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HIV Study Tutorial
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"FileSet_FileUpload_Stacktrace.txt" attached to message "Error when trying to use FileSet"

ERROR DavController 2013-04-10 09:04:49,039 http-8080-2: unexpected exception java.lang.NullPointerException at org.labkey.api.util.FileUtil.getAbsoluteCaseSensitiveFile(FileUtil.java:738) at org.labkey.filecontent.FileContentServiceImpl.fireFileCreateEvent(FileContentServiceImpl.java:791) at org.labkey.core.webdav.DavController.fireFileCreatedEvent(DavController.java:2619)...

"cpas.log" attached to message "500: Unexpected server error"

11 Jan 2006 14:02:23,381 DEBUG ModuleLoader : ModuleLoader init 11 Jan 2006 14:02:23,568 DEBUG CoreModule : Ensuring databases are present 11 Jan 2006 14:02:23,578 ERROR ModuleLoader : Failure ocurred during ModuleLoader init. java.lang.NoClassDefFoundError: org/apache/tomcat/dbcp/dbcp/BasicDataSource at org.fhcrc.cpas.module.CoreModule.ensureDataBases(CoreModule.java:86) at org.fhcrc.cpas.module.ModuleLoader.doInit(ModuleLoader.java:145)...

Error at startup after upgrading to the trunk version: 27583

500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoSuchMethodError: org.labkey.api.ehr.EHRService.registerSimpleFormType(Lorg/labkey/api/ehr/EHRService$FORM_TYPE;Lorg/labkey/api/module/Module;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V        at org.labkey.onprc_ehr.ONPRC_EHRModule.registerEHRResources(ONPRC_EHRModule.java:184)        at...

NIMHPortions.xls

Sheet1 SubjectID SampleID PortionID DateSeparated Division 20021 789 7891 5/2/71 Half 20001 456 4561 5/2/71 Half 20022 786 7861 5/2/71 Half 20023 450 4501 5/2/71 Half 20024 342 3421 5/2/71 Half 20025 783 7831 5/2/71 Half 20002 890 8901 5/2/71 Half 50002 990 9901 5/2/71 Half 50003 129 1291 5/2/71 Half 10001 617 6171 5/2/71 Half 10002 712 7121 5/2/71 Half 50001 888 8881 5/2/71 Half 10003...

NIMHPortions.xls

Sheet1 SubjectID SampleID PortionID DateSeparated Division 20021 789 7891 5/2/71 Half 20001 456 4561 5/2/71 Half 20022 786 7861 5/2/71 Half 20023 450 4501 5/2/71 Half 20024 342 3421 5/2/71 Half 20025 783 7831 5/2/71 Half 20002 890 8901 5/2/71 Half 50002 990 9901 5/2/71 Half 50003 129 1291 5/2/71 Half 10001 617 6171 5/2/71 Half 10002 712 7121 5/2/71 Half 50001 888 8881 5/2/71 Half 10003...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

NIMHSlides.xls

Sheet1 SubjectID SampleID PortionID SlideID StainPositive StainDate 20021 789 7891 1 Y 5/3/71 20001 456 4561 2 Y 5/3/71 20022 786 7861 3 Y 5/3/71 20023 450 4501 4 Y 5/3/71 20024 342 3421 5 Y 5/3/71 20025 783 7831 6 Y 5/3/71 20002 890 8901 7 Y 5/3/71 50002 990 9901 8 N 5/3/71 50003 129 1291 9 N 5/3/71 10001 617 6171 10 N 5/3/71 10002 712 7121 11 N 5/3/71 50001 888 8881 12 N 5/3/71 10003...

NIMHSlides.xls

Sheet1 SubjectID SampleID PortionID SlideID StainPositive StainDate 20021 789 7891 1 Y 5/3/71 20001 456 4561 2 Y 5/3/71 20022 786 7861 3 Y 5/3/71 20023 450 4501 4 Y 5/3/71 20024 342 3421 5 Y 5/3/71 20025 783 7831 6 Y 5/3/71 20002 890 8901 7 Y 5/3/71 50002 990 9901 8 N 5/3/71 50003 129 1291 9 N 5/3/71 10001 617 6171 10 N 5/3/71 10002 712 7121 11 N 5/3/71 50001 888 8881 12 N 5/3/71 10003...

"reload.txt" attached to message "expXML property declaration import errors"

12 Jan 2006 11:59:59,838 INFO : Experiment Import for Uploaded file: 1/12/2006 11:59:59 12 Jan 2006 11:59:59,838 INFO : ======================================= 12 Jan 2006 12:00:00,410 INFO : Rolling back transaction in experiment loader. 12 Jan 2006 12:00:00,410 ERROR: Exception during load org.fhcrc.cpas.exp.XarFormatException: java.sql.SQLException: ERROR: insert or update on table "objectproperty"...

Step 2: Study Reports

In this step we will look at the variety of reports available in the online example. We will look at both built-in reports (automatically available in all study folders) and custom reports (created by the study researchers or data analysts). As you progress with the walkthrough, notice two things: First, all of these reports are 'live', that is, they represent the current state of the underlying...

Query Metadata: Examples

This topic provides examples of metadataSql used to change the display and behavior of fields in tables and queries. Auditing Level Conditional Formatting Include Row Selection Checkboxes Hide a Field from Users Show/Hide Columns on Insert and/or Update Use a Format String for Display Use a Text Expression for Display Set a Display Width for a Column Display Columns in Specific Order...

Ontology Lookup

Premium Feature — Available in the Enterprise Edition of LabKey Server. Learn more or contact LabKey. Ontology Lookup Data Type Lookup Rules Usage Example Concept Picker for Insert/Update with Type-ahead Initialize Expected Vocabulary Ontology Lookup Data Type Once an ontology has been loaded and the module enabled in your folder, the fieldEditor will include an Ontology Lookup data...

"cpas.log" attached to message "Manual Unix Install (500: Unexpected server error)"

17 Jan 2006 11:18:37,092 DEBUG ModuleLoader : ModuleLoader init 17 Jan 2006 11:18:37,198 DEBUG CoreModule : Ensuring databases are present 17 Jan 2006 11:18:37,204 ERROR ModuleLoader : Failure ocurred during ModuleLoader init. java.lang.NoClassDefFoundError: org/apache/tomcat/dbcp/dbcp/BasicDataSource at org.fhcrc.cpas.module.CoreModule.ensureDataBases(CoreModule.java:86) at org.fhcrc.cpas.module.ModuleLoader.doInit(ModuleLoader.java:145)...

"Assay UI.pptx" attached to message "Suggestions for Extensible Assays"

Interacting with Assay Data 1 Basic Ways to Interact: Experiment: cuts across all assay types Assay: by batch, run or sample 2 Assay View: Most of this already exists in labkey Should give user a grid of data from one assay by either batch, run or sample (like grid here: /assay/home/assayRuns.view) I believe much of this already is possible in text-assays, but we should be able to define the...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

drt problem

I'm trying to run the drt targets from the command prompt, from the LABKEY_HOME/server/test/build.xml, in release 8.3 and I'm getting and error. ... [junit] Loading scripts from seleniumHelpers.js [junit] testSteps(org.labkey.test.drt.XTandemTest) [junit] com.thoughtworks.selenium.SeleniumException: ERROR Server Exception: sessionId should not be null; has this session been started yet? [junit]...

job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

"catalina.out" attached to message "Labkey error"

Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server version: Apache Tomcat/7.0.62 Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server built: May 7 2015 17:14:55 UTC Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server number: 7.0.62.0 Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener...

NIMHSamples.xls

Sheet1 SubjectID SampleID DateObtained SampleType Volume VolumeUnits 20021 789 5/1/71 Blood 2 ml 20001 456 5/1/71 Blood 2 ml 20022 786 5/1/71 Blood 1 ml 20023 450 5/1/71 Blood 1 ml 20024 342 5/1/71 Blood 1 ml 20025 783 5/1/71 Blood 1 ml 20002 890 5/1/71 Blood 2 ml 50002 990 5/1/71 Blood 2 ml 50003 129 5/1/71 Blood 2 ml 10001 617 5/1/71 Blood 2 ml 10002 712 5/1/71 Blood 2 ml 50001 888...

NIMHSamples.xls

Sheet1 SubjectID SampleID DateObtained SampleType Volume VolumeUnits 20021 789 5/1/71 Blood 2 ml 20001 456 5/1/71 Blood 2 ml 20022 786 5/1/71 Blood 1 ml 20023 450 5/1/71 Blood 1 ml 20024 342 5/1/71 Blood 1 ml 20025 783 5/1/71 Blood 1 ml 20002 890 5/1/71 Blood 2 ml 50002 990 5/1/71 Blood 2 ml 50003 129 5/1/71 Blood 2 ml 10001 617 5/1/71 Blood 2 ml 10002 712 5/1/71 Blood 2 ml 50001 888...