see below:

(1) ws-workspace command will not work as it currently stands in IRIS, and this basically breaks all the modeling commands unless the user supplies the -w option
        -this is because it wants to stash the currently selected workspace in the config file, which does NOT exist in IRIS


hmm- the new ws-workspace actually does try to detect when it is in the IRIS environment, and when it does it sets an environment variable.  I had copied this behavior from the original kbws-workspace script but never actually had time to test it in my own IRIS deploy.  I must have done something incorrectly.  Is there any documentation on using environment variables in IRIS?  I think others may be trying to use this feature as well. 

But I guess in the short run, it sounds like Chris has a handle on this.  Thanks.  Longer term I was thinking we might switch to using the user state service for some of these user settings.


That should fix everything except any issues that cropped up in the modeling make file.
I will do (3) and (4) immediately and send an email when it's done. Hopefully Mike or Dan can do (2).

(2) is done in branch deprecated-script-hotfix in workspace_deluxe.  We can deploy these scripts now just for the Iris deployment, and then actually come up with a real solution for handling deprecated scripts in KBase...  We should not redeploy the production workspace or production FBA service.

 
Dan can you fix the modeling makefile? The key thing is that we need to create "kbfba-*" commands for each "fba-" command so we stay true to the documentation.

Chris

On Feb 10, 2014, at 7:50 PM, "Murphy-Olson, Daniel E." <dolson@mcs.anl.gov> wrote:

> Here is what happened.  The Iris -> IRIS change happened last Thursday in git.
>
> I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo.
> The Iris that was in testing (from 1/9) was pushed into production.
>
> We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed.  Is there?
>
> We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list.  Miriam would know for sure.
>
> ----
> Daniel Murphy-Olson
> Sr. Systems Administrator
> Mathematics & Computer Science Division
> Argonne National Laboratory
> 630-252-0055
> From: release-team-bounces@lists.kbase.us [release-team-bounces@lists.kbase.us] on behalf of Brettin, Thomas S. [brettin@cels.anl.gov]
> Sent: Monday, February 10, 2014 7:40 PM
> To: Nomi Harris
> Cc: Jim Thomason; Henry, Christopher S.; release-team@kbase.us; Gordon, India S.
> Subject: Re: [Release-team] IRIS testing needed
>
> Right. Useless trivia. There was no point.
>
> Sent from my Verizon Wireless 4G LTE DROID
>
>
> Nomi Harris <nlharris@lbl.gov> wrote:
>
> So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed.
>
> Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first.
>
>      Nomi
>
>
> On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <brettin@cels.anl.gov> wrote:
> IRIS
>
> In the beginning IRIS was an acronym for interactive remote invocation service.
>
> Useless trivia.
>
>
>
>
> Sent from my Verizon Wireless 4G LTE DROID
>
>
> Nomi Harris <nlharris@lbl.gov> wrote:
>
> I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html:
> Iris/iris.html:                                    tab : 'IRIS Terminal',
> Iris/iris.html:        <title>KBase IRIS Terminal</title>
> Iris/splash.html:    <title>KBase IRIS Terminal</title>
> but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”.
>
> I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release.
>
> In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme).
>
> Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services?
>
> Nomi
>
> On Feb 10, 2014, at 5:09 PM, Shane Canon <scanon@lbl.gov> wrote:
>
>> I don't think you would see any of ws-* commands if this wasn't the latest version.  So I'm pretty sure it is up to date.
>>
>> --Shane
>>
>>
>> On Feb 10, 2014, at 5:00 PM, Nomi Harris <nlharris@lbl.gov> wrote:
>>
>>> On Feb 10, 2014, at 4:43 PM, Michael Sneddon <mwsneddon@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@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
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