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February 2014

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Re: [Release-team] IRIS testing needed
by Christopher Henry 10 Feb '14

10 Feb '14

So my deepest apologies for being offline all afternoon - I was busy at the meeting. But I know exactly what the problem(s) are. (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 (2) The old workspace commands should no longer be deployed to IRIS, with the exception of kbws-jobs, kbws-checkjob, kbws-resetjob (3) The new workspace commands should be wrapped by versions of those commands that start with "kb" (e.g. ws-list should also have a "kbws-list") -This is for reverse compatibility, and we should just do it for a while until people get used to the ws commands and we have time to adapt the documentation -Again, this means the new workspace commands (for the most part) should replace the old workspace command -From the users prospective, this transition should be essential transparent… they should just see the ws-* and fba-* commands appear (4) There are also issues with the modeling makefile - I am completely mystified by the new deploy system and can use Dan's help here. ********************************************************************************************************************************* My proposed solution: 1.) We no longer deploy any scripts from the old workspace (but PLEASE DO keep the old workspace service running) -I will clean out the scripts directory and empty the commands file and check that into master 2.) We adjust the makefile on the new workspace to deploy kbws-* binaries in addition to the ws-* binaries 3.) I will add a "kbws-workspace" command to the modeling repo that should be deployed to IRIS, and it will work in IRIS 4.) I will also add the kbws-jobs, kbws-checkjob, kbws-resetjob to the modeling repo and commands file 5.) We redo the client deploy of the modeling service and workspace deluxe in invocation 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). 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.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

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Re: [Release-team] IRIS testing needed
by Thomason, James 10 Feb '14

10 Feb '14

There wasn’t a scheduled invocation deploy, this was a newly discovered bug regarding the tutorials not showing up on the live site. Looks like some sort of CORS type issue because iris runs off of kbase.us<http://kbase.us> but was fetching tutorials from www.kbase.us<http://www.kbase.us> and failing to load. I have no clue why this didn’t pop up until now. Simultaneously, since that needed to go out, we tossed in the cosmetic change to turn Iris into IRIS, since that matches the spelling on the posters and slides at the demo. I wasn’t aware that there was a discrepancy between the posters and the software until Friday, I think. These were both last-minute discovery quick-fix sort of things. Sorry for the last minute nature of things. The only mods in iris are changing the URL for the tutorials, the capitalization of the name, and as of tonight, the version number. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 7:50 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 Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

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<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 Shane Canon 10 Feb '14

10 Feb '14

I stand corrected. We redeployed, but we didn't do a fresh git pull. It looks like the last commit went up until December 13 and missed the changes done on Feb 6. Dan or I will redeploy tonight. --Shane On Feb 10, 2014, at 5:36 PM, 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 >>>> 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 Brettin, Thomas S. 10 Feb '14

10 Feb '14

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<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 10 Feb '14

10 Feb '14

Our messages crossed. Glad to hear I wasn't hallucinating, and IRIS really does not seem to have been updated. I wrote: > Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. You already updated the whatsnew. I just updated the release notes for you. Nomi On Mon, Feb 10, 2014 at 5:36 PM, 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 Nomi Harris 10 Feb '14

10 Feb '14

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 Thomason, James 10 Feb '14

10 Feb '14

I can confirm that iris was definitely not updated. The version number wasn’t revved from 0.0.6, but that was just an oversight on my part, but nothing new went out regardless. Anyway, since I did a fresh git pull (and did see the changes), I went ahead and kicked to v0.0.7, so that’s incremented at least. But the changes definitely did not go out and it’d need a fresh deploy regardless. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 7:19 PM, 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

1 0

Re: [Release-team] IRIS testing needed
by Brettin, Thomas S. 10 Feb '14

10 Feb '14

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<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

1 0

Re: [Release-team] IRIS testing needed
by Nomi Harris 10 Feb '14

10 Feb '14

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 >>> 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 >

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