Problems running eTRIKS transmart release (1.2.2.e)

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Karl Forner

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Jan 30, 2015, 1:28:02 PM1/30/15
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Hello,

I gave another try running transmart for our IMI project (http://www.precisesads.eu). I've been suggested to use the latest eTRIKS version (1.2.2.e):
http://owncloud.etriks.org/public.php?service=files&t=fa3130b3ab0e2649489b641e8293e9c9&download

I followed the installation instructions from: https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205

0) Warnings in /var/log/tomcat7/transmart.log, probably harmless but I'd like to be sure

30-01-2015 17:58:54,894  WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.StatusOfExport has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
30-01-2015 17:58:54,907  WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.GalaxyUserDetails has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
30-01-2015 17:58:56,518  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [org.transmart.biomart.BioAssayAnalysisExt]; using defaults.
30-01-2015 17:58:56,656  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagTemplateAssociation]; using defaults.
30-01-2015 17:58:57,238  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [fm.FmFile]; using defaults.
30-01-2015 17:58:57,276  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagDisplayValue]; using defaults.
30-01-2015 17:58:57,424  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagTemplate2]; using defaults.
30-01-2015 17:58:57,851  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagAssociation]; using defaults.
30-01-2015 17:58:57,874  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagItem]; using defaults.
30-01-2015 17:58:58,229  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagTemplate]; using defaults.
30-01-2015 17:58:58,271  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [org.transmartproject.db.accesscontrol.SecuredObjectAccessView]; using defaults.
30-01-2015 17:59:00,332  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [fm.FmFolderAssociation]; using defaults.
30-01-2015 17:59:00,578  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [org.transmart.biomart.Observation]; using defaults.
30-01-2015 17:59:00,673  WARN AbstractEhcacheRegionFactory - Couldn't find a specific ehcache configuration for cache named [annotation.AmTagValue]; using defaults.
30-01-2015 17:59:06,814  WARN DefaultGrailsApplicationAttributes - ApplicationContext not found in org.codehaus.groovy.grails.APPLICATION_CONTEXT attribute of servlet context.
30-01-2015 17:59:07,924  WARN ModuleDeclarationsFactory - 'grails.resources.modules' in config does not define any modules
30-01-2015 17:59:11,854  WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.StatusOfExport has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.
30-01-2015 17:59:11,887  WARN GrailsUtil - [WARNING] Property [id] of domain class blend4j.plugin.GalaxyUserDetails has type [int] and doesn't support constraint [nullable]. This constraint will not be checked during validation.




1) Error on login: No such property: bioDataUid

Just after login, I get this error in transmart.log

30-01-2015 17:59:30,438 ERROR GrailsExceptionResolver - MissingPropertyException occurred when processing request: [GET] /transmart/RWG/getFilterCategories
No such property: bioDataUid for class: org.transmart.biomart.ConceptCode. Stacktrace follows:
groovy.lang.MissingPropertyException: No such property: bioDataUid for class: org.transmart.biomart.ConceptCode
    at org.transmart.SearchKeywordService.findFilterCategories(SearchKeywordService.groovy:115)
    at RWGController$_closure11.doCall(RWGController.groovy:531)
    at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
    at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)
    at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)


2) If I click "Sample Explorer", the page is empty with a never ending "Loading..." message. In the log:
 
30-01-2015 18:19:42,450 ERROR GrailsExceptionResolver - HttpResponseException occurred when processing request: [POST] /transmart/sampleExplorer/showTopLevelListPage
Not Found. Stacktrace follows:
groovyx.net.http.HttpResponseException: Not Found
    at groovyx.net.http.HTTPBuilder.defaultFailureHandler(HTTPBuilder.java:636)
    at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:492)
    at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:278)
    at SolrService$_facetSearch_closure1.doCall(SolrService.groovy:40)
    at SolrService.facetSearch(SolrService.groovy:35)
    at SampleExplorerController$_closure5.doCall(SampleExplorerController.groovy:59)
    at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
    at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)
    at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)


3) If I click on GWAS: empty page and in the log:

This seems related to solr, which is running on 8983 according to its log

30-01-2015 18:22:14,888 ERROR GrailsExceptionResolver - Exception occurred when processing request: [GET] /transmart/GWAS/getFacetResults
SOLR Request failed! Request url:http://localhost:8080/solr/rwg/select/?#  Response code:404  Response message:Not Found. Stacktrace follows:
java.lang.Exception: SOLR Request failed! Request url:http://localhost:8080/solr/rwg/select/?#  Response code:404  Response message:Not Found
    at GWASController$_closure8.doCall(GWASController.groovy:553)
    at GWASController$_closure13.doCall(GWASController.groovy:847)
    at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
    at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)
    at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
30-01-2015 18:22:14,944 ERROR GrailsExceptionResolver - Exception occurred when processing request: [GET] /transmart/GWAS/getDynatree
SOLR Request failed! Request url:http://localhost:8080/solr/rwg/select/?#  Response code:404  Response message:Not Found. Stacktrace follows:
java.lang.Exception: SOLR Request failed! Request url:http://localhost:8080/solr/rwg/select/?#  Response code:404  Response message:Not Found
    at GWASController$_closure8.doCall(GWASController.groovy:553)
    at GWASController$_closure14.doCall(GWASController.groovy:912)
    at GWASController$_closure3.doCall(GWASController.groovy:316)
    at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
    at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)
    at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)


4) If I click on "Upload data", It get a "An error has occured page"
in transmart.log:
30-01-2015 18:26:27,095 ERROR GrailsExceptionResolver - QueryException occurred when processing request: [GET] /transmart/uploadData/index
could not resolve property: platformType of: org.transmart.biomart.BioAssayPlatform [SELECT DISTINCT vendor FROM org.transmart.biomart.BioAssayPlatform as p WHERE p.platformType='Gene Expression' ORDER BY p.vendor]. Stacktrace follows:
org.hibernate.QueryException: could not resolve property: platformType of: org.transmart.biomart.BioAssayPlatform [SELECT DISTINCT vendor FROM org.transmart.biomart.BioAssayPlatform as p WHERE p.platformType='Gene Expression' ORDER BY p.vendor]
    at com.recomdata.grails.plugin.gwas.UploadDataController.addFieldData(UploadDataController.groovy:335)
    at com.recomdata.grails.plugin.gwas.UploadDataController$_closure1.doCall(UploadDataController.groovy:59)
    at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53)
    at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49)
    at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)



Could you help me figuring out what's wrong ?
Thanks,

Karl Forner






Florian Guitton

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Jan 30, 2015, 2:34:01 PM1/30/15
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Your thread on the eTRIKS bug reporter suggests that you are not importing seed data.
Could you please verify that you do ?

Best,

Karl Forner - Quartz Bio

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Feb 2, 2015, 4:58:00 AM2/2/15
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Hi,
I do not know what is seed data, and this is not mentioned in the instructions. What should I do ?
Thanks,
Karl

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Florian Guitton

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Feb 4, 2015, 11:53:54 AM2/4/15
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Information about populating the database for first use can be found here :

Karl Forner - Quartz Bio

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Feb 6, 2015, 5:22:04 AM2/6/15
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Hi Florian,
I uploaded the sample data, as explained in the installation instructions: https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205

sudo -u postgres bash -c "source vars; PGSQL_BIN=/usr/bin/ PGDATABASE=template1 make -C ddl/postgres/GLOBAL tablespaces"
make postgres
make -C samples/postgres load_clinical_GSE8581
make -C samples/postgres load_ref_annotation_GSE8581
make -C samples/postgres load_expression_GSE8581


Karl Forner

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Feb 16, 2015, 12:20:05 PM2/16/15
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Following up on my issues: Florian helped me solving the main issues CATALINA_TMPDIR not set when launching tomcat, and a bad solR port in the groovy config.
I setup a docker github and dockerhup: https://registry.hub.docker.com/u/quartzbio/transmart/ and https://github.com/quartzbio/transmart-docker

Where I stand regarding the reported issues:

  • issue 0 (warnings) - probably harmless
  • issue 1: No such property: bioDataUid - still no clue
  • issue 2: Sample details not working - still there
  • issue 3: GWAS --> Apparently expected, should be hidden in the general config
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