From 8836bd0cbacc879ab71f6e36c362711ba3a8da29 Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Sat, 11 Apr 2020 15:27:03 +0200 Subject: [PATCH 1/4] fix: remove dash from Human-GEM in short_name field dash causes problems when exporting to SBML --- ModelFiles/yml/HumanGEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ModelFiles/yml/HumanGEM.yml b/ModelFiles/yml/HumanGEM.yml index c9f305a9..a398547f 100644 --- a/ModelFiles/yml/HumanGEM.yml +++ b/ModelFiles/yml/HumanGEM.yml @@ -1,9 +1,9 @@ !!omap - metaData: - short_name : "Human-GEM" + short_name : "HumanGEM" full_name : "Generic genome-scale metabolic model of Homo sapiens" version : "" - date : "2020-03-21" + date : "2020-04-11" authors : "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas" email : "jonrob@chalmers.se" organization: "Chalmers University of Technology" From 83c7ddfcdf5942a718068337c2c7bf2e0c2f336f Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Tue, 21 Apr 2020 14:34:49 +0200 Subject: [PATCH 2/4] fix: revert removal of dash from model ID except in SBML file --- ModelFiles/yml/HumanGEM.yml | 2 +- code/io/exportHumanGEM.m | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/ModelFiles/yml/HumanGEM.yml b/ModelFiles/yml/HumanGEM.yml index c4e0ea3c..4a76a3bc 100644 --- a/ModelFiles/yml/HumanGEM.yml +++ b/ModelFiles/yml/HumanGEM.yml @@ -1,6 +1,6 @@ !!omap - metaData: - short_name : "HumanGEM" + short_name : "Human-GEM" full_name : "Generic genome-scale metabolic model of Homo sapiens" version : "" date : "2020-04-05" diff --git a/code/io/exportHumanGEM.m b/code/io/exportHumanGEM.m index 21dad3ab..3cd24aae 100755 --- a/code/io/exportHumanGEM.m +++ b/code/io/exportHumanGEM.m @@ -109,6 +109,7 @@ model = simplifyModel(ihuman,false,false,true); % remove inactivated rxns model = annotateModel(model); % add annotation data to structure model = rmfield(model,'inchis'); % temporarily remove inchis until export function is updated + model.id = regexprep(model.id,'-',''); % remove dash from model ID since it causes problems with SBML I/O exportModel(model,fullfile(path,'modelFiles','xml',strcat(prefix,'.xml'))); end From 0bb5238f1c11e08447872b06a039e3af628f6568 Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Tue, 21 Apr 2020 14:40:01 +0200 Subject: [PATCH 3/4] style: prevent change of modelFiles directory name --- {ModelFiles => odelFiles}/yml/HumanGEM.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {ModelFiles => odelFiles}/yml/HumanGEM.yml (100%) diff --git a/ModelFiles/yml/HumanGEM.yml b/odelFiles/yml/HumanGEM.yml similarity index 100% rename from ModelFiles/yml/HumanGEM.yml rename to odelFiles/yml/HumanGEM.yml From 250757b356d543da428361b5d6fbf5bce4a7a85f Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Tue, 21 Apr 2020 14:40:20 +0200 Subject: [PATCH 4/4] style: prevent change of modelFiles directory name --- {odelFiles => modelFiles}/yml/HumanGEM.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {odelFiles => modelFiles}/yml/HumanGEM.yml (100%) diff --git a/odelFiles/yml/HumanGEM.yml b/modelFiles/yml/HumanGEM.yml similarity index 100% rename from odelFiles/yml/HumanGEM.yml rename to modelFiles/yml/HumanGEM.yml