Hi Shane,
Alexey (cc-ed) was the primary developer of meme, cmnokey and inferelator services. Please talk to Alexey.
Thanks,
P.
On Jan 31, 2014, at 1:01 PM, Shane Canon <scanon(a)lbl.gov> wrote:
>
> Pavel,
>
> I'm working through the services. I have cmonkey and meme deployed. I've noticed a few things that we will need to fix, but I'm working around for
> now. Some of these are artifacts due to we no longer install into /kb/deployment. So if the code or tests assume that, then it can cause problems.
> We also install as a non-root user. So this can sometime lead to problems too. If you or Roman grep through the code and look for references
> to /kb/deployment, then you will see what needs to be addressed. I also noticed that the tests have hard coded references for a magellan host.
> So that needs to be fixed.
>
> After deploying meme, I am seeing the following failures when I run make test. I could use some help to understand how to deal with these.
>
> For now, I will work on bambi and inferelator.
>
> --Shane
>
> ubuntu@t46:/kbase/deployments/20140109-prod/dev_container/modules/meme$ make test
> ../../tools/Makefile.common.rules:36: warning: overriding commands for target `deploy-libs'
> Makefile:47: warning: ignoring old commands for target `deploy-libs'
> # run each test
> /kbase/runtimes/20140109-prod/bin/perl test/script_tests-command-line.t ; \
> if [ $? -ne 0 ] ; then \
> exit 1 ; \
> fi \
>
> 1..24
> ok 1 - creating Test::Cmd object for find_motifs_with_meme_from_ws
> not ok 2 - Running find_motifs_with_meme_from_ws
> # Failed test 'Running find_motifs_with_meme_from_ws'
> # at test/script_tests-command-line.t line 32.
> MemeRunResult ID: {"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id cannot be null or the empty string","error":"us.kbase.common.service.ServerException: id cannot be null or the empty string\n\tat us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat us.kbase.meme.MemeServerImpl.findMotifsWithMemeJobFromWs(MemeServerImpl.java:594)\n\tat us.kbase.meme.MemeServerImpl.findMotifsWithMemeFromWs(MemeServerImpl.java:559)\n\tat us.kbase.meme.MemeServerCaller.findMotifsWithMemeFromWs(MemeServerCaller.java:60)\n\tat us.kbase.meme.MEMEServer.findMotifsWithMemeFromWs(MEMEServer.java:103)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.lang.reflect.Method.invoke(Method.java:606)\n\tat us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat java.lang.Thread.run(Thread.java:744)\n"},"id":"995521465406405"}
>
> not ok 3 - MEME run successfuly
> # Failed test 'MEME run successfuly'
> # at test/script_tests-command-line.t line 35.
> ok 4 - creating Test::Cmd object for find_motifs_with_meme_job_from_ws
> ok 5 - Running find_motifs_with_meme_job_from_ws
> Job ID: 52ebf83ee4b0b278264a5393
>
>
> ok 6 - MEME run successfuly
> ok 7 - creating Test::Cmd object for get_pspm_collection_from_meme_result_from_ws
> not ok 8 - Running get_pspm_collection_from_meme_result_from_ws
> # Failed test 'Running get_pspm_collection_from_meme_result_from_ws'
> # at test/script_tests-command-line.t line 50.
> MemePSPMCollection ID: {"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id cannot be null or the empty string","error":"us.kbase.common.service.ServerException: id cannot be null or the empty string\n\tat us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeJobResultFromWs(MemeServerImpl.java:917)\n\tat us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeResultFromWs(MemeServerImpl.java:882)\n\tat us.kbase.meme.MemeServerCaller.getPspmCollectionFromMemeResultFromWs(MemeServerCaller.java:488)\n\tat us.kbase.meme.MEMEServer.getPspmCollectionFromMemeResultFromWs(MEMEServer.java:338)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.lang.reflect.Method.invoke(Method.java:606)\n\tat us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat java.lang.Thread.run(Thread.java:744)\n"},"id":"633289031774389"}
>
> not ok 9 - MEME PSPM collection generated successfuly
> # Failed test 'MEME PSPM collection generated successfuly'
> # at test/script_tests-command-line.t line 53.
> ok 10 - creating Test::Cmd object for get_pspm_collection_from_meme_result_job_from_ws
> not ok 11 - Running get_pspm_collection_from_meme_result_job_from_ws
> # Failed test 'Running get_pspm_collection_from_meme_result_job_from_ws'
> # at test/script_tests-command-line.t line 59.
> Job ID: {"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"MemeRunResult download error","error":"java.lang.Exception: MemeRunResult download error\n\tat us.kbase.meme.MemeServerImpl.getPspmCollectionFromMemeJobResultFromWs(MemeServerImpl.java:919)\n\tat us.kbase.meme.MemeServerCaller.getPspmCollectionFromMemeResultJobFromWs(MemeServerCaller.java:502)\n\tat us.kbase.meme.MEMEServer.getPspmCollectionFromMemeResultJobFromWs(MEMEServer.java:358)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.lang.reflect.Method.invoke(Method.java:606)\n\tat us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat java.lang.Thread.run(Thread.java:744)\n"},"id":"656565433923738"}
>
> ok 12 - MEME PSPM collection generated successfuly
> ok 13 - creating Test::Cmd object for compare_motifs_with_tomtom_by_collection_from_ws
> not ok 14 - Running compare_motifs_with_tomtom_by_collection_from_ws
> # Failed test 'Running compare_motifs_with_tomtom_by_collection_from_ws'
> # at test/script_tests-command-line.t line 69.
> TomtomRunResult ID: Failed to acquire token: Failed to get auth token: Failed to query Globus Online: 500 read timeout at /kbase/deployments/20140109-prod//lib/Bio/KBase/AuthToken.pm line 574.
>
>
>
> not ok 15 - TOMTOM run successfuly
> # Failed test 'TOMTOM run successfuly'
> # at test/script_tests-command-line.t line 72.
> ok 16 - creating Test::Cmd object for compare_motifs_with_tomtom_job_by_collection_from_ws
> ok 17 - Running compare_motifs_with_tomtom_job_by_collection_from_ws
> Job ID: 52ebf85be4b0b278264a5395
>
>
> ok 18 - TOMTOM run successfuly
> ok 19 - creating Test::Cmd object for find_sites_with_mast_by_collection_from_ws
> not ok 20 - Running find_sites_with_mast_by_collection_from_ws
> # Failed test 'Running find_sites_with_mast_by_collection_from_ws'
> # at test/script_tests-command-line.t line 87.
> MastRunResult ID: {"version":"1.1","error":{"name":"JSONRPCError","code":-32500,"message":"id cannot be null or the empty string","error":"us.kbase.common.service.ServerException: id cannot be null or the empty string\n\tat us.kbase.common.service.JsonClientCaller.jsonrpcCall(JsonClientCaller.java:155)\n\tat us.kbase.userandjobstate.UserAndJobStateClient.completeJob(UserAndJobStateClient.java:400)\n\tat us.kbase.meme.MemeServerImpl.finishJobWithError(MemeServerImpl.java:113)\n\tat us.kbase.meme.MemeServerImpl.findSitesWithMastJobByCollectionFromWs(MemeServerImpl.java:1298)\n\tat us.kbase.meme.MemeServerImpl.findSitesWithMastByCollectionFromWs(MemeServerImpl.java:1260)\n\tat us.kbase.meme.MemeServerCaller.findSitesWithMastByCollectionFromWs(MemeServerCaller.java:287)\n\tat us.kbase.meme.MEMEServer.findSitesWithMastByCollectionFromWs(MEMEServer.java:279)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.lang.reflect.Method.invoke(Method.java:606)\n\tat us.kbase.common.service.JsonServerServlet.doPost(JsonServerServlet.java:303)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:688)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:770)\n\tat org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)\n\tat org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)\n\tat org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)\n\tat org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)\n\tat com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)\n\tat java.lang.Thread.run(Thread.java:744)\n"},"id":"125399939805853"}
>
> not ok 21 - MAST run successfuly
> # Failed test 'MAST run successfuly'
> # at test/script_tests-command-line.t line 90.
> ok 22 - creating Test::Cmd object for find_sites_with_mast_job_by_collection_from_ws
> ok 23 - Running find_sites_with_mast_job_by_collection_from_ws
> Job ID: 52ebf86ce4b0b278264a5396
>
>
> ok 24 - MAST run successfuly
> # Looks like you failed 9 tests of 24.
> make: *** [test-scripts] Error 1
>
