I just landed. I'll take a close look when I get to the office. Couple hrs at most Thanks Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <[email protected]> wrote: Right, I know. I didn't elaborate on that distinction in the message about name cleanup, since it was already a long message. Do you want me to make any edits before I send the message? Nomi On Wed, Feb 12, 2014 at 5:46 AM, Brettin, Thomas S. <[email protected]<mailto:[email protected]>> wrote: There is not one to one relationship between iris command set and service and repo. Can we discuss on Devel call today. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <[email protected]<mailto:[email protected]>> wrote: Yes, it would be nice if the services could be grouped by functionality in some way, but as you note, that would require some discussion, and many services don't fit cleanly into one category. The name cleanup I'm proposing is pretty straightforward. Nomi On Tue, Feb 11, 2014 at 1:25 PM, Murphy-Olson, Daniel E. <[email protected]<mailto:[email protected]>> wrote: What you're proposing sounds good to me.
From an end users perspective, some consolidation around workflow categories might improve usability - but we might want phase in a change like that.
---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ From: Nomi Harris [[email protected]<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 3:09 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; Jim Thomason; [email protected]<mailto:[email protected]>; Nomi Harris Subject: Re: [Release-team] IRIS testing needed If you can wait a few days before redeploying IRIS, that will give me a chance to fix something else: IRIS has a list of services that it supports. I noticed recently that the names that IRIS displays for these services (see screenshots below) often don’t match the names used in the Master tab of the Services spreadsheet (https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBc...), which is what is used on the Services web page (http://kbase.us/developer-zone/services/, though note that it hasn’t been updated—I have a lot of changes to it once we finish this IRIS release). I think the names for services should be the same in IRIS and the Services page. (There are also the names used in the URLs for services, service docs, etc--but I’m not going to try to fix that now.) I thought a few of the service names in IRIS were better than the ones that we had on the Services page (for example, “Tree Service” -> Phylogenetic Trees and Alignments), so I updated the Master spreadsheet and will update the names on the Services page when the release is done. In other cases, though, the names used for services in IRIS are inconsistent (they variously are called “Service”, “Scripts”, “Tools”, or “commands”) and in some cases odd (why is the first one called “Assembly-RAST scripts”?). [cid:[email protected]][cid:[email protected]][cid:[email protected]] I propose to remove the word service/commands/scripts from all of the service names, so they will say (for example) “Assembly”, “Annotation” (or should that be “Genome Annotation”?), “Compression-Based Distance”, etc. I would like to send out a note to all the developers with the proposed “clean” names of all the services, and give them a chance to reply if they want to change any of them, and if I don’t hear otherwise, then on Wed. I will change the COMMANDS file in each service repo to match the cleaned-up service name. Sound ok? By the way, in terms of timing, I will be offline all day Thurs (until about 3pm PT). Nomi On Feb 10, 2014, at 11:19 PM, Murphy-Olson, Daniel E. <[email protected]<mailto:[email protected]>> wrote: Ok.. I plan on doing the redeploy in test early in the morning, and holding the push to production until Thursday morning unless some new information arises. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> ________________________________________ From: Christopher Henry [[email protected]<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 12:43 AM To: Murphy-Olson, Daniel E. Cc: Nomi Harris; Jim Thomason; [email protected]<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Okay. I checked the fixes in. As Nomi says, we don't need it for the demo, but we should fix IRIS ASAP. Just a client deploy of the modeling and workspace_deluxe stuff in IRIS should do it. And we should clean out the old workspace scripts in invocation. I made those changes in the old workspace repo as well (cleaned out the commands file and scripts directory). Chris On Feb 11, 2014, at 12:18 AM, "Murphy-Olson, Daniel E." <[email protected]<mailto:[email protected]>> wrote: Nomi, According to the stated dependencies in each services master:/DEPENDENCIES file, the FBA service is the only one dependent on the old workspace. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> From: Nomi Harris [[email protected]<mailto:[email protected]>] Sent: Tuesday, February 11, 2014 12:10 AM To: Murphy-Olson, Daniel E. Cc: Jim Thomason; Henry, Christopher S.; [email protected]<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed The DOE meeting demos are not relying on IRIS, so I don't think it needs to be redeployed instantly. However, lots of people probably will be hitting IRIS (and the FBA service) as a result of the meeting, so it would be good to get some of these issues worked out soon. The FBA service is one of our most used services. Users complain if it doesn't work as advertised. We've now uncovered issues with the FBA commands that relate to the WS upgrade (and Chris has a plan for fixing them)--but won't the WS upgrade affect other services as well? FBA can't be the only service that uses workspaces, can it? Nomi On Mon, Feb 10, 2014 at 5:50 PM, Murphy-Olson, Daniel E. <[email protected]<mailto:[email protected]>> wrote: Here is what happened. The Iris -> IRIS change happened last Thursday in git. I had thought Jim was asking for the deploy of invocation that was in testing, not a re-pull from a repo. The Iris that was in testing (from 1/9) was pushed into production. We really shouldn't make a last minute change unless there is something in the demo this week that needs to get fixed. Is there? We had asked weeks ago for notification if there were going to be any last minute updates, and I don't believe invocation was on the list. Miriam would know for sure. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> From: [email protected]<mailto:[email protected]> [[email protected]<mailto:[email protected]>] on behalf of Brettin, Thomas S. [[email protected]<mailto:[email protected]>] Sent: Monday, February 10, 2014 7:40 PM To: Nomi Harris Cc: Jim Thomason; Henry, Christopher S.; [email protected]<mailto:[email protected]>; Gordon, India S. Subject: Re: [Release-team] IRIS testing needed Right. Useless trivia. There was no point. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <[email protected]<mailto:[email protected]>> wrote: So I heard. Anyway, my point was not to discuss the merits of Iris vs IRIS, but just to point to a trivial but visible change that I expected to see when IRIS was redeployed. Jim, if there's going to be another IRIS redeploy, you should update the release notes and the whatsnew file (Iris/whatsnew.html) first. Nomi On Mon, Feb 10, 2014 at 5:29 PM, Brettin, Thomas S. <[email protected]<mailto:[email protected]>> wrote: IRIS In the beginning IRIS was an acronym for interactive remote invocation service. Useless trivia. Sent from my Verizon Wireless 4G LTE DROID Nomi Harris <[email protected]<mailto:[email protected]>> wrote: I’m hoping that Jim will weigh in on this, but besides the fact that he fixed the tutorial function and it’s not fixed at http://kbase.us/services/docs/invocation/Iris/iris.html, here’s a totally trivial change that I see in git but not oniris.kbase.us<http://oniris.kbase.us>. We decided to switch back to calling it IRIS rather than Iris (since Jim and I were the only people who ever called it Iris), and Jim changed that in the html: Iris/iris.html: tab : 'IRIS Terminal', Iris/iris.html: <title>KBase IRIS Terminal</title> Iris/splash.html: <title>KBase IRIS Terminal</title> but http://kbase.us/services/docs/invocation/Iris/iris.html still says “Iris Terminal”, not “IRIS Terminal”. I do see ws-* functions in IRIS but I’m pretty sure at least some of those were there before the recent release. In the list of services, I see that http://kbase.us/services/docs/invocation/Iris/iris.html has services that are out of order and have been retired (e.g., PROM, Experiment, Metagenomic Sequence QC), while I don’t see some of the new services (e.g., cMonkey, Expression, Meme). Basically, http://kbase.us/services/docs/invocation/Iris/iris.html looks to me like it did in December (though I have no way of proving that). Maybe some of it got redeployed but other parts didn’t? Maybe something special (in addition to the normal deploy) has to happen to refresh the html and get rid of the defunct services and bring in the new services? Nomi On Feb 10, 2014, at 5:09 PM, Shane Canon <[email protected]<mailto:[email protected]>> wrote: I don't think you would see any of ws-* commands if this wasn't the latest version. So I'm pretty sure it is up to date. --Shane On Feb 10, 2014, at 5:00 PM, Nomi Harris <[email protected]<mailto:[email protected]>> wrote: On Feb 10, 2014, at 4:43 PM, Michael Sneddon <[email protected]<mailto:[email protected]>> wrote: I forgot to mention that ws-workspace not working means you will have to pass the -w [ws_name] flag to all the WS and FBA scripts whenever a workspace name is required. I suppose we could temporarily remove that method from IRIS until we have it fixed. Hmm. Sounds like that will require some work from Jim. There’s also a lot of documentation that will need to be changed to reflect the changes (kbws-* no longer supported; need to use ws-*; need to create a new ws in WS deluxe; need to use “-w ws_name” flag for all WS and FBA scripts). Also, it doesn’t look to me like IRIS is really the latest version. I know Jim fixed the tutorial, but it doesn’t work: / tutorial Could not load tutorial and there are other changes that I would expect to see if this were really the latest version that I’m not seeing. Nomi On Mon, Feb 10, 2014 at 4:40 PM, Michael Sneddon <[email protected]<mailto:[email protected]>> wrote: Sorry I wasn't following this thread closely enough earlier, but I think at least part of the problem may be related to pointing to the correct WS service. The 'kbws-*' scripts point to the old WS, but the fba methods point to the new WS deployment (kbase.us/services/ws<http://kbase.us/services/ws>). So methods will fail unless you have a workspace created with the correct name in the new WS, and your objects are in that workspace. We should remove the 'kbws-*' scripts from the IRIS deployment. See below for the working commands to import the E.coli genome and create a model. A sidenote is that the 'ws-workspace' command is not functioning properly to set the default WS. This method works by setting/reading an environment variable, but I know this wasn't tested very thoroughly. There is probably a bug or a change in which environment variables are set. / ws-createws IrisTestWS Workspace created with name: IrisTestWS and id: 818 Command Completed / kbfba-loadgenome "kb|g.0" -w IrisTestWS Genome successfully loaded to workspace: Object Name: kb|g.0 Object ID: 2 Type: KBaseGenomes.Genome-1.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:34:06+0000 Saved by: wstester1 Checksum: 9e4a09bf26ae131d3982517006d3b100 Size(bytes): 3625772 User Meta Data: none. Command Completed / kbfba-buildfbamodel "kb|g.0" -w IrisTestWS Model successfully generated in workspace: Object Name: kb|g.0.fbamdl Object ID: 3 Type: KBaseFBA.FBAModel-2.0 Version: 1 Workspace: IrisTestWS Save Date: 2014-02-11T00:35:09+0000 Saved by: wstester1 Checksum: ee99d7b7017766c8efef87519de37c2e Size(bytes): 1673278 User Meta Data: none. Command Completed / ws-listobj -w IrisTestWS ID ObjName Vers Type WS Last_modby Moddate Size(bytes) 3 kb|g.0.fbamdl 1 KBaseFBA.FBAModel-2.0 IrisTestWS wstester1 2014-02-11T00:35:09+0000 1673278 2 kb|g.0 1 KBaseGenomes.Genome-1.0 IrisTestWS wstester1 2014-02-11T00:34:06+0000 3625772 1 kb|contigset.10186 1 KBaseGenomes.ContigSet-1.1 IrisTestWS wstester1 2014-02-11T00:34:02+0000 4639516 Command Completed On Mon, Feb 10, 2014 at 3:30 PM, Murphy-Olson, Daniel E. <[email protected]<mailto:[email protected]>> wrote: I think at some point workspace commands required specifying the -w <workspace> option. However, even with that I'm getting errors in Iris / kbfba-loadgenome -e "kb|g.0 " -w IrisTut Genome failed to load to workspace! JSONRPC error: Attribute (md5) does not pass the type constraint because: Validation failed for 'Str' with value undef at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 38 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at reader Moose::Exception::trace (defined at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Moose/Exception.pm line 12) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x1eae12c0)') called at /kbase ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> From: [email protected]<mailto:[email protected]> [[email protected]<mailto:[email protected]>] on behalf of Murphy-Olson, Daniel E. [[email protected]<mailto:[email protected]>] Sent: Monday, February 10, 2014 5:14 PM To: Nomi Harris Cc: Henry, Christopher S.; Thomason, James; [email protected]<mailto:[email protected]> Subject: Re: [Release-team] IRIS testing needed That version string is hardcoded in the latest master.. I had the same thought. Iris was re-deployed this morning. I think errors were introduced in the FBA scripts. We still don't have a fix for them, and I'm growing concerned. It looks like changes were made last week to FBA, which changed the deploy Makefile in such a way that things deploy properly into the test environment, but don't work in production. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055<tel:630-252-0055> From: Nomi Harris [[email protected]<mailto:[email protected]>] Sent: Monday, February 10, 2014 4:27 PM To: Murphy-Olson, Daniel E. Cc: Henry, Christopher S.; [email protected]<mailto:[email protected]>; Thomason, James Subject: Re: [Release-team] IRIS testing needed I’m still not able to run kbfba-loadgenome—see trace below. Has IRIS been redeployed? It still says v0.0.6 - 12/13/2013. / kbws-workspace Current workspace is: nomitest2 Command Completed / kbfba-loadgenome -e "kb|g.0" Genome failed to load to workspace! JSONRPC error: _ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 JSONRPC error code: -32603 JSONRPC error data:_ERROR_Mandatory arguments workspace missing._ERROR_ Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 2088 Bio::KBase::fbaModelServices::Impl::_error('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'Mandatory arguments workspace missing.', '_validateargs') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 846 Bio::KBase::fbaModelServices::Impl::_validateargs('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)', 'ARRAY(0x2648f030)', 'HASH(0x19f09e60)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Impl.pm line 5181 Bio::KBase::fbaModelServices::Impl::genome_to_workspace('Bio::KBase::fbaModelServices::Impl=HASH(0x84e0b60)', 'HASH(0x274c9500)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 399 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Server.pm line 397 Bio::KBase::fbaModelServices::Server::call_method('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x229b2958)', 'HASH(0x2104c650)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 33 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/RPC/Any/Server.pm line 26 RPC::Any::Server::handle_input('Bio::KBase::fbaModelServices::Server=HASH(0x84e0968)', 'HASH(0x15ef3c38)') called at /kbase/deployments/20140109-prod/lib/fbaModelServices.psgi line 20 Plack::Sandbox::_2fkbase_2fdeployments_2f20140109_2dprod_2flib_2ffbaModelServices_2epsgi::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Middleware/CrossOrigin.pm line 115 Plack::Middleware::CrossOrigin::call('Plack::Middleware::CrossOrigin=HASH(0x8505930)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Component.pm line 50 Plack::Component::__ANON__('HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Util.pm line 142 Plack::Util::run_app('CODE(0x7f26e68)', 'HASH(0x15ef3c38)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 273 Starman::Server::process_request('Starman::Server=HASH(0x27805a8)', 'Net::Server::Proto::TCP=GLOB(0x1924c380)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 75 Net::Server::run_client_connection('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 eval {...} at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 229 Net::Server::PreFork::run_child('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 187 Net::Server::PreFork::run_n_children('Starman::Server=HASH(0x27805a8)', 5) called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server/PreFork.pm line 111 Net::Server::PreFork::loop('Starman::Server=HASH(0x27805a8)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Net/Server.pm line 61 Net::Server::run('Starman::Server=HASH(0x27805a8)', 'port', 'ARRAY(0x2c28270)', 'host', '*', 'proto', 'tcp', 'serialize', 'none', 'min_servers', 5, 'min_spare_servers', 4, 'max_spare_servers', 4, 'max_servers', 5, 'max_requests', 1000, 'user', 200, 'group', '1003 1003', 'listen', 1024, 'check_for_waiting', 1, 'no_client_stdout', 1, 'pid_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/service.pid', 'setsid', 1, 'background', 1, 'log_file', '/kbase/deployments/20140109-prod//services/fbaModelServices/error.log') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Starman/Server.pm line 84 Starman::Server::run('Starman::Server=HASH(0x27805a8)', 'CODE(0x2780488)', 'HASH(0x277c008)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Handler/Starman.pm line 18 Plack::Handler::Starman::run('Plack::Handler::Starman=HASH(0x2780548)', 'CODE(0x2780488)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Loader/Delayed.pm line 20 Plack::Loader::Delayed::run('Plack::Loader::Delayed=HASH(0x2792c50)', 'Plack::Handler::Starman=HASH(0x2780548)') called at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/Plack/Runner.pm line 277 Plack::Runner::run('Plack::Runner=HASH(0x27d6898)') called at /kbase/runtimes/20140109-prod/bin/starman line 38 Trace begun at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/Client.pm line 2434 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x29a0978)', 'HASH(0xbc12d0)') called at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 165 eval {...} at /kbase/deployments/20140109-prod/lib/Bio/KBase/fbaModelServices/ScriptHelpers.pm line 158 Bio::KBase::fbaModelServices::ScriptHelpers::runFBACommand('HASH(0xbc12d0)', 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0xbc3790)') called at /kbase/deployments/20140109-prod/plbin/ fba-loadgenome.pl<http://fba-loadgenome.pl> line 58 On Feb 10, 2014, at 1:39 PM, Michael Sneddon <[email protected]<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. <[email protected]<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 [email protected]<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team ` _______________________________________________ Release-team mailing list [email protected]<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list [email protected]<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list [email protected]<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team
