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How is Study Data Stored in LabKey Server?

This topic answers a few questions about how study data is stored inside the server: When you create a study dataset and import data to it, how is that data stored and managed in the system? How is data from different studies related? Is the data from different studies physically or logically separated? Topics Data Tables within Schema Import Process System Tables Visit Labels ...

"labkey-errors.log" attached to message "Why build Labkey but the ./build/deploy/modules is empty?"

ERROR ModuleLoader 2016-12-07 12:12:54,844 localhost-startStop-1 : Unable to instantiate module C:\LabKey16.1-42836.12-src\build\deploy\modules\adjudication org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 31 in XML document from URL [file:/C:/LabKey16.1-42836.12-src/build/deploy/modules/adjudication/config/module.xml] is invalid; nested exception is org.xml.sax.SAXParseException;...

"labkey-errors (4).log" attached to message "500: CONFIGURATION ERROR"

ERROR DbScope 2016-04-20 08:19:47,687 localhost-startStop-1 : Connection to "labkeyDataSource" at jdbc:postgresql://localhost:5432/labkey failed with the following error: ERROR DbScope 2016-04-20 08:19:47,688 localhost-startStop-1 : Message: El intento de conexi�n fall�. SQLState: 08001 ErrorCode: 0 org.postgresql.util.PSQLException: El intento de conexi�n...

"labkey-errors.log" attached to message "Why build Labkey but the ./build/deploy/modules is empty?"

ERROR ModuleLoader 2016-11-29 18:34:43,304 localhost-startStop-1 : Unable to instantiate module C:\LabKey16.1-42836.12-src\build\deploy\modules\adjudication org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 31 in XML document from URL [file:/C:/LabKey16.1-42836.12-src/build/deploy/modules/adjudication/config/module.xml] is invalid; nested exception is org.xml.sax.SAXParseException;...

"labkey-errors.log" attached to message "Why build Labkey but the ./build/deploy/modules is empty?"

ERROR ModuleLoader 2016-12-10 12:57:11,548 localhost-startStop-1 : Unable to instantiate module C:\LabKey16.1-42836.12-src\build\deploy\modules\adjudication org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 31 in XML document from URL [file:/C:/LabKey16.1-42836.12-src/build/deploy/modules/adjudication/config/module.xml] is invalid; nested exception is org.xml.sax.SAXParseException;...

Problem loading the yeast_a.xml file for the demo

I get the following output in the error log: ERROR ionUploadManager 2007-09-28 17:19:01,234 AnnotLoader1 : Failed to parse file C:\CPASDemo\databases\yeast_a org.xml.sax.SAXException: Can't open file 'C:\CPASDemo\databases\yeast_a'     at org.labkey.ms2.protein.XMLProteinLoader.parseFile(XMLProteinLoader.java:105)     at org.labkey.ms2.protein.AnnotationUploadManager$AnnotationLoadJob.run(AnnotationUploadManager.java:132)...

"labkey-errors.log" attached to message "LabKey Server Not Starting on Tomcat Intiation..."

ERROR ModuleLoader 2016-02-11 13:43:30,647 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException: DataSources are not properly configured in labkey.xml. at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:887) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:319) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:231)...

"labkey.log" attached to message "LabKey Server Not Starting on Tomcat Intiation..."

INFO ModuleLoader 2016-02-11 13:43:27,618 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR ModuleLoader 2016-02-11 13:43:30,647 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException:...

Configuration error deteced at LabKey Server Startup

Hello,   I am trying to install a local LabKey server on a machine running CentOS 6. I went through the installation steps, but am receiving this error when I go to open labkey in my browser. Also, I am only able to start up postgres when I am logged in as root; does this have something to do with the error? I am relatively new to Linux so please bear with me.   org.labkey.api.util.ConfigurationException:...

"labkey-errors.log" attached to message "Caused by: java.lang.IllegalStateException: Why am I in a transaction?"

ERROR ModuleLoader 2015-07-17 11:53:05,852 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException: Cannot connect to DataSource "labkeyDataSource" defined in labkey.xml. Server cannot start. at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:985) at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:890)...

"labkey.log" attached to message "LabKey Server Not Starting on Tomcat Intiation..."

INFO ModuleLoader 2016-02-11 13:43:27,618 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR ModuleLoader 2016-02-11 13:43:30,647 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException:...

"labkey.log" attached to message " You must have a DataSource named "labkeyDataSource" defined in labkey.xml."

INFO ModuleLoader 2015-06-30 15:28:00,878 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR ModuleLoader 2015-06-30 15:28:03,239 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException:...

"cpas.log" attached to message "CPAS MS2 problem"

09 Mar 2006 22:48:22,687 ERROR ViewServlet : error javax.servlet.ServletException: Servlet execution threw an exception at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:275) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)...

"labkey.log" attached to message "LabKey Server Not Starting on Tomcat Intiation..."

INFO ModuleLoader 2016-02-11 13:43:27,618 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR ModuleLoader 2016-02-11 13:43:30,647 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException:...

"vector_import.tsv" attached to page "Bulk Registration of Entities"

name description nucSeqId selectionMethods tstV-101 pACYC177 Vector Sequence NS-25 ["kanamycin", "ampicillin"] tstV-102 pET-24(+) Vector Sequence NS-26 ["kanamycin"] tstV-103 pLysS sequence NS-27 ["chloramphenicol"] tstV-104 pPCR-Script NS-28 ["ampicillin"] tstV-105 thoroughly made up NS-24 ["blasticidin", "bleomycin"]

Creating New Modules

Hi guys, Wondering if I can get any guidance on coding my own module. I've compiled 1.4 from source code, tinkered with the demo module, and taken a look at the build scripts. As a first step, I copied the demo module into another directory in the modules folder and modified the build script: added <antcall target="myModule"/> to "build_module_classes" target 2. added   <target name="myModule"...

"labkey-db-error-report.txt" attached to message "DB related problem"

ERROR DbSchema 2008-04-10 15:16:04,331 8180-Processor24 : Exception loading schema core java.lang.NullPointerException at org.labkey.api.module.ModuleLoader.getModuleForSchemaName(ModuleLoader.java:1193) at org.labkey.api.data.DbSchema.getModuleForSchemaName(DbSchema.java:182) at org.labkey.api.data.DbSchema.getXmlStreamIfChanged(DbSchema.java:170) at org.labkey.api.data.DbSchema._get(DbSchema.java:105)...

"labkey-errors.log" attached to message "New Install Fails with "Caused by: java.lang.IllegalStateException: Why am I in a transaction?""

ERROR ModuleLoader 2015-04-24 09:04:17,545 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException: Cannot connect to DataSource "labkeyDataSource" defined in labkey.xml. Server cannot start. at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:974) at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:864)...

First-time Setup redirects me to home, unable to complete administration set up, cannot log in

Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://<server-name>:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://<server-name>:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in...

Status Assessment.xls

data Participant ID Source Lsid Date Day Meets Criteria for Acute Agrees to Acute Schedule Agrees to Provide Partner Info Partner #1 ID Partner #2 ID Cohort 249318596 2008-08-04 79 true true true 249320489 1 249318596 2008-11-23 190 true true true 249320489 1 249318596 2008-09-02 108 true true true 249320489 1 249318596 2009-04-17 335 true true true 249320489 1 249318596 2009-01-18...