Home

TIBCO® Spotfire® DecisionSite® 9.1.1

1. Dr PARAMVALUE AS SELEC PRT ID PT NAME P STRING VALUE FROM AADM SCHEMA PARAMETER P AADM SCHEMA PARAMETER TEMPLATE PT AADM SCHEMA PROTOCOL PRT AADM SCHEMA PROTOCOL TEMPLATE PRTT WHERE PRT ID P PROTOCOL ID AND PRTT ID PRT TEMPLATE ID AND PT PROTOCOL TEMPLATE ID PRTT ID AND PT PARAMETER IDX P PARAMETER IDX EXPERIMENT ANALYSIS View CREA OR REPLACE VIEW V EXPERIMENT ANALYSIS A PROTOCOL ID E PROTOCOL ID TARGET ID PHYSICAL CHIP ID EXPERIMENT NAME ANALYSIS ID ANALYSIS NAM ANALYSIS DATI E Fl 27 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 3 5 2 3 3 5 3 28 AS SELECT ACHP PROTOCOL ID EXP PROTOCOL ID EXP TARGET ID EXP PHYSICAL CHIP ID EXP NAME ACHP ID ACHP NAME ACHP ANALYSIS DATE FROM AADM SCHEMA EXPERIMENT EXP AADM SCHEMA ANALYSIS DATA SET DSCEL AADM SCHEMA ANALYSIS ACEL AADM SCHEMA ANALYSIS DATA SET DSCHP AADM SCHEMA ANALYSIS ACHP WHERE EXP ID DSCEL EXPT ID AND ACEL DATA SET COLLECTION ID
2. 59e372a0 d517 11d5 f16b 0010ac110306 name join Dons employee names in EMP and Hurnan_Resources Employees lt Select Iv Save Copy Save Clear 89 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 4 4 3 3 3 4 1 90 Option Add gt Remove Select Freehand Case sensitive Tables to join GUID Name Description Parent domain lt Select Default join Save Copy Save Clear Description Select a column from Data Sources and then click this button to include it in the join Removes a column from the list of columns included in the join Select this button to choose from standard joins in the drop down list Select this button to enter your own join definition Select this check box to make the join case sensitive Select one table from each drop down list If you are only using two columns in the join then do not alter the default choices If more than two columns are included in the join condition for example an intermediate table then it is important to select the two tables that are to be joined A unique identifier used internally to identify the data elements The name of the join to be saved edited A free text description of the join The maximum limit of the description is 255 characters The name of domain folder where you want to save the join Select a domain in the Information Model then click here to place the
3. 7 Click the Add gt button to add the selected users to the Group members list Note You cannot add any users to a group that is configured to synchronize with an external LDAP server 8 Select one or more Products to which you wish to grant the group members access 9 From the DecisionSite level drop down list select the level of access granted to the group members 10 Click Save This Configuration Logging User Activity Viewing Log Files Log files register user activity on your Spotfire Analytics Server They allow you to keep track of when users log on when users fail to log on etc The log files are located in the directory lt installation directory gt spotfire logs There are several log files that you can configure and view DecisionSite Log Actual file dss log is located in the logs directory This file logs all activity on the server except the events recorded by the DecisionSite Access Log and the DecisionSite Client Log It includes the SQL log and a simplified version of the Access log You can set the detail level of what this file shall log by selecting different Log Configuration Files DecisionSite Access Log Actual file located in lt installation directory spotfire administrator dssaccess log This file logs all logins and logouts from DecisionSite Clients to the Spotfire Analytics Server It shows which user logged in out and when It is always enabled and is unaffected by Log Configuration File setti
4. A location in a record where data is stored used in some database systems to mean column Although the terms field and column have slightly different meanings in formal database theory in most instances they are used synonymously Spotfire DecisionSite Administration Filter A set of criteria applied to records to show a subset of the records or to sort the records GUID Global Unique Identifier A GUID establishes a unique identity for elements in the Information Model For example f9717cc0 e965 11d4 941b 0010ac110117 Information Builder A tool for creating and executing information links in Spotfire DecisionSite Information Model The Information Model consists of the data integration layer which manages connections with the various data sources and the data access layer which associates database identifiers with user friendly column names Appears to the user as a folder structure Information Services A suite of tools for accessing databases Includes Information Designer Information Builder and Information Library Information Library A tool for executing information links Information link A predefined database query including all required connection information When opened executed will retrieve data from databases and visualize it in DecisionSite Join An element used to describe how tables relate to one another Tables are typically joined using data that they have in common see Primary key Jo
5. Syntax The syntax for the personalized information link parameters is CURRENT USER and CURRENT GROUPS Adding a Structure Search Filter Users of DecisionSite for Lead Discovery can use structure search in run time filters This means using substructure or similarity search to limit the data set to chemical structures of a particular type Structure search can be used on BLOB Integer and Real column elements For Integer and Real it is important that the values in the column are valid compound identifiers gt Tosetup a run time filter with structure search 1 Create a new information link or modify an existing link 2 Adda column element of the type BLOB Binary Large Object Integer or Real Comment For column elements of the type BLOB a structure search run time filter is automatically enabled The Retrieve box on the Advanced tab will be disabled BLOB data cannot be retrieved or visualized in DecisionSite but can be used for filtering 3 If the column type is Integer or Real go to the Advanced tab and select the Structure Search prompt 4 Savethe information link or open it Adding Procedures Procedures are added to an Information Link in the same way as any other element such as a column or filter You select them from the Elements Pane and click Add to Link The procedure icon looks like this E 126 4 4 3 2 10 4 4 3 2 11 Spotfire DecisionSite Administration Priority of Exec
6. You can enter other text freely in this field Note One can create additional default naming schemes that will always appear in the Column names drop down list box for all users Talk to your Spotfire Analytics Server administrator to do this and read more about the procedure in the Spotfire Spotfire Analytics Server Administrator s Manual Example If we look at the example from Example of Pivoting again The following table is transformed by pivoting City Month Temp London February 4 New York February 6 London May 16 New York May 19 London August 28 New York August 26 London November 13 New York November 11 By using the Expression Month C Average V we would get the following table with column names Month Month August Month Month May City February November Average Temp EE Average Temp Average Temp London 4 16 28 13 New wok d 19 26 11 Since we knew that this transformation was about average temperature we choose to write the text Average instead of including the Computation Parameter M in the column name 4 4 4 5 6 Set Filter for Column Dialog The Set Filter for Column dialog appears when an information link is being opened and a column is encountered that has been set up with a run time filter The dialog may take various forms depending on the type of prompt selected Strings containing commas can be included both as values as well as range limits by escaping the comma with a bac
7. lt reference column gt CDBREGNO lt id column gt CDBREGNO lt structure column gt MOLFILE lt pl constant name idColumn gt CDBREGNO lt pl constant name structureColumn CTAB lt pl constant MOLSIMILARITY name similarityScoreColumn lt data column gt Other columns you want to display one row for each column If your MDL Direct setup includes a column containing structure keys it needs to be identified by a lt meta data gt tag to be recognized by the Add Structure Keys tool For the data column containing structure keys add a meta data tag according to the following example lt data column column guid aaedcad0 5ea3 1 1aa 20ae 00a0ac 1 10a07 gt lt ISIS2DKEYS gt lt meta data name S potfire Chemistry Framework StructureKeysColumn gt true lt meta data gt lt data column gt The column guid attribute in the example should be replaced with your guid for the structure keys column Save the file to the same location on the server lt install directory gt server application data chemistry framework 3 4 12 Adding Licenses for the Users gt To enable MDL Direct features for users or groups 1 pe NS 5 In DecisionSite Administrator click on Groups or Users to open the properties for the group or user you wish to give access to DecisionSite for Lead Discovery Make sure that the DecisionSite for Lead Discovery check box is selected Make sure the DecisionSite level
8. 1 Create a new information link or edit an existing link see Modifying an Information Link In the Information Link pane click Edit on the Conditioning line Response The Data Conditioning dialog opens Select Distinct as conditioning type Click OK Response In the Information Link pane Conditioning has been set to Distinct This means that duplicate records will be removed from the data set returned by this information link when it is opened 4 4 3 4 2 Pivoting Data Pivoting is a method of rearranging rows into columns This flexibility allows you to rotate row and column headings around the core data In general pivoting is used to be able to carry out 137 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 3 4 3 138 visual analyses on data that originally reside in a tall skinny format Pivoting may also be used to create more query devices by splitting a column into several other columns gt To pivot data 1 10 11 Create a new information link or edit an existing link see Modifying an Information Link In the Information Link pane click Edit on the Conditioning line Response The Data Conditioning dialog opens Select Pivot as conditioning type Click Configure Response The Pivot dialog opens In the Identity section select the columns that you want to use to identify records Comment Each unique value in the chosen identity column produce
9. 5 Click Save or Save Copy Tip Use conversion functions in the calculation field to map CLOB columns to String Real to Integer etc Just setting the Type is not recommended See Creating a Column Element for more information 70 4 3 2 4 7 4 3 2 4 8 4 3 2 4 9 4 3 2 4 9 1 Spotfire DecisionSite Administration Defining a Column Filter Column filters are automatically applied when the column is retrieved Such filters unlike filters that are defined and saved as separate elements filter elements cannot be disabled by the user Column filters are defined as the column element is being created The following steps should be taken in addition to what is described in Creating a Column Element gt To define a column filter 1 In the Filter section click the Show gt gt button to show the filtering controls 2 Inthe Data Sources pane select a column and then click the Add gt button to add the column to use in the filter condition Comment Repeat this step if you need to include more columns in your filter condition 3 In the Condition field define a filter condition based on the chosen column or columns for example C1 lt 2000 or if you are using two columns C1 lt C2 Comment To combine conditions use the AND or operators for example C1 gt 2000 AND C2 lt 1000 Comment You can also add a personalized filter condition that limits data depending on the currently logged in user See Personalized Informat
10. In the latter case it is important to select which tables to join the tables in which C1 and C2 occur The other columns included in the join condition C3 and C4 are found in an intermediate table No join is created between this table and the other two Example In the following tables we want to create a join that links T1 and T3 In this way we will be able to query the database for say the address of the person who earns 1400 To achieve this T2 is used as intermediate table The tables T1 and T3 should be selected from the Tables to join drop down lists see Creating a join The join again is defined as C1 C3 AND C4 C2 T1 T2 T3 Name Salar Name Number Number C2 Address C1 Y C3 C4 1 Boston John 1000 John 1 2 Stockholm Steve 1400 Steve D 3 Tokyo Lisa 1200 Lisa 3 65 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 3 4 4 3 2 3 5 4 3 2 3 6 66 Editing a Join gt To edit a join 1 In the Information Model pane select the join that you want to edit 2 Click the Edit button in the Information Model pane Response The join is loaded and enabled for editing 3 Modify the desired fields Comment To move an existing join between domains select a new domain in the Information Model pane then click the lt Select button 4 Click Save or Save Copy Comment Use Save Copy if you want to keep the old join as well as the edited one Tip To see fro
11. all elements based on that data source will be automatically updated so that they keep referring to the same underlying database Note If you rename a data source so that the new name is identical to the name of another already existing data source that data source will be replaced with the data source you changed the name for Hence it is important to verify that the changes you have made are correct before clicking Save Removing a Data Source gt To remove a reference to a database 1 From the Select workbench drop down list select Data Source 2 Click Change 3 Inthe Defined data sources list box select a data source 4 Click Remove Note Elements based on a data source that is removed will remain in the Information Model However they will not work unless a new data source is defined using the same name as the deleted data source Issues when Creating an ISIS Direct Data Source When creating a data source for ISIS Direct it is necessary to make the following setting in the Data Source Definition workbench under New connection initialization commands select cdcaux ctenvinit schema dbname from dual Creating a Table Alias You can create a duplicate reference to a database table from Information Designer This duplicate is called a Table Alias and references the very same data only using an alias This can be useful in certain cases most often when in need of a self join within a table below gt Creating a
12. click the Groups tab In the Search for groups pane enter a search criteria for finding a group Comment To see all groups enter an asterisk wildcard The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Click Search In the Matching Groups list click a group name Response The properties of the selected group are displayed Click Rename Group Response The Rename Group dialog is displayed Enter a new group name Click OK Response The Group Name is changed 4 2 2 4 4 Setting Group Privileges gt To assign users products and DecisionSite level to the members of a group 1 2 At the top of the page click the Groups tab In the Search for groups pane enter a search criteria for finding a group Comment To see all groups enter an asterisk wildcard The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Click Search In the Matching Groups list click a group name Response The properties of the selected group are displayed In the Search for available users field enter a search criteria for finding users 51 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 2 2 5 4 2 2 5 1 52 Comment To see all users enter an asterisk wildcard 6 In the Available users list box select the users that you want to include in the group
13. ics New connection init commande 61 Nominal Level nter one i erri 48 Nope Level 1 iere ibd be Mer iaia 48 VUEN 96 NVARCHAR type o eesscsseeseesessecssessesstsstsstsstsstssesseesesseeseeseees 68 NV BE 104 o Open importing a list of users cccseessessteeeseeeseeesteesseeenes 50 opening information links od vg 132 OperatOrs 4c niter reta tide ti ide vetet dirus 75 Oracle Hints Edit Oracle Hints dialog esses 145 Cu sive DL 127 View SQL and Edit Oracle Hints dialog 144 P Passwords ade WERE EN EU 49 Permissions EXPONE oido ce re e ete importing setting user interface Personalized Information Links creating CBE M Rab GEM 102 USING sey 124 Pivot el EU 146 example eee a a aa a 138 139 UE 137 ND Ee 106 Ne DC 18 Post update procedure sss 75 Power Level ion adeste io ERU IAHRORERES 48 Preconditions 3e ca E RE RE te 47 Pre update proced re etes 75 Privileges setting group privileges 51 setting user privileges sesssseesssesereesererrrssrrrsereesee 49 Procedure Join icai grep d e E 96 Procedures Information Builder ene 120 126 Information Designer 75 Product Bicence tenete RA ged eer 48 Prompted filters ieee ene 132 Properties setting group Drivileges esee EN setting user privileges 49 QUGety iiidciaiasn c Ree edis creating definition ie ee
14. regardless of whether the later prompt steps are independent or not It may also be of interest to use the independent setting on an element that is not prompted e g on a column with a hard filter Example Say that you have information about your employees and their salaries stored ina STAR schema database with a layout similar to the one below Male Female Name Salary Smith 2300 Jones 1200 Anderson 2500 Kline i DeptNo 10 z0 30 Location Chicago Dallas New York Now you want to retrieve information about the salary of your employees in the Chicago office with the possibility to filter using DeptNo and Gender upon running the information link gt These are the steps you would perform to retrieve this type of information 1 Create an information link by adding all the interesting columns to the Information Link pane Select the values Filter type for the Location column 3 Enter Chicago in the text box Filtertype Limits 23 Depto ame ZE 46 Gender a ZF 4b Location values cnicaeo E Salary france zl 4 Switch to the Advanced tab 5 Select suitable Prompt options e g List Box for the DeptNo and Gender columns 134 4 4 3 3 5 Spotfire DecisionSite Administration 6 Select the Independent option for the Location column Retrieve Independent Prompt DeptNo v C List Box Gender v T Liste zl Location v IV None Salary v E None x By making Locat
15. you also need to create user accounts and set the permissions for these accounts This is done using the Permissions workbench e Execute rights permit the user or group to see and use elements of a domain filters columns and information links e Execute Modify rights also permit the user or group to add and remove information links from the domain e Modify rights alone gives no access to the domain The domain will not be visible in Information Builder or Information Designer e The user permissions shown for individual users are only the permissions set explicitly for that user The user may have additional rights if he she belongs to a group e Users that do not have access to a domain will not have access to a sub domain within even if they have been given Modify Execute rights to the sub domain gt To set permissions for users groups 1 From the Select workbench drop down list select Permissions 2 Click Change Response The Permissions workbench is displayed 81 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 10 4 3 2 10 1 82 Click Groups or Users Response All available users or groups appear in the accounts list In the accounts list select the user or group whose permissions you want to edit Click Edit permissions Response The domains and the permissions for the selected user are shown Note that individual users also may have other rights if he she belo
16. 5 2 144 settings regarding hard filters in the Properties tab will be disabled Dialogs Save Information Link Dialog Z Save Information Link X Domains 1 ActivityBase Information Links ActivityBase Query Elements ActivityBase_Stored_Information_Links Bil oiL Hits Information Link Test Occasion filter by Result e Hits Information Link Test Request filter by Result e Results Information Link QC Markers e Results Information Link QC Markers filter by Completion Da e Results Information Link QC Markers filter by Row and Colui DII e Results Information Link Test Occasion MERO M Name Description Retrieve all Test Occasion Results for particular studies protocols and runs with Results greater than 50 Help DK Cancel Option Description Domains Select the domain in which to save the information link Name Enter a name for the link It should not contain any blank spaces Description Describe the information link View SQL and Edit Oracle Hints Dialog Note If an information link has been added to the Information Link pane using Add to Link and no additional elements has been added Edit Oracle Hints will not be available To display the Edit Oracle Hints link use Edit Link when you move the information link to the Information Link pane Note If more than one information link containing hints are added to the Information Link pane all hints wil
17. 950 950 CLARK MANAGER ACCOUNTING 2450 2450 JONES MANAGER RESEARCH 2975 2975 BLAKE MANAGER SALES 2850 2850 KING PRESIDENT ACCOUNTING 5000 5000 ALLEN SALESMAN SALES 1600 1400 WARD SALESMAN SALES 1250 1400 MARTIN SALESMAN SALES 1250 1400 TURNER SALESMAN SALES 1500 1400 To produce this table we must define the Average Salary column with two aggregate keys Job and Department gt To use multiple aggregate keys 1 Selecta value column from the Data Sources pane 2 Click the topmost Add gt button 3 Inthe Calculation field type AVG C1 Comment AVG is the average function You can find more aggregate functions here 4 3 2 4 9 3 Spotfire DecisionSite Administration Click Show gt gt to show the aggregation controls From Data Sources select the first column to aggregate over for example Job Click Add gt Response AC1 will appear in the Aggregation Calculation field 7 Click the Add button on the right hand side of the Calculation field 8 Click Clear Response The Columns field is emptied o e 9 Select the second column to aggregate over for example Department 10 Click Add gt Response AC2 will appear in the Aggregation Calculation field 11 Click the Add button on the right hand side of the Calculation field 12 Enter Name Description etc 13 Click Save Response The resulting column will consist of the average of the value column for each value in the aggregation column Note
18. Calculation field enter ex ACE OU b qx concat concat C1 C2 7 Enter Name and Description 8 Selecta Parent domain 9 Select string from the Type drop down 10 Click Save PL SQL Functions In the following example we will retrieve salary information for employees in both USD and SEK One way of doing this is to write a function in SQLplus that performs the calculation CREATE FUNCTION money converter amount IN NUMBER RETURN NUMBER IS return val NUMBER 10 2 0 BEGIN LEET S amount IM se Return return val END The salary in USD is used as input and the output is a value that is 10 3 times bigger Store the function in the SDP ADMIN schema or elsewhere if a different administrator user name is used to make it accessible by Information Designer Now create a column element as follows 106 Spotfire DecisionSite Administration Columns Add gt SAL C1 Remove Calculation money converter C1 Aggregation Show gt gt Filter Show gt gt GUID Name Salary SEK Description Salary in Swedish Crowns Parent domain DREES lt Select Type real Set Filter devices Also create a column element Employee with employee names and Salary USD with the original salary values When an information link with these three columns is executed from Information Builder the generated SQL looks as fol
19. Domain creating S s is deleting cete eR E A dorriaifis pierde rtt eg rey ERI E FIR ege ER D irc M 63 MOVING suse esee ee ies 64 OVENVIEW ec ae p EROR Qai di ee 63 user interfaces Assia ween eee 89 Drillable columns ires 73 D plicates cto ax EN 137 E Editing columns eler UE lt information link SOL 82 information links 3 et crie e eei 121 IMPERATUM DEUM 66 UI Ccp E H A 81 Elements elements parie ase t ded ORO 141 fundamental concepts esessesseeeereene 119 Eliminating duplicates seen 137 EVeryone ioter eise tenete nte ie tet ace 47 Examples eon M 138 pivoting with aggregation cccccseesteeeseeseeeeees 139 run time filter 4 toto rr Ese 133 Executing information links eene 132 Export Rei Un EE list of users user interface F lg lom 58 Field EE ERR IIR EE ERAT 67 File exporting a list of users 50 importing a list of users sess 50 Filter Spotfire DecisionSite Administration adding a structure search filter 126 135 lu LTE defining rr tenet tts deleting e t RE RS COVICES cese DE ERU E Ces different types nee during retrieval eese editing ra rere o E e re erri vanae element innuit ele ente eds example ix ERE user interface ae using run time filters Freehand joins Func
20. Guides pane is directed to a default server The important difference between home server and default server is that the default server does not have be a Spotfire Analytics Server The default server can be set from the installer when Spotfire DecisionSite Client is installed The setting can also be modified directly in the registry HKLM HKCU Software Spotfire eApplication Servers DefaultServer String lt url gt There is also support for a custom start page The custom start page can be configured from the Options dialog in the Guides pane The dialog is available via the context menu The custom start page can also be configured via the registry HKLM HKCU Software Spotfire eApplication Navigator CustomStartPage String lt url gt 4 5 3 5 The Spotfire Zone Dynamic content in the Guides pane requires access to Spotfire APIs These APIs are not safe for scripting To allow API usage the servers must be trusted This can be done either by adding the servers to the Trusted Sites or by adding the servers to the Spotfire Zone The Spotfire Zone is defined in the registry HKLM HKCU Software Spotfire SecurityManager Spotfire Zone lt server or domain gt lt protocol gt DWORD 0 1 Protocol can be http or https use 0 to allow and 1 to deny 4 5 3 6 Server Display Name By default the Spotfire Analytics Server is identified by its hostname For environments with more than one server this is not very practical To resolv
21. High salary Low salary B C Scott 35 DeptNo Ab Emplove Ab Location 32 Salary eu test query H O STANZA ISIS Edit Link Add to Link 141 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 4 3 142 Option Available elements Details Edit Link Add to Link Description Displays all available information links column elements or filter elements Click on the desired element to select it Displays information about the selected element Click here to edit an information link selected under Available elements Click here to add the selected element to the Information Link pane Icons in the Elements Pane In the Elements pane the following icons may appear Click on a link in the table below to find out more about each element type Icon C3 eL ae ous E m blob det Element type Domain Information link Filter String column Integer column Real column Date column DateTime column Procedure Time column BLOB binary large object column Cannot be retrieved but can be used in the structure search filter condition It can also be used in custom made filter conditions using the API CLOB character large object column Can be retrieved to DecisionSite Client It can also be used in custom made filter conditions using the API Spotfire DecisionSite Administration Information Link Pane Properties tab Propert
22. Only log files that contain logging information will be displayed in the drop down list Click Logging to update the list when you expect that logging information has been written to a previously empty log file gt To view a log file 1 At the top of the page click Logging 2 From the View log files drop down list select a log file 3 Click Refresh Changing Log Configuration File You can set what should be logged in the log files by selecting a certain Log Configuration File This configuration file will set the level of detail for the actual log files There are three levels of logging you can choose between by selecting different Log Configuration Files log4j minimal properties The DecisionSite Log will only log errors and the SQL Log will be deactivated log4j properties The default setting The DecisionSite Log will log warnings errors and basic information The SQL Log will log basic SQL information log4j debug properties The DecisionSite Log will log detailed debug information as well as warnings errors and other detailed information The SQL Log will log more detailed SQL information Warning Only use Debug mode for diagnostics and not for continuous server use It significantly reduces the performance of the server and also produces very large log files If you want to configure the logs in other ways than the above options let you you can create your own Log Configuration File using standard Log4j synt
23. Post update procedure this procedure does not return any data it only performs an operation on one or more databases All post update procedures in an Information Link will always be executed after any query procedure gt To Create a Pre update or Post update procedure 1 From the Select workbench drop down list select Procedures 2 Click Change Response The Procedures workbench is displayed 3 From the Data Sources pane select the database procedure you wish to use Click Add gt Response The database procedure is added to the workbench Information Designer analyzes the database procedure and makes a guess as to whether it is a pre update 76 4 3 2 6 3 10 11 12 13 Spotfire DecisionSite Administration procedure or a query procedure it never sets post procedure by default Procedure Add gt blade2 OE INSERT_INTO_TESTTABLE Type Pre update procedure DI Select the Type of procedure Pre update procedure or Post update procedure Comment Pre update procedures are always executed first in an Information Link Post update procedures are always executed last in an Information Link If the database procedure requires any Input Parameters their name and type are displayed Input Parameters Name Type Default value Permit null Prompt Y string Boston E Single value DI Select whether the input parameter should receive a Default value by entering a value of the appropriate ty
24. T38 RE I37 O0BJDID T38 BJDID Data Source ISIS DIRECT SELECT IS CDBREGNO AS CDBREGNO S108 ISISCPD AS ISISCPD sing NARITO as roman zl Help Copy SOL Close Option Description SQL for the selected Displays the SQL statements used to retrieve the desired Information Link information If several Data Sources are used the SQL statements for the different sources are separated by lines Help Opens this help file Copy SQL Copies the SQL statements to the clipboard 86 4 3 3 3 4 3 3 3 1 Spotfire DecisionSite Administration Workbenches Data Source Definition Workbench Defined data sources Data Source Definition Help MySQL OfficialBugsystem eT sas share ede SQLServer GUID Name Type Connection URL No of connections User name Password User authentication Default data source ISIS_DIRECT Oracle sl jdbc oracle thin isisdirect 1521 isisd Min 2 Max 10 isis 99999 oO oO Default join data source Allow writing in temporary tables New connection initialization commands Fetch size Batch size Option Defined data sources Edit Remove GUID Name Type Connection URL select cdcaux ctenvinit isis isisrc2d from dual Y 10000 100 Description Lists all data sources that have been defined Opens the settings of the selected data source for editing Removes the selected
25. Table Alias 1 Selecta table in the Data Sources pane 2 Right click the table and select Add Alias 61 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 62 Data Sources fad OfficialBugsystem E oracle 1 gy CTXSYS El un SPOTUSEF_IIM BASEBALL IO a CITE DOIT 3 A Table Alias of the table is created B an SPOTUSER IM BASEBALL FILM eed ROUGHNESS DATA SITE_FOUR CITE mar LEECO JTE Self Joins A Self Join is a join from a table to itself In Information Designer this is implemented by using a Table Alias ID Name Manager 1 Sarah 2 2 Mike 3 3 Carla Null 4 Vincent 2 5 Adrian 3 The above database table lists a number of employees at a company and specifies who is the manager of each employee Carla is the head of the department Mike and Adrian report directly to Carla whereas Sarah and Vincent report to Mike In order to produce a list where the ID stated in the Manager column is replaced by a name see below we would need a self join in the table The table needs to look up the ID column in itself Name Manager Sarah Mike Mike Carla Carla Vincent Mike Adrian Carla 4 3 2 2 4 3 2 2 1 4 3 2 2 2 4 3 2 2 3 4 3 2 2 4 Spotfire DecisionSite Administration This is done by first creating a Table Alias of the table and then creating a
26. Tool a Guide or an external link The same extension can be added to several applications and several extensions can be added to the one application If an application or extension is removed all its extensions will also be removed However if an extension is applied to several applications it will not be removed until the last application using that extension is removed If an application or extension is un deployed and has an older version on the server the older version will still be deployed and used gt To Un deploy DecisionSite applications and extensions that are oe At the top of the page click the Deployer tab Response A list of all applications and extensions that are deployed on the server is displayed Select the check boxes of the applications and or extensions you want to un deploy 3 Click Un Deploy Response A new dialog appears listing the contents of the projects about to be un deployed If there are any applications or extensions that are based on a project that are 54 Spotfire DecisionSite Administration about to be un deployed these will be listed under a dotted line Such applications or extensions will also be un deployed 4 Click Un Deploy Response The specified applications and extensions are un deployed If an application or extension is un deployed and has an older version on the server the older version will still be deployed and used 4 2 3 User interface reference 4 2 3 1 User Propert
27. Username and Password that gives access to the data source QUU deus Select whether user must be authenticated when accessing the data source Response If this option is selected authentication is required when accessing this connection either by the user or by a plug in If not selected the credentials supplied above will be used for all users Even if user authentication is selected Username and Password must be supplied since they are used by Information Designer 7 Enter any additional configuration settings 8 Click Save 60 4 3 2 1 3 4 3 2 1 4 4 3 2 1 5 4 3 2 1 6 Spotfire DecisionSite Administration Note Setting up a data source to ISIS Direct requires special attention Click here for more information Note If you are connecting to a non writable data source for example SAS SHARE or ODBC you must clear the Allow writing in temporary tables check box Note For SAS SHARE and ODBC data sources both Min and Max No of connections should be set to 0 in order to disable connection pooling The same holds for other data sources that does not support pooled connection since there is no valid ping command Modifying a Data Source gt To modify an existing data source 1 From the Select workbench drop down list select Data Source 2 Click Change 3 Inthe Defined data sources list box select a data source 4 Change any fields 5 Click Save or Save Copy Note If the name of a data source is changed
28. Vincent 2 5 Adrian 3 The above database table lists a number of employees at a company and specifies who is the manager of each employee Carla is the head of the department Mike and Adrian report directly to Carla whereas Sarah and Vincent report to Mike In order to produce a list where the ID stated in the Manager column is replaced by a name see below we would need a self join in the table The table needs to look up the ID column in itself Name Manager Sarah Mike Mike Carla Carla Vincent Mike Adrian Carla This is done by first creating a Table Alias of the table and then creating a join between the table and its alias WHERE TABLE IDZTABLE ALIASI MANAGER Column Elements Columns Overview All information in a relational database is represented explicitly as values in tables composed of rows records and columns fields Column elements in the Information Model can be based on several database columns For example a column element can be calculated as the sum of the values in two different columns The underlying columns can reside in the same database table in different tables or even on different databases 67 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 4 2 68 Columns can be defined with built in column filters that are automatically applied when the column is retrieved You can also add a personalized column filter condi
29. a more efficient execution plan See Oracle documentation for more information about hints Note In some cases adding a hint can actually decrease the performance of an information link If this is the case click Edit Oracle Hints and remove the hint gt To add hints to an information link 1 Make sure the information link or columns of interest are added to the Information Link pane by clicking Edit Link or Add to Link respectively after selecting the elements 2 Click on the sal button in the toolbar of Information Builder Response The View SQL and Edit Oracle Hints dialog is displayed 3 Click on Edit Oracle Hints next to the data source that you want to annotate with hints Comment If several Data Sources are used each one will have a separate Edit Oracle Hints link Response The Edit Oracle Hints dialog is displayed 4 Enter the hints separated by space and click OK Response The hints are added to the SQL statement 5 Click OK Response The View SQL and Edit Oracle hints dialog is closed 6 Save the information link by clicking H Comment Note that the hint is not saved with the information link until the entire information link is saved Note If an information link has been added to the Information Link pane using Add to Link and no additional elements have been added Edit Oracle Hints will not be available To display the Edit Oracle Hints link use Edit Link when you move the information link to the Info
30. analysis HTS internal Library Section for our internal results Project A Tumor research Users of the DecisionSite applications DecisionSite for Lead Discovery and DecisionSite for HTS quality control would get directed into their corresponding Library Sections 1 5 3 Spotfire Library Database Connections gt To set up Spotfire Library Connections 1 2 Open an Internet Explorer browser Enter the name of your Spotfire Analytics Server in the Address field Example http analyticsserver Response This opens the Spotfire Analytics Server start page Click on Library Administrator and log in with your DecisionSite administrator username password The actual Spotfire Library Database tables have already been created when installing the Spotfire Analytics Server This was done by running the create_library_env sql script by the person who installed the server What you need to do now is to enter the same information in the panel below to connect the Spotfire Library to its database To find the information you need to enter below see the Installation Procedures chapter of the Spotfire Analytics Server Installation and Configuration Manual where the person who installed the Spotfire Analytics Server should have written down the settings Find the settings for the Spotfire Library Database Another option is to check the settings made in the file library service xml located in the lt Server Installation Directory
31. and Administration Manual e A group is a collection of users e Ausercan be a member of one or many groups e A group cannot be a member of another group e All users are members of the Everyone group e The Everyone group cannot be deleted and will always contain all users You can add new products for it and change the DecisionSite level 4 2 2 2 Setting up Access to DecisionSite Products The task of assigning users and groups access to the products purchased from Spotfire is done in the DecisionSite Administrator There are two things that determine which functionality a user group have access to Product licenses and DecisionSite Levels Product license The Product license determines which collection of tools and Guides that will be available for the user group see License information for more information e DecisionSite for Functional Genomics e DecisionSite MapConnect e DecisionSite Statistics e Computation Services Designers e DecisionSite for Lead Discovery e DecisionSite Posters e Spotfire Library e DecisionSite for Lead Discovery no ISIS Host If you develop your own custom DecisionSites these will be available here as well Note Assigning the DecisionSite Posters license to a user will automatically assign the user a license for Spotfire Library as well DecisionSite Levels For each user or group you also set a DecisionSite Level This is the level of access a user should have to the fundamental data retrieva
32. be stored as the login information for the user 4 Click OK Response The new user account is created 4 2 2 3 2 Deleting Users This can only be done when using Database Authentication gt To delete a user account 1 At the top of the page click the Users tab 2 Click Remove a User Response The Remove a User dialog is displayed 3 Enter the user name and click OK Response The user is removed 4 2 2 3 3 Changing User Passwords This can only be done when using Database Authentication gt To change the password of a user 1 At the top of the page click the Users tab 2 Inthe Search for users pane enter a search criteria for finding a user Comment To see all users enter an asterisk wildcard The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Comment If you are using Database Authentication this may take some time if there are many users 3 Click Search In the Matching Users list click a user ID Response The properties of the selected user are displayed 5 Click Change password Response The Change User Password dialog is displayed 6 Enter a new password and click OK 4 2 2 3 4 Setting User Privileges gt To assign groups products and DecisionSite level to a user 1 At the top of the page click Users 2 Inthe Search for users pane enter a search criteria for finding a user 49 TIBCO Spotfire amp DecisionS
33. click on the information link designated by the ILicon that you wish to edit Click the Edit button or right click on the information link and select Edit SQL from the context menu Response The Edit SQL workbench is displayed with details of the selected information link Select the Data source that you want to work against from the drop down list box Comment Complex information links may contain elements from several different data sources You can only edit the SQL part of the query that belongs to a single data source at a time After you have saved your first changes you can switch to another data source to edit the rest of the SQL To edit Pre Updates SQL or Post Updates click the corresponding radio button Comment Use SQL to modify the SELECT statement of the information link Use Pre Updates or Post Updates to add new statements or scrips to be run before or after the data retrieval Edit the SQL statement or add Pre or Post Updates in the Modified SQL text box Spotfire DecisionSite Administration Comment You can compare the changes that you have made in the Modified SQL to the Original SQL at all times Multiple SQL statements are allowed as long as they are separated with a semicolon and new line except the last statement in sequence Click Save Comment If you change your mind and want to start over with the original SQL click Reset to Original If you want to start over with a previously modified SQL click R
34. data source Unique identifier of the selected data source The name of the data source as you want it to appear in the Data Sources pane Type of database Choose from Oracle DB2 SQL Server MySQL SAS SHARE or ODBC For information about how to set up other types of databases please refer to the Spotfire Analytics Server Installation and Administrator s guide URL of database The format of this URL depends on the type of database Change the placeholders in the default URL so that it links to 87 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 88 No of connections Username Password User authentication Default data source Default join data source Allow writing in temporary tables New connection initialization commands Fetch size Batch size Save Copy Save Clear your selected database Min is the minimum number of users that can submit queries at any one time Max is the maximum number of users that can submit queries at any one time Additional users will be put in a queue Set both min and max to 0 for SAS SHARE ODBC and other data sources that does not support pooled connections i e there is no valid ping command Username Password Use individual user names to authenticate users when running Information Links By default this will prompt the user for credentials when running the Information Link against this data source for the first tim
35. details 4 5 6 4 Failed to Load User Profile Problems during installation and upgrade or in the interaction between Spotfire DecisionSite Client and Spotfire Analytics Server often result in Failed to load user profile The profile drives both the client user interface and the installation Packages required by the current profile are automatically installed and verified during login This error is very general and does not provide any details about what actually happened Often the detailed error message will provide enough information to track the problem but is quite difficult to interpret The recommendation is to look at the bottom of the detailed error message The message is built from the bottom up and the last line or section often provides the most valuable information for solving the problem 4 5 7 Further Reading 4 5 7 1 Further Reading For further reading see Spotfire Developer Network for a technical reference and description of the APIs that are available from the DecisionSite ApplicationManager 4 6 Changing the Unsupported Client Info When a user tries to log into Spotfire Analytics Server from a DecisionSite Client which is installed on a machine that does not comply to the minimum system requirements an error dialog is displayed 166 Spotfire DecisionSite Administration Ea x Possible problems detected Your computer does not meet the requirements for Spotfire DecisionSite 7 2 You can still l
36. domain in the Information Model 4 3 2 4 4 Editing a Column gt To edit a column 1 In the Information Model pane select the column that you want to edit 2 Click the Edit button at the top of the Information Model pane Response The column information is loaded and enabled for editing 3 Modify the desired fields Tip To move a column to a different domain select a new domain in the Information Model pane then click the lt Select button 4 Click Save to save update the column or click Save Copy to create a copy Comment Use Save Copy if you want to keep the old column definition unchanged Tip To see from which table and database a column has been taken click the column name The path to the data source appears at the bottom of the page Add gt IDNAME C1 a Remove 4 3 2 4 5 Deleting a Column gt To delete a column 1 In the Information Model pane select the column that you want to delete 2 Click the Delete button at the top of the Information Model pane Response The column is deleted from the Information Model 4 3 2 4 6 Calculating a Column gt To calculate a column 1 Start by adding a column from Data Sources 2 If you want a column to be calculated enter the expression in the Calculation field for example C1 C2 3 Use the two Show gt gt buttons to access functions for aggregating data or for creating a built in filter Enter Name and Description and choose a parent directory
37. element should contain the information of the individual pathways This must include a the pathway identifier e g pathwayid map00010 b one coordinate file containing the PathwayID and the xy box coordinates e g coordinatefile sample coord c one image file e g imagefile sample gif 31 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual d the pathway name as it will be displayed to the end users in the user interface of the tool e g pathwayname NK cell mediated cytotoxicity There may be many pathways included in each subgroup Once you have added the pathway information for the individual pathways they should show up in the pathway tree Add pathways e g KEGG to data directory Place any pathway image and pathway coordinate files that you want the end users to have access to in the following directory on the Spotfire Analytics Server e install directory gt server application data pathwayviewer data Construct an idmapping xml file Contact a person knowledgeable in the end user s data formats to assist in creating or editing the file named idmapping xml This file should contain many to many mappings of internal IDs used in the data set and PathwayIDs You can edit the enclosed idmapping xml file in the directory e install directory gt server application data pathway viewer The file needs the following structure tab separated data PathwayIDNam
38. entering C1 C2 More In the Aggregation section click Show gt gt to show the aggregation controls More In the Filter section click Show gt gt to show the filtering controls More In the last section enter the name for the new column in the Name field Comment Curly brackets are not allowed in column names In the Description field enter your own description of the column Comment The maximum limit of the description is 255 characters In the Information Model pane select a domain to save the column in and then click the lt Select button Select the data Type of the column element 4 3 2 4 3 Spotfire DecisionSite Administration Comment It is recommended that you use conversion functions for mapping columns See notes below 12 Click Set to modify the set of run time filters allowed for this column in Information Builder Comment By default all available filter types are enabled except for the Structure Search filter Structure Search filters can be added to columns of type blob integer and real Make sure that a valid structure or structure ID is included in the column prior to adding a structure search filter Comment It is not possible to combine Drillable with any of the filter devices list box check boxes or radio buttons 13 Click Save to save update the column or click Save copy to create a copy Response The column is saved in the Information Model and will receive a GUID and an icon
39. gt This is where you will add the addresses to all R servers on your company 3 For each R server that you want to add to the list specify an element as follows lt server gt lt address gt YOUR_SERVER_ADDRESS lt address gt lt server gt where YOUR_SERVER_ADDRESS should be the address to the R server e g http myRserver 4 Save the file 3 2 5 S PLUS Connector gt To configure the S PLUS connector 1 Make sure you have followed the general steps above 2 In the file compserv servers xml locate the following section lt category gt Spotfire Category CompServ PreDefined SPlusServer lt category gt This is where you will add the addresses to all S PLUS servers on your company 3 For each S PLUS server that you want to add to the list specify an element as follows lt server gt lt address gt YOUR_SERVER_ADDRESS lt address gt lt server gt where YOUR_SERVER_ADDRESS should be the address to the S PLUS server e g http mysplusserver 908 1 4 Save the file 3 2 6 Custom Connectors If you or your company have developed any type of custom connectors you should be able to specify a list of servers the same way as for the out of the box alternatives above In this case you must probably create the category element for your custom connector yourself 3 3 Configuring DecisionSite for Functional Genomics 3 3 1 DS for Functional Genomics Prerequisites Before you begin To make the full set of tools
40. in DecisionSite for Functional Genomics is called e affymetrix aadm xml Copy the affymetrix aadm xml file from 26 Configuring DecisionSite installation directory gt server application data iis application iimNaffymetrix aadmN to installation directory gt server application data iis export This allows you to perform any necessary changes to the XML file that you will use in the export directory while keeping the original XML file intact All IMs that are to be imported by the Information Designer must be placed in this directory 3 3 5 Importing the Information Model 3 3 5 1 Creating Views Note The following steps are applicable on Oracle databases only The AADM IM includes references to the AADM database and to a set of views in the AADM database instance These three views need to be created before the IM can be used The SQL code for the views is shown below Replace AADM SCHEMA in the example views with the name of your own AADM schema The views can be created either in the AADM schema or in another schema where the schema owner has amp rsquor select privileges to the AADM schema You also need to change the placeholder AADM VIEWS SCHEMA in the affymetrix aadm xml file to the schema name that you are using See amp rdquor Editing the IM XML File for more information PROTOCOL PARAMETER View CREATE OR REPLACE VIEW V PROTOCOL PARAMETER PROTOCOL ID PARAMNAMI
41. is normally no need to edit any XML files to make it work gt To import a domain 1 Place the file to be imported in the directory lt installdir gt spotfire application data iis export Comment On WebSphere web servers the path to the directory varies with the server name and may look something like this lt installdir gt installedApps lt server name gt Spotfire_DecisionSite_Analytics_Server ear application data iis export From the Select workbench drop down list select Import 3 Click Change Response The Import Workbench is displayed Enter a filename e g abase50 xml 5 Select Import mode Comment See Import Workbench for more information on the available options Note that joins cannot be overwritten 6 Select Include permissions if you want to include the permission settings for the imported elements 7 Inthe Information Model pane select the domain under which you want to store the imported domain 8 Click Select 9 Click Import Response The saved domain is added to the Information Model Note When importing elements that were exported from the 7 0 version of Information Designer or that were exported from the 6 3 version and then upgraded these will be associated with the current default data source Select a suitable default data source prior to importing such elements Permissions Setting Permissions When you have set up the Information Model with appropriate columns and filters
42. is set to at least DecisionSite Nominal Click Save This Configuration Repeat for other users or groups if applicable Explanation of the different licenses 39 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Check box in Things that the user or group will have DecisionSite access to Administrator DecisionSite for Lead Select this check box to ensure access to all possible Discovery structure providers All DecisionSite for Lead Discovery features will be available including the Chemistry Services and hence the possibility to use ISIS Host and MDL Direct as well as custom structure providers DecisionSite for Lead Select this check box to allow users to run against MDL Discovery no ISIS Host Direct or custom structure providers only All tools will be available except those that are specific to ISIS Host since this structure provider will be prohibited If both of the above check boxes are selected the user or group will have access to everything described under DecisionSite for Lead Discovery above the latter check box is ignored 3 4 13 Troubleshooting MDL Direct Connections Some of the problems that may occur when you configure a connection to MDL Direct may be detected by the Structure Analytics Diagnostics tool This tool is available in DecisionSite Client under Help Structure Analytics Diagnostics and it can be a valuable help in detecting what m
43. join in the selected domain Select this check box if you want this join to be the default one if two different joins between the same tables exist Click Save Copy to create a copy with a new GUID Click Save to save or update the join This button clears all fields without saving Column Workbench Column Workbench Overview The column workbench allows you to compose column elements It is divided into three sections 1 Column Composition 2 Filter Composition 3 Save Column 4 3 3 3 4 2 Spotfire DecisionSite Administration Column Workbench Column Composition Columns Calculation Aggregation Hide lt lt Columns Add gt SAL C1 remove avG ci G Add gt DEPTNO AC1 remove Clear T Calculation ACL Add OH SS DEPTNO Remove Edit 19 12 I Drillable Option Description 1 Add gt Select a column from Data Sources and then click this button to include in the new column 2 Remove Deletes the selected column from the composition 3 Calculation 4 Show Hide 5 Add gt 6 Remove 7 Clear 8 Add 9 Remove 10 Edit 11 Calculation 12 Drillable To calculate the column enter the expression in this text box Click this button to show hide the aggregation controls Adds the columns selected in Data Sources to the aggregation Deletes the selected column from the aggregation Removes all columns from the list of aggregation columns Adds the r
44. mechanisms e MSI Install kit e Repackaging Plug in Enabled Framework The DecisionSite ApplicationManager constitutes a framework which can be extended in terms of the software functionality it offers to the connecting DecisionSite clients This can be done through a plug in mechanism with the following characteristics e All features defined as resources e Abstract addressing of resources e Hierarchical definition of resources e General extendibility at any level of the hierarchy e Support for custom application defined resources e General mechanism for replacing and or extending existing resources Developer Support DecisionSite ApplicationManager also provides an environment and tools with which developers can e Build and test client features without server available through Spotfire Developer Network e Create and deploy extensions to a Spotfire Analytics Server via the DecisionSite ApplicationManager software distribution mechanism Configuration Parameters Install Folder Software distributed by DecisionSite ApplicationManager is silently installed to the current install folder The install folder can be configured separately for machine and user packages HKLM Software Spotfire Distribution InstallFolder String lt path gt HKCU Software Spotfire Distribution InstallFolder String lt path gt HKLM Software Spotfire Distribution PerUserInstallFolder String lt path gt By default the install folder is b
45. molname with the structure name for example amp rdquor 3 5 Dichlorobenzoic acid Name Key The column cdbregno Column with the unique numbers identifiers for Or the structure corpid names strings FROM isisrc2d mol WHERE cdbregno 12 Retrieval B When a record is marked in a DecisionSite Poster this SQL statement is executed to retrieve name of the chemical structure in MDL Chime 21 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 1 4 3 22 10 11 Click on the Save button to save the ISIS Direct connection It will appear in the list at the top of the screen You can now test the ISIS Direct connection by entering a compound ID in the field next to URL for testing configuration mysearch using compound at the top of the screen This displays a hyperlink just below the field Click on this to launch a new Internet Explorer window in which the chemical structure should appear if the connection has been set up correctly Verifying the DecisionSite Posters Installation To verify that DecisionSite Posters has been installed and is ready to use you can perform the following procedure in which you will create a new Poster publish it in the Spotfire Library and finally delete it again gt How to verify the DecisionSite Posters installation 1 2 CoS x e 10 11 12 13 14 15 16 Open an Internet Explorer brows
46. of the annotation files will be visible to the end users of the tool in a drop down list This means that the file names should be unique and make sense to the end users so that they can select the correct annotation for their current analysis For more information regarding supported annotation file formats see the chapter amp rdquor Gene Annotation File Formats in the Spotfire DecisionSite for Functional Genomics User s Manual Configuring DecisionSite for Lead Discovery DS for Lead Discovery Prerequisites Before you begin To use the Information Model for ActivityBase you must have access to e ActivityBase 4 0 4 1 or 5 0 database To use MDL Direct as a structure provider for the Structure Analytics tools you must have access to e MDL Direct 2 0 through 5 1 Molecules database Checklist e Make sure Information Services is installed and running and that you are authorized to make changes to the data sources e Log into Windows on the Spotfire Analytics Server machine using a user account that has local administrative privileges DS for Lead Discovery Overview The DecisionSite for Lead Discovery consists of the following configurable components Component Description ActivityBase IM In the ActivityBase Information Model columns filters and joins are conceptionally organized into domains For instance a set of columns may be considered relevant for a particular task and are therefore saved in the same do
47. should be available depends on the decision process at your company The default levels are Open For review and Closed 19 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 1 4 2 20 Use the Add new Edit and Remove buttons to change the available levels 14 One Decision Status level must be set as Default Do this by selecting it from the list and clicking on the Set as default button 15 Use the Move up and Move down buttons to position the Decision Status levels in the order you want The order they are positioned in the list is the same order they will appear in the Posters menu 16 Click on the Save button to make your changes take effect 17 Click on the Start button to start the Poster service Setting Up ISIS Direct Connections If you want to setup an ISIS Direct connection in order to show chemical structures in the Details on Demand window of the Poster then perform the steps below An ISIS Direct Details on Demand created in this way will be available to anyone creating a Poster If the Poster author wants to setup a certain Poster with an ISIS Direct Details on Demand he can do so and it will be displayed for anyone opening the Poster later Note A Poster author can also create various web searches for the Details on Demand window when publishing a Poster Such a web search can for instance connect to a chemical structure database other than ISIS link to an intern
48. top of the Information Model pane Response The filter is deleted from the Information Model Relational Operators The following operators can be used in filters Equal or Not Equal Less Than gt Greater Than lt Less Than or Equal To gt Greater Than or Equal To e Generally with text columns it is best to use or e Make sure that any text that appears in the statement is surrounded by single quotes OC e Tocombine multiple conditions use the AND or operators for example C1 gt 2000 AND C2 1000 Procedures Procedures Overview Database Procedures A database procedure is a set of SOL statements that can be stored in the database Once this has been done clients do not need to keep reissuing the individual statements but can refer to the database procedure instead Database procedures can be useful in many situations e When multiple client applications are written in different languages or work on different platforms but need to perform the same database operations e Some institutes like banks where security is important use database procedures for all common operations This provides a consistent and secure environment and procedures can ensure that each operation is properly logged In such a setup applications and users would not get any access to the database tables directly but can only execute specific database procedures e Database procedures can provide improved performance bec
49. work you need access to the following key pieces e Affymetrix AADM database or GCOS e Pathway map and coordinate files e Gene ontology and annotation files Checklist e Make sure Information Services is installed and running and that you are authorized to make changes to the AADM database instance e Log into Windows on the Spotfire Spotfire Analytics Server using a user account that has local administrative privileges 25 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 3 2 DS for Functional Genomics Overview The DecisionSite for Functional Genomics consists of the following configurable components Component Description AADM IM In the AADM Information Model AADM based columns filters and joins are conceptionally organized into domains After setting up the IM some information links are available and new ones can be created using Information Builder Retrieve from Database tool Affymetrix data integration After configuring this tool it is possible to retrieve both summary and analysis data directly into DecisionSite Client Configuration of this tool is normally handled during installation of the server Updates are managed using an XML file on the server Pathway Viewer Connects map information files to the data set in DecisionSite Client The Pathway Viewer tool will not work without pathway maps and coordinate files on the server Gene Onto
50. 1 Select string from the Type drop down 12 Click Save Combining ISIS and ActivityBase Data In the Data Sources pane select the structure BLOB column again The following example describes how to combine data from ISIS and ActivityBase databases It represents a typical use case where the user wants to access ActivityBase data while using structure search to filter for certain chemical structures in ISIS gt To set up an Information Link for combining ActivityBase and ISIS 1 Setup two data sources one for the ISIS database and one for the ActivityBase database Spotfire DecisionSite Administration Comment See Creating a Data Source 2 Create the following joins between the two databases Join column With column Data Data Table Column Table Column Source Source ActivityBase STUDY STDYID ActivityBase PROTSTDY STDYID ActivityBase TOCCASON TOCCID ActivityBase TOTSODRS TOCCID ActivityBase PROTSTDY PROTID ActivityBase TOCCASON PROTID ActivityBase TOTSODRS OBJDID ISIS ISISRC2D MOL CORP ID 3 Create column elements as follows Data Filter Name Table Column Source Device Study ActivityBase STUDY STDYID Protocol ActivityBase PROTSTDY PROTID Run ActivityBase TOCCASON TOCCID Plate ID ActivityBase TOTSODRS OLPTID Compund ID ActivityBase TOTSODRS OBJDID Batch ActivityBase TOTSODRS OBJDBATCHREF Result ActivityBase TOTSODRS TTORRSLTVALUE Well Row ActivityBase TOTSODRS substr TTORWELLREFERENCE 1 1 Well_
51. 4 4 3 4 4 Spotfire DecisionSite Administration As we add more observations the table grows taller but remains three columns wide While useful during data collection this format may not be appropriate for certain types of calculations or visualizations For example the entities that interest us are the different cities so we may want a representation with a single record for each city Pivoting this table produces the following note that avg Temp is the average of a single cell City avg Temp avg Temp avg Temp RE for February for May for August E London 4 16 o 7 New York 19 26 T Each city is now represented by a single record which makes this format very suitable for Spotfire DecisionSite profile charts The following steps have been performed during the pivoting e A row has been created for each unique value in City e A column has been created for each unique value in Month e A value from Temp has been entered for each cell in the resulting grid The following settings were made in the Pivot dialog to produce this result e Identity City e Category Month e Values Temp Example of Pivoting with Aggregation Note To understand this example it is recommended to read Example of Pivoting first Apart from changing format from tall skinny to short wide pivoting can be used to create a more compact table Consider the following table based on a series of temperature measurements City Month Day Temp London Fe
52. Add Licenses All interaction with the Spotfire Analytics Server depends on what licenses the users have access to The licensing is also handled in DecisionSite Administrator If you grant a product license to a user or group the functionality is automatically presented to them in the appropriate way No functionality that requires a license can be used before you unlock it Example Acme Corp has decided that sales and management use the standard DecisionSite application which only requires the default license They will also use DecisionSite Posters to communicate analysis results efficiently This tool does need a license which Tom grants them By granting this license the DecisionSite Poster functionality will appear for these users Research uses DecisionSite Posters and the DecisionSite for Functional Genomics which includes a number of useful tools when working with genes Both require a license so Tom unlocks these for the Research department group 4 1 4 Set Up the Spotfire Library The Spotfire Analytics Server from version 8 0 features a Library which provides convenient publishing of analysis data Using the Spotfire Library the users can publish and share all their analysis material The Spotfire Library is divided into Library Sections where all access permissions are set It is the Library Sections which contains the analysis material and folders The permissions apply to the entire Library Section regardless of the folder
53. Builder They can be gt High salary added to any information link just like column elements Sr Low salary but cannot be modified See Creating a new information link to find out how to include a filter element Filter type Limits Hard filters are set up as you define the information link z values al EH and are saved with the link This means that they cannot be 5 aes reused in other links Also hard filters can only specify a E range range or a list of values and so are less versatile than filter elements See Adding Hard Filters for more details Run time filters are also set up when you create an v B information link However the actual conditions are CHICAGO entered by the user only when the link is opened E DALLAS executed For each column that has been set up like this a dialog will appear allowing the user to enter threshold T NEW YORK values or select individual values See Adding Run time Filters for more details 4 4 2 5 Domains Ba St i Sie Domains are containers similar to file folders that are used to organize CH information links and other elements such as filters and columns The A domain structure is independent of the physical location of data d E Domains are created by the administrator using Information Designer 4 4 2 6 Procedures Database Procedures in Information Services Using Information Designer and Information Builder you select pre made database procedu
54. Column ActivityBase TOTSODRS substr TTORWELLREFERENCE 2 2 Completion Date ActivityBase TOCCASON TOCCDATEACTUALCOMP ctab ISIS ISISRC2D MOL CTAB pce Search 4 Launch Information Builder 5 Create an information link using all the columns in 3 6 Forthe columns Study Protocol Run and Plate ID enable run time filtering by selecting a suitable prompt method Comment See the help file for Information Builder for more information This is reached by launching the tool and clicking Help 7 For the column ctab select prompt method Structure Search 8 Click Open to execute the query 4 3 5 Troubleshooting 4 3 5 1 Troubleshooting Please note To run Information Designer you need DecisionSite Client installed on the same machine 115 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 6 4 3 6 1 116 If you get error messages from Microsoft Internet Explorer IE when trying to run Information Designer you should check your security settings You must allow ActiveX controls to run All ActiveX controls in Information Designer are signed and safe to run gt To enable ActiveX controls 1 Launch Information Designer 2 Inthe bottom right hand corner of the IE window containing Information Designer check the web zone for example Local intranet In IE click Tools gt Internet Options and go to the Security tab Select the web zone of Information Designer for example Local intranet C
55. DSCEL COLLECTION ID AND DSCHP ANALYSIS ID ACEL ID AND ACHP DATA SET COLLECTION ID DSCHP COLLECTION ID ANALYSIS TYPE View CREATE OR REPLACE VIEW V ANALYSIS TYPE ID TYPE AS SELEC DISTINCT ANALYSIS ID ID STAT TYPE FRO AADM SCHEMA ABS GENE EXPR RES STAT UNIO SELECT U EMP TYPE FRO ADM SCHEMA ABS GENE ISTINCT ANALYSIS ID ID EXPR RESULT Editing the IM XML File Before importing the IM you must make sure that you have edited the affymetrix aadm xml file to point to your current AADM schema and to the schema where you created the views The following references should be changed in the affymetrix aadm xml file schema AADM VI to schema YOUR AA and schema AADM SC to schema YOUR AA EWS SCHEMA H D Schema VIEWS SCH EMA lt schema gt EMA lt schema gt SCHEMA lt schema gt where YOUR_AADM_VIEWS_SCHEMA is the schema where you created the views and YOUR AADM SCHEMA is the name of the AADM schema used at your company Importing the IM Import the Information Model using the Information Designer Configuring DecisionSite Import Help Filename affymetrix aadm xml Import mode Replace all Add overwrite conflicting elements C Add keep conflicting elements Include z permissions Parent domain x Select Import Clear Once the Model is imported you
56. Data source 1SIS_DIRECT C Pre Updates SQL Post Updates M Synchronized scrolling Modified SQL Original SQL SELECT SELECT I1 CDBREGNO AS Cdbregno I1 CDBREGNO AS Cdbregno TZ A uditmodifiedtime AS A T2 uditmodifiedtime AS A FROM FROM ISIS ISISRC2D ACTIVITY I ISIS ISISRC2D ACTIVITY I TEMPORARY RESULT i T2 TEMPORARY RESULT 1 T2 WHERE WHERE I1 CDBREGNO TZ ACTION I1 CDBREGNO T2 ACTION ls fe e43f4900 4bdc 11d7 26fd 0010ac110132 My Information Link Parent domain user Annica Information Links Save Option Description Data source Displays the data sources used by the current information link in a Pre Updates SQL Post Updates Synchronized scrolling Modified SQL Original SQL Reset to Saved Reset to Original GUID Name Parent domain Save Spotfire DecisionSite Administration drop down list You can only edit the SQL of one data source at the time Click this radio button to enter statements to be executed before the data retrieval For example this could be a call to a stored procedure or statements such as CREATE TABLE or INSERT Click this radio button to display and modify the SQL of the information link Click this radio button to be able to enter statements to be executed after the data retrieval For example DROP TABLE Select this check box to simultaneously scroll both the Modified SQL and the Original SQL text box
57. Deployment and Administration Manual 4 3 2 4 9 2 72 Click the topmost Add button 3 Inthe Calculation field type AVG C1 Comment AVG is the average function Click Show gt gt to show the aggregation controls St om Select the column to aggregate over from Data Sources 6 Click Add gt Response AC1 will appear in the Aggregation Calculation field You can use this field to modify the chosen column using mathematical expressions 7 Click the Add button on the right hand side of the Calculation field Enter Name Description and Domain 9 Click Save Response The resulting column will consist of the average of the value column for each value in the aggregation column Ge Tip Rather than hard coding the columns to aggregate over you may consider marking the column as Drillable The column will then be aggregated over any other columns retrieved in the same information link Note When a query is executed aggregation is always applied before a column filter Aggregating Over Many Columns There may be situations where it is necessary to use more than one aggregation column In the following table for example we can compare the salary of each employee with the average salary of employees at the same department and job SCOTT ANALYST RESEARCH 3000 3000 FORD ANALYST RESEARCH 3000 3000 MILLER CLERK ACCOUNTING 1300 1300 SMITH CLERK RESEARCH 800 950 ADAMS CLERK RESEARCH 1100 950 JAMES CLERK SALES
58. Description Select a Parent domain Select real from the Type drop down Click Save por e A 4 3 4 11 2 Creating a Molecular Formula Column Databases with the ISIS Direct Cartridge allow you to use C2H4 ISIS Direct operators to extract information from a BLOB C2 H5N 02 column that contains binary chemical structures The molfmla C3H3N 0 operator returns the molecular formula of a structure In the C2H50T example below we also use the operator fmla like to limit C2H50 Na the results to compounds with a specific number of carbon C2H402 and hydrogen atoms 113 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 4 11 3 114 gt To create a molecular formula column Column Element Help Columns Add gt Remove Calculation molfmla C1 Aggregation Show gt gt Filter Hide lt lt Columns Add gt Remove Condition fmla_like FC1 C 1 3 H 1 5 1 e 1 From the Select workbench drop down list select Column and click Change 2 Inthe Data Sources pane select the structure BLOB column In this example it has the name CTAB 3 Click Add gt In the Calculation field enter molfmla C1 Expand the filter section by clicking Show gt gt Click Add in the Filter section In the Condition field enter Oe Ed fmla like FC1 C 1 3 H 1 5 1 9 Enter Name and Description 10 Select a Parent domain 1
59. E o rei EU ERU ERU 137 146 CONVERSION 202 aget ib oet cepe eI eit E dE 68 Creating ell CG 68 dotrialris rere de ai ea 63 PIERS occ rn tec bo e iet 74 information link tete 121 JOINS d stone cei eec nde des 64 multiple col miis REESEN SEET 69 D Data Conditioning dialogi mee Eee 155 el lee GE 137 de 137 Data sources el TEE 60 details on data sources and Ms 107 modifying uero rei 61 e ET 60 removing ce adis BERE ee 61 serinterface ere eee dee 83 Database Proced res ceteri 75 Databases connecting e EE 60 Creating zelo ets IU TIBERI MEE 60 Dates parse methods ceres using in hard filters DecisionSite deploying ie tee eet tette es 54 DecisidnSite level cei iii ceo eH 48 Definitions fundamental concepts cecceeseesessteesseesseesseeeenes 119 glossary te o CR e s 157 Deleting pel PL 70 elen UC 63 filters nuire ert e d a td 75 JAKOL aA tpe OCHO 51 information links eeeseeeeeeeenennennennnn 122 nre RE 66 IrcR M n 49 Deployment deploying NOW tO orte iy Ete Intt 54 deployment pane eu 58 Dialog data conditioning ssseeesssessseresserssersssrrerrssrenserenes 155 get values from data set cccecsecsseesssessessteeeseeees 154 OU 146 save information link eeeennn 144 146 set filter for column view SQL and edit oracle hints 144 RI ol Le eei ee e regi p 137
60. E ACTIVITYBASE 40 E ActivityBase Information Links aiL QC Markers e BC Markers by Completion Date cip QC Markers by Compound ID oiL QC Markers by Plate ID aiL Test Occasions e Test Occasions by Completion Date aiL Test Occasions by Compound ID aiL Test Occasions by Plate ID aiL Test Request aiL Test Request by Completion Date aiL Test Request by Compound ID aiL Test Request by Plate ID ActivityBase Query Elements Filters QC_Results Test_Occasion Test_Request j Protocolloin PROTSTDY TOCCASON PROTID E Protocolloinm PROTSTDY TREGTSET PROTID E Protocolloim PROTSTDY TSETCSRS PROTID E Runloin TOCCASON TOTSODRS TOCCID Sea Runloin TREGTSET TOTSODRS TRTSID Studyoin STUDY PROTSTDY STDYID ActivityBase 4 0 Information Model ll ZS After importing the 4 1 Model you should see the following Information Links and Query Elements in the Information Designer 35 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual CJ amp CTVITYBASE 41 Information Links diL Results Information Link QC Markers diL Results Information Link Test Occasion e Results Information Link Test Request Query Elements Filters QC Results Test ccasion Test Request prpmno PROTPARM TOTSODRS ode TEST TREQTSET ttordimo TEST TOCCASON ttordimo TEST TOTSODRS ttordimo TEST TSETCSRS ttordimo TSETSCRS TREQSET KREE ActivityBase 4 1 Information Model After import
61. Edit Displaying SQL Statements for an Information Link Sometimes it may be of interest to view the SQL statements generated for an information link gt To view the SQL behind an information link 1 Make sure the information link or columns of interest are added to the Information Link pane by clicking Edit Link or Add to Link respectively after selecting the elements 2 Click on the sal button in the toolbar of Information Builder Response The View SQL and Edit Oracle Hints dialog is displayed 3 Look at the generated SQL in the text field Click OK when finished Comment If several Data Sources are used the SQL statements for the different sources are separated by lines Comment Click Copy SQL to copy the information in the text field to the clipboard Editing Oracle Hints If you are working against an Oracle database that rarely updates its statistics or if you are querying operational databases with complex schemas adding one or more Oracle hints to the information link can improve the overall performance of the information link 127 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Oracle hints are comments included in an SQL statement that are used in the choosing of execution plan for the statement If you have detailed information about your data that a certain index is more selective for certain queries for example including hints to the information link can result in
62. IEEE sequential aep ede what are vis Information Mode details on data sources and IMs pop up menu user interface Information Services uge telle el WEE 118 Install DecisionSite Deployment pane sssesssssssssessersssrresreeee 58 deploying se ic tete etes 54 ISIS adding a structure search Tlter 126 filtering using structure search 135 ISIS Dit amp ct i ooh een eee 61 Issues when Creating an ISIS Direct Data Source 87 J Join Path sie css er eterne ERO IRE 128 Joins Creatingsais cte HR Ste EP 64 ETag ugeet ewig 64 Gel nge 66 editis RR UR EEN 66 freehand ice e erae 65 join Dathisx i irre een enn eene 128 Self JOITi 5i ae Aenea ean SNe a eS 61 66 user interface eie iiit ee Eater iet 89 Where tO StOre entre rnin oa iei 102 L Lead DISCOVOry s sese et HERR teresa sais hates 33 EE 48 Limiting number of record 105 Limits adding hard filters ode aded 122 adding run time filters eese 123 filters description of 120 uito set limits i iuto cete tercii 143 LINKS i rne e EE ERIS ER 64 Log files changing log configuration file 53 logging pane 255 eed oibus 57 viewing log les 52 176 M Microarray Analysis eese 41 Modifying information links essen 121 Molecular formula 2 n be e RU 113 Molecular weight 113 Multiple Columns el TE 69 user interface see lapiel iet e lernen 94 N Name changing group names naming sch tme
63. It would not have been possible to produce the table above using the Drillable option If the Average Salary column element had been drillable it would have appeared identical to the Salary column Using Drillable When creating an aggregated column it is possible to specify aggregate keys the columns over which to aggregate This is done from the Column Element workbench under Aggregation It is also possible to ignore the aggregation settings altogether by selecting the Drillable check box This way the column will be aggregated over all other columns being retrieved in the same information link The following table illustrates this Average Salary Drillable is calculated using the AVG function No aggregate keys have been specified and instead the Drillable check box has been selected ANALYST 3000 CLERK 1037 5 MANAGER 2758 33333333333 PRESIDENT 5000 SALESMAN 1400 As we see above the average salary is computed for each value in Job We could just as well have defined a salary column explicitly aggregated over Job However by using the Drillable option we can now retrieve a different set of columns and still get a useful answer ANALYST RESEARCH 3000 CLERK ACCOUNTING 1300 CLERK RESEARCH 950 CLERK SALES 950 MANAGER ACCOUNTING 2450 MANAGER RESEARCH 2975 MANAGER SALES 2850 PRESIDENT ACCOUNTING 5000 SALESMAN SALES 1400 Note It is not possible to combine Drillable with any of the filter devices list box check boxes or radio bu
64. Log on as service privilegie Leave both fields empty to execute under the Local System account Enter AUserName to use a local user User Domain User Name Password Installshield lt Back Cancel The user must also have amp rdquor Full Control permission to the installation target folder The default option is to leave both fields empty which will run the service under the amp rdquor Local System account which always has the needed privilege On some systems you may need to make sure that the corresponding user amp rdquor System has Full Control permission to the installation target folder If you wish to specify another user the username should be preceded by the Domain it belongs to lt domain gt lt username gt If the user is a local user the user name must be preceded by a dot and a backslash lt username gt Note If you intend to use HTTPS with Client Certificates do not use the Local System account Instead specify a user name and password of the user who s client certificate should be used for the communication between Visualization Services and the Spotfire Analytics Server Click Next to continue 15 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 12 Select whether to do a Complete or Custom install and click Next ie isualization Services InstallShield Wizard Setup Type Choose the setup type that best suits your needs
65. M Xmx256M Duser language en Duser country US Save the file Open the file lt server install dir gt bin service bat Edit the following line so that it specifies the language and country you want EXECUTABLE US SERVICE_NAME JvmOptions Djava io tmpdir CATALINA_BASE temp JvmMs 256 JvmMx 256 XX DisableExplicitGC Duser language en Duser country US Save the file and restart the Tomcat server Configuring DecisionSite Posters for the First Time Configuring Poster Settings gt To configure Posters 1 2 Open an Internet Explorer browser Enter the name of your Spotfire Analytics Server in the Address field Example http spotfireanalyticsserver Note The URL you enter will be the actual URL Visualization Services will use to communicate with the Spotfire Analytics Server Do not use amp rdquor localhost always specify a full server URL Response The Spotfire Analytics Server start page is opened Click on Library Administrator and log in with your DecisionSite administrator username password 4 10 11 12 13 Configuring DecisionSite From the Select workbench drop down menu select Poster Options OSpotfire age Select workbench Poster Options DecisionSite Administrator DecisionSite Library Poster Options th Visualization Services Connection This is required to allow the DecisionSite Analytics Server to connect to Spotfire Visualization Services which p
66. NOT LIMITED TO ANY RELEASE NOTES AND READ ME FILES TIBCO Spotfire DecisionSite is covered by U S Patent No 6 014 661 and U S Patent No 7 216 116 Other patent s pending TIBCO Software Inc Confidential Information Table Of Contents Table of Contents 1 DEPLOYING DECISIONSITE FOR THE FIRST TIME 1 Deployment Procedure uoo e EE Alte iene teen 1 Updating the PDF Manuals on the Gerver eters ee eineeeeeeieeeeetieeeeetiieeeeesieeeeeeeneeeee 1 Unlocking Administrator Privileges A 1 Deploying Software Packages iii atre EE dee led ei ied aden 2 Spotfire LIDA EE 3 Configuring Additional Functionality sssseee eem emnes 7 UPGRADING DECISIONSITE eire rete pirRbxea derer lotus biet bes pedi E inis 8 Upgrading Procedure uen tne tera taire ano eder onere 8 Updating the PDF Manuals on the Gerver ene nennen 8 Deploying Software Packages dnce Paediatric dede 8 Configuring Additional Functionality sssseeeeeeenm emm emm nennen 8 CONFIGURING DECISIONSITE 6c eccc e ecce e esee e cese ce e cese ecce eie ecce ccce eee cese 10 DecisionSite POSIGrS nocet eter es et ird eet ia eei aeree ert T epe cu de 10 Configuring Computation Services m nennen nemen enne nnns 23 Configuring DecisionSite for Functional Genomics eee 25 Configuring DecisionSite for Lead Discovery sssssse enne emere 33 Configuring DecisionSite for Micro
67. O NOT AGREE WITH THE TERMS AND CONDITIONS SET FORTH BELOW YOU SHOULD PROMPTLY RETURN THE SOFTWARE PACKAGE UNOPENED OR DISCONTINUE THE INSTALLATION AND USE THE TERM Customer BELOW REFERS TO YOUR COMPANY ITS OFFICERS E nTnhromnonc Act AMD CUNT car AMD repens Iaccept the terms in the license agreement C Ido not accept the terms in the license agreement Installshield lt Back Cancel 10 Enter the port number on which Visualization Services should listen This is the port Visualization Services will use to communicate with the Spotfire Analytics Server Make sure the port number you specify is not already used by some other application ie isualization Services InstallShield Wizard Visualization Services Enter the port number Enter the port number on which Visualization Services should listen Port 12000 Installshield lt Back Cancel It can be any unused port from 1 65535 Default is 12000 Click Next to continue 14 Configuring DecisionSite 11 Enter the user name and password to be used for running the Windows service This user must have the amp rdquor Log on as service privilege InstallShield Wizard fe isualization Services Visualization Services Enter the user name and password Enter the user name and password to be used when executing Visualization Services Contact your system administrator to make sure that this user has the
68. Please select a setup type Complete All program features will be installed Requires the most disk space C Custom Choose which program Features you want installed and where they will be installed Recommended for advanced users InstallShield Custom will let you specify the folder where you want to install Visualization Services where as Complete will install it in the predefined folder C Program Files Spotfire VisualizationServices Apart from that the two options are the same 13 Click Install to begin the installation jp Visualization Services InstallShield Wizard Ready to Install the Program The wizard is ready to begin installation Click Install to begin the installation If you want to review or change any of your installation settings click Back Click Cancel to exit the wizard Installshield 16 Configuring DecisionSite 14 Visualization Services is installed InstallShield Wizard iz isualization Services Installing isualization Services The program features you selected are being installed Please wait while the InstallShield Wizard installs Visualization Services This may take several minutes Status InstallShield Back Next gt Visualization Services a Windows service is automatically started after the installation is complete 15 The installation is complete and Visualization Services is started ie isualization Servic
69. TIBCO Spotfire DecisionSite 9 1 1 Deployment and Administration Manual D TIBCO The Power of Now Important Information SOME TIBCO SOFTWARE EMBEDS OR BUNDLES OTHER TIBCO SOFTWARE USE OF SUCH EMBEDDED OR BUNDLED TIBCO SOFTWARE IS SOLELY TO ENABLE THE FUNCTIONALITY OR PROVIDE LIMITED ADD ON FUNCTIONALITY OF THE LICENSED TIBCO SOFTWARE THE EMBEDDED OR BUNDLED SOFTWARE IS NOT LICENSED TO BE USED OR ACCESSED BY ANY OTHER TIBCO SOFTWARE OR FOR ANY OTHER PURPOSE USE OF TIBCO SOFTWARE AND THIS DOCUMENT IS SUBJECT TO THE TERMS AND CONDITIONS OF A LICENSE AGREEMENT FOUND IN EITHER A SEPARATELY EXECUTED SOFTWARE LICENSE AGREEMENT OR IF THERE IS NO SUCH SEPARATE AGREEMENT THE CLICKWRAP END USER LICENSE AGREEMENT WHICH IS DISPLAYED DURING DOWNLOAD OR INSTALLATION OF THE SOFTWARE AND WHICH IS DUPLICATED IN TIBCO BUSINESSWORKS CONCEPTS USE OF THIS DOCUMENT IS SUBJECT TO THOSE TERMS AND CONDITIONS AND YOUR USE HEREOF SHALL CONSTITUTE ACCEPTANCE OF AND AN AGREEMENT TO BE BOUND BY THE SAME This product includes software licensed under the Common Public License The source code for such software licensed under the Common Public License is available upon request to TIBCO and additionally may be obtained from http wtl sourceforge net This document contains confidential information that is subject to U S and international copyright laws and treaties No part of this document may be reproduced in any form without the written authorizati
70. To create a configuration file 1 Use Explorer or another file browser to browse to the directory on the server called install directory gt server application data chemistry framework Copy the file template mdl direct xml and name the new copy mdl direct xml Open the mdl direct xml file in your favorite editor 4 Change the name title description and tooltip tags to display suitable information E Comment The name must be unique for each connection It is used by the Structures in Table tool The title is what the end users will see as an option in the drop down list of the Structure Connection dialog The description is also shown to the end users in this dialog and should contain more information about the selected connection The 38 Configuring DecisionSite ToolTip is shown when an end user is hovering with the mouse pointer over the database connection link in Structure Viewer If no ToolTip has been specified the description is used instead 5 Now you need to add the guid for each column element that should be used by the Structure Analytics tools to suitable positions in this file Comment The guids can be obtained from the Information Model tree view in Information Designer Right click on the desired element in the tree view select Copy Guid from the pop up menu and paste the guid in the mdl direct xml file Example Tag in configuration file Element in Information Model
71. a complete join path between the tables 130 CT x d E Available Joins G Join Path Selected Joins TB1 joined TB2 demo Baseball Film larstest Pharma Sales WindSit S TB2 joined TB4 TB3 joined TB4 Add EI b3 Help If you want to make sure the second join is always used in the join path even if the default join is changed you must move it to the Selected Joins list Select the join from the Additional Default Joins list Database Marketing Add to selected joins Spotfire DecisionSite Administration Details TB1 joined TB2 Join condition oracle 1 SPOTUSER IM BASEBALL NAME oracle 1 SPOTUSER IM FILM ACTOR onal Default Joins TB2 joined TB4 Je Update continuously OK Cancel Note Even if you do not move the second join to the Selected Joins list the join path is still complete The information link will then always use the Selected Join and then form a complete join path using the default joins which may have been changed later on from Information Designer Click on the lt arrow button to move the join to the Selected Joins list 131 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 3 3 4 4 3 3 1 4 4 3 3 2 132 6 Response The join path is complete and will always use the selected joins 7 Join Path Select
72. ackage registration The tool can be obtained from Spotfire Support The tool will clean up any corrupted package and COM registration The tool can also be run in diagnostic mode to check for problems See tool documentation for details Support Pages Each installation of Spotfire Analytics Server provides a set of support tools available via Microsoft Internet Explorer The Support Pages are located at http lt server gt spotfire support The Support Pages offer the following functionality e List all installed packages Usage To see what is actually installed e Uninstall all packages Usage To forcefully uninstall packages e Repair installation Usage To repair broken COM and package registrations 4 5 5 3 4 5 5 4 4 5 5 5 4 5 6 4 5 6 1 4 5 6 2 Spotfire DecisionSite Administration e Install Application Manager and other packages Usage To administratively bootstrap DecisionSite on a machine The Support Pages can be used for diagnostics and problem solving The Support Pages rely on some ActiveX components that will be installed automatically when needed The user must have sufficient privileges to install ActiveX components to use the Support Pages Client Logging The Application Manager has support for client side logging The logging is disabled by default Logging can be enabled through the registry HKLM HKCU Software Spotfire eApplication Log String path When enabled the client log will grow indefinitel
73. adding a structure search filter Displays the filter devices that are enabled for the column This means that the selected devices will be presented as prompting type options when defining a prompted information link in Information Builder Adds the selected device to the list of selected devices Removes the selected device from the list of selected devices gt To reach the Set Filter Devices for Column Element dialog 1 Select the Column workbench and create a new column element or edit an existing column element from the Information Model 2 Click on Set 93 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 5 94 Multiple Columns Workbench Add gt Remove LE Remove Al Column elements Column element properties Name Accountno Balance Empno Ename Data type real Sal Source name BALANCE Description SCOTT ACCOUNT BALANCE foply Changes Parent domain Scott Select Option Add gt lt Remove Remove All Name Data type Source name Description Apply Changes Save Clear Description Select one or more tables or columns from Data Sources and then click this button to include the columns as new column elements Whole databases or schemas cannot be added To select more than one column press Ctrl and click on the desired columns in the Data Sources pane before clicking Add Del
74. ager works and is intended for administrators who whish to learn more about the inner workings of the DecisionSite environment The DecisionSite ApplicationManager provides functionality and service for configuration versioning and delivery of DecisionSite guided analytic applications from server to client DecisionSite ApplicationManager has a client server architecture and thus has both DecisionSite Client and Server components It provides powerful functionality for delivering and upgrading applications with new functionality in the DecisionSite Client end user environment DecisionSite Application Delivery and Update The DecisionSite ApplicationManager delivers new and or updated functionality to DecisionSite Client in the form of tools guides and applications when the user logs in Upon first login after a fresh installation of DecisionSite Client all tools guides and applications that 4 5 1 3 4 5 1 4 4 5 2 4 5 2 1 4 5 2 2 4 5 2 3 Spotfire DecisionSite Administration the user is licensed to are delivered to the client The licensed tools guides and applications are specified in a user profile that is delivered to the client If the user profile changes such that additional tools guides and or applications are assigned to the user the new applications and its components are delivered at the next login If an application has been extended to contain a new tool or guide all end users with access to that application will a
75. ailable Joins list Note Use right click and Refresh to update only the selected element Displays the View SQL and Edit Oracle Hints dialog Lists the available joins that can be added to the information link Displays details about the SQL for the currently selected join in the Available Joins list Adds the selected join from the Available Joins list to the Selected Joins list Lists the joins that will always be used in the join path between the tables in the information link Moves a join up or down in the list This is used to control the order the joins are performed when the information link is executed Joins higher up in the list have higher priority The order of the joins may improve Spotfire DecisionSite Administration performance of the information link Ex Removes the selected join from the Selected Joins list D Moves the selected join from the Additional Default Joins list to the Selected Joins list so that it will always be used in the information link Additional Lists the additional default joins that are used to complete the join path of Default Joins the tables in the information link This list is updated and based on the joins that has been selected so far Update When selected this option continuously updates the Additional Default continuously Joins list with appropriate joins However since this might be time consuming on some systems there is an option to turn it off gt To reach the Join Pa
76. al rock sample database or to a general search engine such as Google gt To set up ISIS Direct connections 1 From the Select workbench drop down menu select ISIS Direct Configuration 2 Click on the Change button Spotfire Select workbench ISIS Direct Configuration DecisionSite Administrator DecisionSite Library Poster ISIS Settin Ni The end Defined ISIS Direct connecti ISIS String ID Remove URL for testing configuration ISIS Web Search using compound id 100 spotfire ws servlet protected isis cmd qget amp dbid isis connection amp molid 100 Connection configuration ISIS table names Connection name SIS arch Main table Connection description Structure table Structure column Oracle server Structure key column Oracle port Oracle SID sisd Name table Oracle user name isis Name column Un Oracle password Name key column name cdbreano Number of connections Connection initialization e substituted with the current main table You can create one or more ISIS Direct connections Each one will appear in the topmost list after you have created and saved it 3 Click on the New button This clears all fields and lets you enter parameters for a new connection 4 Entera Connection name This is the name that will be seen by the end users when they wish to create a Poster with an ISIS Direct connection 5 Optionally enter a Connection description explaining more details about t
77. alog will use lt h2 gt Please log into Spotfire DecisionSite lt h2 gt 4 5 3 8 Announcing Peers Spotfire Analytics Server has support for announcing other Spotfire Analytics Servers AII announced servers are listed in the Login dialog Servers are announced by adding a peers section to the manifest stored in e WebLogic installation directory gt spotfire spotfire WEB INF manifest xml e WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war WEB INF manifest xml See example below for details lt manifest gt lt peers gt lt server gt lt title gt My Other Spotfire Analytics Server lt title gt lt address gt http hostname spotfire manifest lt address gt lt server gt lt server gt 162 lt server gt lt peers gt lt manifest gt Support Policy Spotfire DecisionSite Administration Starting with DecisionSite v7 2 the client server protocol includes features for implementing a support policy Spotfire use this technology to prevent usage of DecisionSite on Microsoft Windows platforms that are no longer supported The current server side implementation is split up into three parts e Detection script embedded in WebLogic installation directory gt spotfire spotfire WEB INF manifest xml WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war WEB INF manife
78. ame instance of Visualization Services Requirements for the Spotfire Analytics Server The requirements which must be met in order to run Spotfire DecisionSite Posters can be found at http www spotfire com sr e It is recommended that Oracle not be running on the machine running Visualization Services since both applications are memory intensive which might affect performance e Ifyou intend to use the ISIS Details on Demand it requires ISIS Direct 2 0 or MDL ISIS 5 0 Client requirements The requirements which must be met in order to use Spotfire DecisionSite Posters on a client machine can be found at http www spotfire com sr Note that amp rdquor MDL Chime Pro 2 6 SP5 for Web must be installed on the client if you intend to view ISIS structures in the Details on Demand window in DecisionSite Posters 10 Configuring DecisionSite 3 1 1 3 Communication The Spotfire Analytics Server and Visualization Services uses standard HTTP for communication The port used is configured when installing Visualization Services 3 1 2 Installing Visualization Services gt Installing Visualization Services 1 Log into the Windows server as a user with Admin privileges 2 Copy the file setup exe for Visualization Services to the local disk of the intended server 3 Run the setup exe file Response The installer starts InstallShield Wizard Preparing to Install Spotfire Visualization Services Setu
79. anuals from the Spotfire DecisionSite Client you must copy these manuals to the server gt To copy the Spotfire DecisionSite manuals 1 From the documentation folder on the Spotfire DecisionSite deployment kit copy all the PDF manuals and the file called manuals jsp 2 Paste these into the following folder on the Spotfire Analytics Server machine lt installation directory gt server webapps spotfire support manuals 1 3 Unlocking Administrator Privileges gt To define an Admin user and unlock administrator privileges for that user 1 You will need the unlock codes provided in the documentation folder of the deployment kit in the file codes txt Open this file and print it for future reference Open an Internet Explorer browser 3 Enter the name of your Spotfire Analytics Server in the Address field Response This opens the Spotfire Spotfire Analytics Server start page TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual E Spotfire DecisionSite Microsoft Internet Explorer E lO xj File Edit View Favorites Tools Help EI Back gt O A A Asearch XjFavortes media C4 B 5 38 Links pvoForun Address fa http ganetdev spotfire spotnet htm zl Go Spotfire DecisionSite Librar Browse search and manage items published to DecisionSite Library Support pages Verify packages downloaded to this client Check system requirements Administration De
80. any However depending on which person from the sales department accesses an analysis using this information link only the sales figures pertaining to the region that sales person is assigned to should be retrieved For example if a sales person is working in the East region she should only be allowed to see sales figures made in that region by any person The Spotfire Administrator has created groups on the Spotfire Analytics Server named SalesForce East SalesForce West SalesForce South and SalesForce North Each sales person is a member of one or more of these Note You can also create a Lookup table just as in the first example in which you assign various users or groups to categories that match your Sales table That way you do not need to create superfluous groups on the Spotfire Analytics Server if groups with matching names are not already available You then take a look at the Sales table containing the total sales of every person in the sales force Order ID Employee Region Product Sale ID 1 101 SalesForce Cornflakes 100 East 2 150 SalesForce Soda 550 103 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 4 5 West 3 244 SalesForce Cornflakes 160 North 4 101 SalesForce Mineral Water 400 East 5 101 SalesForce Soda 120 East 6 339 SalesForce Mineral Water 200 East Next you add an Information Servi
81. appears click Get Values or Get Range 4 4 4 5 8 Data Conditioning Dialog A batacondtionng Conditioning type Help OK Cancel Configure Option Description Conditioning type None No conditioning Pivot Allows you to transform your data from a tall skinny format to a short wide format by rotating row and column headings around the core data Select which columns to work on by clicking Configure Distinct Removes all duplicate records records where all fields are identical from the returned data set Configure Opens the Pivot dialog gt To reach the Data Conditioning dialog Click Edit in the Information Link pane 155 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 4 5 9 156 Join Path dialog x d sql Available Joins Details El demo 5 TB1 joined TB2 Baseball 5 d Database Marketing pe ae Film SPOTUSER_IIM larstest BASEBALL Pharma Sales hire windSit Oracle Le ei ined TU SPOTUSER_IIM m T81 joined TB2 FILM TB1 joined TBS ACTOR TB2 joined TB4 TB3 joined TB4 Add Join Path Selected Joins TB1 joined TB2 Additional Default Joins TB2 joined TB4 C X I Update continuously Help DK Cancel Option kJ sal Available Joins Details Add Selected Joins ERI Description Refreshes the entire tree structure in the Av
82. ard gt To reach the View SQL and Edit Oracle Hints dialog 1 Make sure the information link or interesting columns are added to the Information Link pane by clicking Edit Link or Add to Link after selecting elements 2 Click on the 8 button in the toolbar of Information Builder 4 4 4 5 3 Edit Oracle Hints Dialog Edit Oracle Hints Enter Oracle hints of ActivityB FIRST_ROWS Help OK Cancel 145 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 4 5 4 146 Enter the Oracle hints that you wish to add to the SQL statement separated by a space and will be automatically added to the entered hints Note In some cases adding a hint can actually decrease the performance of an information link If this is the case click Edit Oracle Hints and remove the hint gt To reach the Edit Oracle Hints dialog Click Edit Oracle Hints next to the data source of interest in the View SQL and Edit Oracle Hints dialog Pivot Dialog LI NENNEN 00 Identity Identify records by the columns Name Type Age group Customer age First buy Electronics real real datetime real z r Category Age group Customer age T First buy I Electronics Create a new column for each value in real real datetime real sl Values Use values in Name Computation Type Age group C
83. array Analysis sseeeeeeen emen 41 SPOTFIRE DECISIONSITE ADMINISTRATION eeeeeeeeenennnn 43 Setting Up the Environment aririk e tiat ee de e dpt etaed n ur e dpt tad d 43 DecisionSite Administrator EE 47 DecisionSite Information Designer 59 DecisionSite Information Builder sssseeeee enne 118 DecisionSite Appltcatonkanager eene nennen rne 158 Changing the Unsupported Client Info 166 Changing the Remember Me Time 167 Spotfire Support Pages for Packages eene n nnne 167 Connecting to Spotfire Analytics Server menm enn 168 Listing Which Users Have Access to a Certain Application ssssssssssesee 170 INDEX e S 174 Deploying DecisionSite for the First Time 1 Deploying DecisionSite for the First Time 1 1 Deployment Procedure This chapter explains how to deploy and set up TIBCO Spotfire DecisionSite on a Spotfire Analytics Server for the first time It is required that you have already installed and configured the Spotfire Analytics Server itself If you already have a version of Spotfire DecisionSite on the server and which to deploy a later version of DecisionSite then please follow the instructions in chapter 2 Upgrading DecisionSite instead 1 2 Updating the PDF Manuals on the Server In order for the end users to get access to the Spotfire DecisionSite manuals when they select Help gt PDF M
84. ased on folder settings for the operating system Machine SPROGRAMFILES Spotfire Packages User SUSERPROFILE S Local Settings Application Data Spotfire Packages Spotfire DecisionSite Administration 4 5 3 2 Install Mode The DecisionSite ApplicationManager can install packages per machine and per user Per user installation is not supported for Microsoft Windows NT 4 The effective install mode is determined based on system capabilities user privileges and local settings The default install mode has been changed over time e DecisionSite v7 1 1 and earlier Prefer per user installation e DecisionSite v7 2 and above Prefer per machine installation Some settings to control the install mode were introduced for DecisionSite v7 1 1 HKLM Software Spotfire Distribution AllowPerUserInstall DWORD 0 1 HKLM Software Spotfire Distribution PreferredInstallMode String User Machine 4 5 3 3 Roaming Profiles Microsoft Windows roaming profiles are supported for DecisionSite 7 2 and above Due to compatibility issues with previous versions this support must be enabled manually Please contact Spotfire Support for current information and assistance on using roaming profiles 4 5 3 4 Server Addresses The Spotfire DecisionSite Client is associated with a home server Choosing a different server in the Login dialog changes the current home server At initial start up after installation there is no home server Instead the
85. ata file this is the data that is opened up in DecisionSite Client and will be linked to the pathway maps All files involved in the configuration of the tool should be placed in the following directory on the Spotfire Analytics Server install directory gt server application data pathwayviewer 3 3 8 3 Configuring the Pathway Viewer When the tool is shipped in DecisionSite for Functional Genomics there is no pathway information installed on the server except for a limited example configuration Real pathway information must be added as part of the product configuration gt The following items must be configured e Configure the pathway settings xml file e Add pathway image maps and coordinate files to the data directory on the server e Construct an idmapping xml file based on the end user s data format Configure the pathway settings xml file This is the example pathway settings xml file Xpathway settings admin true gt maingroups name Cancer gt subgroups name Immunity lt pathway pathwayid map00010 filedir coordinatefile sample coord imagefile sample gif pathwayname NK cell mediated cytotoxicity gt lt subgroups gt lt maingroups gt lt pathway_settings gt Edit the lt maingroups gt and lt subgroups gt elements to contain the folder names and information about the pathway maps and coordinates that you want to display to the end users of the tool For each subgroup the lt pathway gt
86. ation link that contains run time filters Response The system will begin to retrieve data For each column with run time filter see Adding Prompted Filters a dialog will appear asking you to specify the filter conditions for this column Enter the filter conditions that you want to apply Comment If you are using the List Box Check Boxes or Radio Buttons prompt methods then you will find that only values that have not been eliminated by previous filter conditions are shown Click Next gt gt or Finish when you have come to the last column Response The data is retrieved and displayed in DecisionSite 4 4 3 3 3 4 4 3 3 4 Spotfire DecisionSite Administration Note Dialogs are displayed in the order the columns appear in the Information Link pane In other words the first column for which Prompt has been set to anything but None will be the first to display a dialog Run time Filter Example Information links may include more than one column with run time filters In this case each filter will reduce the data set such that subsequent prompts may present fewer values This can be overridden by treating the columns as independent Consider the following example This is the data as it would look if no filters were being applied Name Salary Location Prompt None Range Check Boxes Miller 1300 New York King 1400 New York Clark 700 New York Ford 1100 Dallas Adams 900 Dallas Scott 1300 Dallas Jones 1200 Dallas Jame
87. ause less information needs to be sent between the server and the client However this increases the load on the database server system because more of the work is done on the server side and less is done on the client application side Consider this if many client machines such as Web servers are serviced by only one or a few database servers 75 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual e Database procedures also allow you to have libraries of functions in the database server This is a feature shared by modern application languages that allow such design internally for example by using classes Database Procedures in Information Services Using Information Designer and Information Builder you select pre made database procedures and configure these to be accessible in Information Links These Information Links are available to the DecisionSite Client users to retrieve or manipulate data In Information Designer you select a database procedure from your available data sources and define which input parameters that the procedure should prompt for and any potential resulting columns and joins In Information Builder you configure a complete Information Link with one or more combinations of procedures and columns from other tables The Three Kinds of Procedures Information Services defines three kinds of procedures e Pre update procedure this procedure does not return any data it only perfo
88. aw values from two or more different tables Joins can be set up between tables in different data sources In the Information Model joins are represented by this icon Creating a Join If you want to combine columns from two disparate data sources for example if one field is in a different table than the rest of the information you need to create a join between two columns gt To create a join 1 From the Select workbench drop down list select Join 2 Click Change Response The Join Element workbench is displayed From the Data Sources pane select the first column to include in the join operation Click Add gt Select the second column to include in the join operation Click Add gt Optionally repeat steps 4 and 5 for any additional columns to be included in the join Click either Freehand or Select Select join operator from the Condition drop down list or type a freehand join ci c2 SEX 00 SION tAv UM Comment There are two basic types of joins that can be done between tables inner joins and outer joins An inner join will return records for which only the matching 4 3 2 3 3 Spotfire DecisionSite Administration fields in both tables are equal An outer join will return all the records including NULL values from one table and only the matching records from the other table In the Condition drop down list outer joins include the character The position of the plus sign indicates which table wil
89. ax more info at http jakarta apache org log4j docs index html Placing a new log4j configuration file with a name matching the pattern log4j properties in the installation directory spotfire spotfire WEB INF directory will cause it to appear in the drop down list among the other Log Configuration Files and can thus be selected gt To change current log setting 1 At the top of the page click Logging 2 From the Current log configuration file drop down list select the required logging level 3 Click OK All the DecisionSite log files will now begin logging the messages according to the new log setting Note Only use Debug mode for diagnostics and not for continuous server use It significantly reduces the performance of the server and also produces very large log files Viewing Current Users Viewing Current Users You can view a list of all users that are logged on to your Spotfire Analytics Server gt To view current users 1 At the top of the page click the Current Users tab 2 Click Refresh Response A list of the currently logged in users is displayed The format is User Machine and Logged in since 53 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 2 2 7 Deploying New DecisionSite Applications 4 2 2 7 1 Viewing the Current Deployments gt To view which DecisionSite applications and extensions that are Ee At the top of the page click Deployer Respons
90. ax count gt 10 lt max count gt Z4min ronnt 24 min eonnt Note If there are other catalog references in the file that link to oracle 1 the oracle 1 data source must be kept and you should instead create a new ACTIVITYBASE data source 4 3 4 10 Examples of Generated SQL 4 3 4 10 1 SQL Filters In this example we will define a column element with a filter The column should only return commissions above 1000 109 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Columns Add gt Remove Calculation Aggregation o Show gt gt Filter Hide lt lt Columns Add gt COMM FC1 Remove Condition rci gt 1000 GUID Name High Commission Description Commission greater than 1000 Test lt Select real Parent domain Type Check boxes Filter Listbox devices Radio butto ns Save Clear The column element defined above will result in the following SQL when executed as part of an information link SE Car E1 COMM AS High Commission FROM n LEMEE TTNA AE WHERE E1 COMM gt 1000 4 3 4 10 2 In the following example SQL GROUP BY we will use aggregation to calculate the average salary for employees in various departments We are assuming that the database provides the salary SAL and department DEPTNO for each employee Define a column element 110 as follows Sp
91. ay have gone wrong during the configuration Missing Columns When the configuration is read the guids are confirmed in the Information Model If a guid cannot be located that column element is discarded from the configuration If the id column e g CDBREGNO is missing the Structure Analytics Diagnostics tool will state it is missing and the configuration will not be shown in the drop down list of the Structure Connection dialog If the structure column e g MOLFILE is missing the Structure Analytics Diagnostics tool will state it is missing and the configuration will not be shown in the drop down list of the Structure Connection dialog If the reference column is missing the Structure Analytics Diagnostics tool will state it is missing and the configuration will not be shown in the drop down list of the Structure Connection dialog If there is no reference column at all in the configuration the id column will be used instead A column might be missing due to either of the following e The guid entered in the configuration file mdl direct xml is wrong misspelled e The user does not have Execute permissions on that particular column element e The column element is missing removed from the database Configuration File Issues If the file name mdl direct xml is wrong the Structure Analytics Diagnostics tool should say it failed to find it 40 Configuring DecisionSite If the XML in the configuration file mdl dir
92. bruary 1 5 London February 15 8 London May 1 15 London May 15 22 New York February 1 9 New York February 15 7 New York May 1 18 New York May 15 24 Tall Skinny gt Short Wide conversion lets us pivot and aggregate this table producing the following 139 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual City avg Temp for February avg Temp for May London 6 5 18 5 New York 8 21 A smaller table has been created summarizing the original table The following settings were made in the Pivot dialog to produce this result e Identity City e Category Month e Values Temp 4 4 4 User interface reference 4 4 4 1 User Interface Overview B X 2 sd Elements Available elements Details 21 ACTBASE 40 Information Links Query Elements Filters eee Hits Filler TOTS k Unverified Protac Valid Protocols Fi Valid Studies Filte gt Verified Protocol QC Results m Ga T M Edit Link Add to Link Information Link Properties OMETE Clear Link Filter type Limits WB Plate ib range ll ECK ap Compound range ll ERK Ab Batch ase ll IT EE 2 Result range Z ECK Conditioning None Edit Join Path Default Edit Open 140 Spotfire DecisionSite Administration Option Description m Displays the Save Information Link dialog which saves the configuration current
93. ces Filter or Column that constrains the Region column so that it only returns values if the currently logged in user is a member of a group with that exact name Filter Element Columns wu gem Condition FCL in CURRENT_GROUPS An example of the resulting SQL of this would be SalesTable Region SalesForce East SalesForce North Now the information link is ready to be used and will only retrieve data for groups that the currently logged in user is a member of Syntax The syntax for the personalized information link parameters is CURRENT USER and CURRENT GROUPS Replacing Null Sometimes a column returns null values By using the Oracle SQL function NVL null values can be replaced with another value Note The following example only applies to data retrieved from an Oracle database gt To modify a column to replace null values with 0 zero 1 Select the column in the Information Model IM 2 Click Edit 3 Inthe Calculation field type NVL CI 0 4 Click Save 104 Spotfire DecisionSite Administration Note Sometimes a null value has a meaning different from zero such as value unknown Make sure you understand how the data is meant to be interpreted before replacing values 4 3 4 6 Limiting the Number of Records Returned The Oracle pseudo column ROWNUM makes it possible to use a filter to control the number of records returned by an information link Note Th
94. cisionSite Administrator Administrate users groups and licenses Deploy custom DecisionSites View logs Library Administrator Edit who is allowed to create new Library Sections Configure DecisionSite Library and Poster settings Information Designer Administrate the connections to the databases used by Information Services First Time Administrator Access 1 Create user 2 Unlock Administrator privileges About DecisionSite Analytics Server ie 4 Ifyou are using Database Authentication you must create a new user who will be the Admin of the Spotfire Analytics Server If you are using Windows Authentication or LDAP Authentication proceed to the next step Click on Create user and enter a username Preferably admin or similar and a password Then click OK 5 Click on the Unlock Administrator privileges link 6 You will be required to log in If you are using Database Authentication enter the user you created above otherwise pick an already existing user to be Admin of the Spotfire Analytics Server and log in 7 You will now be able to unlock Administrator Privileges for that user Unlock Administrator Privileges This page allows you to unlock and assign Administrator Privileges to the logged in user Please enter the Product Unlock Codes provided on the installation media Product Unlock Code EE Unlock 8 Enter the codes provided in the codes txt file and click on Unlock Respon
95. ctivitybase to installation directory gt server application data iis export This allows you to perform any necessary changes to the XML file that you will use in the export folder while keeping the original XML file intact All IMs that are to be imported by the Information Designer must be placed in this directory Importing Information Models Editing Information Models ActivityBase 4 0 4 1 or 5 0 IM Before importing the selected XML file make sure to change the following references in the abase40 xml abase41 xml or abase50 xml file lt schema gt ACTIVITYBASE_SCHEMA lt schema gt to lt schema gt YOUR_ACTIVITYBASE_SCHEMA lt schema gt where YOUR_ACTIVITYBASE_SCHEMA is the name of the schema that ActivityBase uses at your company Importing the DSLD IM Import the desired Information Model using the Information Designer Configuring DecisionSite Import Help Filename abaseso xml Import mode C Replace all Add overwrite conflicting elements C Add keep conflicting elements Include Iz permissions Parent domain L Select Import Clear Import workbench in Information Designer Once the Model is imported you will be asked to update the ACTIVITYBASE Data Source information with a user name password server port and SID After importing the 4 0 Model you should see the following Information Links and Query Elements in the Information Designer
96. cute advanced database queries without any knowledge of SQL or the underlying database structures Information Designer is part of a suite of tools called Information Services The other tools directed at end users are Information Library and Information Builder While Information Builder is used to create information links queries from columns and filters Information Library is used only for executing these links and retrieving the data Note To run Information Designer you need DecisionSite Client installed on the same machine 4 3 1 2 General Workflow This is the general workflow for using Information Designer 1 Set up the data sources Enter the information required to connect to the databases which will be accessed through the Information Model 2 Create domains for storing elements The Information Model is a hierarchical structure where domains correspond to folders on a file system 3 Combine tables by creating joins If you want to work with data from different tables you first need to create joins 4 Define column elements from available data sources Define the column elements to be shown to the user These columns can be taken directly from tables in one or more databases They can also be calculated filtered or otherwise modified 5 Create filter elements to be used in the domain Create filter elements with descriptive names to be applied by the user at will 6 Set permissions for individual users or us
97. d to force the install mode for packages Note If the Application Manager is not installed on the system then certain things are needed to run the support web pages Internet Explorer must allow download of signed ActiveX controls The ActiveX control that is used on the support pages is named SfUpgrade cab 4 9 Connecting to Spotfire Analytics Server Starting with DecisionSite version 7 2 the client server protocol includes features for implementing a support policy Spotfire uses this technology to ensure that clients who connect to a Spotfire Analytics server meet the system requirements enforced by that server Clients that do not meet the system requirements are denied access to that Spotfire Analytics server gt Connecting a DecisionSite Client to a Spotfire Analytics Server 1 A DecisionSite Client connects to a Spotfire Analytics Server for the first time Spotfire Please login to Spotfire DecisionSite Server dsas82 User ID Ile smith Register a new user Password eeeeesece IT Remember me Login Cancel 2 The client environment is detected and compared to the system requirements that the Spotfire Analytics Server requires 168 Spotfire DecisionSite Administration Alternative A If the client environment meets the system requirements enforced by the server the client is connected to the server and the upgrade process continues downloading the rest of the packages that need to be upg
98. data access layer as a folder structure It is possible to drag an element from one place to an other in the tree structure Select none Edit Delete A ActivityBase 2 ActivityBaseE El CT Clinical 7 CT Phasel H C Filters ig ActTime 2 Diastolic igo HeartRate 1 Systolic i23 SampTime 53 Infusion H Phase2 Item Description Select none To save something at the root level instead of selecting a domain click this button Edit Select an existing element domain join filter or column and click Edit to load the settings for viewing and editing Delete Select an element and click Delete to remove it 1 Domain An expanded domain Click the plus and minus to browse the tree 2 Column element A column element 4 3 3 2 2 Icons in the Information Model In the Information Model the following icons may appear Click on a link in the table below to find out more about each element type Icon Element type Domain 84 det Spotfire DecisionSite Administration Information Link Join Filter String column Integer column Real column Date column DateTime column Time column Procedure BLOB binary large object column Cannot be retrieved but can be used in the structure search filter condition It can also be used in custom made filter conditions using the API CLOB character large object column Can be retrieved to DecisionSite Client It can also be used in custom made f
99. denoting its type Comment Use Save Copy if you want to keep the old column definition unchanged Note If the column in the database is of the type Real and you want to create a column element of the type Integer then set the Type step 11 above to Integer Similarly if the column in the database is of the type Unknown you must manually choose an appropriate type before the column can be saved It is also strongly recommended that you use an Oracle conversion function for example ROUND in the Calculation field step 5 above Note For the Unicode data type NVARCHAR convert lt column name gt UTF 8 should be entered in the Calculation field or else it will not be possible to filter on the column Creating Multiple Column Elements The Multiple Columns Workbench can be used if you want to create many column elements in one operation Note Whole databases and schemas cannot be added only columns and tables are available using this Workbench gt To add multiple columns to the IM 1 From the Select workbench drop down list select Multiple Columns 2 Click Change Response The Multiple Column Elements workbench is displayed 3 Select the columns of interest leaf nodes in the Data Sources tree Comment In the Data Sources pane to the left click the El signs to browse databases and tables You can select several columns at once by pressing Ctrl and clicking on the desired columns It is also possible to select an entire
100. duction DecisionSite Administrator is a tool for managing DecisionSite users and groups You can organize users into groups define profiles for the individual user and group and assign licenses to groups and users Preconditions Installation DecisionSite Administrator is automatically installed together with the Spotfire Analytics Server To run DecisionSite Administrator the Spotfire Analytics Server and the Spotfire Analytics Server database must be running Licensing The user must have a license for DecisionSite Administrator to run the tool A user can ask for a DecisionSite Administrator license from the system administrator After getting a license for DecisionSite Administrator a user can unlock the license by opening DecisionSite Client and clicking on the File gt DecisionSite Login gt Unlock New License Another way to unlock the license is to open a new Internet Explorer window enter the URL to the Spotfire Analytics Server for example http myserver 8080 spotfire and then click on the Unlock Administrator privileges link Related reading For detailed accounts of setting up the server side of Spotfire DecisionSite please consult the Spotfire Analytics Server Installation and Configuration Manual Using DS Administrator Users and Groups e A user is a DecisionSite user whose login name is registered in the Spotfire Analytics Server system 47 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment
101. e 157 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 5 4 5 1 4 5 1 1 4 5 1 2 158 Information Services A suite of tools for accessing databases Includes Information Designer Information Builder and Information Library Information Library A tool for executing information links Information Link A predefined database query including all required connection information When opened executed the information link will retrieve data from databases and visualize it in DecisionSite Pivoting Choosing dimensions from the set of available dimensions in a multidimensional data structure for display in the rows and columns of a cross tabular structure Query A specific request or set of instructions for retrieving modifying inserting or deleting data in a database Record A term used in some database systems to mean row Although record and row have slightly different meanings in formal database theory in most instances they are meant synonymously Row In a table a set of related columns of information that are treated as a unit and that describe a specific entity A row is the logical equivalent of a record SQL Structured Query Language a database query and programming language DecisionSite ApplicationManager General Information and Background General Information and Background This chapter provides information about how the DecisionSite ApplicationMan
102. e A list of all applications and extensions that are deployed on the server is displayed 2 Select one or more items from the list and click View Details Response More detailed information about the applications and extensions are displayed such as the version number etc If the item is based on another application or extension this will be shown If there are any other applications or extensions that are applied to the item this will be shown too 4 2 2 7 2 Deploying a New DecisionSite Application or Extension Prerequisite A file named distribution zip has been created using DecisionSite Builder See DecisionSite Developer for documentation gt To deploy a DecisionSite application or extension distribution file 1 At the top of the page click the Deployer tab 2 Click Browse and select a distribution zip file to deploy 3 Click Deploy Response A new dialog appears listing the contents of the distribution zip file The New Version column indicates if the packages about to be deployed are of a later version than the packages already installed All packages that have a later version will be installed 4 Click Deploy Response The packages are installed 4 2 2 7 3 Un Deploying a DecisionSite Application or Extension An application represents a running instance of Spotfire DecisionSite that is a predefined selection of Tools and Guides An extension is an add on to an existing application or extension It may be a
103. e Optionally a plug in can be used to retrieve the credentials The default data source will be used by all imported elements when importing an Information Model from Spotfire Analytics Server 7 1 1 or older The default join data source is used for creating temporary tables and joining the final result when running an Information Link It is used when running against several data sources where no data source allows writing in temporary tables Allows the Information Services to create temporary tables in this data source This is needed when running Information Links that joins data from several data sources or has a large number of filter values To guarantee full compatibility between Information Services and Oracle databases it is recommended that the compatible setting in init ora for the databases is set to compatible 8 1 0 0 0 Command executed when initializing a database connection This is needed when setting up a data source to ISIS Direct see Issues when Creating an ISIS Direct Data Source for details The maximum number of values in each block of data retrieved from the database Used for performance tuning In general use higher values for physically distant databases Use lower values when the number of users is high Entering the value zero will make the JDBC driver use its default value The maximum number of values in each block of data written to the database Used for performance tuning In general use higher va
104. e PathwayID gt String String String 293241 3 6 1 34 Oxidative phosphorylation Photosynthesis ATP Synthase 283821 2 3 1 37 Glycine serine and threonine metabolism Z18785 1 11 1 7 Phenylalanine metabolism Methane metabolism Flavonoids stilbene and lignin biosynthesis lt data gt The mapping information between the internal identifiers in the data sets used by the end users and the pathway identifiers many to many should be pasted between the data elements and the first line should be String to import the data into the DecisionSite Client as strings 3 3 8 4 Upgrading a Previous Version of Pathway Viewer If you have been using the Pathway Viewer tool previously on a Spotfire Analytics Server your old data and settings files will remain in their old directories during a server upgrade To use the old files on a later Spotfire Analytics Server you should copy all image maps and coordinate files from their old location to e install directory gt server application data pathwayviewer data You should also copy the idmapping xml and pathway_settings xml file to e install directory gt server application data pathway viewer and make sure to remove any defaultdir and pathwayid to clientid file attributes from the pathway settings element of the pathway settings xml file 3 3 9 Gene Ontology Browser 3 3 9 1 Gene Ontology Browser Introduction The Gene Ontology Browser tool is used to connect a data set in DecisionSit
105. e The procedure will receive a GUID in the selected domain and will be denoted with the 8it icon Note that the procedure object will be visible to the end user in the list of Information Links You can also make larger more complex Information Links using the procedure when creating an Information Link in Information Builder Creating a Query Procedure Using Information Designer and Information Builder you select pre made database procedures and configure these to be accessible in Information Links These Information Links are available to the DecisionSite Client users in order to retrieve data In Information Designer you select a database procedure from your available data sources and define which input parameters the procedure should prompt for and any potential resulting columns and joins T7 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 78 The Three Kinds of Procedures Information Services defines three kinds of procedures Pre update procedure this procedure does not return any data it only performs an operation on one or more databases All pre update procedures in an Information Link will always be executed before any query procedure Query procedure just like a database table this procedure returns data Post update procedure this procedure does not return any data it only performs an operation on one or more databases All post update procedures in an Information Link will a
106. e Administration gt To add new columns 1 2 Compose a new information link For details see Creating a new information link Click Open Comment The data retrieved using the current information link is visualized in DecisionSite Create new visualizations and apply suitable settings for color and size Return to the Information Builder and add any additional columns to the information link Click Open Click Yes when prompted about whether or not you want to add the result as new columns to the current data set Response The changes will be reflected in the query devices but the data will still be displayed using the plots that you created Note The steps above only apply when a column element is added to an information link If a filter is added or if a column element is removed from the information link then the entire data set will be retrieved again Any visualization settings axes colors etc that have been made will then be lost 4 4 3 4 Transforming the Data 4 4 3 4 1 Eliminating Duplicates Eliminating duplicates means removing all duplicate records from the returned data set By duplicates we mean records where all fields are identical to all fields of another record Consider the following example Before removing duplicates After removing duplicates Name Income Name Income Smith 1200 Smith 1200 Jones 700 Jones 700 Banks 700 Banks 700 Smith 1200 Smith 900 Smith 900 gt To eliminate duplicates
107. e Client to gene ontologies provided by the Gene Ontology Consortium or other ontology files with the same structure via an annotation file that links the different files together The tool can be run using local files but setting up files on the server simplifies the use of the tool for the end users Note On WebSphere servers you may have to create the following directory structure under the application data directory for yourself geneontology annotations 32 3 3 9 2 3 3 9 3 3 4 3 4 1 3 4 2 Configuring DecisionSite ontologies See Note under amp rdquor Copying the DSFG Information Model for more information regarding WebSphere paths Adding Ontology Files to the Server Place the ontology files in the following directory on the Spotfire Analytics Server e install directory gt server application data geneontology ontologies Note There should only be one set of ontology files on the server This means one component ontology one function ontology and one process ontology The file names are not important The tool will always try to parse all available ontology files in this folder Hence old files should be replaced or removed from this folder upon update to avoid trouble when running the tool Adding Annotation Files to the Server Place the annotation files in the following directory on the Spotfire Analytics Server e install directory gt server application data geneontology annotations Note The names
108. e WEB INF manifest xml e WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war WEB INF manifest xml 163 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 5 3 10 4 5 4 4 5 4 1 4 5 5 4 5 5 1 4 5 5 2 164 Trust Policy DecisionSite ApplicationManager relies on Microsoft Authenticode for validating packages There are two settings for controlling the validation for code trust HKLM HKCU Software Spotfire Distribution WinTrustUI String All None NoGood NoBad HKLM HKCU Software Spotfire Distribution CheckRevocations DWORD 0 1 WinTrustUI e All Always display dialog when a package is verified e None Never display dialog when a package is verified e NoGood Do not display any positive dialog e NoBad Do not display any negative dialog Technical Details Technical Details Per user and per machine installations Package Contents e DHTML Script e WSC e COM DLL OCX e EXE e HTA e Basically any file can be included e Signatures and trust model e Local application registration e Integration between DecisionSite Client and DecisionSite ApplicationManager Troubleshooting CleanUpPackages The installation can be corrupted by altering the package folders in the file system or by changing the package registration in the registry Spotfire provides a tool to help resolving problems with corrupted p
109. e following example only applies to data retrieved from an Oracle database gt To create a filter that limits the number of records returned by an information link Filter Element Help Columns Add gt Remove Condition RowNUM 11 x 11 GUID 23af4a90 SS5cf 11d6 a548 0010acii03f5 Name First Ten Description Returns only the first ten rows Parent domain Filters lt Select Save Copy Save Clear 1 From the Select workbench drop down list select Filter and click Change 2 In the Condition field type ROWNUM lt 11 3 Enter Name and Description Select a Parent domain 5 Click Save 4 3 4 7 Concatenating Strings The Oracle SQL function CONCAT lets you create a column by concatenating strings from different tables Note The following example only applies to data retrieved from an Oracle database 105 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 4 8 gt To combine strings from two different tables into a single column element Column Element Help Columns FirstName C1 LastName C2 Add gt Remove Calculation concat concat C1 C2 Aggregation ji Show gt gt From the Select workbench drop down list select Column and click Change In the Data Sources pane select the first column e g FirstName Click Add gt Select the second column e g LastName Click Add gt In the
110. e for Functional Genomics DecisionSite for Lead Discovery DecisionSite for Microarray Analysis If any of these features are relevant for you proceed to chapter 3 Configuring DecisionSite where you will find instructions on how to set them up TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 2 Upgrading DecisionSite 2 1 Upgrading Procedure This chapter explains how to upgrade the DecisionSite version on your Spotfire Analytics Server by deploying a new version of Spotfire DecisionSite It is required that you have already installed and configured the Spotfire Analytics Server itself If you have never before had Spotfire DecisionSite on the server and wish to deploy and set up the system for the first time then please follow the instructions in chapter 1 Deploying DecisionSite for the First Time instead 2 2 Updating the PDF Manuals on the Server In order for the end users to get access to the Spotfire DecisionSite manuals when they select Help PDF Manuals from the Spotfire DecisionSite Client you must copy these manuals to the server gt To Copy the Spotfire DecisionSite Manuals 1 From the documentation folder on the Spotfire DecisionSite deployment kit copy all the PDF manuals and the file called manuals jsp 2 Paste these into the following folder on the Spotfire Analytics Server machine installation directory gt server webapps spotfire support manuals 2 3 Deploying Soft
111. e this each server can by given a display name that is used instead manifest server info lt title gt My Informative Server Name lt title gt 161 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual server info lt manifest gt 4 5 3 7 Changing the Text in the Login Dialog It is possible to change the text that is displayed in the server login dialog This is done by editing the manifest xml file gt To Change the Text in the Login Dialog 1 Open the following file in a text editor WebLogic installation directory gt spotfire spotfire WEB INF manifest xml WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war WEB INF manifest xml 2 Insert the following passage into the manifest xml file anywhere within the lt manifest gt tag lt server info gt lt welcome message gt New login text lt welcome message gt lt server info gt 3 Save the file Restart the DecisionSite Server for the changes to appear Example of a login text lt welcome message gt Welcome to the Spotfire Server Please Login with the same username and password as you use for Windows welcome message You can also use HTML formatting lt welcome message gt lt CDATA lt h2 gt Welcome to the Spotfire Serverc h2 welcome message If no lt welcome message gt has been added the Login di
112. ect xml is incorrect the Structure Analytics Diagnostics tool should say it is invalid Specification of Rules For information on how to specify mandatory and recommended rules see Spotfire Developer Network 3 5 Configuring DecisionSite for Microarray Analysis 3 5 1 Introduction This chapter describes how to install and configure Spotfire DecisionSite for Microarray Analysis which provides multiple levels of probe level analysis normalization quality assessment and advanced statistics for secondary analysis of both Affymetrix and 2 Channel microarray experiments Important Spotfire DecisionSite for Microarray Analysis requires Spotfire Analytics Server 9 0 or higher Before you begin make sure that you have access to the latest software distribution archive from the Spotfire download site It contains the following files e The file TIB_DSMA_9 1 1_distribution zip which is what you will deploy on the server e The release notes for DecisionSite for Microarray Analysis 9 1 1 3 5 2 Installation If you should need more information on how to deploy zip files on the server please see chapter DecisionSite Administrator gt To deploy the DecisionSite for Microarray Analysis distribution file 1 Make sure that the Spotfire Analytics Server is running 2 Unzip the downloaded installation archive file for DecisionSite for Microarray Analysis to a temporary folder 3 Start the DecisionSite Administrator tool eith
113. ed Joins Additional Default Joins TB1 joined TB2 TB2 joined TB4 Add calculated join to selected joins CI X V Update continuously Click OK to save the information link Comment The Selected Joins will be saved for the information link and will always be used when retrieving data via the information link Any default joins will not be saved as these may change and are determined on the fly when using the information link Note When executing an Information Link against several data sources all subqueries are run first and then the main query joining all subresults This means that the joins in the main query are performed after all joins in the subqueries In each where clause in the subqueries the order of the joins is preserved from the chosen join path in the Information Link Opening Information Links Opening Information Links Information Builder allows you to open information links This means accessing data sources and executing a query gt To execute an information link 1 Create a new information link or edit an existing link see Modifying an Information Link Click Open Response The query is executed and the data is shown in DecisionSite If the information link includes prompted filters one or more dialogs will appear before the data is loaded See Using Prompted Filters for details Using Run time Filters gt To specify filter parameters during retrieval 1 Open an inform
114. ed by all users to access data Setting up the data views are done by designated people and only rarely when new views are needed 3 Use of data on a daily basis in Information Library IL by everyone The access to all databases and their content is established with Information Designer Here the database connections are set up with relevant database information The administrator does this once and no decisions about the actual data retrieval are made Actual data links are designed in Information Builder this is done occasionally when the information model needs to be modified Designing data links is normally done by users with in depth knowledge of the data infrastructure of the company who set up the links needed for their colleagues The daily data retrieval is made with Information Library in which users click on predefined links to load data Example Acme Corp uses two databases with a number of tables in them Tom sets up connections to both of these databases in Information Designer Tom does not have to work with the actual information model when he does this Instead two members of the development team are assigned the responsibility of setting up the data links needed by the researchers These two use IB to set up a number of links identified to capture the data demand at each research project Having done this all researchers are now able to analyze the research data with simple clicks in Information Library 4 1 7 Customi
115. eee bete eXecUtllig eter ERREUR RR ER Ne 132 predefined siste ee 119 TG 121 Query procedure eee etienne 75 R R Corinector une reti tee cre ee eds Ranges dete ie e TRE CER IE UHR eee Record References Relational Operators Remember Me Replacing values E Reguirementz EEN Retrieve data user interface overview seen 140 using the Information Builder sssss 132 Rights setting group Drivlleges 51 setting user privileges ssssssessrsssesrssrsrrerrerrsrrsresee 49 Roaming Profiles e eI p ended 161 Run time filters adding to a column sse 123 END e 133 information designer eese 93 user interface setting up 143 Using iden tb i RR aen ANTE 132 using structure search 135 What ate sedie or ERE URGERE 120 S KEE Le 24 SUE 50 Saving a domain to file i apeieeteeeipenen 80 atroot level iiir 63 ell ul 68 information links 121 144 Selected H TC 128 Selecting Join Path eet coe 128 SOLES OI inrer eer ee EEE 61 66 Sequential information links adding to a column Spotfire DecisionSite Administration Server activity EE 52 Set Filter for Column dialog esses 148 Setting limits using hard filters eee 122 using run time filters eese 123 Settings cot obe teat Nee 53 Short Wide example of pivoting eseesseeeen 138 example of pivoting with aggrega
116. egen eite e e b ER RM eg 47 deleting eee ete 49 VAN View SQL and Edit Oracle Hints ial OB rp 144 displaying SQL statements 127 editing Oracle hints essere 127 View SQL dialog conteret eicere es 86 Visualization Services s sessseseessessrsrerrerrrsererrerrerensrrnrreses 10 Vocabulary sien ehe A 157 Vocabulary for Information Designer 116 deg au VE 59 Z ZIP file i pi debe be ee ie IE 54 178
117. elements in this domain When this check box is selected the user has access to the contents of this domain Saves the settings for the selected user Note The user permissions shown for individual users are only the permissions set explicitly for that user The user may have additional rights if he she belongs to a group Spotfire DecisionSite Administration 4 3 3 3 9 Export Workbench Export Help Include Iz permissions Filename filter backup xml Domain trnp Filters Select Export Clear Option Filename Include permissions Domain lt Select Export Clear Description Enter a filename No path is required Select this check box to include information about the permissions associated with the domain and its content The domain selected for exporting see below Select a domain in the Information Model and then click this button Exports the specified domain and its contents in an XML file to the directory lt installdir gt spotfire application data iis export on the server Clears all fields without saving 4 3 3 3 10 Import Workbench Import Filename Import mode Include permissions Parent domain Help filter backup xml Replace all Add overwrite conflicting elements Add keep conflicting elements Iv o lt Select Import Clear Option Filename Import mode Description Enter the name of the file to be im
118. er Enter the name of your Spotfire Analytics Server in the Address field Example http analyticsserver Response The Spotfire Analytics Server start page is opened Click on DecisionSite Library and log in with your DecisionSite administrator username password Click on New Library Section Select the No create a blank Library Section radio button and click Next Enter a Title Description and Keywords and click Next Return to the Spotfire Analytics Server start page Step 2 Click on DecisionSite Administrator and select the Admin user Response A new Product License can be seen DecisionSite Posters Products DecisionSite for Functional Genomics DecisionSite for Lead Discovery I DecisionSite MapConnect M DecisionSite Posters DecisionSite Statistics M DecisionSite Library Assign the DecisionSite Posters and Spotfire Library license to the Admin user Start DecisionSite Client and log into the Spotfire Analytics Server as the user mentioned in the previous step Open a data set for example C Program Files Spotfire DecisionSite Data General Baseball baseball sfs Create a scatter plot and select File gt Publish Poster to Library Response The Publish Poster to Library step 1 3 dialog opens Response If the Unsupported Items dialog appears just click Close Click the Next button Response The Publish Poster to Library step 2 3 dialog opens Click on the Library Section you created previously C
119. er and group organization affects users in two ways e The DecisionSite application Different users at your site can use different DecisionSite applications DecisionSite Base DecisionSite for Lead Discovery and DecisionSite for Functional Genomics are examples of DecisionSite applications Each has its own set of tools aimed at its field The DecisionSite application determines which tools your users has access to e The analysis access in the Spotfire Library The Spotfire Library will be discussed later but is a publishing area for analysis material Access to this material can be controlled by granting access to the users and groups The user organization is done in DecisionSite Administrator where users can be added and made part of groups Example Tom decides to create a group for each department and one for each project in the research department By creating these groups Tom wants to ensure that each group gets the tools needed for their specific needs without the distraction of unnecessary items Tom also creates a group consisting of the development team at the research department With this group the developers can create an environment of Guides applications and extensions not ready for production 43 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Sales Marketing Department Department Research Department Development Team Project A Project B 4 1 3
120. er conditions while the information link is being executed These filters are added when an information link is created in Information Builder Row In a table a set of related fields that are treated as a unit and that describe a specific entity A row is the logical equivalent of a record Server A computer on a network that controls access to data SQL Structured Query Language a database query and programming language Table A collection of associated columns The logical equivalent of a database file 4 4 DecisionSite Information Builder 4 4 1 Introduction 4 4 1 1 Introduction to Information Builder Information Builder is a tool for creating and opening information links An information link is a database query specifying the columns to be loaded and any filters needed to narrow down the data set prior to visualization in Spotfire DecisionSite Information Builder is built on top of the Information Model IM This model resides on your server and is a representation of one or more databases which may be geographically dispersed It allows you to execute advanced database queries without any knowledge of the underlying database structures The model appears as a folder structure see Element Pane which is set up by the administrator Information Builder is part of a suite of tools called Information Services The other tools are Information Library and Information Designer While Information Builder is used to create inf
121. er groups Different groups of users are given different levels of access to data These permissions are administered in Information Designer 59 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 1 3 Related Reading To find out more on how to use the Information Builder and Information Library please use the online help for these products For information on how to use Spotfire DecisionSite please consult the Spotfire DecisionSite Client User s Guide and Reference Manual For detailed accounts of setting up the server side of Information Services see the Spotfire Analytics Server Installation and Administrator s Guide 4 3 2 Using Information Designer 4 3 2 1 Data Sources 4 3 2 1 1 Data Sources Overview Data sources are the physical units from which data can be retrieved usually databases Connecting to a database requires technical know how not always found among end users Therefore Information Designer lets the administrator make all the required settings in advance including database name user name password etc This information becomes part of the Information Model so that when an end user executes an information link the connection with any required databases is established automatically and invisibly User authentication to the data source can be made in two ways Either once when creating the data source connection In this case all users connect with the same credentials Thi
122. er on the server using Internet Explorer or in DecisionSite select Tools gt Administration gt DecisionSite Administrator Note You must have administrator s privileges to run this tool Select Deployer from the top menu frame 5 Browse to the temporary folder where you unzipped the Spotfire DecisionSite deployment kit 6 Select and open the file TIB DSMA 9 1 1 distribution zip 7 Click on Deploy 8 The contents of the distribution are again shown in a separate window All software components of DecisionSite for Microarray Analysis 9 1 1 will now be installed 3 5 3 Configuration gt To make the new features of DecisionSite for Microarray Analysis available to users 1 InDecisionSite Administrator select Users or Groups from the top menu frame 41 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 42 Select the DecisionSite for Microarray Analysis check box for the users and or groups that you wish to have permission to use each feature For more information on how to configure Users or Groups see chapter DecisionSite Administrator Click on the Save this Configuration button The users whose permissions you have set will now get access to the new functionality of DecisionSite for Microarray Analysis the next time they connect to the Spotfire Analytics Server Spotfire DecisionSite Administration 4 Spotfire DecisionSite Administration 4 1 Setting Up the Environment 4 1 1 In
123. es Modify the SQL of the information link in this text box Multiple SQL statements are allowed as long as they are separated with semicolons and new line Displays the original SQL of the information link so that you can immediately see the differences that you have made upon your modification Resets the Modified SQL to the last saved SQL Resets the Modified SQL to the SQL originally created in the Information Link A unique identifier used internally to identify the information link The name of the information link to be saved edited The name of domain folder where the modified information link will be saved Click Save to save the modified information link 4 3 4 4 3 4 1 Tips and Examples General Guidelines for Setting Up an Information Model The Information Model IM concept aims to supply each end user with the data they need with a minimum of effort and confusion Consequently when building an IM it is important to understand who the end users are and what data they require for their work Who are the end users Permissions are set on the domain level Finding groups of users who work on related data will give you a good clue about the domain structure you should implement Do not give all users access to everything this will only cause confusion What data do they need What information is needed How much data can users handle in a single request Are there any commonly used threshold values Answering t
124. es InstallShield Wizard InstallShield Wizard Completed The InstallShield Wizard has successfully installed Visualization Services Click Finish to exit the wizard i Gancel Click Finish to exit the installer 17 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 1 3 3 1 4 3 1 4 1 18 Setting Up Language and Country The following instructions need only be performed for WebLogic on Solaris Tomcat on Solaris In order for DecisionSite Posters to display values and dates in your country s preferred way you may need to set some options on the Spotfire Analytics Server By default the Spotfire Analytics Server is set to use Language English and Country US gt Setting up WebLogic on Solaris 1 2 3 Start a text editor and open the file installation dir gt weblogic spotfire startWebLogic sh Edit the following line among the java options JAVA_OPTIONS Duser language en Duser country US and specify the language and country you want Example JAVA_OPTIONS Duser language ja Duser country JP JAVA_OPTIONS Duser language sv Duser country SE Restart the WebLogic server gt Setting up Tomcat on Solaris 1 2 Ee Open the file lt server install dir gt bin catalina bat in a text editor Edit the following line among the java options so that it specifies the language and country you want set JAVA_OPTS server XX DisableExplicitGC Xms256
125. eset to Saved instead of Save Note The modified SQL is not validated before execution For this reason you should not alter the name of a column the AS part of SELECT xxx AS yyy alter the number of columns returned alter the datatype of columns returned alter the order of columns returned remove lt temporary_result_ gt from the FROM clause in information links that go against multiple data sources remove the trailing WHERE lt conditions gt as it will be replaced by any conditions applied at runtime 4 3 3 User Interface Reference 4 3 3 1 Data Sources Pane Item e HIREDATE 45 SAL 5 COMM gt DEPTNO o Pa SALGRADE Description 1 Database instance The name of the database instance 2 Database link Catalogue A link to another database 3 Schema The owner or database administrator that has set up the different tables 4 Table A set of columns 5 Column The column has an icon that denotes the column type Available types are AbString 23Integer 83 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 1 2Real m DateTime B bBinary Large Object dob Character Large Object 3 Unknown 6 Table Alias A Table Alias You can create a duplicate reference to a database table from Information Designer This duplicate is called a Table Alias 4 3 3 2 Information Model Pane 4 3 3 2 1 Information Model Pane The Information Model pane displays the
126. estart the server nw 4 8 Spotfire Support Pages for Packages Located on every Spotfire Analytics Server are Support web pages which are used to manage the Application Manager and the software packages that are downloaded from the server to each DecisionSite client If a DecisionSite Client should experience problems related to packages then these Support pages can be used to locate the cause of the problem and possibly correct it From the client computer enter the name of the Spotfire Analytics Server in Microsoft Internet Explorer for example 167 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual http home spotfire net This will take you to the Spotfire Analytics Server start page There you will find a link to the Support pages Detailed information about when and how to use the Support pages is provided in each web page From the Support pages you can Show information about installed packages Use this page to check which packages are installed on a client and how they are installed All packages are listed with their name and version number Repair installation Use this page when packages have been installed successfully but problems occur after using the product for a while Uninstall all packages Use this page in combination with the Install packages page to be sure that a known set of packages are installed on the client Install packages Use this page to install packages an
127. esult of the calculation to the list of aggregate keys Removes an aggregate key from the list of aggregate keys Edits an aggregate key Enter an expression here to calculate a column to aggregate over Check if you want the column to aggregate over all other columns that the user selects at run time See Using Drillable for more information 91 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 4 3 4 3 3 3 4 4 92 Column Workbench Filter Composition Filter Hide lt lt Columns Remove Add gt LOC FC1 Condition FC1 CHICAGO Option Show gt gt Hide lt lt Add gt Remove Condition Description Click this button to show hide the filter controls Select a column from Data Sources and then click this button to include in the filter Deletes the selected column from the composition In this field enter a condition containing the selected column or columns Column Workbench Save Column GUID Name 7e 0f0e00 5424 11d6 a548 0010acii03f5 Average Salary Description Average salary for each departmer Parent Departments Human Resources damen Departments Humrnan Resources Select Type Filter devices Check boxes sl Save Copy Save Clear Option Description GUID A unique identifier used internally to identify the data elements Name The name of the column to be saved edited ma
128. etes the selected columns from the Column elements list Clears the Column elements list The name of the column to be saved Click on a column element to display its name in the text box The default name is the same as the name in the database but with _ and replaced by space and only the first character capitalized The maximum limit of the name is 30 characters Displays the data type of the selected column element Displays the source name of the selected column element A short description of the purpose of the column max 255 characters The default description is the path to the column Click this button to apply any changes to the name or description of the selected column element Note that no changes will be made to the Spotfire DecisionSite Administration column element unless this is done Parent domain The name of the domain folder where you want to save the columns lt Select Select a domain in the Information Model then click lt Select to place the columns in the selected domain Save Save the columns to the Information Model Clear Clears all fields without saving 4 3 3 3 6 Filter Workbench Filter Element Help Columns Add SAL FC1 Remove Condition IFc1 31000 GUID Mame High salary Description Salaries over 1000 Parent domain trp Employees Option Add gt Remove Condition GUID Name Description Select Parent domain Save C
129. figuring DecisionSite 6 Click OK when the installation is complete i Microsoft NET Framework 1 1 Setup wll xl Installation of Microsoft NET Framework 1 1 is complete 7 You may need to restart Windows after this step You will be prompted to do so if that is the case Restart windows and proceed below afterwards as the Visualization Services installer will automatically continue If you are not prompted to restart Windows just continue below 8 With Microsoft NET 1 1 installed on the machine the Visualization Services installer continues i isualization Services InstallShield Wizard Welcome to the InstallShield Wizard for Visualization Services The InstallShield R Wizard will install Visualization Services on your computer To continue click Next WARNING This program is protected by copyright law and international treaties Click Next to continue 13 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 9 Read the license agreement select I accept and click Next i Visualization Services InstallShield Wizard License Agreement Please read the Following license agreement carefully BY OPENING THE SOFTWARE PACKAGE OR INSTALLING THE SOFTWARE ON YOUR COMPUTER OR USING THE SOFTWARE DELIVERED HEREWITH YOU ACKNOWLEDGE THAT YOU HAVE READ THIS AGREEMENT UNDERSTAND ITS CONTENTS AND AGREE TO BE BOUND BY ITS TERMS AND CONDITIONS IF YOU D
130. for MDL Direct To use MDL Direct as a structure provider for the Structure Analytics tools the data source or data sources must first be defined according to amp rdquor MDL Direct Data Integration Then continue by creating column elements according to the following process gt Create column elements 1 Open the Information Designer 2 Inthe Select workbench drop down list choose Multiple Columns 3 Click Change 4 In the Data Sources tree view to the left click to select the molecule table This is usually called MDL environment MOL e g ISISRC2D MOL 5 Click Add gt 6 In the Information Model tree view to the right create a new domain by right clicking and selecting New Domain from the pop up menu Comment The new domain will be created under the domain that you currently have selected To place your new domain at the root level first click Select None 7 Inthe Information Model tree click on your newly created domain 8 Inthe Multiple Columns workbench click Select 9 Click Save 3 4 8 Creating a Molfile Column Element gt To create a molfile column element 1 In the Select workbench drop down list choose Column 2 Click Change 3 In the Data Sources tree view under the previously used molecule table click on the blob column that contains structures usually named CTAB 4 Inthe Column Element workbench click Add 5 Change the calculation to molfile C1 Comment The functi
131. gardless of whether the later prompt steps are independent or not Personalized Information Links Using personalized information links you can set up a data source to return only information applicable for a certain User or Group Depending on which user is logged in and accesses the information link different subsets of the data will be available For example you could set up an information link that detects whether the user retrieving data is a member of the sales force for Europe Asia or the US and only return data for that continent Below are two examples of personalized information links The first will retrieve data depending on which user is logged in the second depending on which groups that user is a member of User Name via Lookup Table Scenario You want to set up an information link to a table of data with sales made by all the sales people in his company However depending on which person from the sales department accesses an analysis using this information link only the sales figures pertaining to that single user should be retrieved First take a look at the Sales table containing the total sales of every person in the sales force Order ID Employee ID Product Sale 1 101 Cornflakes 100 2 150 Soda 550 3 244 Cornflakes 160 4 101 Mineral Water 400 5 101 Soda 120 6 339 Mineral Water 200 Then you must create a Lookup Table that matches the Employee ID to the actual Spotfire U
132. gt server webapps spotfire WEB INF folder TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Spotfire Select workbench Connect Library Database v DecisionSite Administrator Spotfire Library Spotfire Library status Running p Spotfire Library Database The Spotfire Library must be stopped before you can edit these settings Make sure that the library is not being used by anyone before you click Stop Database Type Oracle server Oracle port Oracle SID Oracle user name Oracle password Number of connections Minimum B Maximum 5 4 Enter the Spotfire Library database connection settings These must match the settings specified in the Installation Procedures chapter of the Spotfire Analytics Server Installation and Upgrade Manual 5 Click on the Start button to activate the Spotfire Library 6 TheSpotfire Library Status should change to amp rdquor Running 1 5 4 Specifying the Library Section Creators Next you must specify which users and groups will be Library Section Creators These users will be allowed to create new Library Sections As DecisionSite Administrator you already have full access to the Spotfire Library gt To allow users to create Library sections From the Select workbench drop down menu select Library Section Creators 1 Click on the Change button Spotfire Select workbench Library Section Creators DecisionSite Administrator Decis
133. he connection 6 Enter Oracle server Oracle port and Oracle SID Configuring DecisionSite 7 Enter an Oracle user and password which has access rights to the ISIS Direct database 8 Enter the minimum and maximum number of connections 9 Enter the necessary information for the ISIS table names The table below summarizes the ISIS Connection setup in DecisionSite Posters and also shows the executed SQL statements to help you understand the mechanics behind the connections Three SQL statements are constructed based on information entered during the ISIS Connection Setup in DecisionSite Posters ISIS Explanation Example Example ISIS Description Connection Values SQL Statement Items Oracle User A user that has isis user SELECT ISIS Direct Name access rights to cdcaux ctenvinit isis Initialization the ISIS Direct user isisrc2d FROM Command database dual executed once to Main Table The name of the isisrc2d initialize ISIS Database TO DS Direct at first connection Structure The table that isisrc2d mol establishment Table contains the Structure column Structure The column ctab Column with structure information Can be BLOBs or similar Structure Key The column cdbregno Column with the unique numbers identifiers for Or the structures corpid strings Name Table The table that isisrc2d mol SELECT molname Chemical Name contains the Name column Name Column The column
134. he Library Section Owner can also edit the access permissions by adding users to the Library Sections read write and Owner groups Only the Library Section Owner can delete a Library Section Each Library Section has its own set of access permissions and they are enforced in the same way throughout the entire Library Section Example Tom adds the manager of each department Ann for research Peter for sales and Nicole for management as Library Section Creators Eventually Tom might add more people as Creators but for now these people will do The departments will create the Library Sections they need as their work changes For example sales and management create one Library Section each for the publishing of DecisionSite Posters of sales statistics and management reports In Research Ann creates a Library Section for each project in her department adding an extra Library Section Owner for each Peter and Ann assign write access to their staff and read access to management Nicole gives management write access to their Library Section Tom finally adds the members of the developer group at the research department as Library Section Creators They can then create new Library Sections for development purposes Management Sales Nicole Peter Research Ann Development team Project A Project B Project C 45 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual A view of the major Library Sectio
135. he Library is divided into Library Sections where all access permissions are set It is the Library Sections which contains the analysis material and folders The permissions apply to the entire Library Section regardless of the folder structure inside it Library Sections can only be created by Library Section Creators which is a group controlled in the Library Administrator Overview of Library Design Your Library should reflect your company This is a recommended practice This applies to the structure of Library Sections and folders as well as the access permissions of the users The first step of designing your Library after installation is to add users to the Library Section Creators group which is the group that has permission to create Library Sections It is recommended that the members of this group be the same users that manage content and users in your organization It is also recommended that the creators of analysis material such as Guides and Posters become members of this group When you have organized the members of the Library Section Creators group it is recommended that you create a number of Library Sections that reflect your company These will act as a preconfigured structure which the users can use Depending on your company and its business model a few designs are recommended e By DecisionSite Application If the users work in DecisionSite Applications such as DecisionSite for Lead Discovery and or custom DecisionSite A
136. hese questions will guide you in setting up the correct joins columns and filters Will users build their own information links Some end users will want to use the column and filter elements that you design and assemble their own information links queries using Information Builder Others will be less experienced or may perform repetitive tasks For these you should consider preparing complete information links in advance 101 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 4 2 4 3 4 3 4 3 4 4 102 Where to Store Join Elements From a technical point of view join elements can be placed anywhere in the tree structure They are not visible to end users and the system will find the join elements needed for a particular query regardless of location Unlike filter and column elements no control of permissions is performed on join elements Nevertheless it is a good habit to place joins in logical locations so they can easily be found for reconfiguration Consider placing join elements in a special join domain near the root domain for each data source In other words if you have an ISIS Direct data source then create an ISIS root domain with an ISIS joins sub domain Understanding Filters There are two ways to control filtering in Spotfire Information Designer One is to create separate filter elements These will appear as icons and allow the end user to apply them in an informa
137. ies Pane Properties for user toml Search for available groups heme Available groups User included in Pharmacology Team All Licences Enabled Everyone Add gt Products DecisionSite for Functional Genomics Cl DecisionSite for Lead Discovery C Decisionsite MapConnect DecisionSite Posters DecisionSite Statistics DecisionSite Library C Computation Services Designers L Decisionsite for Lead Discovery no ISIS Host DecisionSite level DecisionSite Nominal Iv Option Change password Remove user Save This Configuration Search Available groups User included in Add gt Description Change the password for this user Remove this user Save the settings for this user Populates the Available groups list with groups that match the search criteria The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Groups matching the search criteria Groups to which this user belongs Click to add selected groups to User included in 55 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 2 3 2 56 lt Remove Click to remove selected groups from User included in Products Products to which this user has access DecisionSite Level Level of access gt To reach the User Properties pane 1 2 3 4 At the top of the page click User
138. ies az Clear Link Filter type Limits Ab Employe range Jl EIS 2 Salary range 1100 2200 EEK A Location values cHicaco EA Option Description Filter type Select range or values to add a hard filter to a column Limits Enter upper lower limits for a range filter or list the required values separated by commas for a values filter EE Click to move the elements up or down This is used to control the order of columns with run time filters Filter elements are always applied before run time filters regardless of order X Click to remove an individual element from the link Advanced tab Clear Link Retrieve Independent Prompt Employe v E None Salary IR v Range Location IV m Check Boxes D ICE Advanced Option Description Retrieve Deselect to prevent a column from being loaded Filter conditions will still affect the amount of data loaded Independent If selected the element will be treated as independent in a prompted information link This is used to improve performance of information links when retrieving data from STAR schema databases See Making Elements Independent for more information Prompt Select how each run time filter should appear when the link is opened Select None to disable run time filtering If a run time filter is selected all TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 4 5 4 4 4 5 1 4 4 4
139. ilter conditions using the API 4 3 3 2 3 Information Model Pop up Menu The pop up menu is reached by right clicking in the Information Model tree structure Option Copy GUID New Domain Edit Edit SQL View SQL Delete Rename Select None Description Copies the GUID of the selected element to the clipboard Opens the New Domain dialog where you can enter a name for the new domain folder Clicking OK in the dialog will create the new domain on the level of the selected element Opens the Workbench used to edit the selected element Domain Join Column Filter or Edit SQL Workbench for information links Opens the Edit SQL Workbench Only available for information links Opens the View SQL dialog which displays the SQL statements used in the selected information link Not available for other types of elements Remove the selected element from the Information Model Opens the Rename Element dialog where you can enter a new name for the selected element Deselects all elements Can be used in case you want to save any type of element to the root level 85 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 2 4 View SQL Dialog x SQL for the selected Information Link Data Source ActivityB SELECT I37 ISISCPD AS ISISCPD T38 OBJDID AS OBJID I37 ISISCPD AS ISISMAPPING ISISCPD FROM SYSADMIN ISISMAPPING I37 SYSADMIN TOTSODRS
140. in operator A comparison operator in a join condition that determines how the two sides of the condition are evaluated and which records are returned The most common comparison operator is equivalence Key A column used to identify a record often used as the index column for a table Personalized Information Links An information link that returns a subset of data depending on which user is logged in Pre updates A pre updates element is part of a SQLQuery definition and contains SQL update statements to be executed before a query Post updates A post updates element is part of a SQLQuery definition and contains SQL update statements to be executed after a query 117 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Primary key A column or combination of columns that uniquely identifies rows in a table It cannot contain null values and must always have a unique index A primary key is used to relate a table to foreign keys in other tables Query A specific request or set of instructions for retrieving modifying inserting or deleting data in a database Record A term used in some database systems to mean row Although record and row have slightly different meanings in formal database theory in most instances they are used synonymously In Spotfire terminology usually taken to mean a datapoint in a visualization Run time filters Filters which prompt the user for filt
141. inate from downgrading per user packages The installer gracefully handles upgrade scenarios while downgrade scenarios may require manual steps Incorrect Installation of WSH The Spotfire System Checker can detect most installation problems Still there are some issues that are not handled properly The most common problem originates from insufficient versions of Microsoft Windows Scripting Microsoft Windows Scripting can be installed separately but is generally installed with Microsoft Internet Explorer 165 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Symptom An error dialog when Spotfire DecisionSite Client is started The dialog reports that Spotfire Application Manager Spotfire eAppFramework Loader cannot be created Resolution Install the latest version of Microsoft Windows Scripting The installer can be downloaded from http msdn microsoft com scripting 4 5 6 3 Corrupted Registration The package registration can be corrupted for a number of reasons Common sources are e Uninstall of DecisionSite Client v6 e Restoring an old registry backup e Usage of roaming profiles on Microsoft Windows 2000 or later e Manual removal of files folders and registration The Application Manager silently resolves many errors during start up but severe corruption will require additional attention Spotfire provides a tool for fixing the corrupted registration Please contact Spotfire Support for
142. ing Elements Independent in Prompted Information Links The default behavior of prompted information links is that each subsequent step lists values based on earlier selections See Run time Filter Example However if you are working against a STAR schema database the procedure may require multiple joins since the elements queried for the prompts can only be joined by also joining over the large fact table in the STAR schema This may result in very long times passing between each prompt To avoid the long prompt times it may be useful to treat the various elements as independent and avoid filtering upon each prompt step gt To make an element independent 1 Create a new information link or modify an existing link 2 Inthe Information Link pane go to the Advanced tab 3 Foreach element use the Independent check box to select whether to treat the element as independent or not Comment Note that setting columns or filters as independent may result in no data returned from the information link 4 Save the information link or open it Note Setting an element to Independent will have the effect that no previous selections in the prompt steps will be reflected in the listing for the independent element Neither will any of the 123 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 3 2 7 124 selections made in the prompt step for the independent element be reflected in later prompt steps re
143. ing the 5 0 Model you should see the following Information Links and Query Elements in the Information Designer E ACTIVITYBASE 50 Information Links cip Pivot Compound Run vip QC Markers diL Test Occasion aiL Test Request Query Elements Filters J QC Results Test ccasion TestSet prpmno PROTPARM TOTSODRS ttodimo TEST TREQTSET ttordimo TEST TOCCASON ttordimo TEST TOTSODRS ttordimo TEST TSETCSRS ttordimo TSETSCRS TREQSET ActivityBase 5 0 Information Model 3 4 6 MDL Direct Data Integration ES D EN gt To configure Information Services to connect to MDL Direct 1 Open the Information Designer 2 Create a new data source for the MDL database using the Data Source Definition workbench 3 Set the New connection initialization commands field to select cdcaux ctenvinit isis isisrc2d from dual where amp rsquor isis isisrc2d should be replaced by the name of the MDL environment that is enabled for MDL Direct An MDL environment is a set of tables that contain chemical information and chemically intelligent index mechanisms for binary structures 36 Configuring DecisionSite Note The amp rdquor New connection initialization commands option is used to point out the MDL environment Therefore if you want to use multiple MDL connections you must make a new connection for each MDL environment that you want to use 3 4 7 Creating Column Elements
144. ion Links 4 Write a clear description of how the column is filtered This is important since the user will not be able to disable the filter when using this column element Note When an information link is executed aggregation is always applied before the filter Date and Time Columns A data source provides date and time information as Oracle DATE columns This format can be mapped to either a DATE TIME or a DATETIME data type in the Information Model see Creating a Column Element Note The lowest valid year is 100 gt To find the number of days between two DATE columns 1 From the Data Sources pane select two columns of type DATE 2 Inthe Calculation field enter the expression c c2 Comment By selecting only one column you can also find the elapsed number of days from today using the expression sysdate cl 3 Inthe Save column section set Type to integer gt To generate a Spotfire DecisionSite DATE column from an Oracle DATE column 1 From the Data Sources pane select a column of type DATE 2 Inthe Save column section set Type to date Note Any SQL arithmetic expression may be entered into the Calculation field amp endash however you need to make sure to use the correct syntax since no validation will be performed Working with Aggregation Using Aggregation gt To calculate average values 1 Selecta value column from the Data Sources pane 71 TIBCO Spotfire amp DecisionSite 9 1 1
145. ion independent you avoid having to join to the large fact table for each prompt When the information link is opened you will first be prompted to choose a DeptNo Instead of going through the large fact table to the Location table and filter out all values except the ones for Chicago you will see all values in the DeptNo column For the next prompt step the much quicker connection between DeptNo and Gender is used directly thus improving the performance of the information link Note When Location is made independent you will see all possible values in the prompt step for DeptNo even though some of them perhaps are inapplicable due to the hard filter setting Chicago on the Location column 3 Set Filter for Column Step 1 of 2 Select DeptNo This means that if all employees in the Chicago office belong to department number 30 you might accidentally select number 20 in the prompt step for DeptNo with the result that no data is retrieved from the server If the Independent option had not been selected the hard filter on Chicago would have been applied prior to the first prompting step and DeptNo 30 would have been the only one displayed in the prompt list Retrieve Independent Prompt E Set Filter for Column DeptNo Iv IT List Box Gander KG r us5x 8 Step 1 of 2 Select DeptNo Location E IT None X Salary IV NN None In this case the risk of selecting wrong data in a prompt step is minimized Filtering Using Str
146. ionSite Library Available users and groups E Library Section Creators User spotfire Group Everyone i 1 sp Group g1 User jfk User ui User u2 lt lt Remove Save Cancel 2 Inthe search field type in the name of the group or user you are interested in The groups and users matching the search criteria are displayed in the leftmost list Tip You can use regular expressions to limit the search For example use an asterisk to display all users or append it to a string John to display all users beginning with John 3 Select one or many groups and users from the leftmost list and click on the Add gt gt button to include them as Library Section Creators Deploying DecisionSite for the First Time You can also select one or many groups and or users from the rightmost list of owners and click on the lt lt Remove button to remove them from the list of owners Click on the Save button to make your changes take effect The Spotfire Library has now been set up and is ready to use 1 6 Configuring Additional Functionality You have now deployed DecisionSite Client 9 1 1 on the Spotfire Analytics Server and set up all the basic functionality However there are a number of additional features that you can set up and configure for use on your DecisionSite system if you have purchased the corresponding licenses Additional Features DecisionSite Posters Computation Services DecisionSit
147. isting information links gt To modify an information link 1 In the Elements pane click the information link you wish to edit Response The description of the link appears in the Details pane Click Edit Link Response The content of the information link appears in the Information Link pane Edit the link in the Information Link pane by adding or removing elements or by changing the filtering for a column Open the modified link or save it by clicking the bi button 121 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Comment Replace the old information link by choosing the same name and folder location as the old link Enter a new name or put the link in another folder to keep both the old and the modified information links 4 4 3 2 3 Deleting an Information Link gt To delete an information link from the Information Model 1 Select an information link 2 Click the button on the toolbar Response A dialog appears prompting you to confirm that you want to delete the link 3 Click Yes Note You can only delete information links Column and filter elements cannot be deleted by anyone other than the administrator 4 4 3 2 4 Adding Hard Filters Hard filters are set up as you define the information link and are saved with the link This means that they cannot be reused in other links Also hard filters can only specify a range or a list of values and are therefore less comp
148. isual capabilities of Spotfire DecisionSite to set these values Information Link Ji Sct Filter for Column 5B Let values from Data Set xj Step 2 of 3 Select Salary column 5 Get values from s Selected records OK 7 Cancel gt To use the current visualization for filter definition 1 Open a suitable data set in DecisionSite 2 Choose a subset either by selecting using the query devices or by marking records Comment Marking means clicking and dragging a rectangle around a group of markers in a visualization 3 Open an information link that contains prompted filters When the Set Filter for Column dialog for the desired column appears click Get Values or Get Range Response The Get Values from Data Set dialog is displayed 5 From the Matching column drop down list select the column in the visualized data set from which you want to get the values or the range 6 Click Selected records or Marked records depending on which values you want to use 7 Click OK 8 In the Set Filter for Column dialog click Next gt or Finish if this is the last prompted column 9 Repeat steps 4 to 8 for each prompted column Response The data is loaded and displayed in a visualization Adding Columns to an Existing Data Set As you assemble your data set you may want to create a few intermediate visualizations to see what information needs to be added and what can be left out Spotfire DecisionSit
149. ite 9 1 1 Deployment and Administration Manual 4 2 2 3 5 4 2 2 3 6 4 2 2 4 4 2 2 4 1 Comment To see all users enter an asterisk wildcard The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string 3 Click Search In the Matching Users list click a user ID Response The properties of the selected user are displayed 5 Inthe Search for available groups field enter a search criteria for finding groups Comment To see all groups enter an asterisk wildcard 6 Click Search 7 Inthe Available groups list box select the groups to which you want the user to belong 8 Click Add gt 9 Select one or more Products to which you wish to grant the user access 10 From the DecisionSite level drop down list select the level of access granted to the user 11 Click Save This Configuration Importing a List of Users This can only be done when using Database Authentication gt Toimport a list of users 1 At the top of the page click the Users tab 2 Click Import Users 3 Inthe Import Users from File dialog enter a file name or browse for a file 4 Click OK Response The users listed in the file are added Note The file must be a comma separated text file UTF 8 in this format username l passwordl username2 password2 Exporting a List of Users gt Toexport a list of users 1 At the top of the page click the Users tab Click Expor
150. ized filter condition that limits data depending on the currently logged in user See Personalized Information Links In the Name field enter the name for the new filter In the Description field type your own description of the filter In the Information Model select a domain and then click the Select button Click Save to save the filter in the selected domain folder QOEM 3 4 3 2 5 3 Editing a Filter This section describes how to edit the properties of a filter gt To edit a filter element 1 In the Information Model pane select the filter that you want to edit 2 Click the Edit button at the top of the Information Model pane Response The name of the filter and filter conditions are loaded and enabled for editing 3 Modify the desired fields Tip To move an existing filter to a new domain select a new domain in the Information Model pane then click the Select button 4 Click Save or Save Copy Comment Use Save Copy if you do not want to overwrite the old filter definition Tip To see from which table and database a column has been taken click the column name The path to the data source appears at the bottom of the page 74 4 3 2 5 4 4 3 2 5 5 4 3 2 6 4 3 2 6 1 Spotfire DecisionSite Administration EDTUSES Add gt Remove Deleting a Filter gt To delete a filter 1 In the Information Model pane select the filter that you want to delete 2 Click the Delete button at the
151. join between the table and its alias WHERE TABLE IDZTABLE ALIASI MANAGER Domains Domains Overview Column elements filter elements and joins can be organized into domains in the Information Model the same way files are often organized into folders A domain may contain other domains For example a department may have a domain within which each research group has its own subdomain As an administrator you can control which users have access to specific domains In the Information Model pane you will see that domains have the same collapsible and expandable behavior as folders in a tree structure E C G3 Creating a New Domain To be able to save column and filter elements you must first create a domain in the Information Model gt To create a new domain 1 From the Select workbench drop down list select Domain 2 Click Change Response The Domain Element workbench is displayed 3 Inthe Name field enter the name of the new domain In the Description field enter your own description of this domain 5 Inthe Information Model pane select a parent domain and then click Select The new domain will become a subdomain of the selected domain Comment If no parent domain is selected the created domain will be placed in the root of the Information Model 6 Click Save Response The domain is added to the Information Model Editing a Domain gt To change the name and description of a domain 1 In the Inf
152. k to your usual DecisionSite start page 4 4 3 2 Editing Information Links 4 4 3 2 1 Creating a New Information Link Information Builder allows you to create information links The building blocks are column filter and procedure elements that have been set up by the administrator gt To create an information link 1 In the Elements pane select the column and filter elements that you want to include You can also include procedures Comment To select multiple items hold down the Ctrl key and then click on the desired items Click the symbol to expand a domain Click Add to link Response The selected elements will be added to the Information Link pane Comment If you want to add more elements repeat steps 1 and 2 To remove an item from the information link pane click the X button for the element to be excluded If you want to filter the data set Filter type and Limits Click thell icon Response The Save Information Link dialog appears In the Domains view select where you want the information link to be saved In the Name field enter a name for the information link In the Description field enter some text describing the purpose of the information link This is optional Click OK Response The new information link is added to the Information Model It can now be accessed by other users 4 4 3 2 2 Modifying an Information Link If you have been given permission by the administrator you can edit ex
153. kslash 148 Spotfire DecisionSite Administration Values xi Step 1 of 3 Select Employe Please enter a comma separated list of values below Get values from current visualization Get Values Get values from a text file Browse Help Next gt Cancel Option Description Text field Enter a comma separated list of column values that you want to use as a constraint You can also paste values of a column from a Microsoft Excel sheet Note When using the Get Values feature the characters and V will automatically appear prefixed with a backslash Get Values Use this button to set the column filter by fetching values from the current visualization in DecisionSite Opens the Get Values from Data Set dialog Browse Fetch filter values from a text file 149 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Range A Set Filter for Column Part Description Lower Enter the lower limit for the values of the column Upper Enter the upper limit for the values of the column Get Range Use this button to set the column filter by fetching values from the current visualization in DecisionSite Opens the Get Values from Data Set dialog 150 Spotfire DecisionSite Administration List Box x Step 1 of 3 Select Day 210 F 211 Include empty values for this step Help lt Back Next gt Cancel Option Description Lis
154. l and administration features of Spotfire DecisionSite There are five levels available e None amp endash The default level a user gets before being assigned a proper level If a user or group with no DecisionSite level is assigned a product license for either DecisionSite for Lead Discovery or DecisionSite for Functional Genomics the DecisionSite level of that user or group will be automatically changed to nominal by the admin tool e Nominal amp endash For users who do not use any of the Information Services capabilities but use all of the other fundamental features of DecisionSite e Basic amp endash Users of the Information Library and the fundamental features e Power amp endash Users of the Information Library and Information Builder and the fundamental features e Administrator amp endash Users of Information Library Information Builder and Administration Tools Information Designer and DecisionSite Administrator and the fundamental features Users and groups can have access to multiple product licenses while only one choice of DecisionSite level is applicable 48 Spotfire DecisionSite Administration 4 2 2 3 Managing Users 4 2 2 3 1 Adding New Users This can only be done when using Database Authentication gt To add a new user account 1 At the top of the page click the Users tab 2 Click Create User Response The Create New User dialog is displayed 3 Enter the user name and password This will
155. l be removed from the SQL statement This is due to the fact that the hints in the different information links might conflict with each other and that there is currently no way for the system to figure out if the two hints will work together Spotfire DecisionSite Administration Z View SQL and Edit Oracle Hints my xj SQL for current Information Link elements Data Source ActivityB Edit Oracle Hints SELECT I41 ISISCPD AS ISISCPD 1 T4Zz O BJDID AS OBJID 1 I4Jl ISISCPD AS ISISCPD 2 T42 O BJDID AS OBJID 2 I41 ISISCPD AS ISISMAPPING ISISCPD FROM SYSADMIN ISISMAPPING I4l SYSADMIN TOTSODRS T4Z RE I41 O0BJDID T42 0BJDID Data Source ISIS DIRECT Edit Oracle Hints SELECT E To C ChRDWY N O AS ChRDW NOG SlS n Help Copy SOL OK Cancel Option Description SQL for current Displays the SQL statements behind an information link If several Data Information Sources are used the SQL statements for the different sources are Link elements separated by lines Edit Oracle Displays the Edit Oracle Hints dialog Here you can enter an oracle hint in Hints order to improve performance of the information link when using complex data sources Note In some cases adding a hint can actually decrease the performance of an information link If this is the case click Edit Oracle Hints and remove the hint Copy SQL Copies the SQL statements to the clipbo
156. l contribute only the matching records The column on the opposite side will return all records 10 Select which Tables to join using the two drop down lists Comment This is necessary when more than two tables are involved in defining the join See also Freehand joins 11 If you want the join to be case sensitive select the Case sensitive check box 12 In the Name field enter a name for the join 13 In the Description field enter your own description of the join 14 In the Information Model pane select a parent domain and then click the lt Select button 15 Sometimes you may want to create more than one join between the same two tables In such a situation one of the joins must be the default one that Information Links will use If you want the join you are currently creating to be the default one select the check box Default join 16 Click the Save button to save the join in the selected parent domain Response The join will receive a GUID in the selected domain and will be denoted with the Eicon Note that the join object only appears in the Information Designer and will not be visible to the user Freehand Joins In many situations a join can be defined using one of the operators in the Conditions drop down list However it may sometimes be desirable to use more complex conditions such as e CI 2 C2 mathematical calculation prior to comparison e Cl C3 AND C4 C2 an intermediate table used to set up the join
157. lex than filter elements gt To add hard filters for a column 1 Create an information link 2 Select the Properties tab 3 Foreach column use the Filter type drop down list to select whether to filter by range or by values Comment Filtering by range means entering the upper and lower limits of the desired range Filtering by values means entering the exact values that you want to include in the returned data If no values are entered there will not be any filtering applied to the selected column Strings containing commas can be included as values as well as range limits using backslash as prefix For instance if you want to include the two strings Madonna and Banderas Antonio as values you would need to escape the comma by entering Madonna Banderas Antonio 4 Set the upper and lower limits range or enter the desired values separated with commas values Comment 1 Limits are inclusive In other words if the lower limit is set to 1000 the value 1000 will be included in the data set Comment 2 When setting upper and lower limits on columns of type String A is considered to come before AA and S comes before Smith This means that the name Smith will not be present when choosing names from D to S The order of characters in standard ASCII Comment 3 When setting upper and lower limits on columns of type Date note that only the standard date format yyyy mm dd is recognized Example enter 1969 11 17 for Nove
158. lick Custom Level Under Download signed ActiveX Controls select Prompt Under Run ActiveX controls and plug ins select Enable Under Script ActiveX controls marked safe for scripting select Enable Click OK 10 In the Internet Options dialog click OK Note Enabling ActiveX controls is important also when using Information Builder or Information Library SEN UOS ON pests Glossary Glossary The glossary only contains brief definitions of the terminology You can also use the Index or Search tab to the left to find more information within this help file Column element A list of values A column element can correspond to a database field but can also be the result of calculations performed on multiple fields from several databases What the column element returns is defined by the administrator Database A collection of related data usually in the form of multiple files or tables that are linked to each other Data connection A collection of information required to access a specific database The collection includes a data source name DSN and login information Data connections are stored in a project and are activated when the user performs an action that requires access to the database Data source The entity that provides data similar to the term back end Element Any constituent that can be added to an information link in other words column elements filter elements and other information links Field
159. lick Next Enter a description and a keyword then click Finish Configuring DecisionSite Response The Poster Published dialog is displayed x baseball has been published You can access the Poster via this link Test Section gt baseball Copy Link Send an email to notify users about the Poster Send Email Help Close 17 Click Send Email 18 Enter your own email address in the To field and the From field and click OK 19 Click Close in the Poster Published dialog 20 An email should arrive shortly Verify that is looks good 2 Click on the plot in the email and verify that the Poster is opened in a new browser window Installation verified 3 2 Configuring Computation Services 3 2 1 Setting Permissions for Computation Services Computation Services enables DecisionSite users to connect to various third party statistics servers such as SAS R and S PLUS gt To make the Computation Services features available to users 1 InDecisionSite Administrator select Users or Groups from the top menu frame 2 Selectthe Computation Services Designers check box for the users and or groups that you wish to have permission to use each feature Comment The licence controls which users will have access to the design environment of Computation Services All users of DecisionSite will be able to execute predefined configurations if they are incorporated in a Guide 3 Click on the Save this Configuration b
160. ll automatically upgrade itself and all new applications tools and guides Platform for DecisionSite Client Applications Platform for DecisionSite Client Applications DecisionSite ApplicationManager constitutes the platform for DecisionSite client applications enabling customers and third party companies to extend the existing functionality of DecisionSite Client applications Runtime Components The DecisionSite ApplicationManager provides APIs for managing e URLs e Paths e Files e Registry e Data protection e XML e For handling e and more Spotfire Protocol The DecisionSite ApplicationManager defines its own protocol the spotfire protocol for e Shipping and addressing DHTML and JScript for online and offline usage 159 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 5 2 4 4 5 2 5 4 5 2 6 4 5 3 4 5 3 1 160 e Providing a security model for trusted DecisionSite client applications Software Distribution The DecisionSite ApplicationManager provides the mechanism through which DecisionSite client applications are delivered from the Spotfire Analytics Server to the DecisionSite clients Features provided through this mechanism are e Packaging format e Automatic deployment from server e Strict versioning policy In addition to this built in functionality for DecisionSite client software distribution customers can use the following alternative distribution
161. logy Browser Connects ontology files to the data set via annotation files The Gene Ontology Browser tool can also run using local files but setting up files on the server simplifies the use of the tool for the end user These are the main tasks e Setting up the Retrieve from Database tool during server installation e Setting up the Affymetrix database environment importing the IM for use of information links e Setting up the Pathway Viewer map information e Setting up Gene Ontology Browser ontology and annotation files 3 3 3 Affymetrix Database Configuration Information Models access data through Data Sources defined using the Information Designer See Spotfire Analytics Server Administrator s Guide for more information regarding general concepts of data sources and Information Models The Affymetrix Analysis Data Model AADM is the relational database schema Affymetrix uses to store experiment results The AADM Information Model is used to retrieve Affymetrix Analysis information from the AADM database into Spotfire DecisionSite Client It also includes information links that prompt the end user for metadata information and retrieves the Affymetrix Analysis Information for STAT AADM For a detailed schema of the AADM database see the following link https www affymetrix com support developer aadm content affx 3 3 4 Copying the DSFG Information Model The Information Model for AADM which is included
162. lows SELECT ET ENAME AS Employee jmd Sy Mig AS Wisysvllewes 0S0 H money converter El SAL AS Salary SEK FROM WSOC TR ENEE SES Note Some of the more advanced features of PL SQL are not supported for example stored procedures or executing anonymous PL SQL Blocks 4 3 4 9 Details on Data Sources and Information Models Prior to version 7 1 of Spotfire Analytics Server Information Services used database links to access the data A problem with database links is that they must be defined in the database In DecisionSite 7 1 and later the data sources concept allows direct connection to a separate data source instead of via the database links This makes it a lot easier to move an Information Model IM 107 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual End uzers wanl la Ding in dala fram StS Activity base Data Sources pane Data Sources pane Oracle 1 data epps ISIS catalog ISIS schema Tablet Table2 Activity Base catalog Base schema Table3 Table4 ISIS data source AtivituBase data source Ouer dala Since all references in an exported Information Model go to the data sources object all problems that can occur on import due to changes in database structure can be avoided An Information Model can be imported directly and the data source can later be renamed using the Information Designer Data Sources W
163. lt Select Type ea sz Set Filter devices We create a new column Employees with high salary with the following filter condition FCL gt Select avg SAL from SCOTT EMP DBLINK Note Be careful to include all brackets or it will not work The column element defined above will result in the following SQL when executed as part of an information link notice that the WHERE clause includes the sub query from the filter condition SELECT E1 ENAME AS Employees with high salary FROM een ee eM DEE OASE Ab WHERE US Ste edt Select avg SAL 112 Spotfire DecisionSite Administration from SCOTT EMP DBLINK 4 3 4 11 ISIS Examples 4 3 4 11 1 Extracting Molecular Weight from a Structure Column Databases with the ISIS Direct Cartridge allow you to use ISIS Direct operators to extract information from a BLOB column that contains binary chemical structures The molwt operator for example calculates the molecular weight of a structure gt To create a molecular weight column Column Element Help Columns Add gt CTAB C1 Remove Calculation molwt C1 Aggregation Show gt gt 1 From the Select workbench drop down list select Column and click Change 2 Inthe Data Sources pane select the structure BLOB column In this example it has the name CTAB 3 Click Add gt 4 Inthe Calculation field type molwt C1 Enter Name and
164. lues for physically distant databases Use lower values when the number of users is high Entering the value zero will make the JDBC driver use its default value Click Save Copy to create a copy with a new GUID Click Save to save or update the data source Clears all fields without saving 4 3 3 3 2 4 3 3 3 3 Spotfire DecisionSite Administration Domain Workbench GUID 6613d870 5821 11d6 309e 0010ac110132 Name Human Resources Description Human Resources Department Dat Parent domain Departments lt Select Option GUID Name Description Parent domain cow Description A unique identifier used internally to identify the data elements The GUID appears once the Domain has been created and saved The name of the domain to be saved edited A free text description of the domain The maximum limit of the description is 255 characters The name of domain folder where you want to save the domain lt Select Select a domain in the Information Model and then click this button to retrieve the name Save Copy Click Save Copy to create a copy with a new GUID Save Click Save to save or update the domain Clear Clears all fields without saving Join Workbench Columns Add gt ENAME C1 ENAME C2 Remove Condition Select ci C2 M Case sensitive C Freehand Tables to join BIGEMP EMP z GUID Name Description Parent domain Default join
165. lways be executed after any query procedure gt To Create a Query procedure 1 2 10 From the Select workbench drop down list select Procedures Click Change Response The Procedures workbench is displayed From the Data Sources pane select the database procedure you wish to use Click Add gt Response The database procedure is added to the workbench Information Designer analyzes the database procedure and makes a guess as to whether it is a pre update procedure or a query procedure it never sets post procedure by default M Procedure Add gt blade2 OE INSERT_INTO_TESTTABLE Type Query procedure Select the Type of procedure in this case a Query procedure If the database procedure requires any Input Parameters their name and type are displayed Input Parameters Name Type Default value Permit null Prompt Y string Boston E Single value DI Select whether the input parameter should receive a Default value by entering a value of the appropriate type in the input field If not leave the field blank Select whether you want the end user to be prompted for a single value several values or not at all from the Prompt drop down list box Comment If you select several values the end user will be allowed to enter several values separated by a comma The procedure will run once for each of these values in an iterative loop If you want to allow the input parameter to be Null select the Permit N
166. ly shown in the Information Link pane into a new or updated information link x Deletes the information link selected in the Elements pane H Refreshes the entire tree structure in the Elements pane Note Use right click and Refresh to update only the selected element sql Displays the View SQL and Edit Oracle Hints dialog Elements Contains information about the available elements See the Elements pane topic for more information Information Link Lists the elements included in the current information link See the Information Link Pane topic for more details on the various parts of this pane Clear Link Clears the entire Information Link pane without saving Properties tab This tab is used to define hard filters for any column Advanced tab This tab is used to define run time filters for any column Conditioning Displays which type of conditioning is used for the information link Selected by clicking Edit Conditioning Opens the Data Conditioning dialog where you can select between the Edit conditioning types Distinct or Pivot or None Join Path Edit If there are several possible join paths between the tables in the information link you can specify which join path to use by clicking Edit This opens the Join Path dialog Open Executes an information link and retrieves the data into Spotfire DecisionSite 4 4 4 2 Elements Pane Elements Available elements Details E J Documentation 2 2 Filters gm
167. m which table and database a column has been taken click the column name The path to the data source appears at the bottom of the page Add gt DNAME C1 Remove Deleting a Join gt To delete a join 1 In the Information Model pane select the join that you want to delete 2 Click the Delete button at the top of the Information Model pane Response The join is deleted from the Information Model Creating a Table Alias You can create a duplicate reference to a database table from Information Designer This duplicate is called a Table Alias and references the very same data only using an alias This can be useful in certain cases most often when in need of a self join within a table below gt Creating a Table Alias 1 Select a table in the Data Sources pane 2 Right click the table and select Add Alias Data Sources OfficialBugsystem oracle_1 gy CTXSYS 5 SPOTUSER_IIM BASEBALL FIL CITE NMF 4 3 2 4 4 3 2 4 1 Spotfire DecisionSite Administration 3 A Table Alias of the table is created 2 i SPOTUSER IM E BASEBALL E FILM H PHARMA a Cra PHARMA ALIAST H ROUGHNESS_DATA B SITE_FOUR Fim JA cite NMF Self Joins A Self Join is a join from a table to itself In Information Designer this is implemented by using a Table Alias ID Name Manager 1 Sarah 2 2 Mike 3 3 Carla Null 4
168. main After setting up the IM some information links are available 33 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 4 3 3 4 4 3 4 5 3 4 5 1 3 4 5 2 34 and new ones can be created using Information Builder MDL Direct as The Structure Analytics tools of DecisionSite for Lead structure provider Discovery needs access to structures from a structure provider If MDL ISIS Host is to be used as a structure provider no configuration is necessary on the server However if MDL Direct is to be used you will need to configure the desired connections according to the steps described later in this chapter These are the main tasks e Setting up the ActivityBase database environment importing the IM for use of information links e Configuring MDL Direct to be used as a structure provider for the Structure Analytics tools optional ActivityBase Database Configuration Information Models access data through Data Sources defined using the Information Designer The ActivityBase Information Models are used to retrieve information from the database into Spotfire DecisionSite Client Copying the DSLD Information Model The Information Models available for the different versions of ActivityBase are called e abase40 xml e abase4l xml e abase50 xml Copy the XML file of interest from installation directory gt server application data iis application iim a
169. mber 17th 1969 Note If the Filter type and Limits fields are disabled go to the Advanced tab and select None in the Prompt drop down box for that column It is not possible to combine run time filters with hard filters If this does not help the reason is probably that the administrator disabled Range and or Value filtering when setting up the column element Tip When entering values for filtering you are allowed to use wildcard characters These are matches any characters example mber would return the following months September November and December match any single character example ember would only return the month November 122 4 4 3 2 5 4 4 3 2 6 Spotfire DecisionSite Administration You can also copy columns from Microsoft Excel Mark data in Excel by pressing Ctrl C Paste the data in the values field of the selected column by pressing Ctrl V Adding Run time Filters An alternative to setting filter conditions on the Properties tab see Adding Hard Filters is to configure your information link to prompt for filter values as each column is retrieved This way you do not have to specify filter conditions in advance The data set will be pared down before the next column in sequence is processed unless you have selected to treat the columns as independent See Run time Filter Example for further information gt To enable run time filters 1 Create a new information link or modify an existi
170. n of the procedure In the Information Model pane select a parent domain and then click the lt Select button Click the Save button to save the join in the selected parent domain Response The procedure will receive a GUID in the selected domain and will be denoted with the IMAGE icon Note that the procedure object will be visible to the end user in the list of Information Links You can also make larger more complex 79 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 6 4 4 3 2 6 5 4 3 2 7 4 3 2 7 1 4 3 2 8 4 3 2 8 1 80 Information Links using the created procedure when creating an Information Link in Information Builder Editing a Procedure gt To edit a procedure 1 In the Information Model pane select the procedure that you want to edit 2 Click the Edit button in the Information Model pane Response The procedure is loaded and enabled for editing 3 Modify the desired fields Click Save or Save Copy Comment Use Save Copy if you want to keep the old procedure as well as the edited one Deleting a Procedure gt To delete a procedure 1 In the Information Model pane select the procedure that you want to delete 2 Click the Delete button at the top of the Information Model pane Response The procedure is deleted from the Information Model Export Exporting a Domain A domain including all subdomains and elements joins filters columns contai
171. ned therein can be saved as an XML file on the server gt To export a domain 1 From the Select workbench drop down list select Export 2 Click Change Response The Export workbench is displayed 3 Enter a filename e g abase50 xml Select Include permissions if you want the permission settings to be saved together with each exported element 5 Inthe Information Model pane select the domain that you want to export Click Select 7 Click Export Response The chosen domain and all information in it are saved on the server under lt installdir gt spotfire application data iis export On WebSphere web servers the path to the directory varies with the server name and may look something like this lt installdir gt installedApps lt server name gt Spotfire_DecisionSite_Analytics_Server ear application data iis export a Import Importing Elements A previously exported domain including all subdomains and elements joins filters columns can be imported back into the Information Model For example DecisionSite for Lead Discovery includes a predefined Information Model for ActivityBase This can easily be imported into your new Information Model 4 3 2 9 4 3 2 9 1 Spotfire DecisionSite Administration Note The IM is automatically updated if the name of an existing data source is changed Therefore you can import your IM directly and later change the names of your data source in the Data Sources workbench There
172. new join a complete join path using that join and the resulting default joins will be displayed By selecting additional joins the join path might be updated using other default joins to form the shortest join path given the current selected joins The basic principle of the Join path dialog is this The joins you pick for the Selected Joins list are the ones that will always be used in the join path These are the joins that are actually saved in the information link The joins displayed in the Additional Default Joins list are the joins that will complete the join path at this time Note that these may change if new default joins are created updated in Information Designer gt To Select a Join Path 1 When editing the information link you wish to select a join path for click the Join Path Edit button 129 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Response The Join Path dialog appears and the default join path is displayed in the Additional Default Joins list amp Join path Database Marketing Film larstest Pharma Sales C WindSite P TB1 joined TB2 Ei TB1 joined TB3 By Ja TB2 joined TB4 L E TB3 joined TB4 Select another join you wish to use from the Available Joins list and click Add 3 Response The new join is added to the Selected Joins list and the Additional Default Joins list is updated showing the default joins that will be used to create
173. ng link 2 Inthe Information Link pane go to the Advanced tab 3 Foreach column use the Prompt drop down list to select how you want to be prompted for filter conditions during data retrieval If you do not want run time filtering for a column select None Comment Selecting Values will let you enter a list of values to include Range will let you specify a range of values List Box will display a list box with the available values Check Boxes will display a check box for each value in the column Radio Buttons will display a radio button for each value Structure Search will allow you to filter by substructure or structure similarity see Filtering Using Structure Search 4 Save the information link or open it Note When using run time filters the prompts will appear in the order that the columns appear in the Information Link pane You can use the buttons to move columns up or down Filter elements are always applied before run time filters regardless of order Tip When entering values for filtering you are allowed to use wildcard characters These are matches any characters example mber would return the following months September November and December match any single character example ember would only return the month November You can also copy columns from Microsoft Excel Mark data in Excel by pressing Ctrl C Paste the data in the values field of the selected column by pressing Ctrl V Mak
174. ngs DecisionSite SQL Log Actual file sql log is located in the logs directory This file logs the SQL that is generated each time a user executes an information link You can set the detail level of what this file shall log by selecting different Log Configuration Files below DecisionSite Client Log Actual file dssclient log is located in the logs directory This file logs information each time an unsupported client tries to log on to the Spotfire Analytics Server The log entry will state the Operating System Web browser version etc It is always enabled and is unaffected by Log Configuration File settings DecisionSite Posters Log posteraccess log Actual file posteraccess log is located in the logs directory This file logs an entry every time a user creates or opens a Poster The format is Timestamp User User IP Command GUID Note Spotfire Analytics Server uses rolling logs which means that when a log file gets too big it splits into several files These are indexed by a number the higher the number the older the log and can be selected in the drop down list When a rolling log file reach a certain number it is deleted Note By default the DecisionSite logs use standard ISO 8601 date format If you prefer another date format you can edit the log4j config files For more information see http jakarta apache org log4j docs index html 4 2 2 5 2 4 2 2 6 4 2 2 6 1 Spotfire DecisionSite Administration Note
175. ngs to a group Modify Execute r1 SN C clinical Iv v C Phase1 Iv Iv C Filters O O C Phase2 E E C Phase3 Li C C Phase4 Scroll down to the domain folder that you want to make available for the chosen user and select the check boxes to set the Modify and Execute permissions Comment If you change the permissions for a domain that contains subdomains you will have the option to propagate the change to all the subdomains within that folder When you have set the permissions for the domains that should be available click the Save permissions button to save the settings Response The user will now be able to interact with these domains The level of interaction will depend on the Modify and Execute settings Information Links Editing the SQL of an Information Link Information Links are created using the Information Builder However sometimes there may be situations where complex SQL queries are needed that cannot be generated by Information Builder and the elements in the Information Model An example might be to retrieve information from relational databases or databases with complex schemas where queries generated by Information Builder are not fast enough and need tuning to reach an acceptable performance For those purposes the possibility to manipulate the generated SQL of an information link has been introduced gt To modify the SQL of an information link 1 In the Information Model pane browse the folder structure and
176. ns c ree eec e Ee HEU 72 SOL 110 Pme 71 Annotating information links creating a new information link sesssss 121 save information link dialog ApplicationManager Arithmetic expressions Assigning properties to groups EEN 51 properties to user 49 AVG RC site i RERO HE ote E 71 B Basic Level ep S AFER iE 48 BLOB 67 C Calculating columns nenne n a e 70 W e 67 GIOSING e eck 121 Information Builder eene 121 Column adding iere E eH EE UI eee OR 121 Calculating sisi raa dieses 70 Greatilng Ene 68 creating multiple rhet 69 deleting eR ORTU UE editilig 4 rie peri ar t pU eee re ES LHP ea dA elements ines enr ERE iR filters ueber imr eee rit Lee type date type overview type time oer ere PR TRE COEUR 174 USEF interfaces ase d teet ne 90 Combining data sources sese 64 Comparing ll Tu ee 74 text col minis 5 oH o Ee bd tant eb ts 74 Compound adding a structure search filter ssnssssesseseeseseen eneee 126 filtering using structure search 135 Computation Services esseeeeeeeneenemern 23 Concatenatllig ice to n e pn dee YRRI RES heres 105 Conditioning Leet uge EE 71 data conditioning dialog 155 el lol GE 137 eliminating duplicates 137 filters 5i TE 120 information link D nen 143 DiVO
177. ns at Acme Corp Each solid box represents a Library Section As the business develops more Library Sections can be added by the Library Section Creators 4 1 5 Set Up DecisionSite Posters DecisionSite Posters allows users to mail analysis results and view interactive analyses as web pages The Posters enable a fast and efficient sharing of information If a DecisionSite Poster license has been purchased it must be installed by the administrator before it can be used see the Spotfire Analytics Server Installation and Upgrade Manual When DecisionSite Posters is installed the license can be added to users and groups Example Tom reads the installation manual and follows the instructions on how to configure the company system to use DecisionSite Posters Then he proceeds to add the DecisionSite Posters license to the users from DecisionSite Administrator 4 1 6 Create Information Links To use the DecisionSite analytical platform the users must be able to use their data Since data is normally stored in databases these need to be accessed Spotfire provides the Information Services to do this To access the tools in Information Services licenses need to be unlocked Having done that the data access setup is done in three steps gt Steps 1 Setup connections with database information in Information Designer One person does this once 2 Design data views with Information Builder IB These predefined data views are later us
178. ns include one or more columns and may include one or more filters Stated in English an information link could be Fetch the Name Address and Phone number for employees that pass the filter High Income 45bColumn Elements Column elements in an information link may refer to multiple tables in different databases However Information Builder represents columns as if they were located in the same spreadsheet regardless of the physical location of the data In a Spotfire DecisionSite context columns are entities that can be assigned to the axes in a plot For example data on chemical elements may include element name atomic mass and atomic number Column Element Name Atomic Mass Atomic Number Hydrogen 1 1 Record Carbon BREED e Iron 59 27 Typical column names in other domains are e combinatorial chemistry compound name number of atoms e clinical research age gender histology e HTS plate id percent inhibited e genetics gene name physical location function 119 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 2 4 Filters Filters are conditions that limit the amount of data returned by an information link For example a filter could set the conditions X 10 AND Y 100 There are three ways of filtering data when working with information links Filter elements are set up by the administrator and appear 72 C Filters in the Elements pane of Information
179. nt If desired other useful column elements can be created in a similar way by using the MDL Direct Reference Manual 3 4 10 Setting Permissions for Column Elements When all column elements have been created you need to make sure that all intended end users have access to the elements If a user lacks access to the ID column for a specified connection he she will not have access to that particular connection gt To set permissions 1 In the Select workbench drop down list choose Permissions 2 Click Change 3 Click to select the appropriate Group or User from the list on the left 4 Click Edit Permissions 5 Locate the domain you created under chapter Creating Column Elements for MDL Direct and select the Execute check box for this domain 6 Click Save Permissions 7 Repeat for other users or groups if applicable 3 4 11 Creating and Storing the Configuration File For the connection to an MDL Direct data source to show up in the Structure Connection dialog in DecisionSite Client it is necessary to create a configuration file on the server If you want to set up multiple MDL Direct connections all connections are configured in the same file each under a separate configuration tag You can also create several configurations against the same database For example you might want to set up connections involving a different number of available columns or to use different ID columns for various user groups gt
180. o this Spotfire Analytics Server is restored Naturally it is possible for the user to connect to another Spotfire Analytics Server 169 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 10 Listing Which Users Have Access to a Certain Application 4 10 1 Listing Which Users Have Access to a Certain Application This section describes the steps necessary to import a list of those users who have access to certain applications in DecisionSite Client using Information Services 4 10 2 Import the DS Admin IM gt To import the DS Admin IM 1 In the import workbench import the IM file dsadmin xml using the following import settings Add keep conflicting elements Include permissions Information Designer Microsoft Internet Explorer P nix i Select workbench Import zi Change Import Help OI EG Filename dsadmin xrnl Select None ra Delete H C demo scott gatwin Oracle 8i Import mode C Replace all testdb enterprise420 DracleSi C Add overwrite conflicting elements add keep conflicting elements Include eel IM permissions g Parent domain F lt Select Import Clear 2 Click Import 170 Spotfire DecisionSite Administration Response This dialog appears 4 Spotfire DecisionSite pe 3 Click Close Response The result should be this F Information Designer Microsoft Internet Explorer Select workbench Im
181. ocedure Join column PROC COL STATE1 C2 Remove Add Condition Select ci C2 Case sensitive C Freehand Comment You can only specify one 1 join From the Data Sources pane select the first column to include in the join operation Click Add gt In the Procedure Join column field enter the name of the column in the database procedure you wish to join with Comment This may be one of the columns specified in the Result Columns pane but can also be another column as long as it is available in the database procedure for example and ID column Click Add Click either Select or Freehand Select join operator from the Condition drop down list or type a freehand join Ci C2 M Comment There are two basic types of joins that can be done between tables inner joins and outer joins An inner join will return records for which only the matching fields in both tables are equal An outer join will return all the records including NULL values from one table and only the matching records from the other table In the Condition drop down list outer joins include the character The position of the plus sign indicates which table will contribute only the matching records The column on the opposite side will return all records If you want the join to be case sensitive select the Case sensitive check box In the Name field enter a name for the procedure In the Description field enter your own descriptio
182. ogin to this server as if offline or connect to a different server Message Microsoft Windows 95 98 ME is not supported please upgrade to Microsoft windows 2000 or later Please contact your Spotfire Administrator for upgrading your client system Close You can edit the text at the bottom of this dialog if you want the users to contact a certain person and thus provide an email address or a phone number The file is located at lt installation directory gt server webapps spotfire unsupportedclient htm Be careful only to modify the line of text amp rdquor Please contact your Spotfire Administrator for upgrading your client system not the HTML code itself 4 7 Changing the Remember Me Time If the user selects the Remember Me check box when logging in the server remembers his User ID and Password and automatically logs in the next time DecisionSite Client is started However after a certain time the user is required to re enter his password again By default this is set to 43200 minutes which equals 30 days gt To change the Remember Me time 1 Open the installation directory gt server webapps spotfire WEB INF web xml file in a text editor 2 Find the tag called login remember expiration 3 By default this tag is set to 43200 minutes lt param name gt login remember_expiration lt param name gt lt param value gt 43200 lt param value gt 4 Change it to the preferred value Save the file R
183. on molfile is described in the MDL Direct Reference Manual 6 Give the new column element the name MOLFILE or anything else you can remember later Comment This column element will be referred to as MOLFILE later in this document 7 Inthe Information Model tree click on your newly created domain 8 Inthe Column workbench click Select 9 Click Save Comment If desired other useful column elements can be created in a similar way by using the MDL Direct Reference Manual 3 4 9 Creating a Similarity Score Column Element gt Tocreate a similarity score column element 1 In the Select workbench drop down list choose Column 2 Click Change 37 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 Inthe Data Sources tree view under the previously used molecule table click on the blob column that contains structures usually named CTAB Inthe Column Element workbench click Add 5 Change the calculation to molsim C1 amp rsquor NORMAL Comment The function molsim is described in the MDL Direct Reference Manual 6 Givethe new column element the name MOLSIMILARITY or anything else you can remember later Comment This column element will be referred to as MOLSIMILARITY later in this document 7 Inthe Information Model tree click on your newly created domain In the Column workbench click Select oe 9 Change the Type from blob to real 10 Click Save Comme
184. on of TIBCO Software Inc TIBCO Spotfire and Spotfire DecisionSite are either registered trademarks or trademarks of TIBCO Software Inc and or subsidiaries of TIBCO Software Inc in the United States and or other countries All other product and company names and marks mentioned in this document are the property of their respective owners and are mentioned for identification purposes only This software may be available on multiple operating systems However not all operating system platforms for a specific software version are released at the same time Please see the readme txt file for the availability of this software version on a specific operating system platform THIS DOCUMENT IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE OR NON INFRINGEMENT THIS DOCUMENT COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN THESE CHANGES WILL BE INCORPORATED IN NEW EDITIONS OF THIS DOCUMENT TIBCO SOFTWARE INC MAY MAKE IMPROVEMENTS AND OR CHANGES IN THE PRODUCT S AND OR THE PROGRAM S DESCRIBED IN THIS DOCUMENT AT ANY TIME Copyright 1996 2008 TIBCO Software Inc ALL RIGHTS RESERVED THE CONTENTS OF THIS DOCUMENT MAY BE MODIFIED AND OR QUALIFIED DIRECTLY OR INDIRECTLY BY OTHER DOCUMENTATION WHICH ACCOMPANIES THIS SOFTWARE INCLUDING BUT
185. opy Save Clear Save Clear Description Select a column from the Data Sources and then click this button to include in the filter Deletes the selected column from the composition In this field enter a condition containing the selected column or columns A unique identifier used internally to identify the filter The name of the filter to be saved edited A short description of the purpose of the filter max 255 characters Select a domain in the Information Model and then click this button to retrieve the name The name of domain where you want to save the filter Click Save Copy to create a copy with a new GUID Click Save to save or update the filter Clears all fields without saving 95 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 7 96 Procedure Workbench Procedure Element Help Procedure Add gt blade2 OE INSERT_INTO_TESTTABLE Type Query procedure Name Type Y string r Input Parameters Default value Permit null Prompt Boston O Single value D r Result Columns Insert Original Name PROC COL CITY1 string DI Destination City K Type Label Join Add gt Procedure Join column STATE C1 PROC COL STATE1 C2 Parent domain Remove Add Condition Select ci C2 Case sensitive C Freehand GUID ei759320 4566 11d9 3cOf 0010acii012b Name Destination Ci
186. orkbench without you ever having to edit any XML files It is therefore recommended to use direct connection to a specific data source rather than via database links when you create new Information Models Note In some cases database links may lead to better performance than using direct connection For example this could be the case when you are using information links that join to several databases Import of Information Models that still use database links If an Information Model is imported from a DecisionSite 7 0 or older the desired data source must temporarily be set to the default data source in order for the import to work properly After the import has been made you can go back to your current default data source again Since no user names or passwords are stored at the export you will be prompted to configure the new data source In the XML files of exported Information Models database links are referred to using the tag catalog If you do have catalog references in an exported Information Model you must do one of the following things prior to import e Make sure that the corresponding catalog database link is defined in the database If it does not exist create it or if it exists with a different name change the name on all occurrences in the XML file using Find Replace in your favorite text editor e Replace all catalog references with lt data source gt to switch to the recommended direct connection Thi
187. ormation Model pane select the domain folder icon that you want to edit 2 Click Edit in the nformation Model pane Response The domain information is loaded and enabled for editing 3 Modify the desired fields 4 Click Save Deleting a Domain gt To delete a domain and all its contents 1 In the Information Model pane select the domain that you want to delete 2 Click Delete at the top of the Information Model pane 63 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 2 5 4 3 2 3 4 3 2 3 1 4 3 2 3 2 64 Response The domain is deleted from the Information Model Moving a Domain gt To move a domain and all its contents 1 In the Information Model pane select the domain folder icon that you want to move 2 Click Edit in the Information Model pane Response The domain information is loaded and enabled for editing 3 Select a new parent domain in the Information Model pane Click Select 5 Click Save Response The domain and all its contents are moved to the new location Tip You can also move the domain using a simple drag and drop operation The moved domain will be appended to the contents of the destination domain Joins Joins Overview The SQL join operation defines how rows in different tables relate to one another Normally an identifier column in one table maps to a similar column in another table This allows information links queries to dr
188. ormation links queries from building blocks such as columns and filters Information Library is used only for opening these links and retrieving the data Information Designer is the administrative tool for working with the Information Model It allows the administrator to define columns and filters using joins and aggregation and to set user permissions for accessing various parts of the model 118 4 4 1 2 4 4 2 4 4 2 1 4 4 2 2 4 4 2 3 Spotfire DecisionSite Administration Related Reading Please refer to the Spotfire DecisionSite User s Guide and Reference Manual for information about visualizations query devices and other basic functions not covered in this User s Guide The Spotfire DecisionSite User s Guide and Reference Manual can be reached by clicking Help gt Help Topics in the main menu bar of Spotfire DecisionSite For detailed accounts of setting up the server side of Information Services see the Spotfire Analytics Server Installation and Administrator s Guide Fundamental Concepts Fundamental Concepts Spotfire DecisionSite Information Services requires no prior knowledge of query languages such as SQL However it is important to understand a few terms and concepts as they are used in this product e Information links e Column elements e Filters e Domains e Procedures LInformation Links An information link is a structured request for data which can be sent to the database These specificatio
189. otfire DecisionSite Administration Columns Add gt SAL C1 Remove Calculation avc C1 Aggregation Hide Columns Add gt DEPTNO AC1 Clear Remove Calculation aca Add Aggregate keys DEPTNO Remove Edit Drillable E Filter Show gt gt GUID Name average Salary Description average salary for each departmer Parent domain res o lt Select Type rea zl Set Filter devices We must also define a column element Department Number from DEPTNO which returns department numbers If we define an information link using these two columns the following SQL will be generated notice the GROUP BY clause SELECT E1 DEPTNO AS Department Number AVG E1 SALARY AS Average Salary FROM COTTEN ERODE TENE AEE GROUP BY Ey DEE INO 111 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 4 10 3 SQL Subqueries Information Designer supports subqueries inner SQL In this example we will demonstrate how to retrieve all employees with salary greater than the average Columns Add gt SAL C1 Remove Calculation Aggregation Show gt gt Hide lt lt Columns Add gt SAL FC1 Remove Condition rci Select avg SAL from SCO Filter GUID Name Employees with high salary Description Employees salary above average Parent domain Bey
190. ous projects has write access With this Library Section all users of the application DecisionSite for HTS quality control has direct access to useful Guides e DecisionSite for Lead Discovery This installed Library Section works similarly to DecisionSite for HTS quality control e Project A This Library Section is open for writing by all members of the Project A and reading for Everybody e Project B C e Customer Alpha This Library Section is intended for sharing results with customers Acme has decided to give write access to project mangers and engineers plus the contact persons at the customer company The customers will only see their Library Section Project members have read access to view the project findings e Customer Beta Gamma e HTS internal This is a Library Section used by the HTS scientists for publishing of temporary results and findings in the daily work Everybody has write access to this Library Section Example of how the Library Section view could appear to a user from project A at Acme in this case Deploying DecisionSite for the First Time Spotfire Spotfire Library Help Library Click to select a Library Section X Delete G Copy Link c Access Rights f Properties Refresh Customer Alpha Results for customer Alpha DecisionSite for HTS quality control Guides and Analyses for HTS work DecisionSite for Lead Discovery Additional content for Lead Discovery
191. p is preparing the InstallShield Wizard which will guide you through the program setup process Please wait Configuring Microsoft R NET Framework es Depending on whether Microsoft NET 1 1 is already installed on the machine or not two different dialogs can appear If Microsoft NET 1 1 is not available on the server go to step 4 If Microsoft NET 1 1 is already installed go to step 8 4 If the installer detects that Microsoft NET 1 1 is not installed on the machine it will launch the Microsoft NET 1 1 installer 11 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Microsoft MET Framework 1 1 Setup ell xl a License Agreement g AN Microsoft a 4 copy of this license is available for printing at http en rucrosoft comfylnk LinkId 12283 SUPPLEMENTAL END USER LICENSE AGREEMENT FOR E MICROSOFT SOFTW RE x have read understood and agree to the terms of the End User License Agreement and so signify by clicking agree and proceeding to use this product agree C do not agree Cancel Read the license agreement select I agree and click Install 5 Microsoft NET 1 1 is installed j Microsoft MET Framework 1 1 Setup mi e xl H E Installing Components The following items are being installed on your computer Microsoft NET Framework Files het E UBHHEHEHEEBEEHH Gathering required information 12 Con
192. pe in the input field If not leave the field blank Select whether you want the end user to be prompted for a single value several values or not at all from the Prompt drop down list box Comment If you select several values the end user will be allowed to enter several values separated by a comma The procedure will run once for each of these values in an iterative loop If you want to allow the input parameter to be Null select the Permit Null check box Example 1 Enter Default value and No prompt means that the specified default value will always be used as input parameter Example 2 Leave Default value empty select Permit Null and Single value prompt will cause the end user to be prompted for a value If the end user does not enter a value in the prompt Null will be used Example 3 Leave Default value empty leave Permit Null empty and Single value prompt will cause the end user to be prompted for a value If the end user does not enter a value in the prompt an error message will appear since Null is not allowed Comment You cannot select the combination No Default value Not allow Permit Null and No Prompt since this is a paradox In the Name field enter a name for the procedure In the Description field enter your own description of the procedure In the Information Model pane select a parent domain and then click the lt Select button Click the Save button to save the join in the selected parent domain Respons
193. port Filename asadmin xml J Import mode C Replace all C Add overwrite conflicting elements 3 Add keep conflicting elements Include permissions M eemtbmas E RS 4 10 3 Import Data in DecisionSite Client Using Information Library execute the Information Link List licenses from the DS Admin domain 171 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual A Information Library You will be prompted for what products to list results for 172 Spotfire DecisionSite Administration Set Filter for Column DecisionSite Analysis Builder DecisionSite Basic DecisionSite for Functional Genomics DecisionSite for Functional Genomics SAE DecisionSite for Lead Discovery DecisionSite for Lead Discovery SSV DecisionSite Nominal DecisionSite Power DecisionSite Statistics License Admin Map Interaction Services Web Delivered Software Finished 173 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 5 Index Abbreviations i eren terea Access rights P ActiveX Controls Adding COLUMNS EE ETT domain ul E E ET Fin EST JOINS actui te thee esce tds e tuse multiple columns E Adtninisttatorz irt gae dee Administrator Level 48 Aggregation aggregation in Information Designer 71 example of Pivoting with Aggregation 139 many col mi
194. ported The file must be present in the directory lt installdir gt spotfire application data iis export on the server Controls how conflicts between existing and imported GUIDs are handled Note that elements may have the same name without a conflict arising Replace all The entire current Information Model is replaced by the imported elements Any selection under Parent domain see below is 99 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 11 100 ignored Add overwrite conflicting elements If a GUID already exists the element is overwritten with imported information unless it is a join in which case it must be removed manually The imported element will appear under the imported domain while the old element will be removed from its domain Hence the element will appear to have moved Add keep conflicting elements If a GUID already exists the current element is kept and the imported information is ignored Include permissions Select this check box to include information in the XML file about the permissions associated with the domain and its content Parent domain The domain in which you want to store the imported information This is ignored if Replace All is selected lt Select Select a domain in the Information Model and then click this button Import Imports the specified XML file Clear Clears all fields without saving Edit SQL Workbench Edit SQL Help
195. potfire amp DecisionSite 9 1 1 Deployment and Administration Manual Structure Search Z Set Filter for Column E x Step 3 of 3 Select Structure Search for Substructure Similarity using threshold value 1 100 ao Edit Structure Import Structure lt Back Finish Cancel Option Description Search for Select whether to search using a substructure or to search for structures similar to a master structure If similarity is selected enter a threshold value between 1 and 100 A high value means that only very similar records will be included in the resulting list Edit Structure Launches ISIS Draw where you can edit the master structure before launching the search Import Structure Displays the Open dialog where you can select a MOL file to use in the search 4 4 4 5 7 Get Values from Data Set Dialog E Get Yalues from Data Set xj Matching column rear Get values from E Marked records Selected records OK Cancel 154 Spotfire DecisionSite Administration Part Description Matching column Use the drop down list to select the column in the current data set from which to get the values Get values from Select whether to use Marked records or Selected records as filter values or range limits gt To reach the Get Values from Data Set dialog 1 Open an Information Link with run time filters 2 When the Set Filter for Column dialog for the desired column
196. pplications it is recommended that you create Library Sections with the exact same name as these Library Sections e By project If your company is organized into projects perhaps a Library Section structure with a Library Section for each project is useful This way all users in a specific project can get write access to its Library Section and some other access to other projects TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual e By customer If you work tightly with customers and you want to share analysis material with the customers a Library Section structure for each customer could be useful enabling you to share material with each customer in a secure way e By department allowing for instance all engineers to access the same analysis material e By geography such as for each site e By domain structuring all users working with a specific domain such as Toxicology to work in the same Library Section Linking dynamic Library content to your applications In DecisionSite Client the users have a menu option called Guides gt Run from Library It is a means to access Guides published to the Library in a simple way When the user clicks the menu option an Open from Library dialog appears where users can browse for Guides By default this targets a Library Section with the same name as the current DecisionSite application This is done to minimize the amount of browsing needed for the user in
197. r file types that are important for the Pathway Viewer tool gt Pathway Viewer files 1 Pathway image files in GIF or JPG format These are the actual pathway image maps There is an example file provided by default in the directory install directory server application data pathway viewerMata The example file is called sample gif If you want to download other image maps you can go to ftp ftp genome ad jp pub kegg pathways map 2 Pathway coordinate files containing PathwayID Xmin Xmax Ymin Ymax These are the files on the server that link the PathwayIDs to the coordinates on the pathway 30 Configuring DecisionSite image maps The sample file provided by default is called sample coord It contains the coordinates for PathwayIDs on the sample gif pathway image map Such files can be downloaded from ftp ftp genome ad jp pub kegg pathways map 3 pathway settings xml This is the settings file that links everything together by specifying the image files and coordinate files that should be used as well as specifies the pathway names 4 idmapping xml This is the file on the server that links the records in the end user s data set to the PathwayIDs There is an example file provided by default In the example file the data in the DLBCL data is linked to the PathwayIDs Note This is a manually configured file that is you must edit this file and manually map the end user data to the pathway data 5 The end user s d
198. raded Spotfire Installing packages according to profile Preparing to update 4 packages Retrieving Spotfire Package SciCoVisualUtilities Retrieving Spotfire Package QuickStart Retrieving Spotfire Package ColumnExpression Retrieving Spotfire e amp pp Common Cancel Alternative B If the client environment does not meet the system requirements enforced by the server an error message is displayed providing information about what parts of the client environment do not meet the system requirements enforced by the server as well as information on who to contact for assistance typically the local Spotfire IT administrator The error message also contains information about the fact that the user can log into DecisionSite Client in offline mode or choose another server to connect to This error message can be modified to match each installation by modifying a file on the server Spotfire DecisionSite E x Possible problems detected Your computer does not meet the requirements for Spotfire DecisionSite 8 2 You can still login to this server as if offline or connect to a different server Message Microsoft Windows 95 98 ME is not supported please upgrade to Microsoft Windows 2000 or later Please contact your Spotfire Administrator for upgrading your client system Close If the user chooses to connect as if in offline mode the profile that he she had prior to connecting t
199. res and configure these to be accessible in Information Links These Information Links are available to the DecisionSite Client users in order to retrieve data In Information Designer you select a database procedure from your available data sources and define which input parameters the procedure should prompt for and any potential resulting columns and joins In Information Builder you configure a complete Information Link with one or more combinations of procedures and columns from other tables The Three Kinds of Procedures Information Services defines three kinds of procedures e Pre update procedure this procedure does not return any data it only performs an operation on one or more databases All pre update procedures in an Information Link will always be executed before any query procedure e Query procedure just like a database table this procedure returns data e Post update procedure this procedure does not return any data it only performs an operation on one or more databases All post update procedures in an Information Link will always be executed after any query procedure 120 Spotfire DecisionSite Administration 4 4 3 Using the Information Builder 4 4 3 1 Starting and Closing Information Builder gt To reach Information Builder Select Tools gt Create Information Link in DecisionSite Client gt To close Information Builder Click on the Start Page button above the Guides pane This will bring you bac
200. rmation Link pane Note If more than one information link containing hints is added to the Information Link pane all hints will be removed from the SQL statement This is due to the fact that the hints in the different information links might conflict with each other and that there is currently no way for the system to figure out if the two hints will work together 4 4 3 2 12 Selecting Join Path When you are creating multiple joins between tables in Information Designer you can specify which join will be the default one Sometimes you may want to create an information link that does not use the default join though and this can be done by selecting the join path manually from Information Builder Also when there are several possible join paths between a number of tables you may want to specify which one you want the information link to use Let s say the default join path between Table 1 and Table 4 is via Table 3 and the joins TABLE1 ID TABLE3 ID and TABLE3 NAME TABLE4 NAME 128 Spotfire DecisionSite Administration Ee el Es gi e eg Bra ER W s Res EN fer EH SEU Sg TEMA e Ss For a certain information link this is not what you want instead you wish to configure the link to join via Table 2 using the joins TABLE1 ID TABLE2 ID and TABLE2 COST TABLE4 COST This can be done by clicking on the Join Path Edit button in Information Builder and selecting a different join path than the default one By simply selecting one
201. rms an operation on one or more databases All pre update procedures in an Information Link will always be executed before any query procedure e Query procedure just like a database table this procedure returns data e Post update procedure this procedure does not return any data it only performs an operation on one or more databases All post update procedures in an Information Link will always be executed after any query procedure Note If using Oracle stored procedures that return data Information Services only support procedures that return data of the type REF CURSOR also known as Table Function 4 3 2 6 2 Creating a Pre or Post procedure Using Information Designer and Information Builder you select pre made database procedures and configure these to be accessible in Information Links These Information Links are available to the DecisionSite Client users in order to retrieve data In Information Designer you select a database procedure from your available data sources and define which input parameters the procedure should prompt for The Three Kinds of Procedures Information Services defines three kinds of procedures e Pre update procedure this procedure does not return any data it only performs an operation on one or more databases All pre update procedures in an Information Link will always be executed before any query procedure e Query procedure just like a database table this procedure returns data e
202. rovides the visualizations for DecisionSite Posters To change which port number Spotfire Visualization Services is using please consult the manual Spotfire Visualization Services host localhost Spotfire Visualization Services port 12000 Retails s Visualization Services version 1 0 1818 6115 Poster Service version 14 0 1204 MODIFIED qa ademin 200412230500 Language V SE This will be used for formatting dates and numbers in Visualization Services Poster Email Settings server mnl A Port 75 Default port 25 V Use name and password User name Password Email format HTML with images Email image format PNG a Note Lotus Notes only supports JPEG images Number of included Annotations No enit C Max Note Lotus Notes only supports up to 15 Annotation Notes Decision Status Values Open Default Add new Edit Remove Move down Set as default If the Poster service is running click on the Stop button to stop it Enter the host name of the server where you installed Visualization Services in the designated field If you installed it on the same machine as the Spotfire Analytics Server enter localhost in the field Enter the port number you configured Visualization Services to use when you installed it Default is 12000 Comment Clicking the Details link displays the Visualization Services version the Poster Service version and the Language setting that will be used in Visualization Ser
203. s In the Search for users pane enter a search criteria Click Search In the Matching Users list click a user ID Group Properties Pane Properties for group Pharmacology Team Save This Configuration Search for available users P Available users Group members thorsell toml tomas tommy Products C DecisionSite for Functional Genomics C DecisionSite for Lead Discovery C DecisionSite MapConnect Cl DecisionSite Posters Cl DecisionSite Statistics C DecisionSite Library L1 Computation Services Designers C DecisionSite for Lead Discovery no ISIS Host DecisionSite level None ivl Option Description Change group Change the name of this group name Remove group Remove this group Save This Save the settings for this group Configuration Search Populates the Available users list with users that match the search criteria The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Available users Users matching the search criteria Spotfire DecisionSite Administration Group members Members of this group Add gt Click to add selected users to this active group lt Remove Click to remove selected users from the active group Products Products to which members of this group have access DecisionSite Level Level of access for members of this group gt Toreach the Group Properties pane 1 A
204. s 800 Chicago Turner 1000 Chicago As the information link is opened Salary will be filtered first the order is set in the Information Link pane The user enters the limits 1100 to 1300 After the first filter the following remains Name Salary Location Prompt None Range Check Boxes Miller 1300 New York Ford 1100 Dallas Scott 1300 Dallas Jones 1200 Dallas Several rows including all Chicago employees have been filtered out This means that when the Location filter is shown Chicago will not be presented as an option T DALLAS T NEW YORK When to Use the Independent Setting The Independent setting on the Advanced tab can be used to treat elements columns or filters as independent during the opening of prompted information links The default behavior of prompted information links is that each subsequent step lists values based on earlier selections 133 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual However if you are working against e g a STAR schema database the procedure may require multiple joins since the elements queried for the prompts are linked only by the large fact table in the STAR schema Setting an element to Independent will have the effect that no previous selections in the prompt steps will be reflected in the listing for the independent element Neither will any of the selections made in the prompt step for the independent element be reflected in later prompt steps
205. s a row in the generated table In the Category section select the columns that you want to use for generating new columns in the new table Comment Each unique value in the chosen category column produces a new column in the generated table In the Values section select the continuous column that you want to aggregate Comment The column from which the data is pulled The values in the generated table are computed according to the method selected under Computation Note The computation method depends on what type of column you select If the selected column is numeric the aggregation method will be set to Average Columns of type string will be set to Concatenation In the Other columns section select any other columns that you want to include in the new table Select a naming scheme to use for naming the pivoted columns Click OK Response The Pivot dialog is closed In the Data Conditioning dialog click OK Response In the Information Link pane Conditioning has been set to Pivot This means that the data will be pivoted when the information link is opened Example of Pivoting Pivoting a data set means changing it from a tall skinny format to a short wide format Consider the following tall skinny table based on a series of temperature measurements City Month Temp London February 4 New York February 6 London May 16 New York May 19 London August 28 New York August 26 London November 13 New York November 11
206. s information link only the sales figures pertaining to that single user should be retrieved First take a look at the Sales table containing the total sales of every person in the sales force Order ID Employee ID Product Sale 1 101 Cornflakes 100 2 150 Soda 550 3 244 Cornflakes 160 4 101 Mineral Water 400 5 101 Soda 120 6 339 Mineral Water 200 Then you must create a Lookup Table that matches the Employee ID to the actual Spotfire User Name for each person logging into the Spotfire Analytics Server Spotfire DecisionSite Administration Spotfire Username Employee ID mikesmith 101 lauraclarke 150 sarahdonovan 244 malcomreynolds 339 Next you add an Information Services Filter or Column that constrains the Spotfire Username column to only return values for the currently logged in user Filter Element Columns Spotfire Username FC1 Condition FC1 CURRENT_USER An example of the resulting SQL for this would be LookupTable Spotfire Username malcomreynolds Finally you create an Information Services Join between the Sales table and the Lookup table joining the Employee ID columns Now the Information Link is ready to be used and will only retrieve data for the currently logged in user Group Membership Scenario You want to set up an information link to a table of data with sales made by all of the sales people in the comp
207. s is applicable only to files from version 7 1 or later Give the 108 Spotfire DecisionSite Administration data source definition at the beginning of the file a suitable name e g ACTIVITYBASE Update all data source references and remove the corresponding catalog references Example lt data source gt oracle_1 lt data source gt lt catalog gt ACTIVITYBASE lt catalog gt lt schema gt ABASE lt schema gt should be replaced by data source ACTIVITYBASE data source lt schema gt ABASE lt schema gt Here you should also rename the data source definition at the beginning of the file from oracle 1 to ACTIVITYBASE and replace the URL with the new one linking to the correct data source lt xml version 1 0 encoding UTF 8 gt lt im iis model xmlns im http schemas spotfire com ws 2002 05 im xsd Xen data source guid fd4z bdO0 Sdaf 11d6 1fa0 00108b880f28 lt type gt com spotfire ws im datasource OracleDataSourceFactory lt type gt lt properties gt ne lt name gt write allowed truec write allowed lt shou local tables gt false lt show local tables gt lt fetch size gt 10000 lt fetch size gt lt default data source gt true lt default data source gt lt default join data source gt true lt default join data source gt lt connection pool gt lt driver class gt oracle jdbc driver OracleDriver lt driver class gt lt connection url gt lt connection url gt lt m
208. s is simple way to authenticate users when everyone has the same permissions to the data source The other choice is to require authentication each time a connection is used This is useful when a more detailed security model is required Using user authentication row level security can be obtained The credentials can either be supplied by the user or by a plug in when running an Information Link against this data source A plug in allows the user to log in to the DecisionSite environment only once leaving it up to the plug in to deliver the data source credentials Without a plug in users will have to supply their data source credentials in a prompt Credentials are cached in the data source so that users are prompted only once The layout and handling of the data sources affect most other actions involving the various parts of Information Services Therefore it is most valuable to do a proper planning before starting to work on the layout Modifications to the data sources after the Information Model and information links have been defined will probably mean that some manual work is needed to make sure all information links are still functional 4 3 2 1 2 Creating a Data Source gt To create a new data source 1 From the Select workbench drop down list select Data Source 2 Click Change Response The Data Source Definition workbench is displayed In the Name field enter the name of the new data source Modify the Connection URL Enter a
209. se A message appears stating that you successfully unlocked DecisionSite Administrator 9 Click on the main page link to return to the start page 1 4 Deploying Software Packages gt To deploy new software packages 1 Make sure that the Spotfire Analytics Server is running 1 5 1 5 1 1 5 2 1 5 2 1 1 5 2 2 Deploying DecisionSite for the First Time 2 Start the DecisionSite Administrator tool from the main server page in Internet Explorer 3 Select Deployer from the top menu frame Browse to the temporary folder where you unzipped the installation files from the Spotfire DecisionSite deployment kit 5 Select and open the file ds911_distribution zip Click on Deploy 7 The contents of the distribution are shown in a separate window Click on Deploy in this window All software components of DecisionSite Client 9 1 1 will now be installed e Spotfire Library Setting Up Spotfire Library In order to use Spotfire Library there are additional installation steps that must be performed You need to modify some server settings and initialize the Spotfire Library database Proceed with the instructions below Example of Spotfire Library Design Library Design Introduction For an efficient use of your Library a structure is needed that can accommodate your company s needs This is done in two steps first by giving users access permissions to the Library and second deciding on an efficient layout of the Library T
210. select None and each combination of Identify and Category is not unique This option allows you to include an overall average of a particular measurement for each row in the generated table You can select how the pivoted columns should be named By default there are two predefined options Method Value for Column Category Method Value You can also create a custom naming scheme for your pivoted columns To do this click the Edit button and the Edit Pivot Column Naming Scheme dialog appears After you have created a naming scheme it will be available in the drop down list box as User edited naming scheme Note One can create additional default naming schemes that will always appear in the Column names drop down list box for all users Talk to your Spotfire Analytics Server administrator to do this and read more about the procedure in the Spotfire Spotfire Analytics Server Administrator s Manual 4 4 4 5 5 Edit Pivot Column Naming Scheme Expression Es Z M V Variables Computation Method 4M Value Columns Category Values xL S Sample result Category MethodN amefValueCol Help OK Option Expression Description Enter an expression here which will be used to name the pivoted columns 147 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual There are three parameters that can be used M Computation Method V Value Columns C Category Values
211. ser Name for each person logging into the Spotfire Analytics Server Spotfire Username Employee ID mikesmith 101 lauraclarke 150 sarahdonovan 244 malcomreynolds 339 Next you add an Information Services Filter or Column that constrains the Spotfire Username column to only return values for the currently logged in user Spotfire DecisionSite Administration Filter Element Columns Spotfire Username FC1 Condition FC1 CURRENT_USER An example of the resulting SQL for this would be LookupTable Spotfire Username malcomreynolds Finally you create an Information Services Join between the Sales table and the Lookup table joining the Employee ID columns Now the Information Link is ready to be used and will only retrieve data for the currently logged in user Group Membership Scenario You want to set up an information link to a table of data with sales made by all of the sales people in the company However depending on which person from the sales department accesses an analysis using this information link only the sales figures pertaining to the region that sales person is assigned to should be retrieved For example if a sales person is working in the East region she should only be allowed to see sales figures made in that region by any person The Spotfire Administrator has created groups on the Spotfire Analytics Server named SalesForce East SalesForce West SalesForce Sou
212. ser to be prompted for a single value several values or not at all from the Prompt drop down list box Click the Insert button to add a new line in which to specify a Resulting Column that the query should produce In the Original Name field enter the exact name of a column the database procedure returns This name is specified in the actual database procedure so you have to know this before hand Select the Type the resulting column should have Enter a descriptive Label for the resulting column This Label is the name the end user will see in DecisionSite Client Remove the corresponding Resulting Column row Select a column from Data Sources and then click this button to include it in the join Removes a column from the list of columns included in the join In the Procedure Join column field enter the name of the column in the database procedure you wish to join with This may be one of the columns specified in the Result Columns pane but can also be another column as long as it is available from the database procedure result for example an ID column Click Add to include the column specified in the Procedure Join column field in the join Select this button to choose from standard joins in the drop down list Select this button to enter your own join definition Select this check box to make the join case sensitive A unique identifier used internally to identify the filter The name of the filter to be saved edi
213. ss gt lt server gt lt servers gt lt servers gt lt category gt Spotfire Category CompServ PreDefined SPlusServer lt cate gory gt lt server gt lt address gt http mysplusserver 9081 lt address gt lt server gt lt servers gt lt servers gt category Spotfire Category CompServ PreDefined SASServer catego ry server lt address gt bridge mysasserver 9081 lt address gt lt server gt lt servers gt lt settings gt 2 Continue to the section below describing the connector of interest 3 2 3 SAS Connector gt To configure the SAS connector 1 Make sure you have followed the general steps above 2 In the file compserv servers xml locate the following section lt category gt Spotfire Category CompServ PreDefined SASServer lt category gt This is where you will add the addresses to all SAS servers on your company 3 For each SAS server that you want to add to the list specify an element as follows lt server gt lt address gt YOUR_SERVER_ADDRESS lt address gt lt server gt where YOUR_SERVER_ADDRESS should be the address to the SAS server e g bridge mysasserver 908 1 4 Save the file 3 2 4 R Connector gt To configure the R connector 1 Make sure you have followed the general steps above 24 Configuring DecisionSite 2 In the file compserv servers xml locate the following section lt category gt Spotfire Category CompServ PreDefined RServer lt category
214. st xml e Dialog for notifying the user e Policy settings in the following section of the file WebLogic installation directory gt spotfire spotfire W EB INF web xml WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war WEB INF web xml context param param name supported client min lt param value gt 4 0 lt param value gt context param context param lt param value gt 5 5 lt param value gt context param context param Xparam name supported client min lt param value gt 6 3 lt param value gt context param context param lt param value gt 1 0 0 lt param value gt context param Xparam name supported client min Xparam name supported client min os lt param name gt ie param name dsb param name appmgr param name The detection script can be extended to further restrict usage of Spotfire DecisionSite The dialog is implemented using DHTML The default implementation is located in e WebLogic lt installation directory gt spotfire spotfire unsupportedclient htm e WebSphere lt Directory where Spotfire DecisionSite is deployed gt Spotfire_DecisionSite_Analytics_Server ear spotfire war unsupportedclient htm The default implementation can be overridden by providing a different URL for the dialog in e WebLogic installation directory gt spotfire spotfir
215. structure inside it Library Sections can only be created by Library Section Creators which is a group controlled in the Library Administrator Library Section Creators is a predefined group in the DecisionSite Administrator By adding users to this group they become Library Section Creators Library Section Creators automatically receive the Library Section Owner access privilege in the Library Sections they create It is you the DecisionSite administrator who decides which users should become Library Section Creators This means you do not have to create and manage the Library Sections yourself rather you delegate this to the specified Library Section Creators 44 Spotfire DecisionSite Administration Please refer to Setting up Access to DecisionSite Products for information on how to add users to the Library Section Creators group How are Access Rights used in the Spotfire Library Each time a user attempts to access a Library Section a check is made to see if that user has at least read permission In any tool where Library content is displayed to a user that user is always presented only with the Library Items that he has access to There are three levels of access to Library Sections e Read e Write e Owner Read access means that you can list and view all content in that Library Section However no editing can be done With write privileges you can add content into the entire Library Section and also read the material T
216. t setting name aadm remote lt table owner gt aadm lt table owner gt lt setting gt Note Make sure to edit the table owner for the aadm remote tool 29 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 3 7 Updating AADM Connection Information for Retrieve from Database Local Tool The Retrieve from Database Local tool retrieves data from AADM using an ODBC connection on the client If the user defined in lt user gt is not the owner of the AADM schema the lt table owner gt should be set to the owner of the AADM schema Example lt user gt aadm_not_owner lt user gt setting name aadm local lt table owner gt aadm lt table owner gt lt setting gt Note Make sure to edit the table owner for the aadm local tool Also note that all users of the Retrieve from Database Local tool will be affected by this setting 3 3 8 Pathway Viewer 3 3 8 1 Pathway Viewer Introduction The Pathway Viewer tool maps a location on a pathway image to a specific Pathway identifier PathwayID see picture below The Pathway Viewer tool will allow the end users to select pathways of interest and interact bi directionally between their DecisionSite Client visualization and the display of the Pathway Dv 0 2224 42M amp Ue V LUAM AEFEN T 07 GO PathwayIDs highlighted that are marked in the browser 3 3 8 2 Required Data Files Basically there are 5 files o
217. t Users In the Export List of Users dialog select which group to export Click OK Select where to save the file and click Save Ste EN Response The user names are saved as a new text file Note For security reasons user passwords are not included in the exported file This file contains only user names Managing Groups Creating Groups gt To add a new group 1 At the top of the page click the Groups tab 2 Inthe Groups pane click Create Group Response The Create New Group dialog is displayed 50 Spotfire DecisionSite Administration 3 Enter the group name and click OK Response The new group is created 4 2 2 4 2 Deleting Groups gt To delete a group 1 2 At the top of the page click the Groups tab In the Search for groups pane enter a search criteria for finding a group Comment To see all groups enter an asterisk wildcard The asterisk wildcard represents any letter and or number and can be used in the search before or after a text string Click Search In the Matching Groups list click a group name Response The properties of the selected group are displayed Click Remove Group In the Remove a Group dialog click OK Response The group is removed Note You cannot delete the Everyone group or an group that is configured to synchronize with an external LDAP server 4 2 2 4 3 Changing Group Names gt To change the name of a group 1 2 At the top of the page
218. t box Select the individual values for the column by clicking the entries in the list To select consecutive values click the first item press and hold down SHIFT and then click the last item To select multiple entries that are not consecutive press and hold down CTRL and then click each item To select all the values in the list press CTRL A Include empty Select this check box to also include records that contain no data for this values for this column consequently not available in the list step 151 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 152 Check Boxes O Set Filter for Column im mim m m Ko co m p n p n o La mi EN Part Check boxes Include empty values for this step Description Select individual values for the column by checking the entries in the list To select all the values in the list press CTRL A Select this check box to also include records that contain no data for this column consequently not available in the list Spotfire DecisionSite Administration Radio Buttons O Set Filter for Column e s AS s e A 2 e AS s 2 E Option Description Radio buttons Select a unique value for the column by clicking on an entry in the list Include empty Select this check box to also include records that contain no data for this values for this column consequently not available in the list step 153 TIBCO S
219. t the top of the page click Groups 2 Inthe Search for groups pane enter a search criteria 3 Click Search 4 Inthe Matching Groups list click a group name 4 2 3 3 Logging Pane Logging view log files Current log configuration file 10444 properties Option Description View log files Select a log file Refresh Refresh the log view to display the selected log file Set Configuration Change the current log configuration file gt To reach the Logging pane At the top of the page click Logging 4 2 3 4 Current Users Pane Current Users User Machine Logged in since john_smith L4BCOMPS Nov 16 2005 8 18 49 AM anna clarke LABCOMP2 Mov 16 2005 8 13 07 AM bob anderson LABCOMPS8 Nov 16 2005 8 18 11 AM Option Description Refresh Refresh the list of current users gt To reach the Current Users pane At the top of the page click Current Users 57 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 2 3 5 DecisionSite Deployment Pane DecisionSite Deployment To deploy browse to the distribution zip file created using DS Builder C packages zip Deploy Currently deployed on SpotfireServer1 Name Date Spotfire Deployment DecisionSite Mon 27 Oct 2003 00 52 19 UTC Option Description Browse Click to browse for a distribution zip file Deploy Click to deploy the selected distribution zip file Currently deployed Displays a list of the applications and ex
220. t them up TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 3 X Configuring DecisionSite 3 1 DecisionSite Posters 3 1 1 Spotfire DecisionSite Visualization Services 3 1 1 1 Visualization Services Introduction As of DecisionSite 8 1 the entire function of rendering visualizations for DecisionSite Posters has been separated from the Spotfire Analytics Server to a dedicated application called Visualization Services This can be a installed either on the same machine as the Spotfire Analytics Server if it is a Windows machine or on a separate machine all together Visualization Services runs as a Windows service The Spotfire Analytics Server communicates with Visualization Services which provides visualizations for the Posters opened from the Spotfire Library 3 1 1 2 Requirements Requirements for Visualization Services The requirements which must be met in order to run Visualization Services can be found at http www spotfire com sr Visualization Services must be installed on a Windows machine running e Microsoft Windows Server 2000 SP1 or higher e Microsoft Windows Server 2003 If you are running your Spotfire Analytics Server on a Windows platform it is possible to install Visualization Services on the same machine Hardware requirements vary greatly depending on the number of simultaneous users and the load of the server Note You cannot connect several Spotfire Analytics Servers to the s
221. table by clicking on it in the Data sources pane 4 Click Add gt Comment Columns of type Unknown cannot be added in the Multiple Columns Workbench since they do not automatically map against the datatypes in the IM Response The columns are added to the Column elements list If a table was selected all columns in the table will be added to the list Tip Repeat this step if you want to include more columns 5 Click on an element in the Column elements list to select it or go to step 8 to add the columns using the default settings Comment This step is not necessary unless you want to change the name or description of the element 6 Change the Name of the column element Comment The default name is the same one as in the database but with _ and replaced by space and only the first character in the name capitalized Whitespace characters at the beginning or end of the name are also removed 69 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 7 Change the Description of the column element Comment By default the path to the column is displayed The maximum limit of the description is 255 characters 8 Click Apply Changes Response The name and or description of the selected column element is changed 9 Inthe Information Model pane select a domain to save the columns in and then click the lt Select button 10 Click Save Response The columns are saved to the specified parent
222. ted A short description of the purpose of the procedure max 255 characters Select a domain in the Information Model and then click this button to retrieve the name 97 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 3 3 8 98 Parent domain Save Copy Save Clear The name of domain where you want to save the procedure Click Save Copy to create a copy with a new GUID Click Save to save or update the procedure Clears all fields without saving Permissions Workbench Permissions Administration Help Groups Users Edit Permission Modify Execute Information Interaction Designer Poster Library Administrator Option 1 Groups Users selection 2 Account list 3 Edit permissions 4 Domain folders 5 Modify setting 6 Execute setting 7 Update permissions Permissions for test kaj isis CiSISRC2D FMLA CJigisRC2D MOL a xI a xI viv Clisis test El viv Lies pe d Ka DELTA_MOLTABLE D M CI ISISPLATINUM CM CI DELTA_CTAB ODM C DELTA_FORMULA r 9 CipeLTA Hs EXTREG ri CJDELTA MOLTABLE ono Clos DP Quai DD Leet gt b Description Select to see individual accounts or group accounts Select the account group or individual to modify Loads the current domain settings for the selected user The existing domains in the Information Model When this check box is selected the user has the right to change the
223. tensions that are currently on server deployed on the server Un Deploy Un deploys the applications and extensions selected in the list View details Displays more details such as version number about the applications and extensions selected in the list gt To reach the DecisionSite Deployment pane At the top of the page click Deployer 4 2 4 Troubleshooting 4 2 4 1 Technical support Technical support is available at no charge as described below The best way to report problems is with the support forms available from http support spotfire com gt When reporting problems please include the following information 1 Is the problem reproducible If so how 2 What platform are you running Spotfire Analytics Server on 3 What browser are you using 4 What version of Spotfire Spotfire Analytics Server are you running 58 Spotfire DecisionSite Administration 5 Ifa dialog box with an error message was displayed please include the full text of the dialog box including the text in the title bar Note To get context sensitive help when working with analyses in Spotfire DecisionSite press F1 at any time 4 3 DecisionSite Information Designer 4 3 1 Introduction 4 3 1 1 Introduction to Information Designer Information Designer is an administrative tool for managing the Information Model IM This model is a representation of one or more databases which may be geographically dispersed It allows end users to exe
224. th and SalesForce North Each sales person is a member of one or more of these Note You can also create a Lookup table just as in the first example in which you assign various users or groups to categories that match your Sales table That way you do not need to create superfluous groups on the Spotfire Analytics Server if groups with matching names are not already available You then take a look at the Sales table containing the total sales of every person in the sales force Order ID Employee Region Product Sale ID 1 101 SalesForce Cornflakes 100 East 2 150 SalesForce Soda 550 West 3 244 SalesForce Cornflakes 160 North 4 101 SalesForce Mineral Water 400 East 5 101 SalesForce Soda 120 East 6 339 SalesForce Mineral Water 200 East 125 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 3 2 8 4 4 3 2 9 Next you add an Information Services Filter or Column that constrains the Region column so that it only returns values if the currently logged in user is a member of a group with that exact name Filter Element Columns Region FH i Condition FCL in 95 CURRENT GROUPS 5 An example of the resulting SQL of this would be SalesTable Region SalesForce East SalesForce North Now the information link is ready to be used and will only retrieve data for groups that the currently logged in user is a member of
225. th dialog Click Edit in the Information Link pane 4 4 5 Glossary 4 4 5 1 Glossary The glossary only contains brief definitions of the terminology You can also use the Index or Search tab to the left to find more information within this help file Column element A list of values A column element can correspond to a database field but can also be the result of calculations performed on multiple fields from several databases What the column element returns is defined by the administrator Database A collection of related data usually in the form of multiple files or tables that are linked to each other Element Any constituent that builds up an information link in other words column elements filter elements and other information links Independent An element setting in the Information Link pane Advanced tab If selected the element will be treated as independent in a prompted information link Hereby you can avoid filtering upon each prompt step and thus improve performance of information links when retrieving data from STAR schema databases Information Builder A tool for creating and executing information links in Spotfire DecisionSite Information Model The Information Model consists of the data integration layer which manages connections with the various data sources and the data access layer which associates database identifiers with user friendly column names Appears to the user as a folder structur
226. the Library For example a user who is using the DecisionSite for Lead Discovery application clicks the Guides Run from Library The user is then directed to the installed Library Section DecisionSite for Lead Discovery It is recommended that you create Library Sections corresponding to DecisionSite applications you will use and vice versa Using this functionality the users will have easy access to dynamic Library content 1 5 2 3 Example of a Library Organization Company Acme is a chemistry company working with High Throughput Screening HTS analysis It has developed its own DecisionSite application designed for efficiency called amp rdquor DecisionSite for HTS quality control The company engineers also use DecisionSite for Lead Discovery when performing some surrounding analysis Acme has divided its operations into projects or therapeutic teams with each project working with a specific disease area In this example project A works with tumors Finally the projects involves customers to which Acme publishes results Acme has decided to create a structure following this corporate structure using the following Library Sections with their respective access permissions e DecisionSite for HTS quality control This is viewed as a Library Section containing tools which are used by the scientists New tools might be added by a few power users Because of this the group Everybody has read access and a set of power users from vari
227. tion 139 Similarity search adding a filter ose AAA 126 filtering using ie corem cepe 135 Software Distribution eese 160 S Plus Connector S Spotfire Zone E RR RHOD SQL el DIEN editing filters example group by evample sereine ann 110 in information links eene 119 pl sal example tete 106 subqueries example seen 112 view SQL dialog in Information Builder 144 view SQL dialog in Information Designer 86 STAR schema independent columns in information links 123 143 when to use the Independent setting 133 Stored procedures 5 etit eite es 75 Structure search adding a filter eene 126 filtering Usihg rnit 135 Structures Sub queries SUM iet Support Support Pages s Symbols sientas eii elu T Table alias 4 ev RI DS 61 66 LEIT 83 Tables and columns sese 119 EI Wl EE 138 Technical SUpport eg o tee 58 Temporary tables 5e iiie aeieea 87 U Update all sers rrr eed 98 User activity ce o e res taia aeaeaie a iaiia 52 User permissions ENNEN 81 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual User Properties pane EEN 55 Users ele WEE 49 assigning properties sseseeeeeeeeeenneeene 49 55 definitions be e
228. tion link at will The other method is to associate a filter directly to the column This means that when the column element is used in an information link the column filter is automatically applied Use column filters only when there is no reason to believe the user will ever want to use the column without a filter Make sure the column description makes it clear to the user that a filter is being applied Use filter elements when you want to give users the option to use or not use the filter Again remember to write a good description of the filter Personalized Information Links Using personalized information links you can set up a data source to return only information applicable for a certain User or Group Depending on which user is logged in and accesses the information link different subsets of the data will be available For example you could set up an information link that detects whether the user retrieving data is a member of the sales force for Europe Asia or the US and only return data for that continent Below are two examples of personalized information links The first will retrieve data depending on which user is logged in the second depending on which groups that user is a member of User Name via Lookup Table Scenario You want to set up an information link to a table of data with sales made by all the sales people in his company However depending on which person from the sales department accesses an analysis using thi
229. tion that limits data depending on the currently logged in user see Personalized Information Links Additionally columns can also be set up to include aggregate data In the Information Designer columns are represented by these icons det Real column Integer column String column Date column DateTime column Time column BLOB binary large object column Cannot be retrieved but can be used in the structure search filter condition It can also be used in custom made filter conditions using the API CLOB character large object column Can be retrieved to DecisionSite Client It can also be used in custom made filter conditions using the API Unknown column in the Data Sources pane only Must be set manually to one of the accepted column types above before it can be saved in the IM Creating a Column Element gt To add a column 1 2 10 11 From the Select workbench drop down list select Column Click Change Response The Column Element workbench is displayed Select a column leaf node in the Data Sources tree Comment In the Data Sources pane to the left click the E signs to browse databases and tables Click Add gt Comment Repeat this step if you need to include more data to calculate your column element If you want the column to be calculated enter the expression in the Calculation field Comment For instance if you have added two numerical columns you could calculate the sum by
230. tional Genomics nennen G Get Values from Data Set dialog aano e 154 using current settings as filter 136 Glossary information builder eene 157 information designer cccscccescessesseesesseeseeeseeseees 116 Els UNE 110 Group Properties pane eeeeeeeseeceeeeeeesneeeeeeeeeesneeeeeeeeeees 56 Groups assigning properties eeeeseeseeeneeeeenn 51 56 creating elle E deleting end e e ERR nalmillig z io HERRERA DEI Eed UI IEN H Hard filters adding to an information nk 122 description of erae baies 120 userintertace ci De Ig QE Deis 143 Hints Edit Oracle Hints dalog esses 144 l Icons icons in the elements pane 142 icons in the information model 84 Import details on data sources and INS 107 Elements froma file oem s 80 list of users caeterae ets 50 User interface senec ehe ted 99 Independent columns in prompted information links 123 setting in Advanced tab when to use TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual Information Builder El EEN 140 DEI Ap 121 122 Information Designer c cccscccessesseeseseesseesssecsseessneeseenss 87 Information Library uni cete is 118 Information links annotating c cicer iri emet Greatirig naso Eee esp te t ke bc eee EE EE i iS eXGCUtllg eiie PROPERE Se ATOT e EE E S v OR ORE IO castes ERRAT
231. troduction This section gives a broad overview of the different steps recommended to set up the DecisionSite platform when the Spotfire Analytics Server is installed The intent is to give you as an administrator an understanding of each step and its impact on the environment For details on each step you are recommended to read the Help for the appropriate tool Example An example company Acme Corp is used to exemplify the process of setting up the environment Acme Corp is a company active in the gene exploration field and consists of a research department a sales department and a management department The research department in turn consists of three projects A B and C Analysis results from research and sales needs to be communicated internally as well as to management Research also got a tool development group with representatives from each project Their goal is to develop tools needed to make the gene research more efficient Acme Corp has got a system administrator who is responsible for installing the Spotfire Analytics Server and setting up the DecisionSite platform We will call the administrator Tom 4 1 2 Users and Groups Users and groups of users play an important role in the DecisionSite environment In the DecisionSite Administrator users can be added to the environment and organized into groups The design of the groups affect which tools that become available for the user and what data that can be retrieved The us
232. ttons 73 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 3 2 5 Filter Elements 4 3 2 5 1 Filter Elements Overview Filters correspond to the WHERE clauses in SQL and are used to specify that only certain rows of a table are retrieved from the data source based on the criteria described in the filtering condition Filter elements can be applied as required by the user In the Information Model they are represented by this icon d Filters can also be included as part of a column definition Such filters cannot be disabled by the user Whenever the column is retrieved the data will be filtered 4 3 2 5 2 Creating a Filter Element This topic describes how to create filters as separate elements These can be applied as required by the user See Defining a Column Filter for information on how to add a filter as part of a column definition gt To create a filter 1 From the Select workbench drop down list select Filter 2 Click Change Response The Filter Elements workbench is displayed 3 Inthe Data Sources pane select a column and then click the Add gt button to add the column to use in the filter condition Comment Repeat this step if you need to include more columns in your filter condition 4 Define a filter condition with the chosen columns for example C1 gt 2000 or if you are using two columns C1 C2 See also Relational Operators Comment You can also add a personal
233. ty Description states the Destination City Coverage 1 Save Copy Save Clear Option Add gt Type Description Select a database procedure from the Data Sources list and then click this button to include it Information Services defines three kinds of procedures Pre update procedure this procedure does not return any data it only performs an operation on one or more databases All pre update procedures in an Information Link will always be executed before any query procedure Query procedure just like a database table this procedure returns data Post update procedure this procedure does not return any data it Name Type Default value Permit Null Prompt Insert Original Name Type Label X Add gt Remove Procedure Join column Add Select Freehand Case sensitive GUID Name Description Select Spotfire DecisionSite Administration only performs an operation on one or more databases All post update procedures in an Information Link will always be executed after any query procedure States the name and type of the input parameters detected in the database procedure Select whether the input parameter should receive a Default value by entering a value of the appropriate type in the input field If not leave the field blank If you want to allow the input parameter to be Null select the Permit Null check box Select whether you want the end u
234. ucture Search Users of DecisionSite for Lead Discovery can use structure search in run time filters This means using substructure or similarity search to limit the data set to chemical structures of a particular type gt To use structure search in a run time filter 1 Open an information link that contains columns with structure search run time filters Response The system will begin to retrieve data For each column with a run time filter the Set Filter for Column Dialog will appear asking you to specify the filter conditions for this column 2 Select Substructure or Similarity depending on the type of search you want to perform 135 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 4 4 3 3 6 4 4 3 3 7 136 3 Click Edit Structure Response ISIS Draw is launched 4 Draw a structure to use as search template Comment See ISIS Draw documentation for more information on how to edit structures 5 When you are done drawing the structure click the button in ISIS Draw Response ISIS Draw is closed and the structure appears in the Set Filter for Column dialog 6 Click Next or Finish Response The data is retrieved If this is the last run time filter the data is displayed in a visualization Using Current Query Device Settings as a Filter When opening information links with columns prompted for values or value range see Adding Prompted Filters it is possible to use the v
235. ull check box Example 1 Enter Default value and No prompt means that the specified default value will always be used as input parameter Example 2 Leave Default value empty select Permit Null and Single value prompt will cause the end user to be prompted for a value If the end user does not enter a value in the prompt Null will be used Example 3 Leave Default value empty leave Permit Null empty and Single value prompt will cause the end user to be prompted for a value If the end user does not enter a value in the prompt an error message will appear since Null is not allowed Comment You cannot select the combination No Default value Not allow Permit Null and No Prompt since this is a paradox Click the Insert button to add a new line in which to specify a Resulting Column that the procedure will return 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Spotfire DecisionSite Administration In the Original Name field enter the exact name of a column the database procedure returns This name is specified in the actual database procedure so you have to know this beforehand Select the Type the resulting column should have Enter a descriptive Label for the resulting column This Label is the name the end user will see in DecisionSite Client If you want to specify a Join between the database procedure and another table use the Join pane Join P i Add gt STATE C1 r
236. ustomer age First buy Electronics real Count real Count datetime Count x real Count X x M Other columns Transfer the following column s to the new data set Customer age First buy Electronics Name Type Computation Age group real Count real Count datetime Count H real Count zl Column names Methodi alue for Category Help Option Identity Description Edit OK Cancel Each unique value in the chosen identity column produces a row in the Spotfire DecisionSite Administration Category Values Other columns Column names generated table If you choose more than one column then the new table will have a separate row for each unique combination of values in the chosen columns Each unique value in the chosen category column produces a new column in the generated table Selecting more than one column under means that the new table will have a separate column for each unique combination of values in the chosen columns The column from which the data is pulled The values in the generated table are computed according to the method selected under Computation e g average Note If you are certain that each combination of Identity and Category has a unique value then you can select the Computation None which will not apply any aggregation of the data However the pivot will fail if you
237. ution You can include column elements filter elements and procedure elements in the same Information Link These will be executed in a certain priority order when the Information Link is executed e All pre update procedures will execute in top down order The procedure is executed before any data is retrieved No data is expected from the pre update procedure and no join is performed Any prompting will occur in the top down order e All query procedures and column elements will execute in top down order The procedures run as a part of the data retrieval Data from the procedures is joined with the rest of the columns Any prompting will occur in the top down order e All post update procedures will execute in top down order The procedure is executed after the data has been retrieved No data is expected from the post update procedure and no join is performed Any prompting will occur in the top down order Note that the order of the elements in the user interface only has significance for the elements of the same priority class A pre update procedure will always execute before a query procedure regardless if that pre update procedure is placed at the bottom of the list Information Link Properties PETTEE Clear Link Filter type Limits E Bug Levels DIEN 223 Product range ll NEN IR b Name engl range hd i o DIEN E getBugLev DIEN Ab Identifier range v EK Conditioning None Edit Join Path Default
238. utomatically receive the new content The same applies if new versions of tools guides or applications are deployed on the server Offline Analysis The update and delivery mechanism of the DecisionSite ApplicationManager makes it possible to use DecisionSite and its analytic applications off line Analytic tools and guides can be built for on line only or on line and off line use In other words users can use the off line designed components of DecisionSite applications even if the DecisionSite Client is not connected to the Spotfire Analytics Server The off line use is suitable for travel field use or other activities where access to a Spotfire Analytics Server is not possible Release Upgrade The DecisionSite ApplicationManager enables asynchronous upgrades of Spotfire Analytics Server and Client as new releases are available A new version of the Spotfire Analytics Server can be installed Users can then continue to use it with older versions of DecisionSite Client but with access to all new and updated functionality in the form of tools guides and applications that will be downloaded from the server For example an organization has already deployed a released version of DecisionSite and now wants to roll out a new release of DecisionSite The complete upgrade can be staged by first upgrading the server to the new version All users running the old DecisionSite Client version can access the new server since the application manager wi
239. utton The users whose permissions you have set will now get access to the new Computation Services functionality the next time they connect to the Spotfire Analytics Server 3 2 2 Defining Computation Services Servers When running Computation Services on DecisionSite Client one has to specify on which statistics server to execute the various configurations scripts To simplify for the end users it is possible to preconfigure lists of available servers for all types of connectors This is done in the same file for all connectors Note SAS R and S PLUS are third party software that must be installed separately For detailed system requirements please visit http www spotfire com sr gt To specify which calculation servers should be available for users 23 TIBCO Spotfire amp DecisionSite 9 1 1 Deployment and Administration Manual 1 Open the file compserv servers xml in your favorite editor It is located in the directory lt installation directory gt server application data toolsettings Note If the xml file is not there you probably need to apply the patch A35259 from http support spotfire com patches asp Example lt xml version 1 0 encoding UTF 8 gt lt settings gt lt servers gt lt category gt Spotfire Category CompServ PreDefined RServer lt category lt server gt lt address gt http myRserver lt address gt lt server gt lt server gt lt address gt http Rserver2 8012 lt addre
240. vices Specify the SMTP server and Port you wish to use when sending emails from DecisionSite Posters If your SMTP server does not support anonymous login you can select the Use name and password check box and enter a User name and Password All Poster emails will be send from this account Select Email format The default setting is HTML with images If you prefer to have no images in the emails sent from DecisionSite Posters only a hyperlink to the Poster itself this can be done by changing to Text only This can be useful if many users are burdened by large emails due to slow modem connections or similar Some email systems cannot show images in an email so if your users have such a system set Text only Select Email image format either JPEG or PNG The default setting is PNG which is generally the preferable choice since these images are of better quality than JPEG However if the DecisionSite Posters users are running Lotus Notes as their mail client you must change to JPEG since Lotus Notes does not support PNG images in emails Select the Number of included Annotation Notes in the emails The default is No limit but if the DecisionSite Posters users are running Lotus Notes as their mail client you must change to Max 15 or less since Lotus Notes also has a size limit for emails The next thing to do is to define how many and which Decision Status levels users should be able to set the Posters to Which Decision Status levels that
241. ware Packages gt To deploy new software packages 1 Make sure that the Spotfire Analytics Server is running 2 Start the DecisionSite Administrator tool from the main server page in Internet Explorer 3 Select Deployer from the top menu frame Browse to the temporary folder where you unzipped the installation files from the Spotfire DecisionSite deployment kit 5 Select and open the file ds911 distribution zip Click on Deploy 7 The contents of the distribution are shown in a separate window Click on Deploy in this window All software components of DecisionSite Client 9 1 1 will now be installed a 2 4 Configuring Additional Functionality You have now deployed DecisionSite Client 9 1 1 on the Spotfire Analytics Server and set up all the basic functionality However there are a number of additional features that you can set up and configure for use on your DecisionSite system if you have purchased the corresponding licenses If you have already set up these features for previous versions of Spotfire DecisionSite you do not need to perform the configuration tasks again Additional Features e DecisionSite Posters e Computation Services Upgrading DecisionSite e DecisionSite for Functional Genomics e DecisionSite for Lead Discovery e DecisionSite for Microarray Analysis If any of these features are relevant for you proceed to chapter 3 Configuring DecisionSite where you will find instructions on how to se
242. will be asked to update the AADM Data Source information with a user name password server port and SID Updating AADM Connection Information for Retrieve from Database Remote Tool The Retrieve from Database Remote tool in DecisionSite for Functional Genomics is normally configured in the Affymetrix Database step of the installation process for the Spotfire Analytics Server However there may be times when the connection needs to be updated later on For these occasions you can edit the affymetrix tool settings xml file located in the following directory to update the AADM connection information e install directory gt server application data affymetrix tool lt xml version 1 0 encoding UTF 8 gt lt affymetrix gt connection name aadm remote lt user gt aadm lt user gt lt password gt aadm lt password gt driver class oracle jdbc driver OracleDriver driver class connection url jdbc oracle thin Gqaoracle 1521 qa connection url connection settings setting name aadm remote table owner setting setting name aadm local table owner setting settings lt affymetrix gt Edit the selected element to change the port SID host user or password If the user defined in lt user gt is not the owner of the AADM schema the lt table owner gt should be set to the owner of the AADM schema Example lt user gt aadm_not_owner lt user g
243. x 30 characters Description A short description of the purpose of the column max 255 characters lt Select Select a domain in the Information Model and then click this button Parent domain Type to retrieve the name The name of the domain folder where you want to save the column Use this list box to select the data type of the column Filter devices Spotfire DecisionSite Administration Lists the filter devices that will be available for run time filters in Information Builder Set Opens the Set Filter Devices for Column Element dialog were you can determine which filter devices should be available for the selected column element Save Copy Click Save Copy to create a copy with a new GUID Save Click Save to save or update the column Clear Clears all fields without saving 4 3 3 3 4 5 The Set Filter Devices for Column Element Dialog Set Filter Devices for Column Element E xj Available filter devices Structure Search Radio Buttons Check Boxes Help Selected filter devices List Box Range Add gt gt lt lt Remove OK Cancel Option Available filter devices Selected filter devices Add gt gt Remove Description Displays the filter devices available for the data type of this column The Structure Search filter is available for columns of type blob integer and real Make sure that a valid structure or structure ID is included in the column prior to
244. y The recommendation is to enable logging only when needed and then to disable it again Developers might find it useful to always have the logging enabled Install Log Starting with Application Manager 7 2 all install actions are logged The install log will be written to the packages folder SPROGRAMFILES Spotfire Packages install log SUSERPROFILE Local Settings Application Data Spotfire Packages install log The install log is useful for debugging problems during installation or upgrade The most likely usage scenario is that Spotfire Support will ask for this file if you report an install problem Application Manager Error Messages The Application Manager has a framework for reporting errors Most error dialogs have a Details button that provides access to a detailed error message generated by Application Manager The error message is effectively a high level stack trace of the implementation As a result the original error message can be found at the bottom of the message The detailed message is most useful for developers it is not intended for end users Common Problems Conflict Between User and Machine Packages For Microsoft Windows 2000 and later packages can be installed per user and or per machine User packages always take priority over machine packages This may lead to situations where new packages installed per machine are effectively hidden by old packages installed per user Usually problems orig
245. zing the Environment A number of customizations can be made to the DecisionSite environment An example can be made with a Guide which is basically a series of tools to guide the user through an analysis chain These Guides can be saved in the Spotfire Library 46 4 2 4 2 1 4 2 1 1 4 2 1 2 4 2 1 3 4 2 2 4 2 2 1 Spotfire DecisionSite Administration When the users work with DecisionSite Client helpful Library Guides can be shown in dynamic views to the user Such a view can be set up to display the Guides available in a specified Library Section So using the different access combinations made with the Library Sections different users can see different Guides with the same view For example say that all users get a Guide view added to their common DecisionSite application The view displays all Guides in two Library Sections Research and Sales If a user only has read access to the Research Library Section only Guides from Research Library Section is presented to that user DecisionSite Analysis Builder is needed to create Guide views Example A developer creates a view of Guides for the research department The view displays Guides placed in the Library Sections of any of the research projects With this Guide view each user is only presented with Guides relevant to his or her project since each user only has read access to her own projects Library Section DecisionSite Administrator Introduction Intro

TIBCO® Spotfire® DecisionSite® 9.1.1

Contents

Download Pdf Manuals

Related Search

Related Contents

TIBCO&reg; Spotfire&reg; DecisionSite&reg; 9.1.1

Contents

Download Pdf Manuals

Related Search

Related Contents

TIBCO® Spotfire® DecisionSite® 9.1.1