fix: readYAMLmodel builds correct ec.rxnEnzMat (#568)

* fix: exportForGit correct neverPrefix option

* feat: YAML I/O tests

* fix: exportForGit do not test COBRA if not exist

* fix: readYAMLmodel correct rxnEnzMat

* fix: importExportTests less strict filesize test

Author: edkerk

doc/installation/checkInstallation.html

@@ -53,7 +53,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 <li><a href="checkFileExistence.html" class="code" title="function files=checkFileExistence(files,fullOrTemp,allowSpace,checkExist)">checkFileExistence</a>	checkFileExistence</li><li><a href="exportModel.html" class="code" title="function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)">exportModel</a>	exportModel</li><li><a href="sortIdentifiers.html" class="code" title="function newModel = sortIdentifiers(model)">sortIdentifiers</a>	exportModel</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="SBMLFromExcel.html" class="code" title="function SBMLFromExcel(fileName, outputFileName,toCOBRA,printWarnings)">SBMLFromExcel</a>	SBMLFromExcel</li><li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)">exportForGit</a>	exportForGit</li><li><a href="exportModel.html" class="code" title="function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)">exportModel</a>	exportModel</li></ul>
+<li><a href="SBMLFromExcel.html" class="code" title="function SBMLFromExcel(fileName, outputFileName,toCOBRA,printWarnings)">SBMLFromExcel</a>	SBMLFromExcel</li><li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)">exportForGit</a>	exportForGit</li><li><a href="exportModel.html" class="code" title="function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)">exportModel</a>	exportModel</li></ul>
 <!-- crossreference -->
 
 <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>

doc/io/exportForGit.html

@@ -53,7 +53,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 <li><a href="exportToTabDelimited.html" class="code" title="function exportToTabDelimited(model,path,sortIds)">exportToTabDelimited</a>	exportToTabDelimited</li><li><a href="loadWorkbook.html" class="code" title="function workbook=loadWorkbook(fileName,createEmpty)">loadWorkbook</a>	loadWorkbook</li><li><a href="sortIdentifiers.html" class="code" title="function newModel = sortIdentifiers(model)">sortIdentifiers</a>	exportModel</li><li><a href="writeSheet.html" class="code" title="function wb=writeSheet(wb,sheetName,sheetPosition,captions,units,raw,isIntegers)">writeSheet</a>	writeSheet</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)">exportForGit</a>	exportForGit</li></ul>
+<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)">exportForGit</a>	exportForGit</li></ul>
 <!-- crossreference -->
 
 

doc/io/exportModel.html

@@ -49,7 +49,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 </ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)">exportForGit</a>	exportForGit</li></ul>
+<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)">exportForGit</a>	exportForGit</li></ul>
 <!-- crossreference -->
 
 <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>

doc/io/exportToExcelFormat.html

@@ -682,7 +682,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0625     [~,enzIdx]          = ismember(enzStoich(:,2),model.ec.enzymes);
 0626     coeffs              = cell2mat(enzStoich(:,3));
 0627     model.ec.rxnEnzMat  = zeros(numel(model.ec.rxns), numel(model.ec.genes));
-0628     linearIndices       = sub2ind([max(rxnIdx), max(enzIdx)], rxnIdx, enzIdx);
+0628     linearIndices       = sub2ind([numel(model.ec.rxns), numel(model.ec.genes)], rxnIdx, enzIdx);
 0629     model.ec.rxnEnzMat(linearIndices) = coeffs;
 0630     <span class="comment">%Parse ec-codes</span>
 0631     <span class="keyword">if</span> ~isempty(ecGecko)

doc/io/getToolboxVersion.html

@@ -47,7 +47,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 </ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)">exportForGit</a>	exportForGit</li><li><a href="exportModel.html" class="code" title="function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)">exportModel</a>	exportModel</li><li><a href="exportToExcelFormat.html" class="code" title="function exportToExcelFormat(model,fileName,sortIds)">exportToExcelFormat</a>	exportToExcelFormat</li><li><a href="exportToTabDelimited.html" class="code" title="function exportToTabDelimited(model,path,sortIds)">exportToTabDelimited</a>	exportToTabDelimited</li><li><a href="writeYAMLmodel.html" class="code" title="function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)">writeYAMLmodel</a>	writeYAMLmodel</li></ul>
+<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)">exportForGit</a>	exportForGit</li><li><a href="exportModel.html" class="code" title="function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)">exportModel</a>	exportModel</li><li><a href="exportToExcelFormat.html" class="code" title="function exportToExcelFormat(model,fileName,sortIds)">exportToExcelFormat</a>	exportToExcelFormat</li><li><a href="exportToTabDelimited.html" class="code" title="function exportToTabDelimited(model,path,sortIds)">exportToTabDelimited</a>	exportToTabDelimited</li><li><a href="writeYAMLmodel.html" class="code" title="function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)">writeYAMLmodel</a>	writeYAMLmodel</li></ul>
 <!-- crossreference -->
 
 

doc/io/readYAMLmodel.html

@@ -49,7 +49,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 <li><a href="sortIdentifiers.html" class="code" title="function newModel = sortIdentifiers(model)">sortIdentifiers</a>	exportModel</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)">exportForGit</a>	exportForGit</li></ul>
+<li><a href="exportForGit.html" class="code" title="function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)">exportForGit</a>	exportForGit</li></ul>
 <!-- crossreference -->
 
 <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>

doc/io/sortIdentifiers.html

@@ -42,7 +42,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 
 <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
 <ul style="list-style-image:url(../../matlabicon.gif)">
-<li><a href="#_sub1" class="code">function testExcelImport(testCase)</a></li><li><a href="#_sub2" class="code">function testSBMLImport(testCase)</a></li><li><a href="#_sub3" class="code">function testExcelExport(testCase)</a></li><li><a href="#_sub4" class="code">function testSBMLExport(testCase)</a></li></ul>
+<li><a href="#_sub1" class="code">function testExcelImport(testCase)</a></li><li><a href="#_sub2" class="code">function testSBMLImport(testCase)</a></li><li><a href="#_sub3" class="code">function testYAMLimport(testCase)</a></li><li><a href="#_sub4" class="code">function testExcelExport(testCase)</a></li><li><a href="#_sub5" class="code">function testSBMLExport(testCase)</a></li><li><a href="#_sub6" class="code">function testYAMLexport(testCase)</a></li></ul>
 
 <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
 <div class="fragment"><pre>0001 <span class="comment">%run this test case with the command</span>
@@ -72,31 +72,52 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0025 verifyEqual(testCase,model,modelSBML)
 0026 <span class="keyword">end</span>
 0027 
-0028 <a name="_sub3" href="#_subfunctions" class="code">function testExcelExport(testCase)</a>
+0028 <a name="_sub3" href="#_subfunctions" class="code">function testYAMLimport(testCase)</a>
 0029 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
-0030 load(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'ecoli_textbook.mat'</span>), <span class="string">'model'</span>);
-0031 exportToExcelFormat(model,fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));
-0032 <span class="comment">%File will not be exactly equal as it contains the current date and time,</span>
-0033 <span class="comment">%so md5 or similar would not work. Just check whether file is reasonably</span>
-0034 <span class="comment">%sized.</span>
-0035 s = dir(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));         
-0036 filesize = s.bytes;
-0037 verifyTrue(testCase,filesize&gt;17000);
-0038 delete(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));
-0039 <span class="keyword">end</span>
-0040 
-0041 <a name="_sub4" href="#_subfunctions" class="code">function testSBMLExport(testCase)</a>
-0042 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
-0043 load(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'ecoli_textbook.mat'</span>), <span class="string">'model'</span>);
-0044 evalc(<span class="string">'exportModel(model,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.xml''))'</span>);
-0045 <span class="comment">%File will not be exactly equal as it contains the current date and time,</span>
-0046 <span class="comment">%so md5 or similar would not work. Just check whether file is reasonably</span>
-0047 <span class="comment">%sized.</span>
-0048 s = dir(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xml'</span>));         
-0049 filesize = s.bytes;
-0050 verifyTrue(testCase,filesize&gt;18500);
-0051 delete(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xml'</span>));
-0052 <span class="keyword">end</span></pre></div>
+0030 yamlFile=fullfile(sourceDir,<span class="string">'tutorial'</span>,<span class="string">'empty.yml'</span>);
+0031 evalc(<span class="string">'model=readYAMLmodel(yamlFile)'</span>); <span class="comment">% Repress warnings</span>
+0032 load(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'importExportResults.mat'</span>), <span class="string">'modelYAML'</span>);
+0033 verifyEqual(testCase,model,modelYAML)
+0034 <span class="keyword">end</span>
+0035 
+0036 <a name="_sub4" href="#_subfunctions" class="code">function testExcelExport(testCase)</a>
+0037 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
+0038 load(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'ecoli_textbook.mat'</span>), <span class="string">'model'</span>);
+0039 exportToExcelFormat(model,fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));
+0040 <span class="comment">%File will not be exactly equal as it contains the current date and time,</span>
+0041 <span class="comment">%so md5 or similar would not work. Just check whether file is reasonably</span>
+0042 <span class="comment">%sized.</span>
+0043 s = dir(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));         
+0044 filesize = s.bytes;
+0045 verifyTrue(testCase,filesize&gt;17000);
+0046 delete(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xlsx'</span>));
+0047 <span class="keyword">end</span>
+0048 
+0049 <a name="_sub5" href="#_subfunctions" class="code">function testSBMLExport(testCase)</a>
+0050 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
+0051 load(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'ecoli_textbook.mat'</span>), <span class="string">'model'</span>);
+0052 evalc(<span class="string">'exportModel(model,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.xml''))'</span>);
+0053 <span class="comment">%File will not be exactly equal as it contains the current date and time,</span>
+0054 <span class="comment">%so md5 or similar would not work. Just check whether file is reasonably</span>
+0055 <span class="comment">%sized.</span>
+0056 s = dir(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xml'</span>));         
+0057 filesize = s.bytes;
+0058 verifyTrue(testCase,filesize&gt;18500);
+0059 delete(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.xml'</span>));
+0060 <span class="keyword">end</span>
+0061 
+0062 <a name="_sub6" href="#_subfunctions" class="code">function testYAMLexport(testCase)</a>
+0063 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
+0064 load(fullfile(sourceDir,<span class="string">'tutorial'</span>,<span class="string">'empty.mat'</span>), <span class="string">'emptyModel'</span>);
+0065 evalc(<span class="string">'writeYAMLmodel(emptyModel,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.yml''))'</span>);
+0066 <span class="comment">%File will not be exactly equal as it contains the current date and time,</span>
+0067 <span class="comment">%so md5 or similar would not work. Just check whether file is reasonably</span>
+0068 <span class="comment">%sized.</span>
+0069 s = dir(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.yml'</span>));         
+0070 filesize = s.bytes;
+0071 verifyTrue(testCase,filesize&gt;1290);
+0072 delete(fullfile(sourceDir,<span class="string">'testing'</span>,<span class="string">'unit_tests'</span>,<span class="string">'test_data'</span>,<span class="string">'_test.yml'</span>));
+0073 <span class="keyword">end</span></pre></div>
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>

doc/io/writeYAMLmodel.html

@@ -179,7 +179,7 @@
 end
 
 fprintf(myStr('   > Export Excel format',40))
-if res(3).Passed == 1
+if res(4).Passed == 1
     fprintf('Pass\n')
 else
     printOrange('Fail\n')
@@ -193,20 +193,25 @@
 end
 
 fprintf(myStr('   > Export SBML format',40))
-if res(4).Passed == 1
+if res(5).Passed == 1
     fprintf('Pass\n')
 else
     printOrange('Fail\n')
 end
 
-%Check if it is possible to import an YAML model
-% fprintf(' > Checking import of model in YAML format:\t\t\t');
-% try
-%     readYaml(ymlFile,true);
-%     fprintf('Pass\n');
-% catch
-%     printOrange('Fail\n');
-% end
+fprintf(myStr('   > Import YAML format',40))
+if res(3).Passed == 1
+    fprintf('Pass\n')
+else
+    printOrange('Fail\n')
+end
+
+fprintf(myStr('   > Export YAML format',40))
+if res(6).Passed == 1
+    fprintf('Pass\n')
+else
+    printOrange('Fail\n')
+end
 
 fprintf('\n=== Model solvers ===\n');
 

doc/testing/unit_tests/importExportTests.html

@@ -1,4 +1,4 @@
-function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
+function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)
 % exportForGit
 %   Generates a directory structure and populates this with model files, ready
 %   to be commited to a Git(Hub) maintained model repository. Writes the model
@@ -28,16 +28,13 @@
 %                       Toolbox format using metabolite IDs, instead of
 %                       metabolite names and compartments. (optional,
 %                       default false)
-%   COBRAstyle          true if COBRA-style prefixes should be added to all
-%                       identifiers in the SBML file: R_ for reactions, M_
-%                       for metabolites, G_ for genes and C_ for
-%                       compartments. If all identifiers of a particular
-%                       field already have the prefix, then no additional
-%                       prefixes are added. (optional, default false)
+%   neverPrefixIDs      true if prefixes are never added to identifiers,
+%                       even if start with e.g. digits. This might result
+%                       in invalid SBML files (optional, default false)
 %
 % Usage: exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
 if nargin<8
-    COBRAstyle=false;
+    neverPrefixIDs=false;
 end
 if nargin<7 || isempty(COBRAtext)
     COBRAtext=false;
@@ -73,7 +70,9 @@
 
 %Get versions or commits of toolboxes:
 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
-COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
+if exist('initCobraToolbox.m','file')
+    COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
+end
 
 %Retrieve libSBML version:
 [ravenDir,prevDir]=findRAVENroot();
@@ -142,7 +141,7 @@
 
 % Write XML format
 if ismember('xml', formats)
-        exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),COBRAstyle);
+        exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),neverPrefixIDs);
 end
 
 %Save file with versions:

installation/checkInstallation.m

@@ -625,7 +625,7 @@
     [~,enzIdx]          = ismember(enzStoich(:,2),model.ec.enzymes);
     coeffs              = cell2mat(enzStoich(:,3));
     model.ec.rxnEnzMat  = zeros(numel(model.ec.rxns), numel(model.ec.genes));
-    linearIndices       = sub2ind([max(rxnIdx), max(enzIdx)], rxnIdx, enzIdx);
+    linearIndices       = sub2ind([numel(model.ec.rxns), numel(model.ec.genes)], rxnIdx, enzIdx);
     model.ec.rxnEnzMat(linearIndices) = coeffs;
     %Parse ec-codes
     if ~isempty(ecGecko)