Hi Shane, I changed service URLs in meme and cmonkey tests to http://localhost:service_port_number (assuming that tests will be started on the host where services were deployed). Test logs suggest that meme service failed to read test input from production workspace service at kbase.us/services/ws. Could you please check the access to WS service from the deployment environment? Thank you, Alexey On 1/31/2014 2:50 PM, Pavel Novichkov wrote:

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 <[email protected]> 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