This should be possible *after* the module is first approved for the user's ownership by the workspace admins. Before that, of course, attempted uploads will fail.

-g

On 2/3/2014 6:59 PM, Brettin, Thomas S. wrote:

I want to see the make deploy target depend on a subtarget that registers the typespec.

When make deploy is run in dev, it registers the spec in dev

When make deploy is run in test, it registers the spec in test

and same in prod.

I'm working on a prototype of this that I'll write up as a developer guide and bake into the template makefile.

It should apply to KBase types, not community types.

Deployment to production should be fast, not a cumbersome process

On Feb 3, 2014, at 2:24 PM, Gavin A Price <gavinaprice@gmail.com>

wrote:

Ok, so if you want to exactly duplicate the prod type db in the test server, you have a couple options

1) Blow away the current type db and the workspace db, starting from scratch, and dump the type db from prod and restore it to test. Initialize the workspace db as normal and point it as the restored type db.
2) Go through the standard process of users requesting module ownership, granting them ownership via the admin function, and then have them upload their types as they did in the prod db.

Shortcuts are pretty much what I outlined before:

1) Grab all the most recent modules from the workspace service, a test team member requests ownership of all modules, approves via the admin function, and loads all the modules. This will not load older versions of modules, which may or may not be ok.

2) Give all the users admin access so they can approve their own modules.

See https://atlassian.kbase.us/browse/WOR-80 for a potential long term solution.

Long term, if you guys could outline how you'd like testing of types to work we can try to add the necessary functionality to the service.

-g

On 2/3/2014 9:17 AM, Gavin Price wrote:

No, that's what I was saying in my response to Tom. You'd have to get the types manually, one by one, and have the owners go through the approval process on the test server and redo the uploads if you want to duplicate the prod db. There are short cuts possible, though. I need to deal with some moving stuff now so I'll outline those when I get in.

-g
Sent from my Cray XT30

On Feb 3, 2014 9:10 AM, "Shane Canon" <scanon@lbl.gov> wrote:

I think a dump from prod of the types and load to test makes sense. This allows us to at least be somewhat in sync with the production environment. I don't think it is feasible

to have all the data, but it is reasonable to have the types and maybe some sample data.

Gavin: Do APIs and commands presently exist to do this?

--Shane

On Feb 2, 2014, at 7:56 PM, Gavin Price <gaprice@lbl.gov> wrote:

Sent from my Cray XT30
On Feb 2, 2014 5:07 PM, "Brettin, Thomas S." <brettin@cels.anl.gov> wrote:
>
> --------
> WARNING: At least one of the links in the message below goes to an IP address (e.g.10.1.1.1), which could be malicious. To learn how to protect yourself, please go here: https://commons.lbl.gov/x/_591B
> --------
>
> We need a two step process. Dump all types in prod. Load onto test.
That's not going to happen in the next couple weeks.

> Seems backwards.
It'll do for now. How we manage types in kbase needs an overall rethink, as we discussed.

-g

>
> Sent from my Verizon Wireless 4G LTE DROID
>
>
> Gavin Price <gaprice@lbl.gov> wrote:
>
> You don't need to review them, and the mechanics of approving a type (or
> a set of types) takes a couple seconds. I would just say that if a type
> is available in the prod server it should be available in the test
> server, and the prod server can act as the list of approved types. All
> the test team needs to do is see if the requester owns the type in the
> prod server and if so, approve it on the test server. This could
> probably be scripted easily.
>
> > Why is type registration a risky operation?
> Giving all users admin privileges on the test workspace service is what
> I was saying seems dangerous.
>
> -g
>
> On 2/2/2014 12:19 PM, Murphy-Olson, Daniel E. wrote:
> > --------
> > WARNING: At least one of the links in the message below goes to an IP address (e.g. 10.1.1.1), which could be malicious. To learn how to protect yourself, please go here: https://commons.lbl.gov/x/_591B
> > --------
> >
> > I don't think the test team has the bandwidth to review and approve types. I wouldn't even know where to start with criteria.
> >
> > Why is type registration a risky operation?
> >
> > --Dan
> >
> >> On Feb 2, 2014, at 12:04 PM, "Gavin Price"<gaprice@lbl.gov> wrote:
> >>
> >> Firstly, you may want to check out
> >> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#translateFromMD5Types%28java.util.List%29
> >> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#translateToMD5Types%28java.util.List%29
> >>
> >> These will allow you to translate type names between services even if the types were not loaded in the same order. Generally I'd recommend services use the MD5 style type in their code/settings and translate them to human readable types on startup.
> >>
> >> There are a few options that are possible:
> >>
> >> 1) The test team works with each module author to get the appropriate types installed in the test workspace. That means the module author needs to request the module name on the test server and a test team rep needs to approve that request via the admin interface. Then the module author is free to upload types as necessary.
> >>
> >> 2) The test team sets up a ws admin account and provides the credentials to testers and module authors, who can then approve their own modules. This seems a bit dangerous and I probably wouldn't recommend it
> >>
> >> 3) The test team owns all the modules in the test ws and installs any necessary types for testing themselves.
> >>
> >> -g
> >>
> >>
> >>> On 2/2/2014 8:57 AM, Shane Canon wrote:
> >>> Alexey,
> >>>
> >>> You raise some interesting issues. I hadn't appreciated some of these complexities. I'm glad you included Gavin in the chain. I'm hoping he has
> >>> some ideas. For testing purposes perhaps we could upload a snapshot of the production types into the test workspace.
> >>>
> >>> --Shane
> >>>
> >>>
> >>>> On Feb 1, 2014, at 9:20 PM, Alexey Kazakov<aekazakov@lbl.gov>   wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> workspace service 0.1.x that we use now has several big differences from the previous workspace version. In particular, it requires registration of object types for every module to enable the objects to be saved in workspace, and only module's owner can register typespec for the module. Thus, several actions must be performed before workspace will be populated with data:
> >>>> 1. Module's owner requests an authorship of the module (Workspace.request_module_ownership function).
> >>>> 2. Workspace administrator approves the request (workspace service WILL NOT notify module's owner about it). This step prevents implementation of the whole process as a single script.
> >>>> 3. Module's owner registers typespec file and defines a list of types that will be available in workspace (Workspace.register_typespec function). At this step, typespec from another workspace can be copied by Workspace.register_typespec_copy function.
> >>>> 4. Module's owner releases module for general use of its type (Workspace.release_module).
> >>>>
> >>>> These four steps can be performed once, as a preparation of a new workspace installation for data loading. But version numbers for all registered data types will be 1.0, and I anticipate a potential source of problems here for modules that use previous versions of data types. I do not use hard-coded version numbers in meme, cmonkey and inferelator services, but some other modules may be affected.
> >>>>
> >>>> If execution of a module depends on other modules or their data types, their typespec files must be registered too. For instance, meme module depends on types from KBaseSequences, cmonkey depends on types from MEME, KBaseExpression, KBaseGenomes, KBaseNetworks typespecs, and inferelator depends on types from Cmonkey, KBaseGenomes and KBaseExpression typespecs.
> >>>>
> >>>> Ideally, deployment of workspace 0.1.x in test environment should include requests of authorship for all modules currently registered in production workspace, with subsequent import of all typespecs (including all versions of typespec) in a proper order from production workspace. This will re-create all versions of data types from production workspace to ensure identical behavior of modules in test and production environments. What you think about it?
> >>>>
> >>>> Best,
> >>>> Alexey
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> On 2/1/2014 11:41 AM, Shane Canon wrote:
> >>>>> I'm adding the release-team to the thread so they are in the loop.
> >>>>>
> >>>>> The test workspace is a standard deployment in the test infrastructure. The only difference is it isn't populated with the data that is in the production
> >>>>> instance. In general, it would be best if the tests could assume that there isn't any data pre-loaded into a data store. So if it requires some data in
> >>>>> the workspace, it should populate it as part of the test.
> >>>>>
> >>>>> In looking through the modules I see that there are various references to host in 140.84.*.* and 140.85.*.*. Are these "production" services?
> >>>>> I'm worried that what we are deploying is actually contacting test services on Magellan. Also, we would prefer that URLs not be hard coded
> >>>>> in the source code, but instead be read from the deployment configuration file. Right now it appears that all of this information is hard-coded
> >>>>> in the java files, and we would need to recompile and redeploy if we needed to change a URL.
> >>>>>
> >>>>> By the way, my workaround for the type compiler issue is that I have add the dev branch of the type compiler as a submodule. This isn't ideal but
> >>>>> at least provides a way for us to move forward. I will try to create a branch with these changes so that you can review them and merge them in
> >>>>> if they seem reasonable. Another option would be for you to add the generated code to the module repo and only run the type comp when it
> >>>>> is necessary (i.e. a major change in the type compiler or an API change).
> >>>>>
> >>>>> --Shane
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Jan 31, 2014, at 5:26 PM, Alexey Kazakov<aekazakov@lbl.gov>    wrote:
> >>>>>>
> >>>>>> Hi Shane,
> >>>>>>
> >>>>>> cmonkey and inferelator tests should pass because these services call AWE client which is doing all calculations. Tests of three functions of meme that call AWE client passed too. I am trying to figure out how to deal with other meme functions that run MEME locally. How the workspace service was configured for testing environment? Were modules and object types from production WS made available for the testing WS, or this is only a new clean installation?
> >>>>>>
> >>>>>> Thank you,
> >>>>>> Alexey
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> On 1/31/2014 4:48 PM, Shane Canon wrote:
> >>>>>>> Pavel,
> >>>>>>>
> >>>>>>> Thanks for pointing me to Alexey. I apologize that I keep forgetting who was working on this.
> >>>>>>>
> >>>>>>> BTW, I have inferelator up and running. It seemed to pass the tests easily. There doesn't
> >>>>>>> appear to be any code in bambi (just a spec file). So there isn't anything to deploy there yet.
> >>>>>>>
> >>>>>>> So the only one that we need to figure out is meme. This appears to just be due to testing
> >>>>>>> against a workspace service that isn't the production one. So it is probably missing some
> >>>>>>> objects that are used in the test. I would like to have a test I can run in the test environment
> >>>>>>> just for completeness. But I think we are close.
> >>>>>>>
> >>>>>>> --Shane
> >>>>>>>
> >>>>>>>> On Jan 31, 2014, at 2:50 PM, Pavel Novichkov<psnovichkov@lbl.gov>    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<scanon@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
> su
> >> n.reflect.Deleg
> >>>>>>>>> atingMethodAccessorImpl.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.CoyoteA
> da
> >> pter.service(Coy
> >>>>>>>>> oteAdapter.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.griz
> zl
> >> y.SelectionKeyCo
> >>>>>>>>> ntextTask.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.NativeMethodAccesso
> rI
> >> mpl.invoke(Nati
> >>>>>>>>> veMethodAccessorImpl.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.
> ja
> >> va:331)\n\tat or
> >>>>>>>>> g.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall
> (P
> >> rotocolChainCont
> >>>>>>>>> extTask.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$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:77
> 0)
> >> \n\tat org.apac
> >>>>>>>>> he.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
> .d
> >> oProcess(Process
> >>>>>>>>> orTask.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":"6
> 56
> >> 565433923738"}
> >>>>>>>>> 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.
> in
> >> voke(NativeMeth
> >>>>>>>>> odAccessorImpl.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:3
> 31
> >> )\n\tat org.apac
> >>>>>>>>> he.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)\n\tat com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)\n\tat com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)\n\tat com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)\n\tat com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)\n\tat com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)\n\tat com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)\n\tat com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)\n\tat com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)\n\tat com.sun.grizzly.ProtocolChainContextTask.doCall(Proto
> co
> >> lChainContextTas
> >>>>>>>>> k.java:54)\n\tat com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)\n\tat com.sun.grizzly.ContextTask.run(ContextTask.java:71)\n\tat com.sun.grizzly.util.AbstractThreadPool$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
> >> _______________________________________________
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> >> Release-team@lists.kbase.us
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> >
>
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