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February 2014

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Re: [Release-team] Service name cleanup [was Re: IRIS testing needed]
by Brettin, Thomas S. 11 Feb '14

11 Feb '14

Tomorrow morning accompanied with a thank you. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov> wrote: So, if you want to deploy IRIS on Thursday morning, I need to get the developers to weigh in on the proposed “clean” service names by Wed night, which is tomorrow. Do you think it would be too much of a buzzkill to send out a message about that tonight? Nomi On Feb 11, 2014, at 1:25 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: What you're proposing sounds good to me. >From an end users perspective, some consolidation around workflow categories might improve usability - but we might want phase in a change like that. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Nomi Harris [nlharris(a)lbl.gov<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 3:09 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; Jim Thomason; release-team(a)kbase.us<mailto:[email protected]>; Nomi Harris Subject: Re: [Release-team] IRIS testing needed If you can wait a few days before redeploying IRIS, that will give me a chance to fix something else: IRIS has a list of services that it supports. I noticed recently that the names that IRIS displays for these services (see screenshots below) often don’t match the names used in the Master tab of the Services spreadsheet (https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJB…) which is what is used on the Services web page (http://kbase.us/developer-zone/services/, though note that it hasn’t been updated—I have a lot of changes to it once we finish this IRIS release). I think the names for services should be the same in IRIS and the Services page. (There are also the names used in the URLs for services, service docs, etc--but I’m not going to try to fix that now.) I thought a few of the service names in IRIS were better than the ones that we had on the Services page (for example, “Tree Service” -> Phylogenetic Trees and Alignments), so I updated the Master spreadsheet and will update the names on the Services page when the release is done. In other cases, though, the names used for services in IRIS are inconsistent (they variously are called “Service”, “Scripts”, “Tools”, or “commands”) and in some cases odd (why is the first one called “Assembly-RAST scripts”?). <Screen Shot 2014-02-11 at 10.09.14 AM.png><Screen Shot 2014-02-11 at 10.09.24 AM.png><Screen Shot 2014-02-11 at 10.09.33 AM.png> I propose to remove the word service/commands/scripts from all of the service names, so they will say (for example) “Assembly”, “Annotation” (or should that be “Genome Annotation”?), “Compression-Based Distance”, etc. I would like to send out a note to all the developers with the proposed “clean” names of all the services, and give them a chance to reply if they want to change any of them, and if I don’t hear otherwise, then on Wed. I will change the COMMANDS file in each service repo to match the cleaned-up service name. Sound ok? By the way, in terms of timing, I will be offline all day Thurs (until about 3pm PT). Nomi On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Ok.. I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Service name cleanup [was Re: IRIS testing needed]
by Nomi Harris 11 Feb '14

11 Feb '14

So, if you want to deploy IRIS on Thursday morning, I need to get the developers to weigh in on the proposed “clean” service names by Wed night, which is tomorrow. Do you think it would be too much of a buzzkill to send out a message about that tonight? Nomi On Feb 11, 2014, at 1:25 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > What you're proposing sounds good to me. > > From an end users perspective, some consolidation around workflow categories might improve usability - but we might want phase in a change like that. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > From: Nomi Harris [nlharris(a)lbl.gov] > Sent: Tuesday, February 11, 2014 3:09 PM > To: Murphy-Olson, Daniel E. > Cc: Henry, Christopher S.; Jim Thomason; release-team(a)kbase.us; Nomi Harris > Subject: Re: [Release-team] IRIS testing needed > > If you can wait a few days before redeploying IRIS, that will give me a chance to fix something else: > > IRIS has a list of services that it supports. I noticed recently that the names that IRIS displays for these services (see screenshots below) often don’t match the names used in the Master tab of the Services spreadsheet (https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJB…) which is what is used on the Services web page (http://kbase.us/developer-zone/services/, though note that it hasn’t been updated—I have a lot of changes to it once we finish this IRIS release). > > I think the names for services should be the same in IRIS and the Services page. (There are also the names used in the URLs for services, service docs, etc--but I’m not going to try to fix that now.) I thought a few of the service names in IRIS were better than the ones that we had on the Services page (for example, “Tree Service” -> Phylogenetic Trees and Alignments), so I updated the Master spreadsheet and will update the names on the Services page when the release is done. In other cases, though, the names used for services in IRIS are inconsistent (they variously are called “Service”, “Scripts”, “Tools”, or “commands”) and in some cases odd (why is the first one called “Assembly-RAST scripts”?). > <Screen Shot 2014-02-11 at 10.09.14 AM.png><Screen Shot 2014-02-11 at 10.09.24 AM.png><Screen Shot 2014-02-11 at 10.09.33 AM.png> > > I propose to remove the word service/commands/scripts from all of the service names, so they will say (for example) “Assembly”, “Annotation” (or should that be “Genome Annotation”?), “Compression-Based Distance”, etc. > > I would like to send out a note to all the developers with the proposed “clean” names of all the services, and give them a chance to reply if they want to change any of them, and if I don’t hear otherwise, then on Wed. I will change the COMMANDS file in each service repo to match the cleaned-up service name. > > Sound ok? > > By the way, in terms of timing, I will be offline all day Thurs (until about 3pm PT). > > Nomi > > On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > >> Ok.. >> >> I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. >> >> ---- >> Daniel Murphy-Olson >> Sr. Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055

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Re: [Release-team] IRIS testing needed
by Nomi Harris 11 Feb '14

11 Feb '14

Yes, it would be nice if the services could be grouped by functionality in some way, but as you note, that would require some discussion, and many services don't fit cleanly into one category. The name cleanup I'm proposing is pretty straightforward. Nomi On Tue, Feb 11, 2014 at 1:25 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov > wrote: > What you're proposing sounds good to me. > > From an end users perspective, some consolidation around workflow > categories might improve usability - but we might want phase in a change > like that. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 <callto:630-252-0055> > ------------------------------ > *From:* Nomi Harris [nlharris(a)lbl.gov] > *Sent:* Tuesday, February 11, 2014 3:09 PM > *To:* Murphy-Olson, Daniel E. > *Cc:* Henry, Christopher S.; Jim Thomason; release-team(a)kbase.us; Nomi > Harris > > *Subject:* Re: [Release-team] IRIS testing needed > > If you can wait a few days before redeploying IRIS, that will give me a > chance to fix something else: > > IRIS has a list of services that it supports. I noticed recently that > the names that IRIS displays for these services (see screenshots below) > often don't match the names used in the Master tab of the Services > spreadsheet ( > https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJB…) > which is what is used on the Services web page ( > http://kbase.us/developer-zone/services/, though note that it hasn't been > updated--I have a lot of changes to it once we finish this IRIS release). > > I think the names for services should be the same in IRIS and the > Services page. (There are also the names used in the URLs for services, > service docs, etc--but I'm not going to try to fix that now.) I thought a > few of the service names in IRIS were better than the ones that we had on > the Services page (for example, "Tree Service" -> Phylogenetic Trees and > Alignments), so I updated the Master spreadsheet and will update the names > on the Services page when the release is done. In other cases, though, the > names used for services in IRIS are inconsistent (they variously are called > "Service", "Scripts", "Tools", or "commands") and in some cases odd (why is > the first one called "Assembly-RAST scripts"?). > > I propose to remove the word service/commands/scripts from all of the > service names, so they will say (for example) "Assembly", "Annotation" (or > should that be "Genome Annotation"?), "Compression-Based Distance", etc. > > I would like to send out a note to all the developers with the proposed > "clean" names of all the services, and give them a chance to reply if they > want to change any of them, and if I don't hear otherwise, then on Wed. I > will change the COMMANDS file in each service repo to match the cleaned-up > service name. > > Sound ok? > > By the way, in terms of timing, I will be offline all day Thurs (until > about 3pm PT). > > Nomi > > On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> > wrote: > > Ok.. > > I plan on doing the redeploy in test early in the morning, and holding the > push to production until Thursday morning unless some new information > arises. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: Christopher Henry [chrisshenry(a)gmail.com] > Sent: Tuesday, February 11, 2014 12:43 AM > To: Murphy-Olson, Daniel E. > Cc: Nomi Harris; Jim Thomason; release-team(a)kbase.us; Gordon, India S. > Subject: Re: [Release-team] IRIS testing needed > > Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, > but we should fix IRIS ASAP. Just a client deploy of the modeling and > workspace_deluxe stuff in IRIS should do it. And we should clean out the > old workspace scripts in invocation. I made those changes in the old > workspace repo as well (cleaned out the commands file and scripts > directory). > > Chris > > On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." < > dolson(a)mcs.anl.gov> wrote: > > Nomi, > > According to the stated dependencies in each services master:/DEPENDENCIES > file, the FBA service is the only one dependent on the old workspace. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > From: Nomi Harris [nlharris(a)lbl.gov] > Sent: Tuesday, February 11, 2014 12:10 AM > To: Murphy-Olson, Daniel E. > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, > India S. > Subject: Re: [Release-team] IRIS testing needed > > The DOE meeting demos are not relying on IRIS, so I don't think it needs > to be redeployed instantly. However, lots of people probably will be > hitting IRIS (and the FBA service) as a result of the meeting, so it would > be good to get some of these issues worked out soon. The FBA service is one > of our most used services. Users complain if it doesn't work as advertised. > > We've now uncovered issues with the FBA commands that relate to the WS > upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade > affect other services as well? FBA can't be the only service that > uses workspaces, can it? > > Nomi > > > On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. < > dolson(a)mcs.anl.gov> wrote: > Here is what happened. The Iris -> IRIS change happened last Thursday in > git. > > I had thought Jim was asking for the deploy of invocation that was in > testing, not a re-pull from a repo. > The Iris that was in testing (from 1/9) was pushed into production. > > We really shouldn't make a last minute change unless there is something in > the demo this week that needs to get fixed. Is there? > > We had asked weeks ago for notification if there were going to be any last > minute updates, and I don't believe invocation was on the list. Miriam > would know for sure. > > ---- > Daniel Murphy-Olson > Sr. 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 Brettin, Thomas S. [ > brettin(a)cels.anl.gov] > Sent: Monday, February 10, 2014 7:40 PM > To: Nomi Harris > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, > India S. > > Subject: Re: [Release-team] IRIS testing needed > > Right. Useless trivia. There was no point. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > So I heard. Anyway, my point was not to discuss the merits of Iris vs > IRIS, but just to point to a trivial but visible change that I expected to > see when IRIS was redeployed. > > Jim, if there's going to be another IRIS redeploy, you should update the > release notes and the whatsnew file (Iris/whatsnew.html) first. > > Nomi > > > On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> > wrote: > IRIS > > In the beginning IRIS was an acronym for interactive remote invocation > service. > > Useless trivia. > > > > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > I'm hoping that Jim will weigh in on this, but besides the fact that he > fixed the tutorial function and it's not fixed at > http://kbase.us/services/docs/invocation/Iris/iris.html, here's a totally > trivial change that I see in git but not oniris.kbase.us. We decided to > switch back to calling it IRIS rather than Iris (since Jim and I were the > only people who ever called it Iris), and Jim changed that in the html: > Iris/iris.html: tab : 'IRIS Terminal', > Iris/iris.html: <title>KBase IRIS Terminal</title> > Iris/splash.html: <title>KBase IRIS Terminal</title> > but http://kbase.us/services/docs/invocation/Iris/iris.html still says > "Iris Terminal", not "IRIS Terminal". > > I do see ws-* functions in IRIS but I'm pretty sure at least some of those > were there before the recent release. > > In the list of services, I see that > http://kbase.us/services/docs/invocation/Iris/iris.html has services that > are out of order and have been retired (e.g., PROM, Experiment, Metagenomic > Sequence QC), while I don't see some of the new services (e.g., cMonkey, > Expression, Meme). > > Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks > to me like it did in December (though I have no way of proving that). Maybe > some of it got redeployed but other parts didn't? Maybe something special > (in addition to the normal deploy) has to happen to refresh the html and > get rid of the defunct services and bring in the new services? > > Nomi > > On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > I don't think you would see any of ws-* commands if this wasn't the latest > version. So I'm pretty sure it is up to date. > > --Shane > > > On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > > I forgot to mention that ws-workspace not working means you will have to > pass the -w [ws_name] flag to all the WS and FBA scripts whenever a > workspace name is required. I suppose we could temporarily remove > that method from IRIS until we have it fixed. > > > Hmm. Sounds like that will require some work from Jim. There's also a lot > of documentation that will need to be changed to reflect the changes > (kbws-* no longer supported; need to use ws-*; need to create a new ws in > WS deluxe; need to use "-w ws_name" flag for all WS and FBA scripts). > > > Also, it doesn't look to me like IRIS is really the latest version. I know > Jim fixed the tutorial, but it doesn't work: > > > > / > > tutorial > Could not load tutorial > > > and there are other changes that I would expect to see if this were really > the latest version that I'm not seeing. > > > Nomi > > > > On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov> > wrote: > Sorry I wasn't following this thread closely enough earlier, but I think > at least part of the problem may be related to pointing to the correct WS > service. The 'kbws-*' scripts point to the old WS, but the fba methods > point to the new WS deployment (kbase.us/services/ws). So methods will > fail unless you have a workspace created with the correct name in the new > WS, and your objects are in that workspace. We should remove the > 'kbws-*' scripts from the IRIS deployment. See below for the working > commands to import the E.coli genome and create a model. > > A sidenote is that the 'ws-workspace' command is not functioning properly > to set the default WS. This method works by setting/reading an environment > variable, but I know this wasn't tested very thoroughly. There is probably > a bug or a change in which environment variables are set. > > / ws-createws IrisTestWS > > > Workspace created with name: IrisTestWS and id: 818 > > Command Completed > > / > > kbfba-loadgenome "kb|g.0" > -w IrisTestWS > > Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 > Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: > 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: > 9e4a09bf26ae131d3982517006d3b100 > Size(bytes): 3625772 User Meta Data: none. > > Command Completed > > > / > > kbfba-buildfbamodel > "kb|g.0" -w IrisTestWS > > Model successfully generated in workspace: Object Name: kb|g.0.fbamdl > Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS > Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: > ee99d7b7017766c8efef87519de37c2e > Size(bytes): 1673278 User Meta Data: none. > > Command Completed > > / ws-listobj -w IrisTestWS > > ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 > KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 > 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 > 2014-02-11T00:34:06+0000 > 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS > wstester1 2014-02-11T00:34:02+0000 4639516 > > Command Completed > > > On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. < > dolson(a)mcs.anl.gov> wrote: > I think at some point workspace commands required specifying the -w > <workspace> option. > > However, even with that I'm getting errors in Iris > > / kbfba-loadgenome -e "kb|g.0 " -w IrisTut > > Genome failed to load to workspace! > > JSONRPC error: Attribute (md5) does not pass the type constraint because: > Validation failed for 'Str' with value undef at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm > line > 38 > Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') > called at reader Moose::Exception::trace (defined at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm > line > 12) line 7 > Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') > called at /kbase > > > > ---- > Daniel Murphy-Olson > Sr. 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 Murphy-Olson, Daniel E. > [dolson(a)mcs.anl.gov] > Sent: Monday, February 10, 2014 5:14 PM > To: Nomi Harris > Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us > > Subject: Re: [Release-team] IRIS testing needed > > That version string is hardcoded in the latest master.. I had the same > thought. Iris was re-deployed this morning. > > I think errors were introduced in the FBA scripts. We still don't have a > fix for them, and I'm growing concerned. It looks like changes were made > last week to FBA, which changed the deploy Makefile in such a way > that things deploy properly into the test environment, but don't work in > production. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > From: Nomi Harris [nlharris(a)lbl.gov] > Sent: Monday, February 10, 2014 4:27 PM > To: Murphy-Olson, Daniel E. > Cc: Henry, Christopher S.; release-team(a)kbase.us; Thomason, James > Subject: Re: [Release-team] IRIS testing needed > > I'm still not able to run kbfba-loadgenome--see trace below. > > Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. > > / kbws-workspace > > Current workspace is: nomitest2 > Command Completed > > / > > kbfba-loadgenome > -e "kb|g.0" > > Genome failed to load to workspace! > > JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace > begun at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line > 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'Mandatory arguments workspace missing.', '_validateargs') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line > 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)', > 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line > 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)') > called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 399 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line > 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 33 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 26 > RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > 'HASH(0x15ef3c38)') called at > /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line > 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm > line 115 > Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', > 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm > line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 273 > Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', > 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 187 > Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', > 'ARRAY(0x2c28270)', 'host', '*', 'proto', > 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, > 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', > 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, > 'no_client_stdout', 1, 'pid_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', > 'setsid', 1, 'background', 1, 'log_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', > 'CODE(0x2780488)', 'HASH(0x277c008)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm > line 18 > Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm > line 20 > Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', > 'Plack::Handler::Starman=HASH(0x2780548)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm > line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') > called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error > code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace > missing._ERROR_ Trace begun > at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 2088 > Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'Mandatory arguments workspace missing.', '_validateargs') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 846 > Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line > 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 399 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line > 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 33 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 26 > RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > 'HASH(0x15ef3c38)') called at > /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line > 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm > line 115 > Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', > 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm > line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 273 > Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', > 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 187 > Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', > 'ARRAY(0x2c28270)', 'host', '*', 'proto', > 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, > 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', > 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, > 'no_client_stdout', 1, 'pid_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', > 'setsid', 1, 'background', 1, 'log_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', > 'CODE(0x2780488)', 'HASH(0x277c008)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm > line 18 > Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm > line 20 > Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', > 'Plack::Handler::Starman=HASH(0x2780548)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm > line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') > called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm > line > 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', > 'HASH(0xbc12d0)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm > line 165 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm > line 158 > Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', > 'genome_to_workspace', > 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at > /kbase/deployments/20140109-prod/plbin/ > fba-loadgenome.pl > line 58 > > > > > > On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > > I haven't done a thorough check, but the new WS commands seem to work, and > I can at least successfully run FBA on a model in IRIS. > > > / kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" > > > Flux balance analysis successful: > Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 > Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 > Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): > 267898 User Meta Data: none. > > Command Completed > > > On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. < > dolson(a)mcs.anl.gov> wrote: > Can someone very familiar with FBA test it out in iris and make sure it is > functioning properly? > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team > > ` > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team > > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team > > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team > >

1 0

Re: [Release-team] IRIS testing needed
by Murphy-Olson, Daniel E. 11 Feb '14

11 Feb '14

What you're proposing sounds good to me. >From an end users perspective, some consolidation around workflow categories might improve usability - but we might want phase in a change like that. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Nomi Harris [nlharris(a)lbl.gov] Sent: Tuesday, February 11, 2014 3:09 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; Jim Thomason; release-team(a)kbase.us; Nomi Harris Subject: Re: [Release-team] IRIS testing needed If you can wait a few days before redeploying IRIS, that will give me a chance to fix something else: IRIS has a list of services that it supports. I noticed recently that the names that IRIS displays for these services (see screenshots below) often don’t match the names used in the Master tab of the Services spreadsheet (https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJB…) which is what is used on the Services web page (http://kbase.us/developer-zone/services/, though note that it hasn’t been updated—I have a lot of changes to it once we finish this IRIS release). I think the names for services should be the same in IRIS and the Services page. (There are also the names used in the URLs for services, service docs, etc--but I’m not going to try to fix that now.) I thought a few of the service names in IRIS were better than the ones that we had on the Services page (for example, “Tree Service” -> Phylogenetic Trees and Alignments), so I updated the Master spreadsheet and will update the names on the Services page when the release is done. In other cases, though, the names used for services in IRIS are inconsistent (they variously are called “Service”, “Scripts”, “Tools”, or “commands”) and in some cases odd (why is the first one called “Assembly-RAST scripts”?). [cid:[email protected]][cid:[email protected]][cid:[email protected]] I propose to remove the word service/commands/scripts from all of the service names, so they will say (for example) “Assembly”, “Annotation” (or should that be “Genome Annotation”?), “Compression-Based Distance”, etc. I would like to send out a note to all the developers with the proposed “clean” names of all the services, and give them a chance to reply if they want to change any of them, and if I don’t hear otherwise, then on Wed. I will change the COMMANDS file in each service repo to match the cleaned-up service name. Sound ok? By the way, in terms of timing, I will be offline all day Thurs (until about 3pm PT). Nomi On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Ok.. I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Christopher Henry [chrisshenry(a)gmail.com<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 12:43 AM To: Murphy-Olson, Daniel E. Cc: Nomi Harris; Jim Thomason; release-team(a)kbase.us<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, but we should fix IRIS ASAP. Just a client deploy of the modeling and workspace_deluxe stuff in IRIS should do it. And we should clean out the old workspace scripts in invocation. I made those changes in the old workspace repo as well (cleaned out the commands file and scripts directory). Chris On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Nomi, According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 From: Nomi Harris [nlharris(a)lbl.gov<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 12:10 AM To: Murphy-Olson, Daniel E. Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? Nomi On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Here is what happened. The Iris -> IRIS change happened last Thursday in git. I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. The Iris that was in testing (from 1/9) was pushed into production. We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. ---- Daniel Murphy-Olson Sr. 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 Brettin, Thomas S. [brettin(a)cels.anl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 7:40 PM To: Nomi Harris Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Right. Useless trivia. There was no point. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. Nomi On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: IRIS In the beginning IRIS was an acronym for interactive remote invocation service. Useless trivia. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us<http://oniris.kbase.us>. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: Iris/iris.html: tab : 'IRIS Terminal', Iris/iris.html: <title>KBase IRIS Terminal</title> Iris/splash.html: <title>KBase IRIS Terminal</title> but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? Nomi On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. --Shane On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: / tutorial Could not load tutorial and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. Nomi On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws<http://kbase.us/services/ws>). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. / ws-createws IrisTestWS Workspace created with name: IrisTestWS and id: 818 Command Completed / kbfba-loadgenome "kb|g.0" -w IrisTestWS Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 Size(bytes): 3625772 User Meta Data: none. Command Completed / kbfba-buildfbamodel "kb|g.0" -w IrisTestWS Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e Size(bytes): 1673278 User Meta Data: none. Command Completed / ws-listobj -w IrisTestWS ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 Command Completed On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I think at some point workspace commands required specifying the -w <workspace> option. However, even with that I'm getting errors in Iris / kbfba-loadgenome -e "kb|g.0 " -w IrisTut Genome failed to load to workspace! JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase ---- Daniel Murphy-Olson Sr. 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 Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 5:14 PM To: Nomi Harris Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] IRIS testing needed That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 From: Nomi Harris [nlharris(a)lbl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 4:27 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; release-team(a)kbase.us<mailto:[email protected]>; Thomason, James Subject: Re: [Release-team] IRIS testing needed I’m still not able to run kbfba-loadgenome—see trace below. Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. / kbws-workspace Current workspace is: nomitest2 Command Completed / kbfba-loadgenome -e "kb|g.0" Genome failed to load to workspace! JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/ fba-loadgenome.pl line 58 On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: I haven't done a thorough check, but the new WS commands seem to work, and I can at least successfully run FBA on a model in IRIS. / kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" Flux balance analysis successful: Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): 267898 User Meta Data: none. Command Completed On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Can someone very familiar with FBA test it out in iris and make sure it is functioning properly? ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 _______________________________________________ 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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Re: [Release-team] IRIS testing needed
by Nomi Harris 11 Feb '14

11 Feb '14

If you can wait a few days before redeploying IRIS, that will give me a chance to fix something else: IRIS has a list of services that it supports. I noticed recently that the names that IRIS displays for these services (see screenshots below) often don’t match the names used in the Master tab of the Services spreadsheet (https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJB…) which is what is used on the Services web page (http://kbase.us/developer-zone/services/, though note that it hasn’t been updated—I have a lot of changes to it once we finish this IRIS release). I think the names for services should be the same in IRIS and the Services page. (There are also the names used in the URLs for services, service docs, etc--but I’m not going to try to fix that now.) I thought a few of the service names in IRIS were better than the ones that we had on the Services page (for example, “Tree Service” -> Phylogenetic Trees and Alignments), so I updated the Master spreadsheet and will update the names on the Services page when the release is done. In other cases, though, the names used for services in IRIS are inconsistent (they variously are called “Service”, “Scripts”, “Tools”, or “commands”) and in some cases odd (why is the first one called “Assembly-RAST scripts”?). I propose to remove the word service/commands/scripts from all of the service names, so they will say (for example) “Assembly”, “Annotation” (or should that be “Genome Annotation”?), “Compression-Based Distance”, etc. I would like to send out a note to all the developers with the proposed “clean” names of all the services, and give them a chance to reply if they want to change any of them, and if I don’t hear otherwise, then on Wed. I will change the COMMANDS file in each service repo to match the cleaned-up service name. Sound ok? By the way, in terms of timing, I will be offline all day Thurs (until about 3pm PT). Nomi On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > Ok.. > > I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: Christopher Henry [chrisshenry(a)gmail.com] > Sent: Tuesday, February 11, 2014 12:43 AM > To: Murphy-Olson, Daniel E. > Cc: Nomi Harris; Jim Thomason; release-team(a)kbase.us; Gordon, India S. > Subject: Re: [Release-team] IRIS testing needed > > Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, but we should fix IRIS ASAP. Just a client deploy of the modeling and workspace_deluxe stuff in IRIS should do it. And we should clean out the old workspace scripts in invocation. I made those changes in the old workspace repo as well (cleaned out the commands file and scripts directory). > > Chris > > On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > >> Nomi, >> >> According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. >> >> ---- >> Daniel Murphy-Olson >> Sr. Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055 >> From: Nomi Harris [nlharris(a)lbl.gov] >> Sent: Tuesday, February 11, 2014 12:10 AM >> To: Murphy-Olson, Daniel E. >> Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. >> Subject: Re: [Release-team] IRIS testing needed >> >> The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. >> >> We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? >> >> Nomi >> >> >> On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >> Here is what happened. The Iris -> IRIS change happened last Thursday in git. >> >> I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. >> The Iris that was in testing (from 1/9) was pushed into production. >> >> We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? >> >> We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. >> >> ---- >> Daniel Murphy-Olson >> Sr. 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 Brettin, Thomas S. [brettin(a)cels.anl.gov] >> Sent: Monday, February 10, 2014 7:40 PM >> To: Nomi Harris >> Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. >> >> Subject: Re: [Release-team] IRIS testing needed >> >> Right. Useless trivia. There was no point. >> >> Sent from my Verizon Wireless 4G LTE DROID >> >> >> Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. >> >> Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. >> >> Nomi >> >> >> On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >> IRIS >> >> In the beginning IRIS was an acronym for interactive remote invocation service. >> >> Useless trivia. >> >> >> >> >> Sent from my Verizon Wireless 4G LTE DROID >> >> >> Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: >> Iris/iris.html: tab : 'IRIS Terminal', >> Iris/iris.html: <title>KBase IRIS Terminal</title> >> Iris/splash.html: <title>KBase IRIS Terminal</title> >> but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. >> >> I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. >> >> In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). >> >> Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? >> >> Nomi >> >> On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. >>> >>> --Shane >>> >>> >>> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> >>>>> I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. >>>> >>>> Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). >>>> >>>> >>>> Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: >>>> >>>> >>>>> >>>> / >>>> >>>> tutorial >>>> Could not load tutorial >>>> >>>> >>>> and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. >>>> >>>> >>>> Nomi >>>> >>>>> >>>>> >>>>> On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>>> Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. >>>>> >>>>> A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. >>>>> >>>>>> / ws-createws IrisTestWS >>>>> >>>>> Workspace created with name: IrisTestWS and id: 818 >>>>> >>>>> Command Completed >>>>>> / >>>>> kbfba-loadgenome "kb|g.0" >>>>> -w IrisTestWS >>>>> >>>>> Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 >>>>> Size(bytes): 3625772 User Meta Data: none. >>>>> >>>>> Command Completed >>>>> >>>>> >>>>>> / >>>>> kbfba-buildfbamodel >>>>> "kb|g.0" -w IrisTestWS >>>>> >>>>> Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e >>>>> Size(bytes): 1673278 User Meta Data: none. >>>>> >>>>> Command Completed >>>>>> / ws-listobj -w IrisTestWS >>>>> ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 >>>>> 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 >>>>> >>>>> Command Completed >>>>> >>>>> >>>>> On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>>> I think at some point workspace commands required specifying the -w <workspace> option. >>>>> >>>>> However, even with that I'm getting errors in Iris >>>>>> / kbfba-loadgenome -e "kb|g.0 " -w IrisTut >>>>> Genome failed to load to workspace! >>>>> >>>>> JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>>> 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>>> 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase >>>>> >>>>> >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Sr. 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 Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] >>>>> Sent: Monday, February 10, 2014 5:14 PM >>>>> To: Nomi Harris >>>>> Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us >>>>> >>>>> Subject: Re: [Release-team] IRIS testing needed >>>>> >>>>> That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. >>>>> >>>>> I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Sr. Systems Administrator >>>>> Mathematics & Computer Science Division >>>>> Argonne National Laboratory >>>>> 630-252-0055 >>>>> From: Nomi Harris [nlharris(a)lbl.gov] >>>>> Sent: Monday, February 10, 2014 4:27 PM >>>>> To: Murphy-Olson, Daniel E. >>>>> Cc: Henry, Christopher S.; release-team(a)kbase.us; Thomason, James >>>>> Subject: Re: [Release-team] IRIS testing needed >>>>> >>>>> I’m still not able to run kbfba-loadgenome—see trace below. >>>>> >>>>> Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. >>>>> >>>>>> / kbws-workspace >>>>> Current workspace is: nomitest2 >>>>> Command Completed >>>>>> / >>>>> kbfba-loadgenome >>>>> -e "kb|g.0" >>>>> >>>>> Genome failed to load to workspace! >>>>> >>>>> JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>>> 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', >>>>> 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') >>>>> called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 >>>>> Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>>> 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', >>>>> 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', >>>>> 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/ >>>>> fba-loadgenome.pl >>>>> line 58 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>>> >>>>>> I haven't done a thorough check, but the new WS commands seem to work, and I can at least successfully run FBA on a model in IRIS. >>>>>> >>>>>> >>>>>>> / kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" >>>>>> >>>>>> Flux balance analysis successful: >>>>>> Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): >>>>>> 267898 User Meta Data: none. >>>>>> >>>>>> Command Completed >>>>>> >>>>>> >>>>>> On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>>>> Can someone very familiar with FBA test it out in iris and make sure it is functioning properly? >>>>>> >>>>>> ---- >>>>>> Daniel Murphy-Olson >>>>>> Sr. Systems Administrator >>>>>> Mathematics & Computer Science Division >>>>>> Argonne National Laboratory >>>>>> 630-252-0055 >>>>>> _______________________________________________ >>>>>> Release-team mailing list >>>>>> Release-team(a)lists.kbase.us >>>>>> https://lists.kbase.us/mailman/listinfo/release-team >>>>> ` >>>>> >>>>> _______________________________________________ >>>>> Release-team mailing list >>>>> Release-team(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/release-team >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >

1 0

Re: [Release-team] IRIS testing needed
by Murphy-Olson, Daniel E. 11 Feb '14

11 Feb '14

Ok.. I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Christopher Henry [chrisshenry(a)gmail.com] Sent: Tuesday, February 11, 2014 12:43 AM To: Murphy-Olson, Daniel E. Cc: Nomi Harris; Jim Thomason; release-team(a)kbase.us; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, but we should fix IRIS ASAP. Just a client deploy of the modeling and workspace_deluxe stuff in IRIS should do it. And we should clean out the old workspace scripts in invocation. I made those changes in the old workspace repo as well (cleaned out the commands file and scripts directory). Chris On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > Nomi, > > According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > From: Nomi Harris [nlharris(a)lbl.gov] > Sent: Tuesday, February 11, 2014 12:10 AM > To: Murphy-Olson, Daniel E. > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. > Subject: Re: [Release-team] IRIS testing needed > > The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. > > We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? > > Nomi > > > On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > Here is what happened. The Iris -> IRIS change happened last Thursday in git. > > I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. > The Iris that was in testing (from 1/9) was pushed into production. > > We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? > > We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. > > ---- > Daniel Murphy-Olson > Sr. 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 Brettin, Thomas S. [brettin(a)cels.anl.gov] > Sent: Monday, February 10, 2014 7:40 PM > To: Nomi Harris > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. > > Subject: Re: [Release-team] IRIS testing needed > > Right. Useless trivia. There was no point. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. > > Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. > > Nomi > > > On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: > IRIS > > In the beginning IRIS was an acronym for interactive remote invocation service. > > Useless trivia. > > > > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: > Iris/iris.html: tab : 'IRIS Terminal', > Iris/iris.html: <title>KBase IRIS Terminal</title> > Iris/splash.html: <title>KBase IRIS Terminal</title> > but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. > > I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. > > In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). > > Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? > > Nomi > > On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. >> >> --Shane >> >> >> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>> >>>> I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. >>> >>> Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). >>> >>> >>> Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: >>> >>> >>> > >>> / >>> >>> tutorial >>> Could not load tutorial >>> >>> >>> and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. >>> >>> >>> Nomi >>> >>>> >>>> >>>> On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. >>>> >>>> A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. >>>> >>>> >/ ws-createws IrisTestWS >>>> >>>> Workspace created with name: IrisTestWS and id: 818 >>>> >>>> Command Completed >>>> >/ >>>> kbfba-loadgenome "kb|g.0" >>>> -w IrisTestWS >>>> >>>> Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 >>>> Size(bytes): 3625772 User Meta Data: none. >>>> >>>> Command Completed >>>> >>>> >>>> >/ >>>> kbfba-buildfbamodel >>>> "kb|g.0" -w IrisTestWS >>>> >>>> Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e >>>> Size(bytes): 1673278 User Meta Data: none. >>>> >>>> Command Completed >>>> >/ ws-listobj -w IrisTestWS >>>> ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 >>>> 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 >>>> >>>> Command Completed >>>> >>>> >>>> On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>> I think at some point workspace commands required specifying the -w <workspace> option. >>>> >>>> However, even with that I'm getting errors in Iris >>>> >/ kbfba-loadgenome -e "kb|g.0 " -w IrisTut >>>> Genome failed to load to workspace! >>>> >>>> JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>> 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>> 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase >>>> >>>> >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. 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 Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] >>>> Sent: Monday, February 10, 2014 5:14 PM >>>> To: Nomi Harris >>>> Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us >>>> >>>> Subject: Re: [Release-team] IRIS testing needed >>>> >>>> That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. >>>> >>>> I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. Systems Administrator >>>> Mathematics & Computer Science Division >>>> Argonne National Laboratory >>>> 630-252-0055 >>>> From: Nomi Harris [nlharris(a)lbl.gov] >>>> Sent: Monday, February 10, 2014 4:27 PM >>>> To: Murphy-Olson, Daniel E. >>>> Cc: Henry, Christopher S.; release-team(a)kbase.us; Thomason, James >>>> Subject: Re: [Release-team] IRIS testing needed >>>> >>>> I’m still not able to run kbfba-loadgenome—see trace below. >>>> >>>> Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. >>>> >>>> >/ kbws-workspace >>>> Current workspace is: nomitest2 >>>> Command Completed >>>> >/ >>>> kbfba-loadgenome >>>> -e "kb|g.0" >>>> >>>> Genome failed to load to workspace! >>>> >>>> JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', >>>> 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') >>>> called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 >>>> Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', >>>> 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', >>>> 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/ >>>> fba-loadgenome.pl >>>> line 58 >>>> >>>> >>>> >>>> >>>> >>>> On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> >>>>> I haven't done a thorough check, but the new WS commands seem to work, and I can at least successfully run FBA on a model in IRIS. >>>>> >>>>> >>>>> >/ kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" >>>>> >>>>> Flux balance analysis successful: >>>>> Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): >>>>> 267898 User Meta Data: none. >>>>> >>>>> Command Completed >>>>> >>>>> >>>>> On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>>> Can someone very familiar with FBA test it out in iris and make sure it is functioning properly? >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Sr. Systems Administrator >>>>> Mathematics & Computer Science Division >>>>> Argonne National Laboratory >>>>> 630-252-0055 >>>>> _______________________________________________ >>>>> Release-team mailing list >>>>> Release-team(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> ` >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] IRIS testing needed
by Christopher Henry 11 Feb '14

11 Feb '14

Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, but we should fix IRIS ASAP. Just a client deploy of the modeling and workspace_deluxe stuff in IRIS should do it. And we should clean out the old workspace scripts in invocation. I made those changes in the old workspace repo as well (cleaned out the commands file and scripts directory). Chris On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > Nomi, > > According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > From: Nomi Harris [nlharris(a)lbl.gov] > Sent: Tuesday, February 11, 2014 12:10 AM > To: Murphy-Olson, Daniel E. > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. > Subject: Re: [Release-team] IRIS testing needed > > The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. > > We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? > > Nomi > > > On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > Here is what happened. The Iris -> IRIS change happened last Thursday in git. > > I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. > The Iris that was in testing (from 1/9) was pushed into production. > > We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? > > We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. > > ---- > Daniel Murphy-Olson > Sr. 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 Brettin, Thomas S. [brettin(a)cels.anl.gov] > Sent: Monday, February 10, 2014 7:40 PM > To: Nomi Harris > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. > > Subject: Re: [Release-team] IRIS testing needed > > Right. Useless trivia. There was no point. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. > > Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. > > Nomi > > > On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: > IRIS > > In the beginning IRIS was an acronym for interactive remote invocation service. > > Useless trivia. > > > > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: > Iris/iris.html: tab : 'IRIS Terminal', > Iris/iris.html: <title>KBase IRIS Terminal</title> > Iris/splash.html: <title>KBase IRIS Terminal</title> > but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. > > I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. > > In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). > > Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? > > Nomi > > On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. >> >> --Shane >> >> >> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>> >>>> I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. >>> >>> Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). >>> >>> >>> Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: >>> >>> >>> > >>> / >>> >>> tutorial >>> Could not load tutorial >>> >>> >>> and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. >>> >>> >>> Nomi >>> >>>> >>>> >>>> On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. >>>> >>>> A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. >>>> >>>> >/ ws-createws IrisTestWS >>>> >>>> Workspace created with name: IrisTestWS and id: 818 >>>> >>>> Command Completed >>>> >/ >>>> kbfba-loadgenome "kb|g.0" >>>> -w IrisTestWS >>>> >>>> Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 >>>> Size(bytes): 3625772 User Meta Data: none. >>>> >>>> Command Completed >>>> >>>> >>>> >/ >>>> kbfba-buildfbamodel >>>> "kb|g.0" -w IrisTestWS >>>> >>>> Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e >>>> Size(bytes): 1673278 User Meta Data: none. >>>> >>>> Command Completed >>>> >/ ws-listobj -w IrisTestWS >>>> ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 >>>> 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 >>>> >>>> Command Completed >>>> >>>> >>>> On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>> I think at some point workspace commands required specifying the -w <workspace> option. >>>> >>>> However, even with that I'm getting errors in Iris >>>> >/ kbfba-loadgenome -e "kb|g.0 " -w IrisTut >>>> Genome failed to load to workspace! >>>> >>>> JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>> 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line >>>> 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase >>>> >>>> >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. 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 Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] >>>> Sent: Monday, February 10, 2014 5:14 PM >>>> To: Nomi Harris >>>> Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us >>>> >>>> Subject: Re: [Release-team] IRIS testing needed >>>> >>>> That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. >>>> >>>> I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. Systems Administrator >>>> Mathematics & Computer Science Division >>>> Argonne National Laboratory >>>> 630-252-0055 >>>> From: Nomi Harris [nlharris(a)lbl.gov] >>>> Sent: Monday, February 10, 2014 4:27 PM >>>> To: Murphy-Olson, Daniel E. >>>> Cc: Henry, Christopher S.; release-team(a)kbase.us; Thomason, James >>>> Subject: Re: [Release-team] IRIS testing needed >>>> >>>> I’m still not able to run kbfba-loadgenome—see trace below. >>>> >>>> Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. >>>> >>>> >/ kbws-workspace >>>> Current workspace is: nomitest2 >>>> Command Completed >>>> >/ >>>> kbfba-loadgenome >>>> -e "kb|g.0" >>>> >>>> Genome failed to load to workspace! >>>> >>>> JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', >>>> 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') >>>> called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 >>>> Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', >>>> 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', >>>> 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/ >>>> fba-loadgenome.pl >>>> line 58 >>>> >>>> >>>> >>>> >>>> >>>> On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >>>> >>>>> I haven't done a thorough check, but the new WS commands seem to work, and I can at least successfully run FBA on a model in IRIS. >>>>> >>>>> >>>>> >/ kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" >>>>> >>>>> Flux balance analysis successful: >>>>> Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): >>>>> 267898 User Meta Data: none. >>>>> >>>>> Command Completed >>>>> >>>>> >>>>> On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: >>>>> Can someone very familiar with FBA test it out in iris and make sure it is functioning properly? >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Sr. Systems Administrator >>>>> Mathematics & Computer Science Division >>>>> Argonne National Laboratory >>>>> 630-252-0055 >>>>> _______________________________________________ >>>>> Release-team mailing list >>>>> Release-team(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> ` >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] IRIS testing needed
by Murphy-Olson, Daniel E. 11 Feb '14

11 Feb '14

Nomi, According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Nomi Harris [nlharris(a)lbl.gov] Sent: Tuesday, February 11, 2014 12:10 AM To: Murphy-Olson, Daniel E. Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? Nomi On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Here is what happened. The Iris -> IRIS change happened last Thursday in git. I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. The Iris that was in testing (from 1/9) was pushed into production. We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto: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 Brettin, Thomas S. [brettin(a)cels.anl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 7:40 PM To: Nomi Harris Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Right. Useless trivia. There was no point. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. Nomi On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: IRIS In the beginning IRIS was an acronym for interactive remote invocation service. Useless trivia. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not on iris.kbase.us<http://iris.kbase.us>. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: Iris/iris.html: tab : 'IRIS Terminal', Iris/iris.html: <title>KBase IRIS Terminal</title> Iris/splash.html: <title>KBase IRIS Terminal</title> but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? Nomi On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. --Shane On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: >/ tutorial Could not load tutorial and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. Nomi On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws<http://kbase.us/services/ws>). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. >/ ws-createws IrisTestWS Workspace created with name: IrisTestWS and id: 818 Command Completed ________________________________ >/ kbfba-loadgenome "kb|g.0" -w IrisTestWS Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 Size(bytes): 3625772 User Meta Data: none. Command Completed >/ kbfba-buildfbamodel "kb|g.0" -w IrisTestWS Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e Size(bytes): 1673278 User Meta Data: none. Command Completed ________________________________ >/ ws-listobj -w IrisTestWS ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 Command Completed On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I think at some point workspace commands required specifying the -w <workspace> option. However, even with that I'm getting errors in Iris >/ kbfba-loadgenome -e "kb|g.0 " -w IrisTut Genome failed to load to workspace! JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto: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 Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 5:14 PM To: Nomi Harris Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] IRIS testing needed That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Nomi Harris [nlharris(a)lbl.gov<mailto:[email protected]>] Sent: Monday, February 10, 2014 4:27 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; release-team(a)kbase.us<mailto:[email protected]>; Thomason, James Subject: Re: [Release-team] IRIS testing needed I’m still not able to run kbfba-loadgenome—see trace below. Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. >/ kbws-workspace Current workspace is: nomitest2 Command Completed ________________________________ >/ kbfba-loadgenome -e "kb|g.0" Genome failed to load to workspace! JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/fba-loadgenome.pl<http://fba-loadgenome.pl/> line 58 On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: I haven't done a thorough check, but the new WS commands seem to work, and I can at least successfully run FBA on a model in IRIS. >/ kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" Flux balance analysis successful: Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): 267898 User Meta Data: none. Command Completed On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Can someone very familiar with FBA test it out in iris and make sure it is functioning properly? ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> _______________________________________________ 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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Re: [Release-team] IRIS testing needed
by Nomi Harris 11 Feb '14

11 Feb '14

The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? Nomi On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov > wrote: > Here is what happened. The Iris -> IRIS change happened last Thursday > in git. > > I had thought Jim was asking for the deploy of invocation that was in > testing, not a re-pull from a repo. > The Iris that was in testing (from 1/9) was pushed into production. > > We really shouldn't make a last minute change unless there is something in > the demo this week that needs to get fixed. Is there? > > We had asked weeks ago for notification if there were going to be any last > minute updates, and I don't believe invocation was on the list. Miriam > would know for sure. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 <callto:630-252-0055> > ------------------------------ > *From:* release-team-bounces(a)lists.kbase.us [ > release-team-bounces(a)lists.kbase.us] on behalf of Brettin, Thomas S. [ > brettin(a)cels.anl.gov] > *Sent:* Monday, February 10, 2014 7:40 PM > *To:* Nomi Harris > *Cc:* Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, > India S. > > *Subject:* Re: [Release-team] IRIS testing needed > > Right. Useless trivia. There was no point. > > *Sent from my Verizon Wireless 4G LTE DROID* > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > So I heard. Anyway, my point was not to discuss the merits of Iris vs > IRIS, but just to point to a trivial but visible change that I expected to > see when IRIS was redeployed. > > Jim, if there's going to be another IRIS redeploy, you should update the > release notes and the whatsnew file (Iris/whatsnew.html) first. > > Nomi > > > On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov>wrote: > >> IRIS >> >> In the beginning IRIS was an acronym for interactive remote invocation >> service. >> >> Useless trivia. >> >> >> >> >> *Sent from my Verizon Wireless 4G LTE DROID* >> >> >> Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> I'm hoping that Jim will weigh in on this, but besides the fact that he >> fixed the tutorial function and it's not fixed at >> http://kbase.us/services/docs/invocation/Iris/iris.html, here's a >> totally trivial change that I see in git but not on iris.kbase.us. We >> decided to switch back to calling it IRIS rather than Iris (since Jim and I >> were the only people who ever called it Iris), and Jim changed that in the >> html: >> Iris/iris.html: tab : 'IRIS >> Terminal', >> Iris/iris.html: <title>KBase IRIS Terminal</title> >> Iris/splash.html: <title>KBase IRIS Terminal</title> >> but http://kbase.us/services/docs/invocation/Iris/iris.html still says >> "Iris Terminal", not "IRIS Terminal". >> >> I do see ws-* functions in IRIS but I'm pretty sure at least some of >> those were there before the recent release. >> >> In the list of services, I see that >> http://kbase.us/services/docs/invocation/Iris/iris.html has services >> that are out of order and have been retired (e.g., PROM, Experiment, >> Metagenomic Sequence QC), while I don't see some of the new services (e.g., >> cMonkey, Expression, Meme). >> >> Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks >> to me like it did in December (though I have no way of proving that). Maybe >> some of it got redeployed but other parts didn't? Maybe something special >> (in addition to the normal deploy) has to happen to refresh the html and >> get rid of the defunct services and bring in the new services? >> >> Nomi >> >> On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >> I don't think you would see any of ws-* commands if this wasn't the >> latest version. So I'm pretty sure it is up to date. >> >> --Shane >> >> >> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >> >> I forgot to mention that ws-workspace not working means you will have >> to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a >> workspace name is required. I suppose we could temporarily remove that >> method from IRIS until we have it fixed. >> >> >> Hmm. Sounds like that will require some work from Jim. There's also a >> lot of documentation that will need to be changed to reflect the changes >> (kbws-* no longer supported; need to use ws-*; need to create a new ws in >> WS deluxe; need to use "-w ws_name" flag for all WS and FBA scripts). >> >> >> Also, it doesn't look to me like IRIS is really the latest version. I >> know Jim fixed the tutorial, but it doesn't work: >> >> >/ tutorial >> Could not load tutorial >> >> and there are other changes that I would expect to see if this were >> really the latest version that I'm not seeing. >> >> Nomi >> >> >> >> On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov>wrote: >> >>> Sorry I wasn't following this thread closely enough earlier, but I think >>> at least part of the problem may be related to pointing to the correct WS >>> service. The 'kbws-*' scripts point to the old WS, but the fba methods >>> point to the new WS deployment (kbase.us/services/ws). So methods will >>> fail unless you have a workspace created with the correct name in the new >>> WS, and your objects are in that workspace. We should remove the 'kbws-*' >>> scripts from the IRIS deployment. See below for the working commands to >>> import the E.coli genome and create a model. >>> >>> A sidenote is that the 'ws-workspace' command is not functioning >>> properly to set the default WS. This method works by setting/reading an >>> environment variable, but I know this wasn't tested very thoroughly. There >>> is probably a bug or a change in which environment variables are set. >>> >>> >/ ws-createws IrisTestWS >>> Workspace created with name: IrisTestWS and id: 818 >>> Command Completed >>> ------------------------------ >>> >/ kbfba-loadgenome "kb|g.0" -w IrisTestWS >>> Genome successfully loaded to workspace: Object Name: kb|g.0 Object >>> ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save >>> Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: >>> 9e4a09bf26ae131d3982517006d3b100 Size(bytes): 3625772 User Meta Data: none. >>> Command Completed >>> >>> >/ kbfba-buildfbamodel "kb|g.0" -w IrisTestWS >>> Model successfully generated in workspace: Object Name: kb|g.0.fbamdl >>> Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS >>> Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: >>> ee99d7b7017766c8efef87519de37c2e Size(bytes): 1673278 User Meta Data: none. >>> Command Completed >>> ------------------------------ >>> >/ ws-listobj -w IrisTestWS >>> ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl >>> 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 >>> 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 >>> 2014-02-11T00:34:06+0000 3625772 1 kb|contigset.10186 1 >>> KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 >>> 4639516 >>> Command Completed >>> >>> >>> On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. < >>> dolson(a)mcs.anl.gov> wrote: >>> >>>> I think at some point workspace commands required specifying the -w >>>> <workspace> option. >>>> >>>> However, even with that I'm getting errors in Iris >>>> >/ kbfba-loadgenome -e "kb|g.0 " -w IrisTut >>>> Genome failed to load to workspace! >>>> JSONRPC error: Attribute (md5) does not pass the type constraint >>>> because: Validation failed for 'Str' with value undef at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm >>>> line 38 >>>> Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') >>>> called at reader Moose::Exception::trace (defined at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm >>>> line 12) line 7 >>>> Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') >>>> called at /kbase >>>> >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. Systems Administrator >>>> Mathematics & Computer Science Division >>>> Argonne National Laboratory >>>> 630-252-0055 <callto:630-252-0055> >>>> ------------------------------ >>>> *From:* release-team-bounces(a)lists.kbase.us [ >>>> release-team-bounces(a)lists.kbase.us] on behalf of Murphy-Olson, Daniel >>>> E. [dolson(a)mcs.anl.gov] >>>> *Sent:* Monday, February 10, 2014 5:14 PM >>>> *To:* Nomi Harris >>>> *Cc:* Henry, Christopher S.; Thomason, James; release-team(a)kbase.us >>>> >>>> *Subject:* Re: [Release-team] IRIS testing needed >>>> >>>> That version string is hardcoded in the latest master.. I had the >>>> same thought. Iris was re-deployed this morning. >>>> >>>> I think errors were introduced in the FBA scripts. We still don't have >>>> a fix for them, and I'm growing concerned. It looks like changes were made >>>> last week to FBA, which changed the deploy Makefile in such a way that >>>> things deploy properly into the test environment, but don't work in >>>> production. >>>> >>>> ---- >>>> Daniel Murphy-Olson >>>> Sr. Systems Administrator >>>> Mathematics & Computer Science Division >>>> Argonne National Laboratory >>>> 630-252-0055 <callto:630-252-0055> >>>> ------------------------------ >>>> *From:* Nomi Harris [nlharris(a)lbl.gov] >>>> *Sent:* Monday, February 10, 2014 4:27 PM >>>> *To:* Murphy-Olson, Daniel E. >>>> *Cc:* Henry, Christopher S.; release-team(a)kbase.us; Thomason, James >>>> *Subject:* Re: [Release-team] IRIS testing needed >>>> >>>> I'm still not able to run kbfba-loadgenome--see trace below. >>>> >>>> Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. >>>> >>>> >/ kbws-workspace >>>> Current workspace is: nomitest2 >>>> Command Completed >>>> ------------------------------ >>>> >/ kbfba-loadgenome -e "kb|g.0" >>>> Genome failed to load to workspace! >>>> JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ >>>> Trace begun at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 2088 >>>> Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'Mandatory arguments workspace missing.', '_validateargs') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 846 >>>> Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 5181 >>>> Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm >>>> line 399 eval {...} at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm >>>> line 397 >>>> Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm >>>> line 33 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm >>>> line 26 >>>> RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at >>>> /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 >>>> Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 >>>> Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', >>>> 'HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm >>>> line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line >>>> 142 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line >>>> 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 >>>> Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', >>>> 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line >>>> 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 229 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 187 >>>> Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line >>>> 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', >>>> 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', >>>> 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, >>>> 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', >>>> 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', >>>> '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', >>>> '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm >>>> line 18 >>>> Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', >>>> 'CODE(0x2780488)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 >>>> Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', >>>> 'Plack::Handler::Starman=HASH(0x2780548)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm >>>> line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at >>>> /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: >>>> -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace >>>> missing._ERROR_ Trace begun at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 2088 >>>> Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'Mandatory arguments workspace missing.', '_validateargs') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 846 >>>> Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm >>>> line 5181 >>>> Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', >>>> 'HASH(0x274c9500)') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm >>>> line 399 eval {...} at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm >>>> line 397 >>>> Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm >>>> line 33 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm >>>> line 26 >>>> RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', >>>> 'HASH(0x15ef3c38)') called at >>>> /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 >>>> Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm >>>> line 115 >>>> Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', >>>> 'HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm >>>> line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line >>>> 142 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line >>>> 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 273 >>>> Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', >>>> 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line >>>> 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 229 eval {...} at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 187 >>>> Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm >>>> line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line >>>> 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', >>>> 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', >>>> 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, >>>> 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', >>>> 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', >>>> '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', >>>> 'setsid', 1, 'background', 1, 'log_file', >>>> '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') >>>> called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm >>>> line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm >>>> line 18 >>>> Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', >>>> 'CODE(0x2780488)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm >>>> line 20 >>>> Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', >>>> 'Plack::Handler::Starman=HASH(0x2780548)') called at >>>> /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm >>>> line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at >>>> /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm >>>> line 2434 >>>> Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', >>>> 'HASH(0xbc12d0)') called at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm >>>> line 165 eval {...} at >>>> /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm >>>> line 158 >>>> Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', >>>> 'genome_to_workspace', >>>> 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at >>>> /kbase/deployments/20140109-prod/plbin/fba-loadgenome.pl line 58 >>>> >>>> >>>> >>>> On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> >>>> wrote: >>>> >>>> I haven't done a thorough check, but the new WS commands seem to >>>> work, and I can at least successfully run FBA on a model in IRIS. >>>> >>>> >/ kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" >>>> Flux balance analysis successful: >>>> Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: KBaseFBA.FBA-2.0 >>>> Version: 1 Workspace: wstester1:home Save Date: 2014-02-10T21:34:01+0000 >>>> Saved by: wstester1 Checksum: bf99577941543541d39274ea49dca279 Size(bytes): >>>> 267898 User Meta Data: none. >>>> Command Completed >>>> >>>> >>>> On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. < >>>> dolson(a)mcs.anl.gov> wrote: >>>> >>>>> Can someone very familiar with FBA test it out in iris and make sure >>>>> it is functioning properly? >>>>> >>>>> ---- >>>>> Daniel Murphy-Olson >>>>> Sr. Systems Administrator >>>>> Mathematics & Computer Science Division >>>>> Argonne National Laboratory >>>>> 630-252-0055 >>>>> _______________________________________________ >>>>> Release-team mailing list >>>>> Release-team(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/release-team >>>>> >>>> ` >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> >>>> >>> >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >> >> >> >> >

1 0

Re: [Release-team] IRIS testing needed
by Michael Sneddon 10 Feb '14

10 Feb '14

see below: (1) ws-workspace command will not work as it currently stands in IRIS, and > this basically breaks all the modeling commands unless the user supplies > the -w option > -this is because it wants to stash the currently selected > workspace in the config file, which does NOT exist in IRIS > > hmm- the new ws-workspace actually does try to detect when it is in the IRIS environment, and when it does it sets an environment variable. I had copied this behavior from the original kbws-workspace script but never actually had time to test it in my own IRIS deploy. I must have done something incorrectly. Is there any documentation on using environment variables in IRIS? I think others may be trying to use this feature as well. But I guess in the short run, it sounds like Chris has a handle on this. Thanks. Longer term I was thinking we might switch to using the user state service for some of these user settings. > That should fix everything except any issues that cropped up in the > modeling make file. > I will do (3) and (4) immediately and send an email when it's done. > Hopefully Mike or Dan can do (2). > (2) is done in branch deprecated-script-hotfix in workspace_deluxe. We can deploy these scripts now just for the Iris deployment, and then actually come up with a real solution for handling deprecated scripts in KBase... We should not redeploy the production workspace or production FBA service. > Dan can you fix the modeling makefile? The key thing is that we need to > create "kbfba-*" commands for each "fba-" command so we stay true to the > documentation. > > Chris > > On Feb 10, 2014, at 7:50 PM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> > wrote: > > > Here is what happened. The Iris -> IRIS change happened last Thursday > in git. > > > > I had thought Jim was asking for the deploy of invocation that was in > testing, not a re-pull from a repo. > > The Iris that was in testing (from 1/9) was pushed into production. > > > > We really shouldn't make a last minute change unless there is something > in the demo this week that needs to get fixed. Is there? > > > > We had asked weeks ago for notification if there were going to be any > last minute updates, and I don't believe invocation was on the list. > Miriam would know for sure. > > > > ---- > > Daniel Murphy-Olson > > Sr. 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 Brettin, Thomas S. [ > brettin(a)cels.anl.gov] > > Sent: Monday, February 10, 2014 7:40 PM > > To: Nomi Harris > > Cc: Jim Thomason; Henry, Christopher S.; release-team(a)kbase.us; Gordon, > India S. > > Subject: Re: [Release-team] IRIS testing needed > > > > Right. Useless trivia. There was no point. > > > > Sent from my Verizon Wireless 4G LTE DROID > > > > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > > > So I heard. Anyway, my point was not to discuss the merits of Iris vs > IRIS, but just to point to a trivial but visible change that I expected to > see when IRIS was redeployed. > > > > Jim, if there's going to be another IRIS redeploy, you should update the > release notes and the whatsnew file (Iris/whatsnew.html) first. > > > > Nomi > > > > > > On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. < > brettin(a)cels.anl.gov> wrote: > > IRIS > > > > In the beginning IRIS was an acronym for interactive remote invocation > service. > > > > Useless trivia. > > > > > > > > > > Sent from my Verizon Wireless 4G LTE DROID > > > > > > Nomi Harris <nlharris(a)lbl.gov> wrote: > > > > I'm hoping that Jim will weigh in on this, but besides the fact that he > fixed the tutorial function and it's not fixed at > http://kbase.us/services/docs/invocation/Iris/iris.html, here's a totally > trivial change that I see in git but not oniris.kbase.us. We decided to > switch back to calling it IRIS rather than Iris (since Jim and I were the > only people who ever called it Iris), and Jim changed that in the html: > > Iris/iris.html: tab : 'IRIS Terminal', > > Iris/iris.html: <title>KBase IRIS Terminal</title> > > Iris/splash.html: <title>KBase IRIS Terminal</title> > > but http://kbase.us/services/docs/invocation/Iris/iris.html still says > "Iris Terminal", not "IRIS Terminal". > > > > I do see ws-* functions in IRIS but I'm pretty sure at least some of > those were there before the recent release. > > > > In the list of services, I see that > http://kbase.us/services/docs/invocation/Iris/iris.html has services that > are out of order and have been retired (e.g., PROM, Experiment, Metagenomic > Sequence QC), while I don't see some of the new services (e.g., cMonkey, > Expression, Meme). > > > > Basically, http://kbase.us/services/docs/invocation/Iris/iris.htmllooks to me like it did in December (though I have no way of proving that). > Maybe some of it got redeployed but other parts didn't? Maybe something > special (in addition to the normal deploy) has to happen to refresh the > html and get rid of the defunct services and bring in the new services? > > > > Nomi > > > > On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > > >> I don't think you would see any of ws-* commands if this wasn't the > latest version. So I'm pretty sure it is up to date. > >> > >> --Shane > >> > >> > >> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> > >>> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon(a)lbl.gov> > wrote: > >>> > >>>> I forgot to mention that ws-workspace not working means you will have > to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a > workspace name is required. I suppose we could temporarily remove that > method from IRIS until we have it fixed. > >>> > >>> Hmm. Sounds like that will require some work from Jim. There's also a > lot of documentation that will need to be changed to reflect the changes > (kbws-* no longer supported; need to use ws-*; need to create a new ws in > WS deluxe; need to use "-w ws_name" flag for all WS and FBA scripts). > >>> > >>> > >>> Also, it doesn't look to me like IRIS is really the latest version. I > know Jim fixed the tutorial, but it doesn't work: > >>> > >>> > >>> > > >>> / > >>> > >>> tutorial > >>> Could not load tutorial > >>> > >>> > >>> and there are other changes that I would expect to see if this were > really the latest version that I'm not seeing. > >>> > >>> > >>> Nomi > >>> > >>>> > >>>> > >>>> On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <mwsneddon(a)lbl.gov> > wrote: > >>>> Sorry I wasn't following this thread closely enough earlier, but I > think at least part of the problem may be related to pointing to the > correct WS service. The 'kbws-*' scripts point to the old WS, but the fba > methods point to the new WS deployment (kbase.us/services/ws). So > methods will fail unless you have a workspace created with the correct name > in the new WS, and your objects are in that workspace. We should remove > the 'kbws-*' scripts from the IRIS deployment. See below for the working > commands to import the E.coli genome and create a model. > >>>> > >>>> A sidenote is that the 'ws-workspace' command is not functioning > properly to set the default WS. This method works by setting/reading an > environment variable, but I know this wasn't tested very thoroughly. There > is probably a bug or a change in which environment variables are set. > >>>> > >>>> >/ ws-createws IrisTestWS > >>>> > >>>> Workspace created with name: IrisTestWS and id: 818 > >>>> > >>>> Command Completed > >>>> >/ > >>>> kbfba-loadgenome "kb|g.0" > >>>> -w IrisTestWS > >>>> > >>>> Genome successfully loaded to workspace: Object Name: kb|g.0 Object > ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save > Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: > 9e4a09bf26ae131d3982517006d3b100 > >>>> Size(bytes): 3625772 User Meta Data: none. > >>>> > >>>> Command Completed > >>>> > >>>> > >>>> >/ > >>>> kbfba-buildfbamodel > >>>> "kb|g.0" -w IrisTestWS > >>>> > >>>> Model successfully generated in workspace: Object Name: kb|g.0.fbamdl > Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS > Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: > ee99d7b7017766c8efef87519de37c2e > >>>> Size(bytes): 1673278 User Meta Data: none. > >>>> > >>>> Command Completed > >>>> >/ ws-listobj -w IrisTestWS > >>>> ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 > kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 > 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 > IrisTestWS wstester1 2014-02-11T00:34:06+0000 > >>>> 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS > wstester1 2014-02-11T00:34:02+0000 4639516 > >>>> > >>>> Command Completed > >>>> > >>>> > >>>> On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. < > dolson(a)mcs.anl.gov> wrote: > >>>> I think at some point workspace commands required specifying the -w > <workspace> option. > >>>> > >>>> However, even with that I'm getting errors in Iris > >>>> >/ kbfba-loadgenome -e "kb|g.0 " -w IrisTut > >>>> Genome failed to load to workspace! > >>>> > >>>> JSONRPC error: Attribute (md5) does not pass the type constraint > because: Validation failed for 'Str' with value undef at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm > line > >>>> 38 > Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') > called at reader Moose::Exception::trace (defined at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm > line > >>>> 12) line 7 > Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') > called at /kbase > >>>> > >>>> > >>>> > >>>> ---- > >>>> Daniel Murphy-Olson > >>>> Sr. 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 Murphy-Olson, Daniel E. > [dolson(a)mcs.anl.gov] > >>>> Sent: Monday, February 10, 2014 5:14 PM > >>>> To: Nomi Harris > >>>> Cc: Henry, Christopher S.; Thomason, James; release-team(a)kbase.us > >>>> > >>>> Subject: Re: [Release-team] IRIS testing needed > >>>> > >>>> That version string is hardcoded in the latest master.. I had the > same thought. Iris was re-deployed this morning. > >>>> > >>>> I think errors were introduced in the FBA scripts. We still don't > have a fix for them, and I'm growing concerned. It looks like changes were > made last week to FBA, which changed the deploy Makefile in such a way that > things deploy properly into the test environment, but don't work in > production. > >>>> > >>>> ---- > >>>> Daniel Murphy-Olson > >>>> Sr. Systems Administrator > >>>> Mathematics & Computer Science Division > >>>> Argonne National Laboratory > >>>> 630-252-0055 > >>>> From: Nomi Harris [nlharris(a)lbl.gov] > >>>> Sent: Monday, February 10, 2014 4:27 PM > >>>> To: Murphy-Olson, Daniel E. > >>>> Cc: Henry, Christopher S.; release-team(a)kbase.us; Thomason, James > >>>> Subject: Re: [Release-team] IRIS testing needed > >>>> > >>>> I'm still not able to run kbfba-loadgenome--see trace below. > >>>> > >>>> Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. > >>>> > >>>> >/ kbws-workspace > >>>> Current workspace is: nomitest2 > >>>> Command Completed > >>>> >/ > >>>> kbfba-loadgenome > >>>> -e "kb|g.0" > >>>> > >>>> Genome failed to load to workspace! > >>>> > >>>> JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ > Trace begun at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 2088 > Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > >>>> 'Mandatory arguments workspace missing.', '_validateargs') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 846 > Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)', > >>>> 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 5181 > Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'HASH(0x274c9500)') > >>>> called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 399 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 397 > Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 33 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 26 > RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > >>>> 'HASH(0x15ef3c38)') called at > /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 > Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm > >>>> line 115 > Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', > 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm > line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > >>>> line 273 > Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', > 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 187 > Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > >>>> line 111 > Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', > 'ARRAY(0x2c28270)', 'host', '*', 'proto', > >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', > 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', > 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, > 'no_client_stdout', 1, 'pid_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', > >>>> 'setsid', 1, 'background', 1, 'log_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', > >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm > line 18 > Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', > 'CODE(0x2780488)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm > >>>> line 20 > Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', > 'Plack::Handler::Starman=HASH(0x2780548)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm > line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') > >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC > error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace > missing._ERROR_ Trace begun at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 2088 > >>>> > Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > 'Mandatory arguments workspace missing.', '_validateargs') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 846 > Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > >>>> 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called > at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm > line 5181 > Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', > >>>> 'HASH(0x274c9500)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 399 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm > line 397 > Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > >>>> 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 33 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm > line 26 > RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', > >>>> 'HASH(0x15ef3c38)') called at > /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 > Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm > >>>> line 115 > Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', > 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm > line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line > 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > >>>> line 273 > Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', > 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 eval {...} at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') > >>>> called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > line 187 > Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm > >>>> line 111 > Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line > 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', > 'ARRAY(0x2c28270)', 'host', '*', 'proto', > >>>> 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', > 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', > 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, > 'no_client_stdout', 1, 'pid_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', > >>>> 'setsid', 1, 'background', 1, 'log_file', > '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') > called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm > line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', > >>>> 'CODE(0x2780488)', 'HASH(0x277c008)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm > line 18 > Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', > 'CODE(0x2780488)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm > >>>> line 20 > Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', > 'Plack::Handler::Starman=HASH(0x2780548)') called at > /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm > line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') > >>>> called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace > begun at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm > line 2434 > Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', > >>>> 'HASH(0xbc12d0)') called at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm > line 165 eval {...} at > /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm > line 158 > Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', > >>>> 'genome_to_workspace', > 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at > /kbase/deployments/20140109-prod/plbin/ > >>>> fba-loadgenome.pl > >>>> line 58 > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> On Feb 10, 2014, at 1:39 PM, Michael Sneddon <mwsneddon(a)lbl.gov> > wrote: > >>>> > >>>>> I haven't done a thorough check, but the new WS commands seem to > work, and I can at least successfully run FBA on a model in IRIS. > >>>>> > >>>>> > >>>>> >/ kbfba-runfba -w wstester1:home "kb|g.0.fbamdl" > >>>>> > >>>>> Flux balance analysis successful: > >>>>> Object Name: kb|g.0.fbamdl.fba.2 Object ID: 29 Type: > KBaseFBA.FBA-2.0 Version: 1 Workspace: wstester1:home Save Date: > 2014-02-10T21:34:01+0000 Saved by: wstester1 Checksum: > bf99577941543541d39274ea49dca279 Size(bytes): > >>>>> 267898 User Meta Data: none. > >>>>> > >>>>> Command Completed > >>>>> > >>>>> > >>>>> On Mon, Feb 10, 2014 at 1:07 PM, Murphy-Olson, Daniel E. < > dolson(a)mcs.anl.gov> wrote: > >>>>> Can someone very familiar with FBA test it out in iris and make sure > it is functioning properly? > >>>>> > >>>>> ---- > >>>>> Daniel Murphy-Olson > >>>>> Sr. Systems Administrator > >>>>> Mathematics & Computer Science Division > >>>>> Argonne National Laboratory > >>>>> 630-252-0055 > >>>>> _______________________________________________ > >>>>> Release-team mailing list > >>>>> Release-team(a)lists.kbase.us > >>>>> https://lists.kbase.us/mailman/listinfo/release-team > >>>> ` > >>>> > >>>> _______________________________________________ > >>>> Release-team mailing list > >>>> Release-team(a)lists.kbase.us > >>>> https://lists.kbase.us/mailman/listinfo/release-team > >>>> > >>>> > >>>> > >>> > >>> _______________________________________________ > >>> Release-team mailing list > >>> Release-team(a)lists.kbase.us > >>> https://lists.kbase.us/mailman/listinfo/release-team > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

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