Merge pull request #236 from mihai-sysbio/feat/yaml-validation

feat: add yaml validation

.github/workflows/yaml-validation.yml

@@ -0,0 +1,39 @@
+name: YAML validation
+
+on:
+  push:
+    branches: [ devel ]
+  pull_request:
+    branches: [ master, devel ]
+
+jobs:
+  yaml-validation:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+
+    - name: YAML Lint
+      uses: ibiqlik/[email protected]
+      with:
+        ## File(s) or Directory, separate by space if multiple files or folder are specified
+        file_or_dir: ModelFiles/
+        ## Custom configuration (as YAML source)
+        config_data: "{extends: default, rules: {line-length: disable}}"
+        ## Format for parsing output [parsable,standard,colored,auto]
+        # format: # optional, default is colored
+        ## Return non-zero exit code on warnings as well as errors
+        # strict: # optional, default is false
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Import with cobrapy
+      run: |
+        pip install -r requirements/ci-requirements.txt
+        python -c "import cobra ; cobra.io.load_yaml_model('ModelFiles/yml/yeastGEM.yml')"

ComplementaryScripts/modelCuration/curationsOnV8_4_2.m

@@ -0,0 +1,16 @@
+%% Curations on version 8.4.2
+% This is a list of various smaller curations to be performed on version 
+% 8.4.2 of yeast-GEM. Indicated is what Issue is solved.
+
+% Load model
+cd ..
+model = loadYeastModel;
+
+% Solves #252
+model = changeGeneAssociation(model,'r_4590','YOL130W');
+
+% Solves #254
+model.metNames = regexprep(model.metNames,'^nicotinamide ribose','nicotinamide riboside');
+% All annotations, formula and charge were correct.
+
+saveYeastModel(model);

ComplementaryScripts/saveYeastModel.m

@@ -92,7 +92,8 @@ function saveYeastModel(model,upDATE,allowNoGrowth)
                 num2str(length(model.mets)) '|' ...
                 num2str(length(model.genes)) '|' newline];
         end
-        fwrite(fout,inline);
+        inline=unicode2native(inline,'UTF-8');
+        fwrite(fout,inline,'uint8');
     end
 end
 fclose('all');

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
-MATLAB	9.7.0.1190202 (R2019b)
+MATLAB	9.9.0.1524771 (R2020b) Update 2
 libSBML	5.17.0
-RAVEN_toolbox	2.4.1
-COBRA_toolbox	commit 6c49aaf
+RAVEN_toolbox	commit 5061381
+COBRA_toolbox	commit 800dcfe
 SBML_level	3
 SBML_version	1
 fbc_version	2

ModelFiles/txt/yeastGEM.txt

@@ -3948,7 +3948,7 @@ r_4586	s_3998[c] + s_4192[c]  -> 2 s_4193[c] 		  0.00	1000.00	  0.00
 r_4587	s_0796[e] + s_4199[e]  <=> s_0794[c] + s_3880[c] 	YOL122C	-1000.00	1000.00	  0.00
 r_4588	s_4200[e]  <=> s_3778[c] 	YNL275W	-1000.00	1000.00	  0.00
 r_4589	s_0796[e] + s_4201[e]  <=> s_0794[c] + s_4019[c] 	YOL122C	-1000.00	1000.00	  0.00
-r_4590	s_0796[e] + s_4202[e]  <=> s_0794[c] + s_3801[c] 	YGR191W	-1000.00	1000.00	  0.00
+r_4590	s_0796[e] + s_4202[e]  <=> s_0794[c] + s_3801[c] 	YOL130W	-1000.00	1000.00	  0.00
 r_4591	s_0796[e] + s_4203[e]  <=> s_0794[c] + s_3822[c] 	( YGL255W or YLR130C )	-1000.00	1000.00	  0.00
 r_4592	s_0796[e] + s_4204[e]  <=> s_0794[c] + s_4013[c] 	( YGR191W or YOL130W )	-1000.00	1000.00	  0.00
 r_4593	s_4200[e]  <=> 		-1000.00	1000.00	  0.00

ModelFiles/xml/yeastGEM.xml

@@ -20570,7 +20570,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="s_1218__91__c__93__" sboTerm="SBO:0000247" id="s_1218__91__c__93__" name="nicotinamide ribose [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C11H15N2O5">
+      <species metaid="s_1218__91__c__93__" sboTerm="SBO:0000247" id="s_1218__91__c__93__" name="nicotinamide riboside [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C11H15N2O5">
         <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#s_1218__91__c__93__">
@@ -214436,7 +214436,7 @@
           <speciesReference species="s_3801__91__c__93__" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="G_YGR191W"/>
+          <fbc:geneProductRef fbc:geneProduct="G_YOL130W"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="r_4591" sboTerm="SBO:0000655" id="r_4591" name="Zn(2+) transport" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">