- Release-team - mailman3.cels.anl.gov

Re: [Release-team] Status of some services
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

With only Shane and I working on deployments, we're very resource constrained. I'm going to pause my work on production, and circle back to test. I've already marked 2 out of 6 ready. In the future, we will definitely need more resources for these major pushes, particularly as we've expanded the number of services, and the changes to backend data stores. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov] Sent: Thursday, February 06, 2014 9:26 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us Subject: Re: [Release-team] Status of some services We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 10:05 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 10:05 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Status of some services
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Land, Miriam L. [landml(a)ornl.gov] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi

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Fwd: Modeling ready for deploy
by Brettin, Thomas S. 06 Feb '14

06 Feb '14

FYI to the whole release team. Begin forwarded message: From: Christopher Henry <chrisshenry(a)gmail.com<mailto:[email protected]>> Subject: Modeling ready for deploy Date: February 6, 2014 3:58:41 AM CST To: "Miriam L. Land" <landml(a)ornl.gov<mailto:[email protected]>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>>, "Thomas S. S. Brettin" <brettin(a)cels.anl.gov<mailto:[email protected]>> Hey guys, Modeling services ready for deploy. You can pass make test if you: source /kbase/deployments/20140109-prod/dev_container/user-env.sh cd /kbase/deployments/20140109-prod/dev_container/modules/KBaseFBAModeling export KB_DEPLOYMENT_CONFIG=../../../deployment.cfg make test The production deployment config needs to look like this: [fbaModelServices] fbajobcache=/tmp/fbacache/ jobserver-url=http://kbase.us/services/workspace fbajobdir=/tmp/fbajobs mfatoolkitbin=/kbase/deployments/20140109-prod/bin/mfatoolkit probanno-url=http://localhost:7073 mssserver-url=http://bio-data-1.mcs.anl.gov/services/ms_fba accounttype=kbase workspace-url=https://kbase.us/services/ws defaultJobState=queued gaserver-url=http://kbase.us/services/genome_annotation idserver-url=http://kbase.us/services/idserver Make sure you have KB_SERVICE_NAME set: export KB_SERVICE_NAME= fbaModelServices Chris

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Status of some services
by Nomi Harris 06 Feb '14

06 Feb '14

Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi

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Re: [Release-team] [Kbase-devel] token lifetimes
by Shane Canon 05 Feb '14

05 Feb '14

FYI. I've redeployed on the test cluster. This required updating jars too. --Shane On Feb 5, 2014, at 10:42 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > Re the short term plan, the Java auth libs and workspace service have been updated and I've requested a redeploy. > > -g > > On 2/4/2014 6:49 PM, Gavin A Price wrote: >> I'm moving this conversation from the 'hosed again' thread since otherwise people might miss it based on the title. >> >> In brief: currently the Java auth libs enforce a 3 day lifetime on tokens. The issue is with long running jobs - if a user's token is close to expiry when a job starts, or if the job is days long, the job will not be able to save data to any service that uses the Java auth libs, including the workspace service. From a security perspective, however, 3 days seems like a fairly long time for tokens to live if they start leaking. >> >> The proposal is: >> >> Short term: >> Increase the lifetime to 60 days in the Java auth libs. >> >> Long term: >> Decide on and implement a kbase wide token lifetime. Support necessary functionality for long running jobs given that lifetime. >> >> I'll change the Java libs and request a workspace redeploy tomorrow unless I hear differently. >> >> -g >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel >> > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Release-team] Deploying meme, cmonkey, bambi and inferelator
by Brettin, Thomas S. 04 Feb '14

04 Feb '14

Right. The Devel needs to do this ahead of time. I'm good with that. Sent from my Verizon Wireless 4G LTE DROID Gavin A Price <gavinaprice(a)gmail.com> wrote: 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(a)gmail.com<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> wrote: Sent from my Cray XT30 On Feb 2, 2014 5:07 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> wrote: > >> > >> Firstly, you may want to check out > >> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#trans… > >> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#trans… > >> > >> 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(a)lbl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[email protected]>> 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(a)lbl.gov<mailto:[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 > 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 > >> _______________________________________________ > >> Release-team mailing list > >> Release-team(a)lists.kbase.us<mailto:[email protected]> > >> https://lists.kbase.us/mailman/listinfo/release-team > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us<mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] KBaseExpression GIT PUSHED
by Shane Canon 04 Feb '14

04 Feb '14

It is deployed. I tried running make test. It worked for a good bit, then started failing lots of tests. So you may need to contact the developers. --Shane On Feb 4, 2014, at 7:06 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > KBaseExpression is now ready to be deployed and tested. > > I'll be watching the services spreadsheet to see if there is anything I need to do. > > I'm expecting the last of Pavel's modules to be checked into git by 8am Pacific time. We should be ready to deploy/test and move to prod after that. I'll try to get out a status report in about an hour. > > Miriam > > From: Jason Baumohl <jkbaumohl(a)lbl.gov<mailto:[email protected]>> > Date: Tuesday, February 4, 2014 1:26 AM > To: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]>>, Miriam Land <landml(a)ornl.gov<mailto:[email protected]>> > Cc: Shinjae Yoo <sjyoo(a)bnl.gov<mailto:[email protected]>>, "Thomas S. Brettin" <brettin(a)cels.anl.gov<mailto:[email protected]>> > Subject: Re: GIT PUSHED > > Hi Miriam, > > KBaseExpression is now ready to be tested. It is currently pointing to the dev database. > So later we will need to change the deploy.cfg over. > However in the meantime it can be tested vs the dev DB. > > Thanks, > Jason > > > On Mon, Feb 3, 2014 at 10:26 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > Jason, > > Please send a note to Miriam. > > Thanks, > P. > > On Feb 3, 2014, at 10:21 PM, Jason Baumohl <jkbaumohl(a)lbl.gov<mailto:[email protected]>> wrote: > > OK changes made, tested and committed. > > -Jason > > > On Mon, Feb 3, 2014 at 9:45 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > host = db4.chicago.kbase.us<http://db4.chicago.kbase.us/> > dbname = kbase_sapling_v3_dev > user = kbase_sapselect > pass = oiwn22&dmwWEe > > Please try and be sure that you can see expression data, thanks. > > P. > > > On Feb 3, 2014, at 9:39 PM, Jason Baumohl <jkbaumohl(a)lbl.gov<mailto:[email protected]>> wrote: > > Hi Pavel, > > Please clarify. > Is there a read only account? > If so what is the user name and pwd? > I can put it into the deploy.cfg > > -Jason > > > On Mon, Feb 3, 2014 at 9:25 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > Shinjae, > > We can put MySQL credentials into deploy.cfg files… it can be pointed to kbase_sapling_v3_dev on db4.chicago.kbase.us<http://db4.chicago.kbase.us/> for testing… > and then deployment team will modify it and point to production CS…. > > What do you think? Can you do it? > > > Jason, I think you can do the same… (actually please do it..). Let us use kbase_sapling_v3_dev on db4.chicago.kbase.us<http://db4.chicago.kbase.us/> and "read-only" user name and pwd by default... > > > P. > > > On Feb 3, 2014, at 7:33 PM, "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Pavel, > > I’m playing with dataset and one thing is odd: we lost strength > > From original dataset you loaded: > > {"name":"<->","dataset_id":"kb|g.3899.nds.12","properties":{},"strength":1.04554164409637,"node_id2":"kb|netnode.7691","directed":"false","user_annotations":{},"id":"kb|g.3899.nds.12.edge.12","confidence":0,"node_id1":"kb|netnode.10084”} > > > From networks api output: > > {"id":"kb|netedge.2474","name":"is interact with","node_id1":"kb|netnode.1","node_id2":"kb|netnode.1238","directed":"false","strength":0.0,"confidence":0.0,"dataset_id":"kb|g.3899.nds.12","properties":{},"user_annotations":{}} > > From database table: > > mysql> select * from AssociationFeature where to_link = 'kb|g.3899.CDS.68927' limit 10; > +------------------------------+---------------------+------+---------------+----------+ > | from_link | to_link | rank | stoichiometry | strength | > +------------------------------+---------------------+------+---------------+----------+ > | kb|g.3899.nds.12.edge.93313 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.99086 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.100667 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.115777 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.121994 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.126242 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.127387 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.149415 | kb|g.3899.CDS.68927 | 2 | 0 | 0 | > | kb|g.3899.nds.12.edge.163204 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > | kb|g.3899.nds.12.edge.164735 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | > +------------------------------+---------------------+------+---------------+----------+ > 10 rows in set (0.00 sec) > > > mysql> select * from Association where id = 'kb|g.3899.nds.12.edge.93313'; > +-----------------------------+------------+-------------+-------------+------+-----+ > | id | confidence | directional | description | name | url | > +-----------------------------+------------+-------------+-------------+------+-----+ > | kb|g.3899.nds.12.edge.93313 | 0 | 0 | | <-> | | > +-----------------------------+------------+-------------+-------------+------+-----+ > 1 row in set (0.00 sec) > > It seems we lost strength… > > Thanks, > -SJ > > On Feb 3, 2014, at 9:56 PM, Shinjae Yoo <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Yup, > > mysql> use kbase_sapling_v3_dev; > Reading table information for completion of table and column names > You can turn off this feature to get a quicker startup with -A > > Database changed > mysql> select count(*) from AssociationDataset; > +----------+ > | count(*) | > +----------+ > | 265 | > +----------+ > 1 row in set (0.01 sec) > > > I could see that now… > > I was using v3_empty instead of v3_dev… > > I’m generating test cases… > > Thanks, > -SJ > > On Feb 3, 2014, at 9:57 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > > I just reconnected to db4.chicago.kbase.us<http://db4.chicago.kbase.us/> and kbase_sapling_v3_dev from your instance and see everything: > > mysql> select count(*) from AssociationDataset; > +----------+ > | count(*) | > +----------+ > | 265 | > +----------+ > 1 row in set (0.00 sec) > > > Can you reproduce it? > > > > Unfortunately I thought that the data was not loaded correctly and loaded one JM's PPI dataset: > > kbase_sapling_v3_dev.AssociationDataset: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 > kbase_sapling_v3_dev.IsDatasetFor: Records: 1 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.IsGroupingOf: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 > kbase_sapling_v3_dev.Association: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 > kbase_sapling_v3_dev.AssociationFeature: Records: 220 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.AssociationDetectionType: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 > kbase_sapling_v3_dev.DetectedWithMethod: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 > kbase_sapling_v3_dev.Publication: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 > kbase_sapling_v3_dev.PublishedAssociation: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 > kbase_sapling_v3_dev.Source: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 > kbase_sapling_v3_dev.IsSourceForAssociationDataset: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 > > Most records were fortunately skipped, but for tables they are now duplicated…. So, we might have wrong data for: kb|ppid.0 > > > P. > > > On Feb 3, 2014, at 6:43 PM, "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Ah you directly touched base_sapling_v3_dev… > > I’ll change db from v3_empty to v3_dev… > > Thanks, > -SJ > > > On Feb 3, 2014, at 9:36 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > > I do not undertand that…. > > Yes, I see that there are only 4 datasets… but here is the statistics of loading: > > Mon Feb 3 22:26:32 UTC 2014 > kbase_sapling_v3_dev.AssociationDetectionType: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.DetectedWithMethod: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.Association: Records: 51099805 Deleted: 0 Skipped: 3619 Warnings: 3619 > kbase_sapling_v3_dev.AssociationFeature: Records: 102313637 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.IsGroupingOf: Records: 51099805 Deleted: 0 Skipped: 3619 Warnings: 3619 > kbase_sapling_v3_dev.PublishedAssociation: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.Publication: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.AssociationDataset: Records: 256 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.IsDatasetFor: Records: 258 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.IsSourceForAssociationDataset: Records: 256 Deleted: 0 Skipped: 0 Warnings: 0 > kbase_sapling_v3_dev.Source: Records: 256 Deleted: 0 Skipped: 256 Warnings: 256 > Tue Feb 4 00:41:34 UTC 2014 > > 256 records should be loaded… not warnings, no skipping…. > > P. > > > > On Feb 3, 2014, at 6:21 PM, "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Pavel, > > mysql> select count(*) from AssociationDataset; > +----------+ > | count(*) | > +----------+ > | 4 | > +----------+ > 1 row in set (0.00 sec) > > > mysql> select * from AssociationDataset limit 10; > ERROR 2006 (HY000): MySQL server has gone away > No connection. Trying to reconnect... > Connection id: 2697 > Current database: kbase_sapling_v3_empty > > > > Am I using the same database with you? > > Thanks, > -SJ > > On Feb 3, 2014, at 9:11 PM, Shinjae Yoo <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Great… Thanks… I’ll test it… -SJ > On Feb 3, 2014, at 9:00 PM, Pavel Novichkov <psnovichkov(a)lbl.gov<mailto:[email protected]>> wrote: > > Shinjae, > > All data is loaded to kbase_sapling_v3_dev. > P. > > > On Feb 3, 2014, at 1:04 PM, "Yoo, Shinjae" <sjyoo(a)bnl.gov<mailto:[email protected]>> wrote: > > Pavel, > > I just pushed… > > Now I’m leaving for home… > if you have burning questions, just call me `412-467-6860<tel:412-467-6860>’… > > I should be able to answer your call… > > Thanks, > -SJ > > > > > > > > > > > > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Deploying meme, cmonkey, bambi and inferelator
by Gavin A Price 04 Feb '14

04 Feb '14

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(a)gmail.com > <mailto:[email protected]>> > 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(a)lbl.gov >>> <mailto:[email protected]>> 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(a)lbl.gov >>> <mailto:[email protected]>> wrote: >>> >>>> >>>> Sent from my Cray XT30 >>>> On Feb 2, 2014 5:07 PM, "Brettin, Thomas S." >>>> <brettin(a)cels.anl.gov <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> 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(a)lbl.gov >>>> <mailto:[email protected]>> wrote: >>>> > >> >>>> > >> Firstly, you may want to check out >>>> > >> >>>> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#trans… >>>> > >> >>>> http://140.221.84.209/javadoc/us/kbase/workspace/WorkspaceClient.html#trans… >>>> > >> >>>> > >> 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(a)lbl.gov <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> >>>> 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(a)lbl.gov <mailto:[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 >>>> > 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 >>>> > >> _______________________________________________ >>>> > >> Release-team mailing list >>>> > >> Release-team(a)lists.kbase.us >>>> <mailto:[email protected]> >>>> > >> https://lists.kbase.us/mailman/listinfo/release-team >>>> > > >>>> > >>>> > _______________________________________________ >>>> > Release-team mailing list >>>> > Release-team(a)lists.kbase.us <mailto:[email protected]> >>>> > https://lists.kbase.us/mailman/listinfo/release-team >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us <mailto:[email protected]> >>>> https://lists.kbase.us/mailman/listinfo/release-team >>> >

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