Developer`s manual
Contents
1. 15 3 5 seal 15 16 4 1 Adding a table as an object in 5 16 4 121 USing the Object 16 41 2 Miewing the table se of nee ees 16 4 1 3 Adding or updating 0 4 2244 2 2 1 16 42 Adding a field to a table 2224 0 4 1 17 4 3 Adding field containerContents table 6 0 8 17 44 Adding non containercontents field to containercontents view table optional column 18 1 Environment SLIMS was developed using Java 1 6 0 JSPs Hibernate 3 3 1 GA DB2 and mySQL at different times Apache Tomcat 6 0 18 NetBeans IDE 6 5 Jasper Reports 3 5 1 and JasperSoft s iReport 3 5 1 all on Microsoft Windows XP SLIMS was tested on Mozilla Firefox 3 and Microsoft Internet Explorer 7 2 Database 2 1 Table and Field Descriptions 2 1 1 Common Fields Field Description COMMENTS Any user generated comments for this entry CREATED When was this entry2. 5 hue len 6 2 1 14 thlgenotypingrunsamplestatus 6 2 1 15 thlgenotypingrUNnSNpStatus 10 6 oh seen ee a sh eves 6 2 1 17 eee 6 2 118 151 epee ian te eal ethene 7 2519 7 21 20 0 Aa Ae e E a E Ea deisi 8 21 21 TOIShIPPCOlO diren ieee ae ceeded ee aes a EE 8 2 1 221 8 2 1 23 TOISHOPPINGlISICONTAINGNS iene thie 8 2 124 TDISHOPPINGIISIS 8 2 1 25 1 8 21 26
3. 8 8 21 26 TOISUDJO Cb 9 2 1 291 9 2207 E 9 Zay PAJAN le 9 S Application PIGS 2 9 3 1 9 82121 Nast oct iv he dant 9 3 42 ColuMMDatayavelssssiscciscaidscessseshescesteaasseqedhgnsasdensadesichansajdesessaacibancapdaagesaccehiacasdesessasadbaneatensssenasie 10 3213 eee eae eee ee 10 34 4 FileUploading ava cinvi ise ee A 10 321 5 BilterObject javaiis sce a Se ee 10 3 1 6 ces Acer 10 31 7 10 34 8 SampleSelectOr java sunrises airi 10
4. 3 1 9 SearchObject javaits sri seine 10 3 1 10 SessionListenen java etl 11 3 1 11 0 11 3 1 12 View lt Object gt Manager java eecececeseeeeeneeeeeeeeeneeeeeeeeaeeeeaeeteaeeeeaeeseaeeseaeeseeeseaeeseeeseeeseeeeeeetsas 11 3 2 lCapture hibernate es a tenia eats ead 11 3 2 1 eevee A a eS ee toe 11 3 2 2 lt lt gt eves evened eae et ete eed ee See eee eed 11 3 2 9 Persistent Meta hid C 11 3 2 4 TempMetaData 2 11 3 32 eel 11 3 3 1 lt gt 11 2 9 2 lt gt 12 34 Web Application Files 12 2441 USPS ee 12 5 ee
5. biological material of this sample 2 1 20 tblsampletypes 2 1 21 tblshippedto 2 1 22 tolshoppinglistcontainercontents 2 1 23 tolshoppinglistcontainers 2 1 24 tolshoppinglists Field LISTID LISTNAME INUSEBY Description Primary key The name of the shopping cart list If a user is currently editing this list or using it to populate a container etc anything other than viewing it then this field will have the user s id as a value Other users are only allowed to use a list if this field is null though they can still view it 2 1 25 tolshoppinglistsamples 2 1 26 tblshoppinglistsubjects 2 1 27 tblsimsusers Field SYSID FULLNAME LOGIN PASSW RIGHTS COMMENTARY PARTNER USERTYPEID INITIALS Description Primary key User s full name User s login User s password What level of permissions does this user have a admin no restrictions eu expert user no restrictions dl dry lab limited user can only view data and make lists wl wet lab limited user can only view data make lists and change volumes Comments field Not used in SLIMS What type of user is this The user s initials especially useful for wet lab because this is what is written on plates 2 1 28 tblsubject Field Description SUBJECTID Primary key COHORTID The cohort this subject belongs to ID The subject s ID within its cohort ex 1001 1 called the subject ID in SLIMS FAMILYID The subject s family
6. created CREATED_BY Who created this entry MODIFIED When was this entry last modified MODIFIED_BY Who last modified this entry 2 1 2 Meta_Data Tables SLIMS uses these tables to store information on how to display their parent tables tblcontainers is the parent table of tolcontainers_meta_data They all have the same fields and work the same way except tblcontainercontents_meta_data Each entry meta_data table corresponds to one field of its parent database except tblcontainercontents_meta_data and describes how to display that field In General Field SYSID PROPERTY_NAME SHORT_NAME LONG_NAME VIEW_COLUMN_NUMBER IS_SORTABLE IS_EDITABLE SHOW_IN_REPORTS COMMENTARY Description Primary key The name of the field this entry corresponds to as it appears in SLIMS not the database A user readable short version of this field s name A user readable full version of this field s name When viewing data for the parent table which column will this field be shown in 1 is for the database ID and is only shown to admin users so for most users the left most column shown will be the one with a value of 2 More than once field can have the same value for this field in which case the order of those fields will be alphabetical Values need not be a complete sequence gaps are fine Indicates whether the user can sort by this column O no 1 yes Indicates whether the user can edit this column O no 1 yes Not
7. if you added the new column to your user type s default scheme 17 4 4 Adding non containercontents field to containercontents view table optional column a create the field in fieldname java with its variable name being lt OBJECT gt lt FIELD gt For example adding tblcontainer location would mean a variable name like CONTAINERLOCATION The value of this variable will be lt object gt lt field gt for our example the line in fieldname java would be public static final String CONTAINERLOCATION container location in MetadataManager java method buildContainerContentData add this field to the end of the m key equals Fieldname lt gt statement Take note of the number associated with your new entry Be sure to also update field ccMetaDataAllColCount increase by the number of fields you just added In ContainerContent java method getValueArrayReadable add your new field on to the series of if statements How the string is passed here will be how it shows up in the table so do any formatting at this point Make sure your array index here matches the number you took note of in step b Add an object for your field in the declarations section of ColumnData java this is the data that will be used to create entries in tolcontainercontents_meta_data for your user if they add this field to their view scheme Also add the field to the default views where appropriate if your field is not in tolcontaine
8. information about passwords has been lost lt listener class gt molpage com SessionListener lt listener class gt see SessionListener java listener class gt molpage com ApplicationListener lt listener class gt see ApplicationListener java lt welcome file gt LogIn jsp lt welcome file gt Start page of the application see LogIn jsp lt exception type gt java lang Exception lt exception Error page for unexpected runtime exceptions type gt lt location gt Test_JSP_error jsp lt location gt see Test_JSP_error jsp 15 4 Common Tasks 4 1 Adding a table as an object SLIMS 4 1 1 Using the object gt Create a hibernate mapping file lt Object gt hbm xml so that entries in the table can be interacted with like objects gt Create a java class file to define the object lt Object gt java with all desired fields plus getters and setters gt In constructor UserHttpSess String logPath add the class to hibernate configuration in the line that starts cfg new Configuration addClass User class gt In method UserHttpSess openFactory add the class to hibernate configuration in the line that starts cfg new Configuration addClass User class gt Add new required fields to Fieldname java gt Add methods to UserHttpSess java see other objects versions for template getViewUserManager getCurrentUser getCurrentUse
9. their selection criteria tree SampleSelectorCrtieriaSubChoice jsp Sample selector allows the user to specify details for a criterion selected from SampleSelectorCrtieriaChoice jsp if necessary SampleSelectorCrtieriaChoiceProfile jsp Unused profile based version of SampleSelectorCrtieriaChoice jsp as opposed to the tree version SampleSelectorFetch jsp Sample selector fetches the best match container contents for the current selection profile SampleSelectorSummary jsp Sample selector displays a summary of the selection tree the user has set up and asks if the user wants to continue the process with this tree SampleSelectorViewResults jsp Sample selector shows the user the next batch of best match sample and lets the user accept or reject them Subjects for which no samples have been found accepted are also listed Search jsp Front page for searching data has links to simple search power search and SQL query search SelectReport jsp Shows the user what reports are available 14 SimpleSearch jsp Lets the user perform a single field search of samples containers and subjects Clears the filter object in UserHitpSess and sets the search object Test_JSP_error jsp Error page Page to link to loading containers subjects and samples TOOIS ISP from files View lt Objects gt jsp View table screen for objects View lt Objects gt Lis
10. used in SLIMS Comments Tbicontainercontents_meta_data Specifically Which rows and the order in which they are displayed for tolcontainercontents varies by user Therefore this table is slightly more complex Each user has their own set of entries defining their view scheme which are indicated by the USERID column For example all the entries in this table with USERID 4 define how the user with ID 4 will view the tblcontainercontents table Any entries in this table with USERID not 4 will be ignored when displaying table tolcontainercontents for the user with ID 4 When viewing the samples of the database actually viewing the contents not the DB samples information from other tables than just TBLCONTAINERCONTENTS be displayed This means TBLCONTAINERCONTENTS_META_DATA needs entries corresponding to fields in tables other than its parent table 2 1 3 Log Tables These tables are populated by update and delete triggers on the main four tables tolcontainercontents tblcontainers tolsamples tolsubject Whenever an update or delete is made on one of these tables the pre change version of the entry being changed is stored in the log table along with a timestamp of when the change was being made field UPDATED 2 1 4 tblcontainercontents Field Description CONTAINERID Primary key of tblcontainers the container the content is ROW The row in the container the content is in COLUMN The column in the conta
11. 2 Adding a field to a table in SLIMS a b add a property or many to one tag for the field to lt Table gt hbm xml add the field to lt Table gt java in the declarations section then add getter and setter methods Finally add an if statement to the field in method getValueArrayReadable How the string is passed here will be how it shows up in the table so do any formatting at this point Take not of the array index number you are assigning for your variable Create an entry for your field in fieldname java For example adding field location would mean a line in fieldname java like public static final String LOCATION location In MetadataManager java method build lt Table gt Data add your field to the end of the m key equals Fieldname lt gt statement Make sure the number associated with your field matches the array index number you took note of in step b Note if you are update buildContainerContentData be sure to also update field ccMetaDataAllColCount In database table tblcontainers_meta_data add an entry for your field See Meta Data Tables section for column details Rebuild the application and see your new field 4 3 Adding a field to containerContents table SLIMS a b add a property or many to one tag for the field to lt Table gt hbm xml add the field to lt Table gt java in the declarations section then add getter and setter methods Finally add an if statement to the field in met
12. BIOLOGY RELATED INFORMATION STORAGE KIT Developer s Manual SLIMS tvanrossum SLIMS Developer Manual v1 1 es sooo E E cece dee E A seen date neha aaahden dace 3 2 Database ee i ee 3 21 and Field DeSCTiptions 3 2 Ti C mmoon Fields 3 2 1 2 2 3 253500 Tables ea a ei ee ev ie 4 21 4 tblcontainerc ments eke eet eA 4 2 120 ADICONTAING Ss een ged cei ann eens eee teeth 4 2 1 6 5 eevee edt aa a eb ates eaa sa 5 2 1 8 tolcontrollayoutwells wis eels Se ke ne ho el aL ee aa 5 2 1 9 tblcontrolWell S ares ues Bele Aare mee eee hee 6 2 1 VO tolethnicitylOOKUp a a a AE AE Ar E E 6 A O a EEE dae 6 2 11 12106 6 2 1213 1
13. D SAMPLEPROCESSID PARENTID COLLECTIONDATE SAMPLETYPEYEAR1ID EXTRACTIONDATEYEAR1 COLLECTIONDATEYEAR1 EXTRACTIONDATE Phenotype s abbreviation Description Subject in question part of primary key Phenotype in question part of primary key This subject s affectation status for this phenotype either 0 1 for type 1 phenotypes or a number words for a type 2 Mistaken column should be removed Description Primary key Subject this sample belongs to The name of this sample referred to in SLIMS as the sample ID ex Az1001 1b the root of this ID does not always reflect the subject ID Whether this sample is valid Not used by SLIMS Not used by SLIMS Not used by SLIMS Not used by SLIMS Not used by SLIMS Not used by SLIMS The type of biological material this sample is or was extracted from ie blood epithelial etc Not used by SLIMS The source of this sample if it was created from another sample The date this sample the unextracted version was collected If we have type information for a yr1 sample but aren t sure if the lab has the yr1 sample or the yr7 the yri sample type goes here If we have an extraction date for a yr1 sample but aren t sure if the lab has the yr1 sample or the yr7 the yr1 extraction date goes here If we have a collection date for a yri sample but aren t sure if the lab has the yr1 sample or the yr7 the yr1 collection date goes here The date DNA was extracted from the
14. ID within its cohort ex 1001 GENDER The subject s gender 0 unknown 1 male 2 female CODE Not used in SLIMS Whether we have consent from the subject 0 no 1 yes 2 HASCONSENT ject y The subject s mother s ID field a string representing the MOTHERID subject ID like 1001 4 not the database ID of the subject s mother not a tblsubject subjectID value The subject s father s ID field a string representing the FATHERID subject ID like 1001 5 not the database ID of the subject s mother not a tblsubject subjectID value ETHNICITYID The subject s ethnicity PASSEDQC Not used in SLIMS Not used in SLIMS though it could be if the fields were NUMSAMPLESCOLLECTED populated it represents the number of samples collected from a subject COMMENT Comments 2 1 29 tblusertypes 2 2 Triggers There are update and delete triggers on tblsubject tolsample tblcontainercontents and tolcontainers that log before snapshots of entries when is updated or deleted Previous versions of entries are stored in log tables lt table name gt log see Log Tables 2 3 Diagram For a UML style diagram of the database see file SLIMS_databaseDiagram jpg 3 Key Application Files 3 1 icapture com 3 1 1 ApplicationListener java This class controls opening and closing of hibernate mappings for the web application It should be included in the listener section of the configuration file for the application see list
15. ON ROWS COLUMNS SORTORDER 2 1 7 tblcontrol Field CONTROLID DESCRIPTION TYPE Whether this container has been will be shipped out or not O no 1 yes When this container was will be shipped out Where this container was will be shipped out to Whether the wet lab considers this container only to have stock contents like a box of extracted DNA tubes or a stock 1 1 dilution WGA plate What kind of material is in this container all WGA all genomic a mix of these etc Whether the container is valid explanation of this should be in comments field 0 1 Non systematic name for a container What is actually written on the container if it differs from the systematic name or what the container was once known as The date written on the container The initials of the plate maker s The specifics of where the container is on the shelf in the freezer Description Primary key The description of what kind of container this is ie a 96 well plate a 384 well plate a box of tubes etc The number of rows in this container The number of columns in this container The order in which the entries should appear not used Description Primary key The name of this kind of control Whether it s a negative or positive control 0 is negative control 1 is positive control 2 1 8 tblcontrollayoutwells These are standard control layouts that are used to prompt users to create their actual control wells for a co
16. ds This includes methods to add edit and delete entries in the database fetch all objects of a certain type and potentially only those that satisfy search criteria and get an object by its database ID It also stores current variables shared throughout the application such as power and simple search objects a user s ID type and permission status a plating object the active shopping list and active objects like containers subjects etc though these can be unreliable 3 1 12 View lt Object gt Manager java Manages table view screens particularly multi page navigation of tables with more entries than the set view limit per page usually 1000 ViewContainerContentManager java also manages the processing adding and removing steps involved when a user customizes or resets their columns for that screen 3 2 icapture hibernate 3 2 1 lt Table gt hbm xml Maps database table to java object This file tells SLIMS what each column of a table should be called within SLIMS what type of variable it is optional and whether it can be null If a table has foreign keys these are handled specially see object links 3 2 2 lt Table gt java Java class for the object representation of a table This file has getter setter methods for every field and a getValueArrayReadable method to return an array of values for all the fields that are to be displayed to the user Which fields are to be displayed to users are defined in the _m
17. e is made during the plating job except for the last plate made which brings them to PlatingSummary jsp Index jsp Home page for SLIMS ListTrimTool jsp Allows the user to search for items that either should be kept or remove from their list and lets them either edit their own list to reflect the results or use the results to make a new list ListVolumeUpdate jsp Allows the user to update the volumes and comments of all the containerContents in a list LoadNewContainersCheckFile jsp When bulk loading containers from a file this jsp checks the file for formatting validity of entries etc and shows the users the results of its checks It also allows the user to accept the file given the results of the check and proceed in creating the containers Linked to from LoadNewContainersChooseFile jsp LoadNewContainersChooseFile jsp When bulk loading containers from a file this jsp shows the user what kind of file they can upload and what format is needed The user can choose and attach a file to the request sent to LoadNewContainersCheckFile jsp LoadNewContentsCheckFile jsp When bulk loading contents from a file this jsp checks the file for formatting validity of entries etc and shows the users the results of its checks It also allows the user to accept the file given the results of the check and proceed in creating the contents Linked to from LoadNewContentsChooseFile jsp LoadNewContentsChooseFile js
18. e user what kind of files that can upload and what format is needed for each The user can choose and attach a file to the request sent to CheckFile jsp CloneContainer jsp Allows the user to clone a plate The user must enter the details of the new plate and how much material is to be taken from the source plate CloneContainerE jsp Input form section for CloneContainer jsp DefineFilter jsp Power search interface sets the filter object in UserHttpSess EditBulkContents jsp Allows the user to update the volumes and comments of all the contents in a container 12 EditBulkContentsE jsp Input form section for EditBulkContents jsp Export jsp Prepares a text file version of a search result or browse for download ExportList jsp Prepares a text file version of a list s search result or list browse for download Footer jsp Chunk of html and jsp coding included at the bottom of every page Header jsp Chunk of html and jsp coding included at the top of every page HowManyPlates jsp Used in the tool that makes a plate from a list of samples When first using this it lets the user decide on whether phenotype information should be taken into account during the laying out of samples on plates It also tells the user how many plates they will need to make at least can increase depending on how many controls are used User is brought back to this screen after each plat
19. ener section in web xml 3 1 2 ColumnData java This file enables the adding and removing of columns from a user s view of container contents data It stores the default views for each user type and an array for every possible column to be added 3 1 3 DataExport java When user wants to export a table from search or browse or list of containers etc this file makes appropriate headers for the columns of data in the file and prepared the data to be exported method getHeader After the data is prepared it can be accesses by an iterator and an overridden next method that returns data line by line in tab delimited format 3 1 4 FileUploading java Enables files to be uploaded to create new subjects samples containers and shopping lists Has methods to check a file for upload and return any lines that have problems Also has methods to create elements 3 1 5 FilterObject java Sets up power searches Checks every request field for input and if it is found adds that field to the query method setFilter HttpServletRequest request Prepares strings to add to queries that return search results get lt Object gt String 3 1 6 MetadataManager java This file builds the profiles describing what data a user will view for each object which is based on the Meta Data Tables It gets which fields need to be viewed in what order from the MetaData tables and the actually values for these fields from the Object java s getValueAr
20. eta_data tables see Meta Data Tables and icapture com MetadataManager java see INSERT LINK 3 2 3 Persistent java This is the parent class of objects that represent tables mapped by Hibernate Its common fields are for id visibleName creator modifier createDate modifDate and comment plus it has getters and setters for each 3 2 4 TempMetaData java Object class for meta data tables 3 3 Reports 3 3 1 lt ReportName gt jasper This is the xml file that defines how the report will be filled and will look It must be compiled before the report can be accessed 11 3 3 2 lt ReportName gt jrxml This is the compiled version of the jasper file of the same name it is this file that the user will access when they request a report 3 4 Web Application Files 3 4 1 JSPs File Description Add lt Object gt jsp JSP for generating add edit page for the relevant object and handling validation and execution of add or edit Add lt Object gt E jsp Form section of Add lt Object gt jsp Can be included in Add lt Object gt jsp as many times as necessary in different logic cases Add96WellPlates jsp Customized add container page for 96 well plates Used for plating tool Add96WellPlatesE jsp Input form section for Add96WellPlates jsp AddControlWellsToContainer jsp Allows user to add control wells to a 96 well plate that they are making using an existing control layout Used when ma
21. hod getValueArrayReadable How the string is passed here will be how it shows up in the table so do any formatting at this point Take not of the array index number you are assigning for your variable Create an entry for your field in fieldname java For example adding field location would mean a line in fieldname java like public static final String LOCATION location In MetadataManager java method build lt Table gt Data add your field to the end of the m key equals Fieldname lt gt statement Make sure the number associated with your field matches the array index number you took note of in step b Be sure to also update field ccMetaDataAllColCount increase by the number of fields being added Add an object for your field in the declarations section of ColumnData java this is the data that will be used to create entries in tolcontainercontents_meta_data for your user if they add this field to their view scheme Also add the field to the default views where appropriate if your field is not in tolcontainercontents make sure to preface it with the object that connects it to ContainerContents for our example this would be container location Also add your field to the hashmap in makeHash Add check and num entries to EditColumns jsp and EditColumnsE jsp To see your new field in SLIMS add it to your view scheme through SLIMS interface see User manual or update to your default view settings
22. iner the content is in SAMPLEID Primary key of tblsamples the sample of which the content is an instance VOLUME The volume of the content in ul 1 for unknown CONCENTRATION The concentration of the content in ng ul 1 for unknown CONTAINERCONTENTSID PARENTID CONTAMINATED DILUTION QUANTIFIED MATERIALTYPEID AMPLIFICATIONDATE BARCODE 2 1 5 tblcontainers Primary key The content this content came from ie the tube material was taken from to fill a well 2 tubes have no parents 3 no data available If the tube well is contaminated 0 no 1 yes 2 unknown The dilution of the content ex 1 100 1 1 for stock and blank for unknown or N A The date this content was inventoried What type of material this content is WGA genomic unextracted etc What date this sample was amplified will be null if non WGA The barcode on a tube or plate if the content has one Field Description CONTAINERID Primary key of container CONTAINERTYPEID What type of container this is 96 well plate box of tubes etc CONTAINERNAME The systematic name of this container FREEZERID Which freezer this container is in SHELF The shelf the container is on in the freezer DISCARDED Whether this container has been discarded or not 0 1 SHIPPEDOUT SHIPPEDDATE SHIPPEDTOID STOCK MATERIALTYPEID VALID CONTAINERALIAS DATE INITIALS LOT LOCATION 2 1 6 tblcontainertypes Field CONTAINERTYPEID DESCRIPTI
23. king a new 96 well plate from a list of samples AddControlWellsToContainerE jsp Input form section for AddControlWells ToContainer jsp AddControlWells ToContainerManual jsp Allows user to design a new control layout and add their controls to a 96 well plate that they are making Used when making a new 96 well plate from a list of samples Linked to from AddControlWellsToContainer jsp AddControlWells ToContainerManualE jsp Input form section for AddControlWellsToContainerManual jsp AddListContentsToContainer jsp Allows user to add samples to their new plate specifying how much source material is to be used and what the final volumes and concentrations will be of the samples in their new plate AddListContentsToContainerE jsp Input form section for AddListContentsToContainer jsp AdminMenu jsp Dropdown navigation element for all supporting data view pages AdminPage jsp Front page for Supporting Data Front page for browsing data has links to view pages for Browse JSP subjects contents and containers When making a list from a file this jsp checks the file for formatting validity of entries etc and shows the users the CheckFile jsp results of its checks It also allows the user to accept the file given the results of the check and proceed in creating the list Linked to from ChooseFileToLoad jsp ChooseFileToLoad jsp When making a list from a file this jsp shows th
24. ntainer see TBLCONTROLWELLS Field CONTROLLAYOUTID ROW COLUMN Description Primary key The row this default control well is in The column this default control well is in DEFAULTCONTROL The id of the default control that is in this well LAYOUTNAME The name of this layout of controls 2 1 9 tblcontrolwells These are the entries for the actual controls in plates like a tblcontainercontents for controls Field Description CONTROLWELLID Primary key CONTAINERID The container this control well is in ROW The row this control well is in COLUMN The column this control well is in CONTROLID The id of the control that is in this well VOLUME The volume of the control that is in this well 2 1 10 tblethnicitylookup 2 1 11 tblfreezers 2 1 12 tolgenotypingruncontainers 2 1 13 tblgenotypingruns 2 1 14 tolgenotypingrunsamplestatus 2 1 15 toblgenotypingrunsnpstatus 2 1 16 tolmaterialtype 2 1 17 toblphenotypelookup Field Description PHENOTYPEID Primary key NAME The name of the phenotype The type of phenotype 1 subject either affected or unaffected TYPE binary 2 subject s status requires number or text for classification not binary DESCRIPTION Description of phenotype ABREVIATON 2 1 18 toblphenotypes Field SUBJECTID PHENOTYPEID VALUE ABREVIATON 2 1 19 tolsamples Field SAMPLEID SUBJECTID NAME VALID NUMCALLS LOCATION NUMNOCALLS FREEZERLOCATION CONCENTRATION PARENT SAMPLETYPEI
25. p When bulk loading samples from files this jsp shows the user what kinds of files they need to upload and what format is needed This jsp allows them to load the second of two needed files the one that creates containerContents The user can choose and attach a file to the request sent to LoadNewContentsCheckFile jsp LoadNewSamplesCheckFile jsp When bulk loading samples from a file this jsp checks the file for formatting validity of entries etc and shows the users the results of its checks It also allows the user to accept the file given the results of the check and proceed in creating the samples Linked to from LoadNewSamplesChooseFile jsp When the user accepts their file and proceeds to create the samples they are directed to the second step in creating samples creating 13 contents LoadNewContentsChooseFile jsp LoadNewSamplesChooseFile jsp When bulk loading samples from files this jsp shows the user what kinds of files they need to upload and what format is needed This jsp allows them to load the first of two needed files the one that creates samples The user can choose and attach a file to the request sent to LoadNewSamplesCheckFile jsp LoadNewSubjectsCheckFile jsp When bulk loading subjects from a file this jsp checks the file for formatting validity of entries etc and shows the users the results of its checks It also allows the user to accept the file given the re
26. rayReadable It then consolidates these two information arrays to build an array that will be shown to the user 3 1 7 Plater java Keeps track of plating operations what samples need to be plated what samples have been plated order of samples based on phenotypes what controls need to be plated what controls have been plated how much space there is on a plate after adding controls etc This is used for make 96 well plates from a list of contents as well as making 384 well plates from a list of 96 well plates 3 1 8 SampleSelector java Manages and tracks the decision tree structure being made by the user Prepares and runs queries to fetch the best match or next best match contents Manages accepting and rejecting of contents and storage of those accepted 3 1 9 SearchObject java Sets up simple searches Checks the request field for input and what to search and uses those fields to set up the the query method setUpSearch HttpServletRequest request Prepares strings to add to queries that return search results get lt Object gt String This file is a simplified version of FilerObject java 10 3 1 10 SessionListener java This class supports session management for the web application It should be included in the listener section of the configuration file for the application see listener section in web xml 3 1 11 UserHttpSess java Manages setting up the application and contains nearly all the database querying metho
27. rcontents make sure to preface it with the object that connects it to ContainerContents for our example this would be container location Also add your field to the hashmap in makeHash Add check and num entries to EditColumns jsp and EditColumnsE jsp 18
28. rld getAllUsers int startPosition getAllUsersCount setUserSortCol String sortCol getUserSortld String sortCol setCurrentUser String userID gt Rebuild SLIMS 4 1 2 Viewing the table Do steps in 4 1 1 Add a meta data table to the database for the table you want to add see Meta_Data Tables to control what columns are displayed Create a hibernate mapping file for the meta data table lt Object gt MetaData hbm xml Create a java class file for the meta data table object lt Object gt MetaData java Create a View lt Object gt Manager java file to control pagination of table viewing Create a View lt Object gt s jsp file similar to existing View lt Object gt s jsp files Add methods to MetaDataManager Add to methods of UserHttpSess UserHttpSess HttpSession s buildMetaData resetCurrents setSettings cancelFilter cancelFilterList cancelSearch cancelSearchList gt Rebuild SLIMS VVVVVV Vv 4 1 3 Adding or updating values gt Create an Add lt Object gt jsp file similar to existing Add lt Object gt jsp files Make sure to validate input here gt Create an Add lt Object gt E jsp file similar to existing Add lt Object gt E jsp files This will need to have input elements for every field you want to be able to edit or fill 16 gt Add methods to UserHittpSess java see other objects versions for template checkUserld String userID addUser updateUser gt Rebuild SLIMS 4
29. sults of the check and proceed in creating the subjects Linked to from LoadNewSubjectsChooseFile jsp LoadNewSubjectsChooseFile jsp When bulk loading subjects from a file this jsp shows the user what kind of file they can upload and what format is needed The user can choose and attach a file to the request sent to LoadNewSubjectsCheckFile jsp LogIn jsp First page users sees when visiting SLIMS allows them to log in Make384From96 jsp This file lets the user make a 384 well plate from the 96 well plates in a list of containers It lets them name the new plates and set the layout for the 384 well plate When the user is done this jsp creates the new plates updates the source volumes and directs the user to PlatingSummary jsp Make384From96E jsp Input form section for Make384From96 jsp MakeSDS jsp Code to make an SDS import file for a plate Writes the file to the user s machine This is accessed through a button in the container viewing tables PlatingSummary jsp Shows a summary of the plates just made for each plate it shows name layout and links to reports for them When the user is finished they are directed to SLIMS home page and their active list is closed QueryExport jsp Code to write the results of an SQL query to the user s machine QuerySearch jsp JSP for user to input and run an SQL query SampleSelectorCrtieriaChoice jsp Sample selector allows the user to set up
30. t jsp View table screen for lists of objects Opens in new window from a link on a view containers ViewLayout jsp page Shows a layout of the containers with sample IDs and volumes Jsp for list manager controls loading of premade lists and ViewLists jsp closing lists Has a link to make a new list from a file Lets the user search for lists by name creator and modifier ViewListsE jsp Input form section for ViewLists jsp ViewReport jsp User doesn t see thing page it s responsible for loading the requested jasper report and opening it for the user 3 4 2 Other Files File Description ddsmoothmenu css Css for top menu dropdown functionality ddsmoothmenu js Javascript functions for top menu dropdown functionality formstyle css Css for web application utils js Common javascript functions for application 3 5 Configuration Files web xml sections of note Code Description lt param name gt viewlimit lt param name gt lt param value gt 1000 lt param value gt 1000 number of items viewable per page If more than 1000 items in a view table it will be split among gt 1 page lt param name gt seconduser lt param name gt lt param value gt username password lt param value gt user with username and password will be able to login with administrator rights and will automatically be added to user The option can be useful to get access to database if all
Download Pdf Manuals
Related Search