In addition to the tutorial bug that Jim fixed, here’s another reason to redeploy IRIS: there seems to be a problem with the fba commands. I thought the old command names would work in IRIS (even if they're deprecated)? IRIS seems to recognize kbfba-loadgenome (but it doesn’t work) but it doesn’t recognize fba-loadgenome.
/ fba-loadgenome -e "kb|g.0" fba-loadgenome: invalid command
/ kbfba-loadgenome -e "kb|g.0" Return code from kbfba-loadgenome: 255JSONRPC error: Authentication required for fbaModelServices but no authentication header was passed JSONRPC error code: JSONRPC error data:
Trace begun at /kb/deployment/lib/Bio/KBase/fbaModelServices/Client.pm line 2392 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x252b1c0)', 'HASH(0x25a60f0)') called at /kb/deployment/lib/Bio/KBase/fbaModelServices/Helpers.pm line 118 Bio::KBase::fbaModelServices::Helpers::runFBACommand('HASH(0x25a60f0)', 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0x32c5828)') called at /kb/deployment/plbin/ kbfba-loadgenome.pl line 60 (Yes, I am logged into IRIS.) I tried loading other genome IDs and got the same error. Other kbfba commands (that I could try after kbfba-loadgenome failed—most of the fba commands require a genome or model) didn’t work either.
/ kbfba-exportmedia Carbon-D-Glucose readable -w KBaseMedia Media export failed!
/ kbfba-importpheno "kb|g.0" WT-phenotypes.txt --phenoid Ecoli.Phenos Phenotype import failed!
Nomi On Feb 8, 2014, at 11:17 AM, Thomason, James <[email protected]> wrote:
Could somebody kick out a new iris deploy, please?
There’s no need to do a full invocation release unless one of those is scheduled anyway, just a new iris deploy will suffice.
It fixed a glitch that was preventing tutorials from showing up.
Many thanks,
-- -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/