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&downloadI followed the installation instructions from:
https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=66192050) Warnings in /var/log/tomcat7/transmart.log, probably harmless but I'd like to be sure30-01-2015 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