February 2014 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] IRIS testing needed
by Shane Canon 10 Feb '14

10 Feb '14

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

10 Feb '14

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 > > >

1 0

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

10 Feb '14

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. 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 >> >> >

1 0

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

10 Feb '14

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 > >

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Re: [Release-team] IRIS testing needed
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

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<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 `

1 0

Re: [Release-team] IRIS testing needed
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

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<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 `

1 0

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

10 Feb '14

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 `

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

10 Feb '14

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 >

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IRIS testing needed
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

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

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Re: [Release-team] Many errors on redeployment of IRIS
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

Awesome, that fixed it. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Olson, Robert D. Sent: Monday, February 10, 2014 11:58 AM To: Murphy-Olson, Daniel E. Cc: Thomason, James; release-team(a)kbase.us Subject: Re: Many errors on redeployment of IRIS OK, then my guess was correct - they are not errors but rather lengthy backtraces from this warning: Class::MOP::load_class is deprecated at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Class/MOP.pm line 76. This bug is appropriate: https://rt.cpan.org/Public/Bug/Display.html?id=90983 and means that an update to the perl module Parse::Method::Signatures is needed. The reason it’s not picking up your deployment info is that it’s internally using the name InvocationService for locating the deployment information, so you will need to have a section [InvocationService] with the configuration. We will need to fix this service name / service directory confusion across the board going forward. It’ll require thinking through the desired policy & behavior for names. —bob On Feb 10, 2014, at 11:47 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: Unfortunately, the way we're doing the release - it is a complete redeploy, or iris doesn't get any of the clients. This was necessary because we also upgraded the operating system version. I'm having a hard time figuring out what dependency might be missing from the errors. It is continuing to run with those errors though. One other thing, for some reason it isn't constructing the auth/nonauth storage path properly from the deployment.cfg, even though we have KB_DEPLOYMENT_CONFIG set, and the following defined: [invocation] authenticated-storage-dir = /data/storage-auth nonauthenticated-storage-dir = /data/storage-nonauth authenticated-storage = /data/storage-auth nonauthenticated-storage = /data/storage-nonauth service-url = http://kbase.us/services/invocation ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Olson, Robert D. Sent: Monday, February 10, 2014 11:39 AM To: Thomason, James; Murphy-Olson, Daniel E. Cc: release-team(a)kbase.us<mailto:[email protected]> Subject: RE: Many errors on redeployment of IRIS Those errors look like it's trying to use a build of perl that is missing packages or something. ________________________________________ From: Thomason, James [thomason(a)cshl.edu<mailto:[email protected]>] Sent: Monday, February 10, 2014 11:38 AM To: Murphy-Olson, Daniel E. Cc: Olson, Robert D.; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: Many errors on redeployment of IRIS I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. -- -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 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 <start.log>

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