervo server to run natively on other platforms But to do this you will require a good knowledge of Apache 2 PHP and PostgreSQL Choose the most applicable method and follow the instructions in the following sections 1 1 1 Install as Virtual Appliance recommended method To run the Tellervo server Virtual Appliance you will first need to download and install VirtualBox from http www virtualbox org Installation packages are available for Windows MacOSX OpenSolaris and many Linux distributions Once you have VirtualBox installed you will then need to download the Tellervo server from the Tellervo website http www tellervo org download This package contains a bare bones Ubuntu Linux server Note that the Tellervo appliance is provided in the open standard format OVA You should be able to run the appliance in other Virtual Machine applications e g VMWare Citrix etc but the OVA standard is very young and changing fast We recommend sticking with VirtualBox until the standard stabilizes 6 Tellervo A guide for users and developers with everything required to run the Tellervo server installed and ready to use As VirtualBox the entire Ubuntu operating system and Tellervo server components
191. nch4J BSD MIT NSIS zlib libpng Ant Apache 2 0 Eclipse Eclipse Public License v1 0 ResourceBundle Editor LGPL M2Eclipse Eclipse Public License v1 0 Subversive Eclipse Public License v1 0 Table 13 2 Additional tools libraries typically used in the development of Tellervo 66 Tellervo A guide for users and developers 13 4 Code layout Tellervo has been actively developed since 2000 so has seen contributions by many different developers Coding practices have also changed in this time so inevitably there are some inconsistencies with how the source code is organized For instance the most recent interfaces have been implemented using the Model View Controller MVC architecture whereas earlier interfaces contain both domain and user logic in single monolithic classes Perhaps the most important inconsistency to understand is due to the transistion to the TRiDaS data model In earlier versions of Tellervo used the concept of a Sample to represent each data file Although large portions of Tellervo have been refactored to use the TRiDaS data model classes there are still some places where the Tellervo Sample remain 13 5 Multimedia resources Tellervo includes infrastructure for multimedia resources such as icons images and sounds within the Maven resource folder src main resources The most extensive is the Icons folder which contains many icons at various sizes ranging from 16 x 16 to 512 x 512 as PNG format files The
192. ncies of dependencies automatically Therefore if a developer knows he needs the functions within a particular library he simply needs to supply the details of this library without having to worry about the other libraries that this new library is in turn dependent on Maven also manages versions much more efficiently If a library is dependent on a particular version of another library this is specified within the Maven build mechanism This means it is much easier to keep dependencies up to date without having to worry about the cascading issues that upgrades often have In short Maven is intended to save developers from JAR hell In practice life is not necessarily that simple Although Maven assists developers in many ways it also has its own particular quirks and annoyances The main problem is how to handle the situation when the dependencies you need are not available in central repositories To solve this you either need to install these jars into your local Maven repository or make them available in a 3rd party Maven repository For the ease of developement we have set up a Maven repository as part of the TRiDaS project which can be browsed at http maven tridas org This repository is already configured within the Tellervo project so assuming this repository is still alive then your Tellervo project should automatically build If not then you will need to install the few non standard jars These jars will continue to be maintained in
193. need to open the series you would like to index Next choose Tools gt Index to display the indexing dialog figure 9 1 ndexing Y m Standard Semi log Toothed Pio ERIK Eee SG Roe ps Choose index Algorithm x P Horizontal 430 858 5 0 000 Polynomial 1 94 035 1 0 884 Polynomial 2 77 744 0 0 905 Polynomial 3 75 624 4 0 908 Polynomial 4 69 741 3 0 915 Polynomial 5 64 967 3 0 922 Polynomial 6 63 279 0 0 924 Floating 11 pt 44 812 2 0 947 High pass 1 2 4 2 1 15 248 4 0 982 Cubic Spline 65 508 7 0 921 Series code C ACM 1 A A A Version 2 Help OK Cancel a Figure 9 1 Indexing dialog showing the original data in blue the exponential index of this data in green and the normalized data in red From the indexing dialog you can then choose which type of index to apply to your data The table on the right shows the available options along with the x and p values to help you choose the correct index to use The graph shows your original data the index line and the result of applying the index to the data and changes dynamically as you pick between different indexing methods Once you have decided which index you want to use select it and click OK ensuring that you have given your data series a new version number Chapter 10 Crossdating and chronology building All algorithms work in pretty much the same way There s a fixed sample and there s a moving sample Imagine you have printout
194. nes of metadata Strictly these lines should contain structured metadata but with no software to assist in this users either only partially stick to these rules or reject them entirely instead using the three lines as free text comment lines The metadata should be set out as follows Line 1 Chars 1 6 Site ID 158 Tellervo A guide for users and developers Line 1 Chars 10 61 Site Name Line 1 Chars 62 65 Species Code followed by optional ID number Line 2 Chars 1 6 Site ID Line 2 Chars 10 22 State Country Line 2 Chars 23 30 Species Line 2 Chars 41 45 Elevation Line 2 Chars 48 57 Lat Long in degrees and minutes ddmm or dddmm Line 2 Chars 68 76 1st and last Year Line 3 Chars 1 6 Site ID Line 3 Chars 10 72 Lead Investigator Line 3 Chars 73 80 comp date Then follows the data lines which are set out as follows Chars 1 8 Series ID the series ID should be unique in the file so that it is clear where one series ends and another begins when multiple series are present in the same file Next 4 chars Year of first value in this row Ten data values consisting of a space character and 5 integers The file and last data line for a series may have less than 10 data values so that the majority of lines begin at the start of a decade The final data value should be followed by a a stop marker which is either 999 or 9999 When a stop marker of 999 is used this indicates that th
195. nowing that NAT is being used The URL that you need to use to connect to is http ip of your physical machine 8080 tellervo 1 1 2 Ubuntu native installation If you are fortunate enough to be running Ubuntu then the native Ubuntu deb package is the best and easiest method for installing the Tellervo server otherwise see section 1 1 1 to install the server as a Virtual Appliance To install the Tellervo server in Ubuntu simply download the deb package from the Tellervo server http www tellervo org download and install with your favourite package manager For instance to install from the command line simply type 4 sudo dpkg install tellervo server deb If you haven t got all the required dependencies already installed dpkg will return an error This can be fixed by running Z sudo apt get install f which will install all the missing packages and will automatically allow dpkg to run to completion The package will automatically run a configuration script to assist with creating a database user building the Tellervo PostgreSQL database setting database permissions and setting up the Apache webservice The configuration ends with a test routine to check all services are set up correctly and if so will provide you with the URL of the newly configured Tellervo webservice 8 Tellervo A guide for users and developers 1 1 3 Advanced install on other operating systems As mentioned previously the limited resources available for
196. ns If the platform has the ability to work in different units the UnitMultiplier value must be used to ensure the units set by the user are handled correctly 72 Tellervo A guide for users and developers zeroMeasurement if your platform responds to requests to zero the measurement value this is where you should implement this requestMeasurement if your platform responds to requests to send the current measurement value then you should implement this functionality here Once your new class is complete you need to inform Tellervo that it exists To do this you need to register the device in org tellervo desktop hardware SerialDeviceSelector You should then be able to launch Tellervo and test your new device in the preferences dialog The relevant parts of the dialog will be enabled disabled depending on how you set the corresponding is Editable methods in your class The dialog also includes a seperate test window with a console for debugging the raw data received from the serial port 13 14 Writing documentation The documentation in Tellervo is written in the well established typesetting language ATEX 2e IATEX is a great tool for producing high quality documentation with a good structure and style Unlike standard WYSIWYG what you see is what you get word processing applications like Microsoft Word ATEX uses simple plain text code to layout a document so that it is often described as WYSIWYM what you see is what you mean
197. nst what most dendrochronologists assume and do when using Tucson files For instance most people that work entirely in the BC period use negative integers to represent BC years e g 5 as 5BC With no clear specification and different people interpreting the format in different ways there is no way of being certain what data negative year numbers in Tucson files mean Tucson format places a restriction of just four characters to the year values This means that strictly the earliest value a Tucson file can represent is 999 Some users work around this by steeling the last character of the series ID to give them five characters for the year For example ABCDEFG 9999 This Tucson 159 vvvyv v v conversely limits the series ID to 7 characters To add to the confusion other users have been known to add an arbitrary number e g 5000 to all year numbers to overcome this problem The fact that 999 is used as the stop marker for series in 1 100th mm means that Tucson files cannot store a ring value of 9 99mm In the unlikely event that a sample should have this large a ring it should be rounded up or down to 998 or 1000 Some programs appears to add padding values after the stop marker to fill the rest of the 10 data values in the row Some data files seem to use 9990 as a stop marker Some files appears to use a full stop character to indicate empty data values after the stop marker Data values in RWL files are space delimited however
198. ntain zero Invariant Sections If the Document does not identify any Invariant Sections then there are none The Cover Texts are certain short passages of text that are listed as Front Cover Texts or Back Cover Texts in the notice that says that the Document is released under this License A Front Cover Text may be at most 5 words and a Back Cover Text may be at most 25 words A Transparent copy of the Document means a machine readable copy represented in a format whose specification is available to the general public that is suitable for revising the document straightforwardly with generic text editors or for images composed of pixels generic paint programs or for drawings some widely available drawing editor and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters A copy made in an otherwise Transparent file format whose markup or absence of markup has been arranged to thwart or discourage subsequent modification by readers is not Transparent An image format is not Transparent if used for any substantial amount of text A copy that is not Transparent is called Opaque Examples of suitable formats for Transparent copies include plain ASCII without markup Texinfo input format LaTeX input format SGML or XML using a publicly available DTD and standard conforming simple HTML PostScript or PDF designed for human modification Examples
199. ntial packages to make the server run have been installed This means there is no graphical interface just a command line Hopefully this should not be a problem as once set up the only interaction needed with the Virtual Appliance will be through the normal Tellervo desktop application If you would prefer to use a graphical interface to the server this can be easily installed See chapter 11 for further details There are a number of limitations caused by distribut ing the server software in this way The operating system has already been configured to use network ing without a proxy server so if your computer re quires a proxy then you won t be able to connect to the Internet Please contact the developers for more details VirtualBox has a number of methods for providing network connectivity to the Tellervo virtual appliance The default setup described above is to use bridged networking This makes the virtual server appear as if it was another physical computer on your network with its own IP address This works best in most a Ubuntu Server 11 10 clean_1 Running Oracle VM VirtualBox y Ye Machine Devices Help ould you like the installer to configure Apache to run the webservice Yin y server s fully qualified domain name n be read Conf igurat SUCCESS Your Corina webservice is nou available at http 105 128 cor ina webservice or ina cor ina virtual server usr share cor in APIA BBlRishece
200. od width G max imum density J ring width K minimum density P percentage latewood S width of late wood 13 15 Measurement units 16 20 Length of series 21 24 Species either encoded using ITRDB taxon codes or by using the first two letters of the genus and species 25 30 Year of the last ring 31 50 Description 51 58 Measurement date ddMMyy or ddMMyyyy 59 60 Initials of author 61 68 Last modified date ddMMyy or ddMMyyyy 69 70 VFormat version identifier 00 01 etc 71 73 Estimated number of missing rings as the start of the series gt 74 75 Standard error of this estimate if unknown 76 78 Estimated number of missing rings at the end of the series 79 80 Standard error of this estimate if unknown The second data line is a free text comment up to 80 characters VFormat files from version 10 onwards then contain a third header line This contains 8 floating point numbers of 10 digits each These represent gt gt gt gt gt Longitude Latitude Altitude Height of the tree s measurement Four other user definable numbers VFormat files from version 20 onwards contain a forth header line This is of the same format as line 3 but each of the values is user definable Following the 2 4 header lines come the data lines These lines are made up of 10 data fields each containing 8 characters Each data field is made up as follows gt Two character code fo
201. of a back plate of a string instrument Note that a sample always exists and that it can either be physical e g a core or representative e g a picture A sample is taken from exactly one element and can be represented by one or more radii A radius is a line from pith to bark along which the measurements are taken A radius is derived from exactly one sample It can be measured more than once resulting in multiple measurementSeries A measurementSeries is a series of direct raw measurements along a radius A single measurementSeries can be standardised or a collection of measurementSeries can be combined into a derived Series The measurements themselves are stored separately as values A derivedSeries is a calculated series of values and is a minor modification of the v series concept proposed by Brewer et al 2010 Examples include index average of a collection of measurementSeries such as a chronology A derivedSeries is derived from one or more measurementSeries and has multiple values associated with it A value is the result of a single ring measurement Examples include total ring width earlywood width latewood width The values are related to a measurementSeries or a derivedSeries In case of a mea surementSeries the variable and its measurement unit e g microns 1 100th mm etc are recorded as well For a full description of the standard see Jansma et al 2010 S 2 Example file lt xml version 1 0 enco
202. of transparent image formats include PNG XCF and JPG Opaque formats include proprietary formats that can be read and edited only by proprietary word processors SGML or XML for which the DTD and or processing tools are not generally available and the machine generated HTML PostScript or PDF produced by some word processors for output purposes only The Title Page means for a printed book the title page itself plus such following pages as are needed to hold legibly the material this License requires to appear in the title page For works in formats which do not have any title page as such Title Page means the text near the most prominent appearance of the work s title preceding the beginning of the body of the text The publisher means any person or entity that distributes copies of the Document to the public A section Entitled XYZ means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language Here XYZ stands for a specific section name mentioned below such as Acknowledgements Dedications Endorsements or History To Preserve the Title of such a section when you modify the Document means that it remains a section Entitled XYZ according to this definition The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document These War
203. ollows lt xml version 1 0 encoding UTF 8 gt lt tellervo xmIns http www tellervo org schema 1 0 xmlins gml http ww opengis net gml xmins xlink http www w3 org 1999 xlink xmins tridas http ww tridas org io lt header gt lt header gt lt content gt lt content gt lt tellervo gt The header contains standard information about the request and also includes error and warning messages The content tag contains the actual data being returned 15 2 1 Namespaces For newcomers to XML namespaces and their definition can be quite confusing Namespaces are used in XML to enable us to incorporate multiple schemas within the same XML file In the case of Tellervo that means we can use entities defined in both TRiDaS to describe dendro data as well as for instance GML to describe location information Rather than reinvent the wheel we use established standards like GML so that we can leave the experts in each field to handle their own datastands We need a method of clarifying which schema each entity in the XML file is referring to and for that we use namespaces Namespaces are typically defined in the root tag of the XML file using the attribute xmIns Multiple names paces can be described by adding prefix definitions For example xmins tridas http www tridas org 1 2 2 means that any tag prefixed by tridas in the XML document refers to an entry in the TRiDaS schema Namespace
204. omma character to indicate cell boundaries Support for CSV files in TRICYCLE is limited to a particular layout of data The expected layout is the same as for Excel and ODF spreadsheet files Row 1 Header names for each column gt Column A Year values gt Column B One column for each series containing data values Cells are left empty if no data is available for a series because it does not extend to a particular year Data must be continuous for each series so missing unmeasured rings should be included as zero 114 Tellervo A guide for users and developers F 2 Example file Year MySamplel MySample2 500 0 33 501 0 26 0 26 ORO 2052 503 0 14 0 14 504 0 08 0 08 505 0 02 0 02 506 0 2 0 2 507 0 14 0 14 508 0 08 0 08 509 0 2 510 0 33 511 0 08 512 0 33 513 0 22 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer G 1 Description Corina Corina Legacy Corina Text file Various including raw rec ind cln sum Read and write Corina Data and some structured metadata Gregorian Yes No Yes No Robert Mecki Pohl Appendix G Legacy The Corina Legacy format is the file format used by the Corina software prior to version 2 when it transferred to using TRiDaS The format was origin
205. onent and b serves only to enable use of the work with that Major Component or to implement a Standard Interface for which an implementation is available to the public in source code form A Major Component in this context means a major essential component kernel window system and so on of the specific operating system if any on which the executable work runs or a compiler used to produce the work or an object code interpreter used to run it The Corresponding Source for a work in object code form means all the source code needed to generate install and for an executable work run the object code and to modify the work including scripts to control those activities However it does not include the work s System Libraries or general purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work For example Corresponding Source includes interface definition files associated with source files for the work and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require such as by intimate data communication or control flow between those subprograms and other parts of the work The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source The Corresponding Source for a work in source code form is that same work
206. ooden panel in a painting the left hand back plate of a violin one beam in a roof a tree trunk preserved in the soil a living tree The element is a specific part of exactly one object or 20 Tellervo A guide for users and developers project documentation a dendro research of a particular object or group of objects investigates object documentation an item that is investigated element ER documentation a piece zu of wood originated from one tree sample documentation a physical sample of an element to be measured radius documentation a line from pith to bark from which the measurements are made e g e g paintings of one museum wood in one excavation building living trees in one site e g violin painting excavation site ship church church roof forest dead or alive e g plank of a painting piece of wood from an excavation beam in a church roof live tree in a forest e g wax imprint of a plank picture taken from a painting specimen taken from a beam from an excavation specimen taken from the beam of a church roof specimen taken from a live tree index of a measurementSeries mean of multiple series chronology measurementSeries documentation a series of direct raw measurements of rings seasons Figure 4 1 TRiDaS data model showing the relationships between data entities Most of the entities having a si
207. or 702 Feature not yet implemented 703 Invalid XML being returned by webservice 704 Configuration error User 901 Invalid user parameter s 902 Missing user parameter s 903 No records match 904 Parameters too short 905 Invalid XML request 906 Record already exists 907 Foreign key violation 908 Unique constraint violation 909 Check constraint violation 910 Invalid data type 172 Table Y 1 The Corina webservice provides error feedback by means of an error code and description Section Code Description 911 Series with this version number already exists 912 There must be at least one administrator Appendix Z GNU General Public License The Corina server and desktop client are released under the GNU General Public License GPL version 3 Copyright 2011 Peter Brewer This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details Z 1 Preamble Copyright 2007 Free Software Foundation Inc http fsf org Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed
208. original data and nonces a pseudo random string used just once All hashes used in the Tellervo webservice use the MD5 algorithm This decision will be periodically reviewed to ensure that MD5 is the most appropriate and secure algorithm to use Whilst an MD5 hash of a short phrase can be compromised the length and randomness of the original data means with current cracking techniques this is essentially impossible For a complete description of Tellervo s authentication procedure see section 16 1 The default Tellervo server setup however uses standard HTTP protocol to communicate between the server and the desktop application This is the same protocol used for the majority of web pages on the internet and a determined hacker could eavesdrop on this communication Depending on how important and private you perceive your data you may choose to use Secure Socket Layer SSL to encrypt this communication This is the same technology used by websites such as online banking To make full use of this upgrade in security you will however also require a SSL certificate from an official licensing authority These certificates typically cost several hundred dollars per year 56 Tellervo A guide for users and developers 11 5 Directly accessing the database Although the Tellervo database is designed to only be accessed by the Tellervo desktop application via the Tellervo server s webservice you may decide that you d like to directly access the databas
209. orina Dictionary normalld 4 normal Building gt Building lt type gt lt description gt The White Tower of Thessaloniki was originally constructed by the Ottomans to fortify the city s harbour lt description gt lt coverage gt lt coverageTemporal gt Ottoman lt coverageTemporal gt lt coverageTemporalFoundation gt Stylistic lt coverageTemporalFoundation gt lt coverage gt lt location gt lt locationGeometry xmins gml http www opengis net gml gt lt gml Point srsName urn ogc def crs EPSG 6 6 4326 gt lt gml pos gt 40 6263 22 9485 lt gml pos gt lt gml Point gt lt locationGeometry gt lt locationPrecision gt 20 lt locationPrecision gt lt locationComment gt Thessaloniki Greece lt locationComment gt lt location gt lt object gt lt title gt Fourth floor lt title gt lt type gt Floor lt type gt lt element gt lt title gt C TWI 65 lt title gt lt identifier domain dendro cornell edu gt 89dbd409 03a3 42a0 9391 62c6be7009ad lt identifier gt lt createdTimestamp certainty exact gt 1997 02 01T14 13 51 0Z lt created Timestamp gt lt lastModifiedTimestamp certainty exact gt 1997 02 01T 14 13 51 0Z lt lastModifiedTimestamp gt lt type normalStd Corina Dictionary normalld 3 normal Rafter gt Rafter lt type gt lt description gt 15th Rafter from the south lt description gt lt taxon normalStd Catalogue of Life Annual Checklist
210. ossdate which you ll almost never use It s not terribly useful to dendrochronologists but statisticians might want to know its value so Tellervo makes it available The R value is used in the T Score the T score being defined in terms of the r value and the overlap N If you look at the equations for calculating a T Score you will see on the penultimate line Sry Sea Syy An r value can range from 0 0 no correlation to 1 0 perfect correlation r 10 2 Crossdating series 10 3 Managing chronologies Chapter 11 The Tellervo server For basic day to day running of the Tellervo server you simply need to make sure that the server is running All other interaction and managment creating users granting permissions accessing data is done through the Tellervo desktop application This section however outlines a number of aspects of the server that advanced users may find useful 11 1 Backing up and restoring your database As with any computer system it is important for you to back regular backups of your data to guard against hardware as well as human errors The two main methods for doing this are outlined below 11 1 1 Backup whole Virtual Appliance The simplest method is to make a copy of your entire Virtual Appliance but this does have a number of drawbacks The first is that you need to shut down your server before you can make the backup so this is only possible if server downtime is not a problem for your
211. ox click the Create new box button and enter its details There is no restriction on what boxes should be called but it is probably easiest if you use some sort of numerical sequence to assist with organizing the boxes in your store At Cornell we use a two part name for each the first being the year of collection the second being a sequential number e g 2009 11 The contents tab lists all the samples that have been assigned to this box To add new samples simply click the Add sample to box button and scan the sample s barcode 8 3 2 Inventory An important feature of any collection management system is the ability to perform an inventory on the collection Even with the most robust system samples will always go astray so its important to be able to periodically check that the boxes contain what you expect The Contents tab of the Box details dialog contains a feature to assist with this Next to the list of samples that are recorded as present there is a temporary checklist column By checking the boxes for each sample actually stored in the box it is easy to see which samples have been mislaid If the Mark unchecked as missing from box button is then pressed the date and time the discrepancy was noted is then recorded in the comments field for the box 42 Tellervo A guide for users and developers S f8b 11d iil niii wi i C YMT 1399 A A 2 I Istanbul Yenikapi Metro
212. p id 3 gt lt permission gt lt request gt lt request type read gt lt permission gt lt entity type object id 760a19e2 229c 1lel 8756 03 b2aff2fe33 gt lt securityGroup id 3 gt lt permission gt lt request gt au ae UNB Webservice specifications 89 lt request type update gt lt permission gt lt permissionToCreate gt false lt permissionToCreate gt lt permissionToRead gt false lt permissionToRead gt lt permissionToUpdate gt false lt permissionToUpdate gt lt permissionToDelete gt false lt permissionToDelete gt lt entity type object id 136a70a6 566b 546b a3ae c48cb046e4cd gt lt securityGroup id 1 gt lt securityGroup id 3 gt lt permission gt lt request gt lt request type delete gt lt permission gt lt entity type object id 136a70a6 566b 546b a3ae c48cb046e4cd gt lt securityGroup id 1 gt lt permission gt lt request gt Chapter 16 Systems architecture The centralised nature of the Cornell Tree Ring Lab data required a server client architecture of some type In Corina this was achieved simply by having users save their data in a network folder stored on a central server Whilst this method was adequate it has many data storage issues that can be largely solved by moving the data storage infrastructure to a relational database management sys
213. pages 173 178 so you are welcome to inspect and edit the code The second part of this manual will help you do that Over the years Corina and Tellervo have been developed by Peter Brewer Chris Dunham Aaron Hamid Dan Girshovich Ken Harris Drew Kalina Rocky Li Lucas Madar Daniel Murphy Robert Mecki Pohl and Kit Sturgeon We would like to thank the many people that have tested the applications especially Charlotte Pearson Carol Griggs Brita Lorentzen Jess Herlich LeAnn Canady Kate Seufer and many undergraduate and postgradutes students at Cornell We would also like to thank the College of Arts amp Sciences and the Department of Classics Cornell University the Malcolm H Wiener Foundation and the many patrons of the Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology for their financial support We hope that you find Tellervo useful and look forward to hearing your feedback Part User Guide Chapter 1 Installation Tellervo is made up of two packages the Tellervo desktop application and the Tellervo database server Tellervo was designed primarily for laboratories with multiple users each running the Tellervo desktop application on their own computer connecting to a single central server containing the lab s data In this situation the Tellervo server would be run on a separate computer to those running the desktop client but this need not necessarily be the case It is perfectly
214. parameter contains the default value to return if no preference is found Like the setPref method there are also a host of getPref methods for different data types 13 9 Build script Tellervo is built using Maven and is controlled through the pom xml file stored in the base of the Tellervo source code Previous versions of Tellervo used Ant but managing the increasing number of dependencies as Tellervo has grown become too onerous see section 13 3 for more details Earlier versions of Tellervo were deployed using Java WebStart technology primarily because this is platform independent and requires just a single click for a user to install However this has since been replaced with native installers for the major platforms due to various complications associated with native libraries see section 13 9 5 required for 3D graphics and serial port hardware We have also found most users are more comfortable with the standard install procedures that they are used to on their operating systems While you develop Maven should automatically build Tellervo for you in the background Specific build com mands are only required as you approach a release We use the standard Maven life cycle for building packaging and deploying Tellervo The method for doing this in Eclipse is by right clicking on the pom xml file and selecting Run as gt Maven package etc If the option you want is not displayed you will need to create an entry in the build menu by
215. pg_hba conf Scroll down passed all the comments to the bottom of the file Add the following line host all all IPADDRESS 32 md5 Make sure you replace IPADDRESS with the IP address of the computer you are trying to connect from This is just one style of pg_hba conf entry There are many others which allow you to restrict to specific users computers networks etc See the online PostgreSQL documentation for more details Save your changes and exit by doing CTRL X Next you need to make sure the PostgreSQL server is listening to requests from other IP addresses To do this you need to edit the postgresql conf file like this sudo pico etc postgresql 9 1 main postgresql conf making the following changes Old line listen_addresses localhost I New line listen_addresses Make sure you remove the hash character at the beginning of the line Save the file and finally restart the Tellervo server Z sudo tellervo server restart You should now be able to access your database through PGAdminlll To do this open the application and go to File gt Add server Specify your server s IP address is the host field and your database username and password The Tellervo server 57 11 5 2 ODBC It is also possible to connect to your Tellervo database via an ODBC connection This allows limited access to the database from a variety of database applications including programs like Microsoft Access for which further details a
216. ple should have 100 trend 10 1 3 Weiserjahre The Weiserjahre algorithm is used for crossdating summed samples chronologies against single samples All of the algorithms that have been mentioned so far only compare the ring widths This works fine for raw samples but when crossdating summed samples there s a lot more information available namely the Weiserjahre data Wouldn t it make sense to count a 20 19 x 1 ring more heavily than a 1 1 0 ring 19 out of 20 samples think it s an increasing year not just 1 This is what the Weiserjahre cross does for each possible overlap it starts by counting the number of significant intervals of the master for that overlap A significant interval is one with at least 3 samples where at least 75 of them have the same trend Then it computes the percent agreement like the trend between the master and the raw sample for only those significant years of the overlap Of course for the trend of the master it doesn t use the trend of the master it uses the trend of the majority of its elements They re usually the same but not necessarily Another way to think about the Weiserjahre crossdate is it s like a trend but ignoring years where the sum has only 1 or 2 samples or where there isn t an overwhelming trend in the sum Also like the trend the results are given as a percentage Crossdating and chronology building 51 10 1 4 R Value The R value or correlation coefficient is a cr
217. possible to run both the server and the client on the same computer This is likely to be the situation if you simply want to try out Tellervo if you don t have a separate server or if you do not work in a multi user laboratory 1 1 Server installation For the Tellervo desktop application to be useful you will require access to a Tellervo server If you are running Tellervo in a lab where the Tellervo server has already been set up by your systems administrator you can skip this section The Tellervo server is made up of a number of components which unlike the desktop client can t be easily combined together into cross platform packages Although all the constituent components are open source and available for all major platforms building and maintaining separate packages for each platform is too large a task for a small development team To conserve resources we therefore made the decision to utilize Virtual Machine technology to ensure that the Tellervo server could still be run on all major operating systems This means that we can package the Tellervo server for a single operating system Ubuntu Linux and then distribute it as a Virtual Appliance that can be run as a program on your normal operating system The Tellervo server is therefore available via three methods The first is as a VirtualBox Virtual Appliance which can be run on any major operating system and we strongly recommend that you stick with this option unless you are experie
218. pt e g UPDATE tblsupportedclient SET minversion 2 13 WHERE client Tellervo WSI Run maven package to produce the server deb file Create a clean Ubuntu VirtualBox installation with the user tellervo and the password dendrochronology Install the deb file and dependencies as normal configuring the server with temporary settings Run sudo tellervo server deploy to remove the temporary settings and set up ready for users first run Shutdown the virtual appliance then export Add in all the metadata as required Copy the virtual appliance file and the native deb file to the web server for release The server PHP code will automatically pick up the extra files and offer them to users Update the download index php file to reflect the preferred version choice for users TEST If users are running this as an upgrade then we need to ensure this goes smoothly Although they are told to backup their database before running we should assume they ve ignored the warning and that we are altering precious data Test both a fresh install and an upgrade from the previous version 14 6 Administering the Maven repository The following information is only necessary for the lead developer and outlines the steps necessary to install and maintain the central Maven repository for Tellervo This Maven repository should provide all other developers with the libraries required to develop Tellervo and which are b
219. r of that numbered version or of any later version published by the Free Software Foundation If the Program does not specify a version number of the GNU General Public License you may choose any version ever published by the Free Software Foundation If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used that proxy s public statement of acceptance of a version permanently authorizes you to choose that version for the Program Later license versions may give you additional or different permissions However no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version 15 Disclaimer of Warranty THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 16 Limitation of Liability IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MODIFIES AND OR CONVEYS THE PROGRAM AS PERMIT
220. r validity and importance space full validity not yet used not yet used not yet used no validity for long term evaluations no validity for single value evaluations amp no validity except for cumulative stats no validity at all unknown value The second character is a pseudo binary character used to define a weighting factor For full details of the complex method for calculating this weighting factor see the VFormat documentation gt gt One character user definable code for recording information about the data value Five digit floating point data value which is divided by 100 for interpretation W 2 Example file 1 G1101020 OJmm 81Qusp 1510FLA 02 32 572 HLO1 04 9002 810 10 2 G1101020 0J S20102 0 0J _ VFormat 165 281 132 218 144 64 83 150 123 153 G1101050 G1101050 448 487 179 127 106 93 85 174 152 103 147 174 139 169 175 115 71 61 95 113 145 1516FLA 05 213 323 145 189 198 176 157 125 91 103 133 DO 225 207 176 172 202 116 92 79 72 66 84 108 70 145 112 1 OJmm 121Qusp 10J S20105_0 OJ _ 286 341 353 279 210 277 110 144 101 106 95 83 145 174 132 144 133 117 163 92 127 145 113 112 89 178 126 135 109 62 85 119 164 13 346 422 165 135 191 165 132 83 104 174 155 197 150 130 120 82 94 120 158 586 371 436 261 154 185 193 130 124 99
221. r y Figure 1 1 Screenshot of VirtualBox running the Tellervo server The console contains the results of the tests run at the end of the configuration routine situations but can cause problems if your network administration is particularly strict lt is also not suited to TIf you are using an older version of VirtualBox it may expect an OVF rather than the OVA file provided The OVA file is a tar file containing several files required by VirtualBox including an OVF file If you rename the extension of the OVA file to tar then extract the contents to a folder using a tools like WinRAR you should then be able to continue Installation 7 those installing Tellervo Server on a laptop which is used on different networks especially via wifi If you have problems with bridged networking then it may be better to use one of the alternatives listed below The first network alternative is to use host only networking To use this you simple select your server in VirtualBox click settings then on the network tab choose host only adapter This setting means that your server will only be visible to the physical computer you are running Tellervo server on This may not be a problem it may even be desirable if you are installing for your personal use but of course it is not suitable if you are intending to share the server with colleagues The second network alternative is to use NAT networking NAT stands for Network Address Translation and mean
222. ranslations s dania a A Aa ne 13 7 Logging fixate BA ER Een el re 13 8 Preferentes e See a 13 9 B ild seript 44 64004 464448 A a ahs 13 9 1 Windows installer 2 2 o o o 13 9 2 Mac package aaa 13 9 3 Linux Deb package 0 0 o 000004 13 9 4 Linux RPM package 0 0 e 0000045 13 9 5 Native libraries 2 2 2222 oo oo nn 13 10 Java Architecture for XML Binding JAXB 13311 IV VERSION 2 a ur Sab NE a 13 12 Developing graphical interfaces 0 002000 13 13 Supporting measuring platforms 2 2 2 2 2 nn nn 13 14 Writing documentation oaa 13 15 Recording screencast tutorials ooo aaa 13 16 Making a new release ooa aaa ee 14 Developing Tellervo Server 14 1 Webservicer a da Dd PRE dd A N 14 1 1 Creating new series onen 14 2 Server Package o ee NE ee ed a 14 2 1 Tellervo server script 22 22 oo non 14 3 Handling version dependencies 2 2 non 14 3 1 Client requiring a recent server ooa aa 14 3 2 Server requires a recent client 2 22 22220 14 4 Handling server configuration 0 20 2020000 14 5 Making a new release 2 2 2 CC oo 14 6 Administering the Maven repository 2 ooa 15 Webservice specifications 15 1 Basics of sending requests 2 Comm 15 2 Standard request response 2 2 2 2 oo nn nn 56 56 57 57 57 58 58 59 59 59 vi CONTENTS 15 2 1 Namespaces i iei an
223. ranty Disclaimers are considered to be included by reference in this License but only as regards disclaiming warranties any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License Verbatim copying You may copy and distribute the Document in any medium either commercially or noncommercially provided that this License the copyright notices and the license notice saying this License applies to the Document are reproduced in all copies and that you add no other conditions whatsoever to those of this License You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute However you may accept compensation in exchange for copies If you distribute a large enough number of copies you must also follow the conditions in section 3 You may also lend copies under the same conditions stated above and you may publicly display copies Copying in quantity If you publish printed copies or copies in media that commonly have printed covers of the Document numbering more than 100 and the Document s license notice requires Cover Texts you must enclose the copies in covers that carry clearly and legibly all these Cover Texts Front Cover Texts on the front cover and Back Cover Texts on the back cover Both covers must also clearly and legibly identify you as the publisher of these copies The front cover must present the full title
224. rce If you do not have NSIS installed you will get an error when packaging Tellervo however all other aspects of the development environment including building OSX binaries should work fine if you comment out the NSIS section in the pom xml file Remember not to commit this change to the repository though 64 Tellervo A guide for users and developers Once installed you can then launch Eclipse To access the Tellervo source code you will need to install the Subversive plugin to Eclipse As of Eclipse v3 5 this can be done by going to Help gt Install new software Select the main Update site in the Work with box then locate the Subversive SVN Team Provider plugin under Collaboration If you are using an earlier version of Eclipse you may need to add a specific Subversive update site See the Subversive website http www eclipse org subversive for more details Once installed you will need to restart Eclipse Next you will need to install the m2e Maven plugin to Eclipse This can also be installed by going to Help gt Install new software however you may need to add the Maven update site as this plugin is not currently available in the main Eclipse repository You can do this by click the Add button and using the URL http m2eclipse sonatype org sites m2e Once again you will need to restart Eclipse before continuing Next you need to get the Tellervo source code Go to File New gt Project then in the dialog s
225. rd keywords specified in the documentation but users can extend these with their own This makes the format extremely flexible but the absence of any checking of data types strings numbers categories etc and no method of validation means that there can be problems interpreting metadata entries Heidelberg files can store one or more series in a single file Each series is represented by a header and a data block The header block begins with a line HEADER This is followed by lines of metadata with one field on each line in the format keywords value much like a standard Windows INI file As mentioned previously there are a number of predefined keywords all of which are outlined here AcceptDate Age AutoCorrelation Bark BHD Bibliography Bibliography n BibliographyCount Bundle CardinalPoint Chronology Type VVVVVVVVVVYV ChronoMemberCount ChronoMemberKeycodes Circumference Client ClientNo Collector Comment Comment n CommentCount Continent CoreNo VVVVVVVVVVYV E N N Tellervo A guide for users and developers VVVVVVVVVVVVVYVVYVVYVVVVVVVVYVYVVYVVVYVVVVVVVYVVYVVVVVVVVVYVYVVVVVVVVVVVVVYV Country CreationDate DataFormat DataType DateBegin Dated DateEnd DateEndRel DateOfSampling DateRelBegin n DateRelEnd n DateRelReferenceKey n DateRelCount DeltaMissingRingsAfter DeltaMissingRingsBefore DeltaRingsFromSeedToPith Disk District Edgelnformation EffectiveAutoCorrelation Effective
226. re given here To use ODBC you will need to install the PostgreSQL ODBC driver http www postgresql org ftp odbc on your desktop computer Once you ve installed the driver you can then open a blank database in Access and go to Files Get external data then Link tables In the file dialog box change the file type to ODBC Databases Next select the PostgreSQL Unicode driver then fill out the server details You should then be able to open the tables and views from the Tellervo server database directly from within Access as if they were local tables Be warned though that Access and ODBC have many limitations compared to PostgreSQL especially with regards data types For this reason we strongly recommend using this for read only purposes Using the ODBC connection to write changes to your PostgreSQL database is quite likely to cause serious issues 11 5 3 PSQL The final and most advanced method is to use the psql client on your server This is a command line client which can be used to interrogate the database If you re not already familiar with psql it is unlikely that this is a good method for you to use 11 6 Tellervo server configuration 11 6 1 Standard server configuration The Tellervo server can be configured using the command line tool that is installed on both the Virtual Appliance and native server installs It is the same tool that is run at the end of the native server install but can be run at any time to reconfigure or test
227. reorganization of data in this way is achieved by right clicking on items in the hierarchical tree and choosing either merge or reassign These functions are only accessible to database administrators The reassign option simply moves an entry to a different parent in the database The merge tool handles the more complicated situation where a entry has been made in two different places in the database and they need to be combined For instance in the case described above if the erronously created ABC 138 A after the correct sample ABC 188 A had already been created and populated In this case the A sample from ABC 138 A would be merged into ABC 188 A bringing with it any radii and measurements Hopefully the metadata for the merged series will be identical but in the case of discrepancies details are noted in the comments field of the finished entity You should therefore take the time to check the finished entry and clarify any differences 4 5 Laboratory codes Tellervo uses lab codes to refer to the hierarchical nature of the TRiDaS entities in the database The separate parts of the code are delimited by hyphens and depending on the level of the entity you are referring to will have a different number of parts For instance if you are referring to a tree an element in TRiDaS terminology then the lab code will consist of just two parts the object code and the element code See figure 4 4 for an illustrated example Lab
228. resent rela K K KKK lt 2 lt _ _ 2C z cz tive dates properly Encoding This specified the character encoding to use in the exported text file See section 7 1 2 for more information 7 1 1 Naming conventions The naming convention is used to determine how to name the output files The naming convention relates to the filename itself and not the file extension The file extension is specific to the output format chosen e g Heidelberg files are fh and TRiDaS files are xml Numerical This is the default naming convention It uses the name of the input data file and appends an incrementing number if more than one output file is produced UUID This gives all output files a random named based on Universally Unique Identifiers UUIDs This is a 36 character hexadecimal code which due to the astronomically large number of possible combinations is guaranteed to be universally unique A typical filename will look like 550e8400 e29b 41d4 a716 446655440000 Hierarchical This uses the hierarchical structure of the TRiDaS data model to provide a meaningful name for the output file It joins together the title of each entity in the file beginning with the project name through to the series name For files that contain multiple series the name will contain details of all the entities shared by all the series in the file For example if a file contains several series from the same sample then the file name will be
229. resources schemas folder in the Subversion repository The schema is a detailed representation of what tags are allowed when they are obligatory and what possible values they can contain We strongly suggest getting hold of an XML validation tool to help you check that the requests you send the server are valid The server will do the same and respond with an error message if it is not valid but the textual error is a lot harder to understand than the graphic display of a desktop validation tool The general layout of the request file is as follows lt xml version 1 0 encoding UTF 8 gt lt tellervo xmIns http www tellervo org schema 1 0 xmlns gml http wwmw opengis net gml xmins xlink http www w3 org 1999 xlink xmIlns tridas http www tridas org ioe lt request type gt lt request gt lt tellervo gt Line 1 contains the XML declaration and tells the server that we re using UTF 8 character encoding This is the only encoding currently supported Line 2 starts the root tag and defines the namespaces used by Tellervo In this example the default namespace is the Tellervo schema itself but it also refers to the TRiDaS GML and XLink namespaces that Tellervo also makes use of See section 15 2 1 for more details Line 3 begins the request tag which contains the request itself When you send such a request XML document to the Tellervo server the typical response returned is structured as f
230. rmat designed by over 80 den drochronologists computer scientists and users of dendrochronological data from a variety of associated fields as part of the DCCD project and the Dendro Data Standard forum It is designed to accurately represent any dendro data and metadata and it is hoped over time the dendro community will accept TRiDaS as the de facto standard for all dendro data The format uses extensible markup language XML which means the standard can be extended and evolve as future needs change The format is structured around the eight data entities described below A project is defined by a laboratory and encompasses dendrochronological research of a particular object or group of objects Examples include the dating of a building the research of forest dynamics in a stand of living trees the dating of all Rembrandt paintings in a museum What is considered a project is up to the laboratory performing the research It could be the dating of a group of objects but the laboratory can also decide to define a separate project for each object Therefore a project can have one or more objects associated with it An object is the item to be investigated Examples include violin excavation site painting on a wooden panel water well church carving ship forest An object could also be more specific for example mast of a ship roof of a church Depending on the object type various descriptions are made possible An object can have one
231. rvo Server 77 Images CreatingNewDSeriesWorkflow pdf Figure 14 3 Illustration of the steps that happen during the creation of a new derived series The stages are presented top to bottom in the approximate order in which they are executed Depending on the type of derived series being created a different database function is called to finish the new vmeasurement Figure 14 4 Illustration of the steps that happen during the alteration of an existing derived series The stages are presented top to bottom in the approximate order in which they are executed Note that presently it is not possible to alter the parameters of a derived series 78 Tellervo A guide for users and developers the server packaging will not need to be touched again but if you are making changes and are doing anything more than simple tweaks please consult the Debian policy documentation If changes are required figure 14 5 highlights the order that the pre and post scripts are run and with what parameters The postinst script is used to trigger the interactive script that helps the user configure the Tellervo server described further in section 14 2 1 The steps are as follows Check the user running the script is root as we re doing privileged functions Generated scripts from templates Configure PostgreSQL database creating users and or database if requested otherwise obtaining details if they already exist Configure PostgreSQL to
232. s AFRICA Add layer Altitude 11 567 km Lat 27 5994 Lon 58 3097 Enter place name or coordinate to search for Elev 5 908 meters Figure 5 1 Screenshot showing an example of a site map You can also see a map of your current series if you have latitude longitude metadata by clicking on the map tab on the main data screen 28 Tellervo A guide for users and developers 5 1 Navigation 4 Pan y Zoom C 9 Rotate l Ti It Topography Figure 5 2 On screen navigation controls You can navigate around your maps using the on screen controls figure 5 2 by using your mouse and or your keyboard These controls enable you to explore your location information in 3D such as the example of Mount Vesuvius in figure 5 3 5 1 1 Mouse with scroll wheel Pan Left mouse button click and drag all directions Zoom Use the scroll wheel on the mouse or Left and Right mouse both buttons click and drag up and down Tilt Right mouse button click and drag up and down or use Page Up and Page Down on the keyboard Rotate Right mouse button click and drag left and right Note Crossing the top and bottom half of the screen while rotating will change direction Stop Spacebar Reset Heading N Reset all R 5 1 2 Single button mouse Pan Left mouse button click and drag all directions L left mouse button click once to center view Zoom Hold Ctrl on the keyboard and Left mouse button click and
233. s The first allows the user to choose the format that they would like to export to and the folder into which to save the result Note that the user needs to specify a folder not a filename as many formats are unable to store more than one series in a file When exporting derived series such as chronologies the export dialog may therefore need to create multiple files The second tab contains advanced options for altering the behaviour of the exporter What to export This option enables the user to choose between exporting just the current series or the current series and all associated series Grouping This enables the user to choose to group files into a single export file if possible For formats that do not support more than one series in a file this option is ignored Naming This configures how the output files are named See section 7 1 1 for more details 34 Tellervo A guide for users and developers d Export data from database Y ya Basic settings Advanced options Format Besancon xj Output folder tmp Browse Figure 7 1 Screen showing a se R ries that has been exported to Be Y Y C ACM 1 A A A san on format In the summary of ein Unrepresentable This format does not support relative dates Dates will be output as if undated the export at the bottom of the screen you can see the warning to the user that this format does not Help Convert Save have the ability to rep
234. s are URIs and are typically URLs There is quite often documentation about the schema at the namespace URL au GN Webservice specifications 85 Schema Namespace Tellervo http www tellervo org schema 1 0 TRiDaS http www tridas org 1 2 2 GML http www opengis net gml XLink http www w3 org 1999 xlink Table 15 1 The namespaces used in the Tellervo schema but this is not necessarily the case Information is certainly not retrieved from this location The namespace just needs to be unique and must match what is defined by the schema The prefix itself though can be whatever you want If you have just a few prefixes then it is common to just use a single character prefix perhaps t for TRiDaS to keep the file small Some people prefer to be more explict though and using longer prefixes to ensure there are no confusions Table lists the namespaces used by Tellervo If the majority of your XML file contains tags from one namespace with just a handful of tags from another you may prefer to define a default namespace In this case all tags from the default namespace do not require prefixes The following namespace declarations are therefore all valid and equivalent gt lt tellervo xmIns http www tellervo org schema 1 0 xmIns gml http www opengis net gml xmlns xlink http www w3 org 1999 xlink xmins tridas http www tridas org 1 2 2 gt gt lt t tellervo xmins t http www te
235. s and while you are not asking for a direct contribution we do need your support for future development If there is particular functionality that you would like to see implemented in Tellervo under the open source model this can be done in a number of ways Implement the feature yourself If you are able to program in Java then we would be delighted to assist you to implement new features You could do this in isolation but we hope you will do this collaboratively with us and make the new feature available to the rest of our community Please contact the developers and we will organize a developers SVN account for you to access and contribute to the source code Request a feature from the developers Contact the Tellervo developers and discuss the feature that you would like implemented If the feature is relatively easy to implement and or deemed useful for the laboratories that develop Tellervo then we may be able to implement the feature for you Pay a third party developer If you know a third party developer that can make the changes for you then this is also possible Again we would ask that you do this in consultation with the existing developers so that any improvements can be contributed back to the community Collaborative development If you have an idea for exciting new functionality we would be pleased to discuss the possibility of collaborative development for example as part of a grant funded project The chances of s
236. s are incorrect or have expired the following events occur Server returns an message requesting authentication This message includes a nonce a hash of the current date and time to the nearest minute which we will call server nonce The client creates a second nonce client nonce which is a random hash of it s choosing and a response which is a hash of username hashofpassword servernonce clientnonc It sends this response along with the username and client nonce back to the server but does not send the original server nonce The server computes the same username hashofpassword servernonce clientnonce hash using the in formation it has stored in the database As the server nonce is constant for a minute the two response should match If not the server recomputes the server nonce for one minute ago and tries again This ensures that the server nonce sent to the client is valid for between 1 and 2 minutes Once the server authenticates the user a session cookie is sent to the client On subsequent requests the server recognises the session id and doesn t request authentication again As the user s password is hashed at all points even if the communication is hijacked the attacker will not be able to derive the users password The user s password is also stored in hash form within the database This also means that system administrators do not have access to the passwords either 92 Tellervo A guide for users and de
237. s can be generated metadata entries the sample level must have been made in the database This is typically done using the bulk data entry interface see page 22 If samples are already in the database the user needs to select the object of interest in the label creation dialog to see all the available samples It is then just a matter of selecting the samples of interest and moving them into the selected column Once the list is populated samples from multiple objects can be included then you can either click Preview to see a PDF of the labels or Print to print directly KAA TN C Acm 1 A Figure 8 1 An example of a sample barcode produced by Tellervo for the Cornell lab Note the label also includes the human readable code for the sample The current label style is designed to fit on standard core mounts and most samples There are no widely available die cut labels that fulfill this need so the labels are intended to be printed on archival grade full page sheet labels e g Avery layout 6575 and then manually guillotined 8 2 2 Box labels The procedure for printing box labels is the same as for samples Samples must have already been assigned to boxes before the label is printed see section 8 3 for details To print or preview box labels go to Administration gt Labels gt Box labels The label style is designed to be printed on 5 x st labels two per sheet such as the Avery 6579 layout An example
238. s introduced to Tellervo debugging was often handled through the use of Sys tem out and System err messages To ensure that these messages are not lost we use another package called SysOutOverSLF4J This redirects messages sent to System out and System err to the logging system This is a temporary solution so when working on older classes please take the time to transition these older calls to the proper logging calls We can then remove the need for SysOutOverSLF4J 68 Tellervo A guide for users and developers 13 8 Preferences It is helpful to remember certain user preferences e g colors fonts usernames URLs last folder opened etc so that they don t have to do tasks repeatedly This is achieved through the use of a preferences file This file is stored in a users home folder and consulted to see if a preference has been saved otherwise Tellervo falls back to a default value The preferences are accessed from the static member App prefs To set a preference you can do the following Z App prefs setPref PrefKey PREFKEY the value to set where PrefKey PREFKEY is an enum containing a unique string to identify the preference and the second value is the string value to set There are other specific methods for different data types e g setBooleanPref setIntPref setColorPref etc To retrieve a preference you use a similar syntax 7 App prefs getPref PrefKey PREFKEY default value When you get a preference the second
239. s of 128 bytes If the number of data bytes given in the header at position 45 46 is not a multiple of 128 each block is padded with extra bytes accordingly Padded bytes should be ignored 110 Tellervo A guide for users and developers Bytes Data type Field Description 1 32 C Series name 33 40 C Series code Must be upper case and match file name 41 44 C File extension 45 46 l Series length 47 48 l Sapwood length 49 50 l First valid ring Used if a portion of the series is unreliable 51 52 l Last valid ring Used if a portion of the series is unreliable 53 B Scope 1 pith 2 waldkante 3 pith to waldkante 4 bark 5 pith to bark 54 B State of last ring O last ring complete 1 last ring only early wood 55 56 l First ring Calendar year of first ring O not dated j0 B C O A D 57 B Number of valid characters in series name 58 B Quality code O not known 1 very good 5 uncertain 59 60 l Species code Requires an associated catras wnm file 61 63 D Creation date DMY Y offset 1900 64 66 D Last updated DMY Y offset 1900 67 B Real number format normally 1 IEEE 68 B Type of series O ring widths 1 early wood widths 2 late wood widths 69 81 Reserved 82 C Special sources A averaged D digitized E extern H manual input 83 B Protection O no protection 1 not to be deleted 2 not to be amended 84 B File type O raw 1 tree curve 2 chronology 85 88 C Creator Initials of creator Statistics for total series 89 92 R Arithmetic mean 93
240. s of their graphs on translucent paper The fixed graph is taped to a table and you can slide the moving sample left and right This is actually how it was originally done on graph paper with one inch per decade Start with the moving sample to the left of the fixed sample overlapping it by 10 years Look at how well the graphs match this is the first score that s computed Slide the moving sample to the right one year and so on until you reach the end You could do it all simply by moving graphs and eyeballing the crossdates like this but there are hundreds of sites and millennia of chronologies you ll want to crossdate your samples against so that would take a while Tellervo has a few algorithms to find likely crossdates almost instantaneously They aren t perfect though and all crossdates should be inspected visually to ensure they are a good fit 10 1 Algorithms Tellervo includes a total of five different algorithms for crossdating 10 1 1 T Score The t score is the classic crossdate Unfortunately every dendro program seems to have a slightly different implementation of t score so the numbers you get from Tellervo might not be exactly comparable to the numbers from other programs The version Tellervo uses is based on the algorithms given in Baillie and Pilcher 1973 though with some apparent bugs corrected Ken Harris pers comm In the following equations to 11 X2 are the data of the fixed sample in the overlap yo Y1
241. s that requests and responses sent to from your physical computer are intercepted and forwarded on to the virtual Tellervo server Instead of Tellervo server having its own IP address Tellervo clients wanting to talk to the server send requests to your physical computer This has the benefit of being more likely to work if your institution has strict network policies The main drawback is that it takes a little more effort and perhaps requires a better understanding of systems administration to set up With your virtual machine powered off select it in VirtualBox click settings and go to the network tab Change the network type to NAT and then click the port forwarding button Add an entry to the list Name TellervoHTTP Protocol TCP Host Port 8080 Guest Port 80 You can leave the other fields blank The host port is the port that your Tellervo users connect to The normal port that users connect to for web services is port 80 however on most secure operating systems e g Linux and OSX you cannot port forward to ports below 1024 although it should be possible in Windows If you are running Windows you may therefore be able to use a host port of 80 If you use 8080 or any other port other than 80 you will need to include this in the URL of your webservice when you try to connect The other complication of using NAT networking is that the URL provided by the Tellervo server configuration utility is incorrect as the server has no way of k
242. s the normal sample depth line It begins with 7 spaces followed by each of the sample depth values enclosed in square brackets and left padded with spaces up to 6 characters Data lines continue in pairs until the last line is reached This is the same as a normal data line except it includes an extra data value 9990 as a stop marker This data line may have less than a full decade of values The final sample depth line is the same as normal except it is shifted left by 4 characters A sample depth value is also included for the dummy 9990 stop marker year Following the data block there is a blank line and two option blocks of data that are only included if the file is a chronology file The next block of information in a chronology file is denoted by a line ELEMENTS The following lines contain the file names of the data files that have contributed to the creation of the chronology Following this is an optional block denoted by the line weiserjahre followed by the weiserjahre data Each weiserjahre data line begins with a space followed by a integer year value for the first year in the line The weiserjahre value is left padded with spaces to fill 6 characters and the value itself is written as X Y where X is the number of samples that show an upward trend in width and Y is the number of samples that show a downward trend in width The weiserjahre value is forward facing so the value for ring 1001 shows the trend between ring 1001 and 1002
243. s typically represented by 32 hexadecimal digits and 4 hyphens like this 550e8400 e29b 41d4 a716 446655440000 16 4 Barcode specifications Barcodes in Tellervo are based on the UUID primary keys of database entities Because they are used for different entities in Tellervo boxes samples and series it was also necessary to incorporate a method for determining what type of entity a barcode represents This is done by appending a single character and a colon to the beginning of the UUID B for box S for sample Z for series The barcodes in Tellervo use the Code 128 scheme This symbology was chosen as it allows the encoding of alphanumeric characters in a high density label and can be read by all popular barcode scanners While it would have been possible to create a barcode of plain UUIDs the 36 or even 32 characters would result in a barcode wider than many scanners could read Most scanners on the market have a maximum scan width of at least 80mm so this was used as the baseline to work to Systems architecture 93 To make the barcodes less than 80mm the UUID with prepended entity type character code are Base64 encoded For example the series with UUID 3a8f4336 d17d 11df abde c75e325aebae would be encoded from Z 3a8f4336 d17d 11df abde c75e325aebae to become Wj0o6j0M20X0R36vex14yWuuu Chapter 17 Tellervo Database The database behind Tellervo is run on the popular open source relational database management system Po
244. se Lintab platforms with Tellervo or any software not developed by Rinntech must therefore contact Rinntech and purchase an adapter Measuring platforms typically use serial ports to communicate to computers In recent years computer man ufacturers have been phasing out serial ports so you may need to purchase a serial USB converter Modern MacOSX Linux as well as Windows 7 should support most serial USB adapters out of the box otherwise you must install the relevant drivers before continuing Recent Lintab USB platforms use internal serial USB converters so are treated in exactly the same way by Tellervo To begin shut down your computer attach your platform then reboot and launch Tellervo Next go to the preferences window and open the hardware tab and you should see an interface that looks like figure 3 1 d Preferences yo amp Hardware Preferences Set measuring platform and barcode scanner preferences A Measuring Platform Type Generic ASCII Platform r z 2 gt Port dev ttyUSBO X Data bits Word length 8 r Baud 9600 Handshaking Flow control NONE v Hames Parity None w Line feed CRLF im Stop bits 1 o 2 a 4 a Test connection Barcode scanner Appearance L Disable support for barcode scanner te Mapping Reset all to default OK Figure 3 1 The hardware preferences dialog In the type pull down menu select the type of measuring
245. second reading In this case we are constructing a code for the first reading 1 The second reading would be 2 and so on Figure 4 4 Illustration of the how lab codes are built in Tellervo Figure courtesy of Charlotte Pearson Chapter 5 Mapping Tellervo includes an integrated open source 3D mapping system based on NASA s award winning World Wind Java SDK similar to the program Google Earth which you re no doubt familiar with As mentioned in the installation chapter this mapping system requires an OpenGL 3D capable graphics card Before you can use the mapping in Tellervo you must also have something to map See the chapter on Metadata page 19 for information about adding coordinates to your system There are two ways to map data from your database First of all you can see a map of all the sites i e TRiDaS objects by going to Administration gt Site map This will give you a screen like this 6 Site map vow File Edit View Help Layers Y All objects in database Background layers Y NASA Blue Marble Image Blue Marble WMS 2004 Y i cubed Landsat O USDA NAIP U USDA NAIP USGS U Ms Virtual Earth Aerial usas Topographic Maps 1 250K USGS Topographic Maps 1 100K CU USGS Topographic Maps 1 24K usas Urban Area Ortho Political Boundaries Q Place Names EUROPE poe gi Controls and decorations W Stars Y Atmosphere World Map O Scale bar Y View Controls O Compas
246. sion of the server which could have unexpected side effects Increment the build version number in the pom xml Update the splash screen and background graphics Check the code in Eclipse and eliminate as many warnings as possible Make sure the developers metadata is correct in the pom xml Add any new developers that have joined the project since the last release Run Maven package TEST Deploy to maven tridas org by running Maven deploy Copy target binaries to the http www tellervo org download folder The new release will automatically be added to the options for download If this new release should be the recommmended release for internal and or external uses alter the index php page to reflect this Chapter 14 Developing Tellervo Server The Tellervo server is made up of a PHP webservice run by Apache connecting to a PostgreSQL database The Tellervo webservice is written entirely in PHP Like the Desktop Client the server is developed with Eclipse so most of the setup steps are identical see chapter 13 You will however probably want to install the PHP development plugin so that you get syntax highlighting etc See the Eclipse PDT website http www eclipse org pdt for further information 14 1 Webservice Before making any changes to the webservice you will need to understand its architecture first Chapter 15 contains details of the communications specification 14 1 1 Creating new series Due to th
247. so interpreting the metadata so that it is standardized clean and matches our high data integrity standards As you can imagine this comes at the price although definitely a price worth paying Before continuing you need to have a basic understanding of the TRiDaS data model See chapter 4 page 19 for more information 7 3 1 The import dialog You can launch the import dialog by going to File gt Import data and metadata and then choosing the format that your file is in Ed Import to Database vos TRiDaS representation of file Original file Extracted TRiDaS Metadata TRiDaS Entities Status lla gt i Unnamed project Unsupported ignored cp mimpprinles A Y ij AKK Akkerman Fortress Stored in database Y Element General s Unnamed element Attention required Y X Unnamedsample Attention required Y W Unnamed radius Attention required s F AKKO0010 Attention required Last modified timestam Title Unnamed element Comments Type Description Files Taxon Plantae Dimensions Authenticity Processing Marks A Altitude 999 9 Y Element Other yo y L Merge objects together w Click the lock to edit this entity Conversion warnings Finish Figure 7 2 Screenshot of the import dialog The screen is divided into three main sections The top left contains a TRiDaS representation of the data file that is being imported The top right panel contains the metadata gleaned from each of these TRiDa
248. ssues when reading legacy data files for instance some files do not contain information on the measurement units used In this case Tellervo will make an assumption and warn the user It is important to understand the assumptions and warnings provided by Tellervo in this panel otherwise erroneous meta data may be imported 7 3 2 Importing when entities are already in the database If you already have the object element sample and radius entities entered in your Tellervo database for the series you are trying to import the import process largely involves picking the relevant entities from the database First of all click the most senior entity in the TRiDaS hierarchy on the left which has the status Attention required The dialog will update and the limited metadata that Tellervo has been able to glean from the file will be shown on the right As we already have all the information we need about this entity stored in the database we simply need to replace this skinny entity with the rich one we have in the database This is down by clicking the Change button in the metadata viewer on the right and then by choosing the correct entity from the pull down menu Click the choose button and the swap will be complete Notice now that in the TRiDaS hierarchy that the status for this entity is changed to Stored in database You can continue working down the hierarchy in a similar way 7 3 3 Importing when entities are not in the database
249. standard configuration options offered on the command line there are a number of other options that can be set These are not accessible via the command line because as a rule they should only be altered the Tellervo developers They are primarily for use by the developers as an alternative to hard coding values within the server files For instance one such value is the TRiDaS version being used by the server This value will only ever need to be changed alongside other substantial changes to the code 11 7 Managing map services There is currently no interface in Tellervo that lets you specify the WMS mapping services that should auto matically be available to your Tellervo users Each user can add servers temporarily see section 5 3 but these will disappear at the end of each session Chapter 12 Help and support 12 1 Getting help At the moment your options for getting help are largely limited to contacting Peter Brewer Once the user base of Tellervo expands we will set up forums and mailing lists to assist 12 2 Support for future development Both Tellervo Desktop and Server are free software available under the General Public License v3 see appendix Z This means you are free to use Tellervo in both academic and commercial environments However when we talk about free software as the license explains we are talking about freedom of use not free as in price Tellervo has inevitably cost a great deal to develop over the year
250. stgreSQL Postgres 17 1 Database structure 17 2 Spatial extension Tellervo uses the PostGIS extension to Postgres to store and query spatial data within the database Rather than storing coordinate axis in separate fields a single specialist geometry field type is used 17 3 CPGDB functions The Tellervo Postgresql Database CPGDB functions are a set of functions for searching processing and manipulating the data in the postgresql database All functions are in thecpgdbschema to allow for easy development alongside the database without modifying the database or its structure Thus to execute a cpgdb function you must preface the function name with cpgdb e g SELECT FROM cpgdb GetVMeasurementResult xxxx GetVMeasurementResultID This function populates the tblVMeasurementResult and tblVMeasuremen tReadingResult tables returning a single varchar which contains the tblVMeasurementResult ID You probably want to use GetVMeasurementResult instead GetVMeasurementResult This function returns a table row from tblVMeasurementResult which has been populated with information from the provided VMeasurement ID GetVMeasurementReadingResult This function is provided as a convenience method It requires a VMea surementResultID obtained from one of the above two functions Data is returned sorted by year as cending FindVMChildren This function reverse traverses the database and gives a list of derived V
251. t free under the terms required by the Free Software Foundation Tellervo can still legally be used with the Sun JDK even though it is regarded as proprietary software due to the Major components exception of the GPL license However open source purists find this undesirable and so you may prefer to use open equivalents such as OpenJDK IcedTea or Apache Harmony For this reason we now develop Tellervo against OpenJDK6 Preliminary tests Developing Tellervo Desktop 71 show Tellervo works fine under OpenJDK7 as well however we do not intend to take advantage of Java 7 features in the near future to ensure backwards compatibility for as long as possible The problem of backwards compatibility for MacOSX seems likely to remain for some time 13 12 Developing graphical interfaces Like the rest of the code a number of different styles and methods have been used for the creation of interfaces in Tellervo Many of the earlier interfaces were hand coded but in recent years WYSIWYG graphical designers have been used to enable the creation of more complex designs Most interfaces are now Swing based although AWT widgets are used in places Some interfaces were created using the graphical designed in Netbeans IDE These can be identified by the presence of companion form files and warning comments in the code indicating which sections are autogen erated The major drawback with the Netbeans form designer is that it cannot cope with externa
252. t lt value value 56 gt lt values gt lt measurementSeries gt lt radius gt lt sample gt lt element gt lt object gt lt object gt lt project gt lt tridas gt Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer Appendix T TRIMS TRIMS None known Text file rw Read and write Data only Gregorian Yes Yes No No Unknown This is a simple data only text file format These files were originally produced using the Henson rotary micrometer measuring stages but have largely been phased out Line 1 Initials of user that created the series Line 2 Date the file was created in dd MM YY format Line 4 Space character followed by an integer data value in 1 100th mm gt Line 3 Year of first data value 0 treated as undated series gt gt Final line Space character 999 denoting end of series T 1 Example file pb 05 10 94 1816 169 96 165 85 139 87 112 999 Format name Other name s Type Extension s Read write support Reference implementation Data metadata Appendix U Tucson Tucson Decadal RWL CRN ITRDB Time series format TSF Text file Various including tuc rwl dec crn Read and write COFECHA Data with some stru
253. ta and then choose the format that your file is in If you are unsure you can use appendices A X pages 101 169 to help you You may also like to download TRiCYCLE which includes a file identification tool in the help menu If your file does not explicity indicate what units the measurements are in a dialog box will ask you to specify Once you have done this a standard data editor window will appear with your data in it If the file you import contains multiple series you will have a separate windows for each series If you then go to the metadata tab you will notice that none of the metadata have been set Before you can save to the database you will need to sequentially go through the object element sample radius and series tabs and either choose an existing entry from the database or create a new record if the particular entry is not already represented 7 3 Importing data and metadata The second import method in Tellervo imports both data and metadata into the Tellervo database Unfortu nately this is an unavoidably long winded task For dendro applications that do not manage the underlying TRICYCLE is available from http www tridas org tricycle 36 Tellervo A guide for users and developers data and metadata the task of opening up legacy data files is much simpler In Tellervo however we are more fastidious about our information Importing legacy data files is not just a matter of reading the ring width values but al
254. tained in a Subversion repository at Sourceforget net The simplest way to see the source code is via the web viewer on the Sourceforge website http sourceforge net p tellervo code 0 You can also examine the Javadoc documentation of the code on the Tellervo website If you have Subversion installed you can do an anonymous checkout of the code as follows 7 svn checkout svn svn code sf net p tellervo code O trunk tellervo code 0 An overview of the development can be seen through the Tellervo Ohloh pages at http www ohloh net p tellervo Ohloh provides graphics summarizing the code over time including timelines of commits by user 13 2 Development environment The IDE of choice of the main Tellervo developers is Eclipse http www eclipse org There are many other IDEs around and there is no reason you can t use them instead Either way the following instructions will hopefully be of use We have successfully developed Tellervo on Mac Windows and Linux computers over the years The methods for setting up are almost identical The first step is to install Eclipse Java 6 JDK Subversion Maven and NSIS These are all readily available from their respective websites On Ubuntu they can be install from the command line easily as follows sudo apt get install eclipse subversion sun java6 jdk maven2 nsis Currently there do not appear to be any readily available binaries for NSIS for MacOSX although you can build this from sou
255. tem Although it would be possible and arguably simpler to have refactored Corina to talk directly to one central database server it was decided to go a step further and implement a Web Services orientated server client architecture for Tellervo A web services approach decouples the desktop client from the server so that the server can work on its 16 1 Authentication design The authentication mechanism is loosely based around http digest authentication and uses a challenge and response scheme This makes use of cryptographic hashes a relatively short digital fingerprint of some data but which cannot be decompiled to retrieve the original data and nonces a pseudo random string used just once All hashes used in the Tellervo webservice use the MD5 algorithm Whilst an MD5 hash of a short phrase can be compromised the length and randomness of the original data means that using current cracking techniques would require a very substantial amount of processing power e g supercomputer or large botnet Flaws in the MD5 hash are also mitigated by the time sensitive nature of the Tellervo nonce meaning that any attack would need to be successful within a 2 minute window New weaknesses in security are however revealed on a fairly regular basis so the authentication architecture will be periodically reviewed to ensure that it still meets our needs The first time a client attempts to retrieve data from the webservice or when the client s credential
256. the Tellervo SVN repository and can be installed as follows On your command line navigate to the Libraries folder of your Tellervo source code On Linux and Mac you can then simply run the MavenInstallCommands script On Windows you will need to manually run the commands located in this file For the record Tellervo currently depends upon the libraries listed in table 13 1 The table also specifies the licenses that these libraries are made available under Developing Tellervo Desktop 65 Library License Apache commons lang Apache 2 0 TridasJLib Apache 2 0 Batik Apache 2 0 RXTXcomm LGPL JDOM Apache 2 0 Swing layout LGPL Log4J Apache 2 0 JNA LGPL Apache mime 4J Apache 2 0 Commons codec Apache 2 0 Http Client LGPL Http core Apache 2 0 Http mime Apache 2 0 Jsyntaxpane Apache 2 0 L2fprod common shared Apache 2 0 L2fprod common sheet Apache 2 0 L2fprod common buttonbar Apache 2 0 Text GAPL PDFRenderer LGPL DendroFilelO Apache 2 0 Java Simple MVC MIT JGoogleAnalytics Tracker MIT gluegen BSD JOGL BSD nuclear clause WorldWindJava NOSA SLF4J MIT JFontChooser LGPL MigLayout BSD PLJava BSD PostgreSQL PostgreSQL License BSD MIT Forms BSD JXL LGPL Netbeans Swing Outline GPLv2 Table 13 1 Tellervo s primary and major first order dependencies along with the licenses under which they are used Note there are a total of 82 libraries upon which Tellervo draws Library License Apache commons lang Apache 2 0 Lau
257. the individual works permit Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate 6 Conveying Non Source Forms You may convey a covered work in object code form under the terms of sections 4 and 5 provided that you also convey the machine readable Corresponding Source under the terms of this License in one of these ways a Convey the object code in or embodied in a physical product including a physical distribution medium accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange b Convey the object code in or embodied in a physical product including a physical distribution medium accompanied by a written offer valid for at least three years and valid for as long as you offer spare parts or customer support for that product model to give anyone who possesses the object code either 1 a copy of the Corresponding Source for all the software in the product that is covered by this License on a durable physical medium customarily used for software interchange for a price no more than your reasonable cost of physically performing this conveying of source or 2 access to copy the Corresponding Source from a network server at no charge c Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source This alternative is allowed only occasionally and noncommercia
258. the radii measured or an angle in degrees of the azimuth along the measurement radius Measurement direction Pith to bark 0 Bark to pith 1 Sample height Height at which sample was taken Height code User defined parameters Free text information Number of tree rings in sample Number of rings in sample including those not measured If all rings were measured then this is indicated with a full stop Data type Coded as 90 ring width 91 height shoots 92 volume growths 93 earlywood 94 latewood Defaults to 90 ring width Column with Number of digits the data is stored in Default 3 Number of decimals Number of decimal places the values are stored in Default 2 Number of tree rings measured Number of rings that have been measured J 2 Example file 30 05 09 11 09 05 0 Project Index Timonen 1 30 05 2009 2 4905692 7596282 365 3 100 Kalmankaltio 4 110 1 5 19 6787 61 7 2008 80 9 a 10 Fire scars II 12 25 5 5 NA KINSYS KS 127 94 110 81 108 129 xxx DATA END xxx Appendix K Microsoft Excel 97 2000 XP Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer K 1 Description Microsoft Excel 97 2000 XP Binary Interchange File Format BIFF Binary file
259. them a chance to provide you with an updated version of the Document Modifications You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above provided that you release the Modified Version under precisely this License with the Modified Version filling the role of the Document thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it In addition you must do these things in the Modified Version A Use in the Title Page and on the covers if any a title distinct from that of the Document and from those of previous versions which should if there were any be listed in the History section of the Document You may use the same title as a previous version if the original publisher of that version gives permission B List on the Title Page as authors one or more persons or entities responsible for authorship of the modifications in the Modified Version together with at least five of the principal authors of the Document all of its principal authors if it has fewer than five unless they release you from this requirement State on the Title page the name of the publisher of the Modified Version as the publisher Preserve all the copyright notices of the Document Add an appropriate copyright notice for your modifications adjacent to the other copyright notices nmon Include immediately after the copyright notices a license notice giving the
260. tion the tag also has the following attributes Keycode Name of the series Length Integer for the number of rings Owner Integer index to the group to which this record belongs Chrono TRUE or FALSE indicating whether this record has density information Locked TRUE or FALSE indicating in the record can be moved Filter TRUE or FALSE indicating if an indexing function is appled to the data Filterlndex Integer index for the filter used FilterS1 Parameter 1 for the filter FilterS2 Parameter 2 for the filter FilterB1 Additional filter parameter FilterWeight Additional filter parameter Offset Position of the first ring Color 24bit RGB color for record in Borland format Checked TRUE or FALSE indicating is the record is selected for use in the dynamic group mean IVShift Temporary integer value added to data value to shift vertically in graphs IsMeanValue TRUE or FALSE indicating if this is a dynamic mean value Pith TRUE or FALSE SapWood Integer storing the number of sapwood rings Location String location information Waldkante String description of presence of waney edge FirstValidRing Integer indicating which ring is the first valid ring If O then some rings are discarded LastValidRing Integer indicating which ring is the last valid ring If O then some rings are discarded VVVVVVVVVVVVVVVVVVVVVY PAST4 143 gt gt UseValidRingsOnly TRUE or FALSE internal use only Quality
261. tion for a screenshot of how an ODF spreadsheet should look Format name Other name s Type Extension s Read write support Reference implementation Data metadata Calendar type Absolute dating support Undated series support Relative dating support Multi series support Original designer Appendix O Oxford Oxford Dan Miles Format English Heritage Format Text file Various including dan ddf but often none Read and write Various English Heritage applications Data only Gregorian Yes Yes Yes No Ancient Monuments Laboratory of English Heritage O 1 Description The Oxford format seems to be only currently used in the Oxford Dendrochronology Laboratory It was designed in the 1980s for use with a number of DOS based applications for the English Heritage Ancient Monuments Laboratory It is still actively used by the Oxford Lab with these programs and a number of newer Windows applications The file is a text file format containing two header lines following by a block of data values and an optional block of count sample depth values Some files also contain a number of comment lines at the end of the file Line gt gt gt gt gt vv gt gt gt Line gt 1 contains the following fields Char 1 Apostrophe Chars 2 8 Series name Char 9 10 spaces Char 11 Chars 12 15 First year in sequence when series is securely dated Year should be left padded with spaces i
262. u will see some variation of the measuring panel in figure 2 2 The left display holds the absolute position of the last ring boundary for device that measure cumulatively the middle display holds the last recorded measurement width and the right display holds the current position of the measuring plaform for devices that report live measurements The right hand display is useful for devices that don t have a physical display such as the Lintab Tellervo supports the measuring of rings both individ ually and cumulatively We feel that it is easier and ener oe a more accurate to measure rings individually that is to say the device is reset to zero after each measure ment If a device accepts requests to reset measure tee ee Be ments e g Quadra Chek boxes or if it automatically resets itself to zero after recording a measurement Figure 2 2 Measuring control panel e g EVE IO then this procedure is used by Tellervo In this case the user begins measuring by setting the display to zero then turns the platform to the end of the ring then either presses the measure button on the hardware device or the record button on the screen If your device does not have a physical measure button you don t need to click on the record button each time Instead click on the turn on mouse trigger button and then you can use your mouse s left button as a measure button regardless of where the
263. uccess when applying for infra structure projects from federal agencies are much greater when proposed as part of a collaborative multi laboratory project Note that although the GPL license allows you do develop Tellervo separately it does include clauses that require you to make the source code of the software you create also freely available under GPL or a compatible license If you fork the code in this way you will find it increasingly difficult to benefit from improvements made to the official Tellervo code Part II Developers guide Chapter 13 Developing Tellervo Desktop Tellervo is open source software and we actively encourage collaboration and assistance from others in the community There is always lots to do even for people with little or no programming experience Please get in touch with the development team as we d love to hear from you 13 1 Source code This section describes how to access the Tellervo source code but as you are no doubt aware it is normal if not essential to use a integrated development environment for developing any more than the most simplistic applications If you plan to do any development work it is probably best to skip this section and move straight on to the Development environment section which includes instructions for accessing the source code directly from your IDE If however you just want to browse the source code please continue reading The Tellervo source code is main
264. udes support for menu mnemonics to enable navigation of the menus with the keyboard and accelerator keys to enable keyboard shortcuts to bypass menus Mnemonic are set by adding an ampersand before the letter of interest e g amp File for File in the resource bundle Accelerators are set by adding the keyword accel with the key of interest inside square brackets after the resource bundle entry Some examples include gt amp Graph active series accel G Graph amp component series accel shift G What key the accel keyword refers to depends on the operating system Tellervo is being run on In Windows and Linux it is normally ALT wheras on a Mac it is usually the Apple U 2318 command key There are currently minimal translations for UK English German French Dutch Polish and Turkish These are by no means complete and there are number of interfaces that are not internationalized at all Further assistance is required from native speakers to complete this task 13 7 Logging Logging in Tellervo is handled by the SLF4J and Log4J packages Rather than write debug notes directly to System out Log4J handles logging in a more intelligent way First of all each log message is assigned a log level which are in order of severity fatal error warn info debug and trace Through a log4j xml configuration file contained within the resources folder we can control the level at which messages are displayed For instance wh
265. undled in the release packages The repository tool that we currently use is Apache Archiva Installation is relatively simple 1 Download the zip bundle from the Apache Archiva website 82 Tellervo A guide for users and developers 2 Unzip and place on the server in a suitable location e g usr share apache archiva 3 Run sudo bin archiva start If you have an existing backup of the Archiva database then you can place this in the data folder and you should be good to go If not you will need to do the following steps to configure the repository from scratch 1 Go to http www tridas org 8080 archiva in your web browser and set up the admin account If you re setting this up on another domain remember you ll need to change the repository URLs in both the distributionManagement and repositories sections of your pom file 2 In the repositories tab you need to configure both releases and snapshot repositories 3 Set up users with Repository Manager permissions for each user that would like to deploy to the repository They will need to configure their m2 settings xml file to do this 4 Set up the guest user to have Repository Observer permissions for each repository This means that people can anonymously access artefacts from the repository 5 Add the following remote repositories Geotk Identifier geotk URL http maven geotoolkit org Geomajas repository for JPedal Identifier maven geomajas org U
266. upport OpenGL Most Windows and Linux computers made since 2006 should also support OpenGL however this does require proper drivers to be installed In some cases Windows computers may include a compatible graphics card but may only have the default Windows video drivers installed If you are having trouble with the mapping in Tellervo make sure you have installed the most recent drivers for your graphics card Linux users may be required to install proprietary graphics drivers The mapping component of Tellervo makes use of NASA s open source World Wind Java NASA s website http worldwind arc nasa gov contains further information and instructions that you may find helpful if you are having problems getting the mapping to work 1 3 Upgrading Tellervo desktop There are no special requirements for upgrading the Tellervo desktop client You need simply install the new version over the top of your previous version Any personal settings will be maintained after the upgrade 1 4 Upgrading Tellervo Server The process for upgrading your server is the same regardless of whether it is running in a VirtualBox virtual machine or on a native Linux server As with any upgrade the first thing you need to do is backup your data see section 11 1 1 page 53 We cannot be held responsible for loss of data in the event something goes wrong during the upgrade process Open your Tellervo server and log in to the command line Then type the following commands
267. use of software on general purpose computers but in those that do we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary To prevent this the GPL assures that patents cannot be used to render the program non free The precise terms and conditions for copying distribution and modification follow Z 2 Terms and Conditions 0 Definitions This License refers to version 3 of the GNU General Public License Copyright also means copyright like laws that apply to other kinds of works such as semiconductor masks The Program refers to any copyrightable work licensed under this License Each licensee is addressed as you Li censees and recipients may be individuals or organizations To modify a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission other than the making of an exact copy The resulting work is called a modified version of the earlier work or a work based on the earlier work A covered work means either the unmodified Program or a work based on the Program To propagate a work means to do anything with it that without permission would make you directly or secondarily liable for infringement under applicable copyright law except executing it on a computer or modifying a private copy Propagation includes copying distribution with or without modification making
268. users will be able to use the default Use system default proxy settings option here but if you know that your computer is behind a corporate proxy server you may choose to manually provide the settings Configuring the Tellervo server Tellervo comes in two parts the Tellervo desktop client that you are using and the Tellervo server which runs the database that stores your data If you are working in a lab your systems administrator may have already set up the Tellervo server and given you the URL to connect to Alternatively you may have already installed the Tellervo server yourself If so the installation program should have given you the URL If you don t have access to a Tellervo server yet you should close this wizard then go to the Tellervo website and download it Measuring platform configuration the next page enables you to configure measuring platform hardware attached to your computer Some measuring platforms have fixed settings in which case the port settings will be set automatically but others can be changed in the hardware and must be set explicitly here Use the Test Connection button to make sure that Tellervo can successfully communicate with your platform Once you have completed the wizard you will be presented with a dialog figure 1 3 for logging in to your Tellervo server 10 Tellervo A guide for users and developers The username and password details requested are your Tellervo login credentials
269. using a random color Google Earth KML KMZ file like the ESRI shapefile option this enables you to load spatial data from your computer 30 Tellervo A guide for users and developers 5 3 2 Web Map Service WMS The mapping system in Tellervo includes support for remote map servers that use the OGC Web Mapping Service WMS standard If you go to View gt Layers gt Add remote layers you will get a dialog with a tab for each WMS server configured for your system By default this includes the NASA Earth Observation and Jet Propulsion Lab servers By ticking layers in this list you can add data layers to your map You can add map data from other WMS servers by clicking the tab and entering the URL of the server you would like to use This will give an additional tab with all the available map layers This server will only be available for the duration of your current session so will need to be added each time you start Tellervo If you would like a particular WMS server to be made permanently available your Tellervo administrator can do this see Managing map services on page 58 for further details Additional WMS servers added in this way will be available to all users the next time they connect to your Tellervo server Your system administrator may host a map server specifically for your lab for instance containing high resolution plans of an archaeological site that you are working on or environmental data for your study
270. ut not always 10 per line The file is terminated with 0 1 or 2 free text comment lines A number of Oxford data files have been seen that terminate with the ASCII control character referred to variably as SUB SUBSTITUTE or CTRL Z represented in Unicode as character dec 26 hex 1A It is not clear whether this is necessary for any particular programs to function O 2 Limitations Only holds whole ring width data Does not cope with data values 999 1 100th mm Does not cope with chronologies of 99 samples Does not allow dates before 1AD Oxford 139 0 3 Example file ABCD 75 1850 422 794 464 768 182 191 161 185 NNNNNNNRA 582 611 172 180 201 122 222 151 NNNNNNNN 355 446 190 178 142 223 93 261 NNNNNNNN lt 1850 1925 gt A Fictious NNNNNNNN 266 248 239 168 188 555 100 110 RNNNNNNDN 225 277 128 204 223 123 132 145 NNNNNNN 271 359 153 163 186 126 104 NONNNNNND NNNNNNDN 361 111 234 160 150 108 86 NNNNNNND 235 226 828 255 135 133 277 NNNNNNN 387 189 207 166 134 137 101 395 711 157 136 666 134 141 site abcdl abcd2 Appendix P PAST4 Format name PAST4 Other name s P4P PAST4 Project File Type Text file Extension s p4p Read write support Read and write Reference implementation PAST4 Data metadata Data and some structured metadata Calendar type Gregorian
271. velopers The use of the server nonce within the response means that it will only be valid for a maximum of two minutes This minimizes the possibility of a replay attack 16 2 Database permissions design The database has a user and group based security scheme at three TRiDaS levels object element and series A user can be a member of one or more groups and groups can be members of zero or more other groups The current implementation allows for one nested level of groups within groups however this could be extended if required Security is set on a group by group basis rather than on a single user to ensure ease of management There are five types of permissions granted create read update delete and no permission Each permission is independent of each other with the exception of no permission which overrides all other permissions A group can be assigned one or more of the permissions types to any of the sites trees or measurements in the database Intermediate objects such as subsites specimens and radii inherit permissions from their parent object For instance if a group has permission to read a site then it will have permission to read all subsites from that site It is envisaged that most of the time permissions will be set on a site by site basis It will not be necessary to explicitly assign permissions to trees and measurements as all permissions will be inherited So assuming that no permissions are set on a tree for a part
272. via C YMT 1216 A B 1 Russell Stepp Raw Quercus 2010 04 20 1001 1072 72 x C YMT 1216 A A 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1064 64 x dh YU DOL Bosnia Donja Dolina C VMT 1216 A A 1 Russell Stepp Raw Quercus 2010 04 19 1001 1064 64 di YU KAT Croatia Zagreb Crkva Sv C YMT 1215 A B B Perri Gerard Little Raw Quercus 2010 04 19 1001 1056 56 x dl YU STB Croatia Split Buvina Gate C YMT 1215 A B 1 Sarah Simpson Raw Quercus 2010 04 16 1001 1056 56 x ds YU VIG Croatia Viganj Shipwreck C YMT 1215 A A B Perri Gerard Little Raw Quercus 2010 04 19 1001 1052 52 x dls YUM Mersin Yumuktepe C YMT 1215 A A 1 Sarah Simpson Raw Quercus 2010 04 16 1001 1052 52 x di ZAD Croatia Zadar Relja Liburnia C YMT 1214 A B 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1066 66 x y y s C YMT 1214 A B 1 Leann Canady Raw Quercus 2010 04 19 1001 1066 66 x ZAG Drama Zagradenia Forest C YMT 1214 A A 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1068 68 x di ZAT Croatia Zadar Zaton Ship C YMT 1214 A A 1 Leann Canady Raw Quercus 2010 04 19 1001 1068 68 du ZCM Croatia Zagreb City Museum C YMT 1213 A B 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1049 49 x d a ZEU Gaziantep Nizip Zeugma__ C YMT 1213 48 1 Sarah Simpson Raw Quercus 2010 04 16 1001 1049 49 x lt SSS ey gt C YMT 1213 A A 2 Katherine Seufer Raw Quercus 2010 04 20 1001 1051 51 x p C YMT 1213 A A 1 Sarah Simpson Raw Quercus 2010 04 16 1001 10
273. vo is written in Java it requires a number of native libraries to make use of OpenGL 3D graphics capabilities and to access the serial port of the computer This libraries are different for each operating system and they are also different for 32 and 64 bit machines The correct libraries must be made available to the OS and are therefore typically installed outside of the jar file as part of the installation process On Windows these libraries take the form of Dynamic Link Libraries DLL files which are normally placed in the same folder as the executable gt gluegen rt dll gt jogl_awt dll gt jogl_cg dll gt jogl dll rxtxSerial dll On MacOSX the libraries come as JNILIB files and on Linux as so files e g 70 Tellervo A guide for users and developers libgluegen rt jnilib and libgluegen rt so libjogl_awt jnilib and libjogl_awt so libjogl_cg jnilib and libjogl_cg so libjogl jnilib and libjogl so librxtxSerial jnilib and librxtxSerial so vvvvyv On Linux systems this are installed into the usr lib folder and on MacOSX they are included within the app file We have experimented with techniques for packaging the libraries within the jar then extracting the correct libraries based on architecture and dynamically loaded at runtime This seemed to work relatively well for JOGL Gluegen but not rxtx On certain graphics cards the JOGL Gluegen libraries also caused a SIGSEGV fault All native libraries are therefore now han
274. xel per channel 8 or 16 channel used for analysis Grey RGB R G or B CalibMethod XCal YCal EditedDendro Method of calibration Intr Intrinsic Obj ObjKnownDiam This is followed by the size of a pixel and Y or N indicating if the image has been edited in WinDENDRO ScannerCamera Make Model Software Details about the imaging hardware LensFocLength 35mm The 35mm equivalent focal length of the imaging lens PathBegX BegY EndX EndY Width The coordinates for the start of the path radius followed by the path width RingBoundary AutoMan Meth Precise Details about the path taken Ring boundary Tg tangent to ring or Perp perpendicular to path Detection method A automatic or M manual Ring detection method Int intensity differences or T amp S teach and show whether the more precise detection method is active Y or not N EarlywoodDef Earlywood latewood transition criteria DensActive Media Calib Density Analysis active Y or N Density Media setting F negative file or photo W wood direct xray positive film or photo Light calibration setting Acq after image acquisition Man manual No none DensNSteps MatDens Interpol Number of steps and the density of the step wedge used for calibration followed by the interpolation method used between steps Lin Linear Spl Spline DensStepsThick The thickness of each step of the wedge used for density calibration DensStepsLightInt The light intensity of
275. xls Read and write Microsoft Excel Data only Gregorian Yes No No Yes Microsoft The Excel file format is a widely used format for storing spreadsheet data It is a proprietary binary format created by Microsoft but suppported by many spreadsheet and statistical applications It is not to be confused with the Office Open XML format which was introduced by Microsoft with MS Office 2007 and typically has the file extension xlsx Although Excel files can contain multiple sheets in a workbook only the first sheet is considered Like the CSV and ODF Spreadsheet formats support for Excel files is limited to a particular layout or style of spreadsheet The layout of the data sheet should be as follows Row 1 Header names for each column gt Column A Year values gt Column B One column for each series containing data values Cells are left empty if no data is available for a series because it does not extend to a particular year Data must be continuous for each series so missing unmeasured rings should be included as zero 130 Tellervo A guide for users and developers K 2 Example file A B i c Year MySample1 MySample2 E 1954 0 33 E 1955 0 26 0 26 E 1956 0 2 0 2 sal 1957 0 14 0 14 6 1958 0 08 0 08 Ei 1959 0 02 0 02 E 1960 0 2 0 2 1961 0 14 0 14 E 1962 0 08 0 08 E i 1963 0 2 E 1964 0 33 E 1965 0 08 Dra 1966 0 33 15 1967 0 22 Format name Other name s Type Extension s
276. y et al 2007 There are a number of similar enumerated metadata fields in Tellervo each indicated by a pull down menu When importing these fields will be populated with the non normalized term read by Tellervo but to successfully import the entity into the database you will need to choose the corresponding controlled vocabulary term from the pull down menu Once you have cleaned and normalized your metadata you need to press the Save changes button to upload the entity into the database You will be provided with an error message if you have missed any mandatory fields or if you have not normalized all the data to terms stored in the Tellervo dictionaries Once you have successfully saved the entity the TRiDaS hierarchy on the left will be updated so the status reads Stored in database You will then need to work your way through the remaining entities to finish importing the file 7 3 4 Speeding up the process Manually choosing the relevant entry for each entity is quite a frustrating and time consuming task When importing a file containing multiple series the task is compounded by the fact that Tellervo will often place the series into separate hierarchies Unfortunately many legacy file formats do not contain enough information to enable Tellervo to determine whether they are from the same or different objects To be on the safe side 38 Tellervo A guide for users and developers Tellervo therefore places them in
277. your Tellervo database and all the data it contains Make sure that you export any data you need before doing uninstalling If you are running the Tellervo server as a virtual appliance simply follow the uninstall instructions for VirtualBox If you are running Tellervo server as a native Linux server you should use your preferred package mangement tool e g from the command line Z sudo dpkg remove tellervo server Chapter 2 Getting started Once you have your Tellervo desktop application installed see chapter 1 and you also have access to a Tellervo server either via your lab network administrator or your own on as a Virtual Appliance you are ready to start using Tellervo Below are some basic instructions for performing common tasks in Tellervo followed by a number of more in depth chapters 2 1 Measuring a new sample Once your measuring platform has been configured measuring your first sample is simple To start a new measurement go to File gt New or click the new icon on the home screen A dialog will appear where you can scan your sample s barcode or press the button to enter metadata for your sample later Barcodes minimize data entry errors and also speed up the process of measuring your samples See section 8 2 for more information Once you have scanned your barcode or pressed the button you will then be presented with an empty Tellervo metadata screen The next step is to fill out the metadata information If you h
278. your system It must be run with superuser privileges therefore sudo is required before the command For instance to get help on usage type Z sudo tellervo server help Possible options to pass the server are help Display a list of the possible options gt version Display the version of the Tellervo server webservice and database cur rently installed gt test Run tests on the current configu ration gt configure Configure the Tellervo server from scratch gt reconfigure Reconfigure the Tellervo Images tellervo server terminal png server This should be done if the database name or user credentials change or if the IP address of the machine is altered gt start Start the Tellervo server gt stop Stop the Tellervo server gt restart Restart the Tellervo server Figure 11 1 shows an example of asking the server to test the configuration with all tests passed success fully Figure 11 1 Example of the output from the tellervo server The command line tool stores the majority of settings a est in the config php file stored in the base directory of 58 Tellervo A guide for users and developers your Tellervo webservice In theory you could make changes direct to this file but we do not recommend this unless you know exactly what you re doing 11 6 2 Advanced server configuration In addition to the

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