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@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@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@lists.kbase.us [release-team-bounces@lists.kbase.us] on behalf of Murphy-Olson, Daniel E. [dolson@mcs.anl.gov]
Sent: Monday, February 10, 2014 5:14 PM
To: Nomi Harris
Cc: Henry, Christopher S.; Thomason, James; release-team@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@lbl.gov]
Sent: Monday, February 10, 2014 4:27 PM
To: Murphy-Olson, Daniel E.
Cc: Henry, Christopher S.; release-team@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@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@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@lists.kbase.us
https://lists.kbase.us/mailman/listinfo/release-team

`

_______________________________________________
Release-team mailing list
Release-team@lists.kbase.us
https://lists.kbase.us/mailman/listinfo/release-team