From 3538d8f6d7cafd57766ff14c2d2a185bd1600568 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Wed, 16 Oct 2024 14:21:34 +0200 Subject: [PATCH 1/5] fix: exportForGit correct neverPrefix option --- doc/io/exportForGit.html | 270 ++++++++++++++++---------------- doc/io/exportModel.html | 2 +- doc/io/exportToExcelFormat.html | 2 +- doc/io/getToolboxVersion.html | 2 +- doc/io/sortIdentifiers.html | 2 +- doc/io/writeYAMLmodel.html | 2 +- io/exportForGit.m | 15 +- 7 files changed, 143 insertions(+), 152 deletions(-) diff --git a/doc/io/exportForGit.html b/doc/io/exportForGit.html index 74a90f62..f833f5d1 100644 --- a/doc/io/exportForGit.html +++ b/doc/io/exportForGit.html @@ -24,7 +24,7 @@

PURPOSE ^exportForGit

SYNOPSIS ^

-
function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
+
function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)

DESCRIPTION ^

 exportForGit
@@ -56,12 +56,9 @@ 
DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^

-
0001 function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
+
0001 function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,neverPrefixIDs)
 0002 % exportForGit
 0003 %   Generates a directory structure and populates this with model files, ready
 0004 %   to be commited to a Git(Hub) maintained model repository. Writes the model
@@ -108,140 +105,137 @@ 
SOURCE CODE ^%                       Toolbox format using metabolite IDs, instead of
 0029 %                       metabolite names and compartments. (optional,
 0030 %                       default false)
-0031 %   COBRAstyle          true if COBRA-style prefixes should be added to all
-0032 %                       identifiers in the SBML file: R_ for reactions, M_
-0033 %                       for metabolites, G_ for genes and C_ for
-0034 %                       compartments. If all identifiers of a particular
-0035 %                       field already have the prefix, then no additional
-0036 %                       prefixes are added. (optional, default false)
-0037 %
-0038 % Usage: exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
-0039 if nargin<8
-0040     COBRAstyle=false;
+0031 %   neverPrefixIDs      true if prefixes are never added to identifiers,
+0032 %                       even if start with e.g. digits. This might result
+0033 %                       in invalid SBML files (optional, default false)
+0034 %
+0035 % Usage: exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs,COBRAtext,COBRAstyle)
+0036 if nargin<8
+0037     neverPrefixIDs=false;
+0038 end
+0039 if nargin<7 || isempty(COBRAtext)
+0040     COBRAtext=false;
 0041 end
-0042 if nargin<7 || isempty(COBRAtext)
-0043     COBRAtext=false;
+0042 if nargin<6 || isempty(subDirs)
+0043     subDirs=true;
 0044 end
-0045 if nargin<6 || isempty(subDirs)
-0046     subDirs=true;
+0045 if nargin<5 || isempty(mainBranchFlag)
+0046     mainBranchFlag=false;
 0047 end
-0048 if nargin<5 || isempty(mainBranchFlag)
-0049     mainBranchFlag=false;
-0050 end
-0051 if nargin<4 || isempty(formats)
-0052     formats={'mat', 'txt', 'xlsx', 'xml', 'yml'};
-0053 else
-0054     formats=convertCharArray(formats);
-0055 end
-0056 if any(~ismember(formats, {'mat', 'txt', 'xlsx', 'xml', 'yml'}))
-0057     EM='Unknown file format defined. Only mat, txt, xlsx, xml and yml are allowed file formats.';
-0058     error(EM)
-0059 end
-0060 if nargin<3 || isempty(path)
-0061     path='.';
-0062 else
-0063     path=char(path);
-0064 end
-0065 if nargin<2 || isempty(prefix)
-0066     prefix='model';
-0067 else
-0068     prefix=char(prefix);
-0069 end
+0048 if nargin<4 || isempty(formats)
+0049     formats={'mat', 'txt', 'xlsx', 'xml', 'yml'};
+0050 else
+0051     formats=convertCharArray(formats);
+0052 end
+0053 if any(~ismember(formats, {'mat', 'txt', 'xlsx', 'xml', 'yml'}))
+0054     EM='Unknown file format defined. Only mat, txt, xlsx, xml and yml are allowed file formats.';
+0055     error(EM)
+0056 end
+0057 if nargin<3 || isempty(path)
+0058     path='.';
+0059 else
+0060     path=char(path);
+0061 end
+0062 if nargin<2 || isempty(prefix)
+0063     prefix='model';
+0064 else
+0065     prefix=char(prefix);
+0066 end
+0067 
+0068 %Sort reactions, metabolites and genes alphabetically
+0069 model=sortIdentifiers(model);
 0070 
-0071 %Sort reactions, metabolites and genes alphabetically
-0072 model=sortIdentifiers(model);
-0073 
-0074 %Get versions or commits of toolboxes:
-0075 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
-0076 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
-0077 
-0078 %Retrieve libSBML version:
-0079 [ravenDir,prevDir]=findRAVENroot();
-0080 try % 5.17.0 and newer
-0081     libSBMLver=OutputSBML_RAVEN;
-0082     libSBMLver=libSBMLver.libSBML_version_string;
-0083 catch % before 5.17.0
-0084     fid = fopen('tempModelForLibSBMLversion.xml','w+');
-0085     fclose(fid);
-0086     evalc('[~,~,libSBMLver]=TranslateSBML_RAVEN(''tempModelForLibSBMLversion.xml'',0,0)');
-0087     libSBMLver=libSBMLver.libSBML_version_string;
-0088     delete('tempModelForLibSBMLversion.xml');
-0089 end
-0090 
-0091 % Make models folder, no warnings if folder already exists
-0092 if subDirs
-0093     path=fullfile(path,'model');
-0094     filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'});
-0095     [~,~,~]=mkdir(path);
-0096     for i = 1:length(formats)
-0097         [~,~,~]=mkdir(fullfile(path,formats{i}));
-0098     end
-0099 else
-0100     filePath=cell(1,5); filePath(:)={path};
-0101 end
-0102 
-0103 
-0104 % Write TXT format
-0105 if ismember('txt', formats)
-0106     fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w');
-0107     if COBRAtext==true
-0108         eqns=constructEquations(model,model.rxns,false,false,false);
-0109         eqns=strrep(eqns,' => ','  -> ');
-0110         eqns=strrep(eqns,' <=> ','  <=> ');
-0111         eqns=regexprep(eqns,'> $','>');
-0112         grRules=regexprep(model.grRules,'\((?!\()','( ');
-0113         grRules=regexprep(grRules,'(?<!\))\)',' )');
-0114     else
-0115         eqns=constructEquations(model,model.rxns);
-0116         grRules=model.grRules;
-0117     end
-0118     fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n');
-0119     for i = 1:numel(model.rxns)
-0120         fprintf(fid, '%s\t', model.rxns{i});
-0121         fprintf(fid, '%s \t', eqns{i});
-0122         fprintf(fid, '%s\t', grRules{i});
-0123         fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i));
-0124     end
-0125     fclose(fid);
-0126 end
-0127 
-0128 % Write YML format
-0129 if ismember('yml', formats)
-0130     writeYAMLmodel(model,fullfile(filePath{2},strcat(prefix,'.yml')));
-0131 end
-0132 
-0133 % Write MAT format
-0134 if ismember('mat', formats)
-0135     save(fullfile(filePath{3},strcat(prefix,'.mat')),'model');
-0136 end
-0137 
-0138 % Write XLSX format
-0139 if ismember('xlsx', formats)
-0140     exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx')));
-0141 end
-0142 
-0143 % Write XML format
-0144 if ismember('xml', formats)
-0145         exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),COBRAstyle);
-0146 end
-0147 
-0148 %Save file with versions:
-0149 fid = fopen(fullfile(path,'dependencies.txt'),'wt');
-0150 fprintf(fid,['MATLAB\t' version '\n']);
-0151 fprintf(fid,['libSBML\t' libSBMLver '\n']);
-0152 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']);
-0153 if ~isempty(COBRAver)
-0154     fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']);
-0155 end
-0156 if isfield(model,'modelVersion')
-0157     fields = fieldnames(model.modelVersion);
-0158     for i = 1:length(fields)
-0159         value = model.modelVersion.(fields{i});
-0160         fprintf(fid,[fields{i} '\t' num2str(value) '\n']);
-0161     end
-0162 end
-0163 fclose(fid);
-0164 end

+0071 %Get versions or commits of toolboxes:
+0072 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
+0073 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
+0074 
+0075 %Retrieve libSBML version:
+0076 [ravenDir,prevDir]=findRAVENroot();
+0077 try % 5.17.0 and newer
+0078     libSBMLver=OutputSBML_RAVEN;
+0079     libSBMLver=libSBMLver.libSBML_version_string;
+0080 catch % before 5.17.0
+0081     fid = fopen('tempModelForLibSBMLversion.xml','w+');
+0082     fclose(fid);
+0083     evalc('[~,~,libSBMLver]=TranslateSBML_RAVEN(''tempModelForLibSBMLversion.xml'',0,0)');
+0084     libSBMLver=libSBMLver.libSBML_version_string;
+0085     delete('tempModelForLibSBMLversion.xml');
+0086 end
+0087 
+0088 % Make models folder, no warnings if folder already exists
+0089 if subDirs
+0090     path=fullfile(path,'model');
+0091     filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'});
+0092     [~,~,~]=mkdir(path);
+0093     for i = 1:length(formats)
+0094         [~,~,~]=mkdir(fullfile(path,formats{i}));
+0095     end
+0096 else
+0097     filePath=cell(1,5); filePath(:)={path};
+0098 end
+0099 
+0100 
+0101 % Write TXT format
+0102 if ismember('txt', formats)
+0103     fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w');
+0104     if COBRAtext==true
+0105         eqns=constructEquations(model,model.rxns,false,false,false);
+0106         eqns=strrep(eqns,' => ','  -> ');
+0107         eqns=strrep(eqns,' <=> ','  <=> ');
+0108         eqns=regexprep(eqns,'> $','>');
+0109         grRules=regexprep(model.grRules,'\((?!\()','( ');
+0110         grRules=regexprep(grRules,'(?<!\))\)',' )');
+0111     else
+0112         eqns=constructEquations(model,model.rxns);
+0113         grRules=model.grRules;
+0114     end
+0115     fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n');
+0116     for i = 1:numel(model.rxns)
+0117         fprintf(fid, '%s\t', model.rxns{i});
+0118         fprintf(fid, '%s \t', eqns{i});
+0119         fprintf(fid, '%s\t', grRules{i});
+0120         fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i));
+0121     end
+0122     fclose(fid);
+0123 end
+0124 
+0125 % Write YML format
+0126 if ismember('yml', formats)
+0127     writeYAMLmodel(model,fullfile(filePath{2},strcat(prefix,'.yml')));
+0128 end
+0129 
+0130 % Write MAT format
+0131 if ismember('mat', formats)
+0132     save(fullfile(filePath{3},strcat(prefix,'.mat')),'model');
+0133 end
+0134 
+0135 % Write XLSX format
+0136 if ismember('xlsx', formats)
+0137     exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx')));
+0138 end
+0139 
+0140 % Write XML format
+0141 if ismember('xml', formats)
+0142         exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),neverPrefixIDs);
+0143 end
+0144 
+0145 %Save file with versions:
+0146 fid = fopen(fullfile(path,'dependencies.txt'),'wt');
+0147 fprintf(fid,['MATLAB\t' version '\n']);
+0148 fprintf(fid,['libSBML\t' libSBMLver '\n']);
+0149 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']);
+0150 if ~isempty(COBRAver)
+0151     fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']);
+0152 end
+0153 if isfield(model,'modelVersion')
+0154     fields = fieldnames(model.modelVersion);
+0155     for i = 1:length(fields)
+0156         value = model.modelVersion.(fields{i});
+0157         fprintf(fid,[fields{i} '\t' num2str(value) '\n']);
+0158     end
+0159 end
+0160 fclose(fid);
+0161 end

 
Generated by m2html © 2005

 
 
\ No newline at end of file
diff --git a/doc/io/exportModel.html b/doc/io/exportModel.html
index 34b6f359..57f67266 100644
--- a/doc/io/exportModel.html
+++ b/doc/io/exportModel.html
@@ -53,7 +53,7 @@ 
CROSS-REFERENCE INFORMATION ^
 <li><a href=checkFileExistence	checkFileExistence
  • exportModel	exportModel
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • SBMLFromExcel	SBMLFromExcel
  • exportForGit	exportForGit
  • exportModel	exportModel
    • 
 
 
 
    SUBFUNCTIONS ^
    
diff --git a/doc/io/exportToExcelFormat.html b/doc/io/exportToExcelFormat.html
index b23c701e..bbb64211 100644
--- a/doc/io/exportToExcelFormat.html
+++ b/doc/io/exportToExcelFormat.html
@@ -53,7 +53,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=exportToTabDelimited	exportToTabDelimited
  • loadWorkbook	loadWorkbook
  • sortIdentifiers	exportModel
  • writeSheet	writeSheet
    • 
 This function is called by:
 
+
  • exportForGit	exportForGit
    • 
 
 
 
diff --git a/doc/io/getToolboxVersion.html b/doc/io/getToolboxVersion.html
index 73335a08..54e1744b 100644
--- a/doc/io/getToolboxVersion.html
+++ b/doc/io/getToolboxVersion.html
@@ -49,7 +49,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • exportForGit	exportForGit
    • 
+
  • exportForGit	exportForGit
    • 
 
 
 
    SUBFUNCTIONS ^
    
diff --git a/doc/io/sortIdentifiers.html b/doc/io/sortIdentifiers.html
index 71563563..1198cb31 100644
--- a/doc/io/sortIdentifiers.html
+++ b/doc/io/sortIdentifiers.html
@@ -47,7 +47,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • exportForGit	exportForGit
  • exportModel	exportModel
  • exportToExcelFormat	exportToExcelFormat
  • exportToTabDelimited	exportToTabDelimited
  • writeYAMLmodel	writeYAMLmodel
    • 
+
  • exportForGit	exportForGit
  • exportModel	exportModel
  • exportToExcelFormat	exportToExcelFormat
  • exportToTabDelimited	exportToTabDelimited
  • writeYAMLmodel	writeYAMLmodel
    • 
 
 
 
diff --git a/doc/io/writeYAMLmodel.html b/doc/io/writeYAMLmodel.html
index 77164d47..8aafb9ee 100644
--- a/doc/io/writeYAMLmodel.html
+++ b/doc/io/writeYAMLmodel.html
@@ -49,7 +49,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=sortIdentifiers	exportModel
 This function is called by:
 
+
  • exportForGit	exportForGit
    • 
 
 
 
    SUBFUNCTIONS ^
    
diff --git a/io/exportForGit.m b/io/exportForGit.m
index d90f5b04..0f04406d 100755
--- a/io/exportForGit.m
+++ b/io/exportForGit.m
@@ -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;
@@ -142,7 +139,7 @@
 
 % 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:

From d091b89ab8da0b677d67cca7781a9e1f124852d7 Mon Sep 17 00:00:00 2001
From: Eduard Kerkhoven 
Date: Thu, 17 Oct 2024 20:10:43 +0200
Subject: [PATCH 2/5] feat: YAML I/O tests

---
 doc/installation/checkInstallation.html       | 355 +++++++++---------
 doc/testing/unit_tests/importExportTests.html |  71 ++--
 installation/checkInstallation.m              |  25 +-
 testing/unit_tests/importExportTests.m        |  21 ++
 .../test_data/importExportResults.mat         | Bin 1400 -> 2219 bytes
 tutorial/empty.mat                            | Bin 711 -> 890 bytes
 tutorial/empty.yml                            |  64 ++++
 7 files changed, 326 insertions(+), 210 deletions(-)
 create mode 100644 tutorial/empty.yml

diff --git a/doc/installation/checkInstallation.html b/doc/installation/checkInstallation.html
index 3804091d..3f5370a0 100644
--- a/doc/installation/checkInstallation.html
+++ b/doc/installation/checkInstallation.html
@@ -248,7 +248,7 @@ 
    SOURCE CODE ^end
 0180 
 0181 fprintf(myStr('   > Export Excel format',40))
-0182 if res(3).Passed == 1
+0182 if res(4).Passed == 1
 0183     fprintf('Pass\n')
 0184 else
 0185     printOrange('Fail\n')
@@ -262,186 +262,191 @@ 
    SOURCE CODE ^end
 0194 
 0195 fprintf(myStr('   > Export SBML format',40))
-0196 if res(4).Passed == 1
+0196 if res(5).Passed == 1
 0197     fprintf('Pass\n')
 0198 else
 0199     printOrange('Fail\n')
 0200 end
 0201 
-0202 %Check if it is possible to import an YAML model
-0203 % fprintf(' > Checking import of model in YAML format:\t\t\t');
-0204 % try
-0205 %     readYaml(ymlFile,true);
-0206 %     fprintf('Pass\n');
-0207 % catch
-0208 %     printOrange('Fail\n');
-0209 % end
-0210 
-0211 fprintf('\n=== Model solvers ===\n');
-0212 
-0213 %Get current solver. Set it to 'none', if it is not set
-0214 fprintf(' > Checking for LP solvers\n')
-0215 [~,res]=evalc("runtests('solverTests.m');");
-0216 
-0217 fprintf(myStr('   > glpk',40))
-0218 if res(1).Passed == 1
-0219     fprintf('Pass\n')
-0220 else
-0221     printOrange('Fail\n')
-0222 end
-0223 
-0224 fprintf(myStr('   > gurobi',40))
-0225 if res(2).Passed == 1
-0226     fprintf('Pass\n')
-0227 else
-0228     printOrange('Fail\n')
-0229 end
-0230 
-0231 fprintf(myStr('   > scip',40))
-0232 if res(3).Passed == 1
-0233     fprintf('Pass\n')
-0234 else
-0235     printOrange('Fail\n')
-0236 end
-0237 
-0238 fprintf(myStr('   > cobra',40))
-0239 if res(4).Passed == 1
-0240     fprintf('Pass\n')
-0241 else
-0242     printOrange('Fail\n')
-0243 end
-0244 fprintf(myStr(' > Set RAVEN solver',40))
-0245 try
-0246     oldSolver=getpref('RAVEN','solver');
-0247     solverIdx=find(strcmp(oldSolver,{'glpk','gurobi','scip','cobra'}));
-0248 catch
-0249     solverIdx=0;
-0250 end
-0251 % Do not change old solver if functional
-0252 if solverIdx~=0 && res(solverIdx).Passed == 1
-0253     fprintf([oldSolver '\n'])
-0254 % Order of preference: gurobi > glpk > scip > cobra
-0255 elseif res(2).Passed == 1
-0256     fprintf('gurobi\n')
-0257     setRavenSolver('gurobi');
-0258 elseif res(1).Passed == 1
-0259     fprintf('glpk\n')
-0260     setRavenSolver('glpk');
-0261 elseif res(3).Passed == 1
-0262     fprintf('scip\n')
-0263     setRavenSolver('scip');    
-0264 elseif res(4).Passed == 1
-0265     fprintf('cobra\n')
-0266     setRavenSolver('cobra');
-0267 else
-0268     fprintf('None, no functional solvers\n')
-0269     fprintf('    The glpk should always be working, check your RAVEN installation to make sure all files are present\n')
-0270 end
-0271 
-0272 fprintf('\n=== Essential binary executables ===\n');
-0273 fprintf(myStr(' > Checking BLAST+',40))
-0274 [~,res]=evalc("runtests('blastPlusTests.m');");
-0275 res=interpretResults(res);
-0276 if res==false
-0277     fprintf('   This is essential to run getBlast()\n')
-0278 end
-0279 
-0280 fprintf(myStr(' > Checking DIAMOND',40))
-0281 [~,res]=evalc("runtests('diamondTests.m');");
-0282 res=interpretResults(res);
-0283 if res==false
-0284     fprintf('   This is essential to run the getDiamond()\n')
-0285 end
-0286 
-0287 fprintf(myStr(' > Checking HMMER',40))
-0288 [~,res]=evalc("runtests('hmmerTests.m')");
-0289 res=interpretResults(res);
-0290 if res==false
-0291     fprintf(['   This is essential to run getKEGGModelFromHomology()\n'...
-0292              '   when using a FASTA file as input\n'])
-0293 end
-0294 
-0295 if developMode
-0296     fprintf('\n=== Development binary executables ===\n');
-0297     fprintf('NOTE: These binaries are only required when using KEGG FTP dump files in getKEGGModelForOrganism\n');
-0298 
-0299     fprintf(myStr(' > Checking CD-HIT',40))
-0300     [~,res]=evalc("runtests('cdhitTests.m');");
-0301     interpretResults(res);
-0302 
-0303     fprintf(myStr(' > Checking MAFFT',40))
-0304     [~,res]=evalc("runtests('mafftTests.m');");
-0305     interpretResults(res);
-0306 end
+0202 fprintf(myStr('   > Import YAML format',40))
+0203 if res(3).Passed == 1
+0204     fprintf('Pass\n')
+0205 else
+0206     printOrange('Fail\n')
+0207 end
+0208 
+0209 fprintf(myStr('   > Export YAML format',40))
+0210 if res(6).Passed == 1
+0211     fprintf('Pass\n')
+0212 else
+0213     printOrange('Fail\n')
+0214 end
+0215 
+0216 fprintf('\n=== Model solvers ===\n');
+0217 
+0218 %Get current solver. Set it to 'none', if it is not set
+0219 fprintf(' > Checking for LP solvers\n')
+0220 [~,res]=evalc("runtests('solverTests.m');");
+0221 
+0222 fprintf(myStr('   > glpk',40))
+0223 if res(1).Passed == 1
+0224     fprintf('Pass\n')
+0225 else
+0226     printOrange('Fail\n')
+0227 end
+0228 
+0229 fprintf(myStr('   > gurobi',40))
+0230 if res(2).Passed == 1
+0231     fprintf('Pass\n')
+0232 else
+0233     printOrange('Fail\n')
+0234 end
+0235 
+0236 fprintf(myStr('   > scip',40))
+0237 if res(3).Passed == 1
+0238     fprintf('Pass\n')
+0239 else
+0240     printOrange('Fail\n')
+0241 end
+0242 
+0243 fprintf(myStr('   > cobra',40))
+0244 if res(4).Passed == 1
+0245     fprintf('Pass\n')
+0246 else
+0247     printOrange('Fail\n')
+0248 end
+0249 fprintf(myStr(' > Set RAVEN solver',40))
+0250 try
+0251     oldSolver=getpref('RAVEN','solver');
+0252     solverIdx=find(strcmp(oldSolver,{'glpk','gurobi','scip','cobra'}));
+0253 catch
+0254     solverIdx=0;
+0255 end
+0256 % Do not change old solver if functional
+0257 if solverIdx~=0 && res(solverIdx).Passed == 1
+0258     fprintf([oldSolver '\n'])
+0259 % Order of preference: gurobi > glpk > scip > cobra
+0260 elseif res(2).Passed == 1
+0261     fprintf('gurobi\n')
+0262     setRavenSolver('gurobi');
+0263 elseif res(1).Passed == 1
+0264     fprintf('glpk\n')
+0265     setRavenSolver('glpk');
+0266 elseif res(3).Passed == 1
+0267     fprintf('scip\n')
+0268     setRavenSolver('scip');    
+0269 elseif res(4).Passed == 1
+0270     fprintf('cobra\n')
+0271     setRavenSolver('cobra');
+0272 else
+0273     fprintf('None, no functional solvers\n')
+0274     fprintf('    The glpk should always be working, check your RAVEN installation to make sure all files are present\n')
+0275 end
+0276 
+0277 fprintf('\n=== Essential binary executables ===\n');
+0278 fprintf(myStr(' > Checking BLAST+',40))
+0279 [~,res]=evalc("runtests('blastPlusTests.m');");
+0280 res=interpretResults(res);
+0281 if res==false
+0282     fprintf('   This is essential to run getBlast()\n')
+0283 end
+0284 
+0285 fprintf(myStr(' > Checking DIAMOND',40))
+0286 [~,res]=evalc("runtests('diamondTests.m');");
+0287 res=interpretResults(res);
+0288 if res==false
+0289     fprintf('   This is essential to run the getDiamond()\n')
+0290 end
+0291 
+0292 fprintf(myStr(' > Checking HMMER',40))
+0293 [~,res]=evalc("runtests('hmmerTests.m')");
+0294 res=interpretResults(res);
+0295 if res==false
+0296     fprintf(['   This is essential to run getKEGGModelFromHomology()\n'...
+0297              '   when using a FASTA file as input\n'])
+0298 end
+0299 
+0300 if developMode
+0301     fprintf('\n=== Development binary executables ===\n');
+0302     fprintf('NOTE: These binaries are only required when using KEGG FTP dump files in getKEGGModelForOrganism\n');
+0303 
+0304     fprintf(myStr(' > Checking CD-HIT',40))
+0305     [~,res]=evalc("runtests('cdhitTests.m');");
+0306     interpretResults(res);
 0307 
-0308 fprintf('\n=== Compatibility ===\n');
-0309 fprintf(myStr(' > Checking function uniqueness',40))
-0310 checkFunctionUniqueness();
-0311 
-0312 fprintf('\n*** checkInstallation complete ***\n\n');
-0313 end
-0314 
-0315 function res = interpretResults(results)
-0316 if results.Failed==0 && results.Incomplete==0
-0317     fprintf('Pass\n');
-0318     res=true;
-0319 else
-0320     printOrange('Fail\n')
-0321     fprintf('   Download/compile the binary and rerun checkInstallation\n');
-0322     res=false;
-0323 end
-0324 end
-0325 
-0326 function str = myStr(InputStr,len)
-0327 str=InputStr;
-0328 lenDiff = len - length(str);
-0329 if lenDiff < 0
-0330     warning('String too long');
-0331 else
-0332     str = [str blanks(lenDiff)];
-0333 end
-0334 end
-0335 
-0336 function status = makeBinaryExecutable(ravenDir)
-0337 % This function is required to run when RAVEN is downloaded as MATLAB
-0338 % Add-On, in which case the file permissions are not correctly set
-0339 if ispc
-0340     status = 0; % No need to run on Windows
-0341     return;
-0342 end
-0343 binDir = fullfile(ravenDir,'software');
-0344 
-0345 binList = {fullfile(binDir,'blast+','blastp');                      fullfile(binDir,'blast+','blastp.mac');
-0346            fullfile(binDir,'blast+','makeblastdb');                 fullfile(binDir,'blast+','makeblastdb.mac');
-0347            fullfile(binDir,'cd-hit','cd-hit');                      fullfile(binDir,'cd-hit','cd-hit.mac');
-0348            fullfile(binDir,'diamond','diamond');                    fullfile(binDir,'diamond','diamond.mac');
-0349            fullfile(binDir,'hmmer','hmmbuild');                     fullfile(binDir,'hmmer','hmmbuild.mac');
-0350            fullfile(binDir,'hmmer','hmmsearch');                    fullfile(binDir,'hmmer','hmmsearch.mac');
-0351            fullfile(binDir,'GLPKmex','glpkcc.mexa64');              fullfile(binDir,'GLPKmex','glpkcc.mexglx');                 fullfile(binDir,'GLPKmex','glpkcc.mexmaci64');              fullfile(binDir,'GLPKmex','glpkcc.mexmaca64');
-0352            fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexglx');    fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaci64');  fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaca64');
-0353            fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexa64');    fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexglx');       fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaci64');     fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaca64');
-0354            fullfile(binDir,'mafft','mafft-linux64','mafft.bat');
-0355            fullfile(binDir,'mafft','mafft-mac','mafft.bat');};
-0356 
-0357 for i=1:numel(binList)
-0358     [status,cmdout] = system(['chmod +x "' binList{i} '"']);
-0359     if status ~= 0
-0360         warning('Failed to make %s executable: %s ',binList{i},strip(cmdout))
-0361     end
-0362 end
-0363 end
-0364 
-0365 function printOrange(stringToPrint)
-0366 % printOrange
-0367 %   Duplicate of RAVEN/core/printOrange is also kept here, as this function
-0368 %   should be able to run before adding RAVEN to the MATLAB path.
-0369 try useDesktop = usejava('desktop'); catch, useDesktop = false; end
-0370 if useDesktop
-0371     fprintf(['[\b' stringToPrint,']\b'])
-0372 else
-0373     fprintf(stringToPrint)
-0374 end
-0375 end
    +0308 fprintf(myStr(' > Checking MAFFT',40)) +0309 [~,res]=evalc("runtests('mafftTests.m');"); +0310 interpretResults(res); +0311 end +0312 +0313 fprintf('\n=== Compatibility ===\n'); +0314 fprintf(myStr(' > Checking function uniqueness',40)) +0315 checkFunctionUniqueness(); +0316 +0317 fprintf('\n*** checkInstallation complete ***\n\n'); +0318 end +0319 +0320 function res = interpretResults(results) +0321 if results.Failed==0 && results.Incomplete==0 +0322 fprintf('Pass\n'); +0323 res=true; +0324 else +0325 printOrange('Fail\n') +0326 fprintf(' Download/compile the binary and rerun checkInstallation\n'); +0327 res=false; +0328 end +0329 end +0330 +0331 function str = myStr(InputStr,len) +0332 str=InputStr; +0333 lenDiff = len - length(str); +0334 if lenDiff < 0 +0335 warning('String too long'); +0336 else +0337 str = [str blanks(lenDiff)]; +0338 end +0339 end +0340 +0341 function status = makeBinaryExecutable(ravenDir) +0342 % This function is required to run when RAVEN is downloaded as MATLAB +0343 % Add-On, in which case the file permissions are not correctly set +0344 if ispc +0345 status = 0; % No need to run on Windows +0346 return; +0347 end +0348 binDir = fullfile(ravenDir,'software'); +0349 +0350 binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); +0351 fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac'); +0352 fullfile(binDir,'cd-hit','cd-hit'); fullfile(binDir,'cd-hit','cd-hit.mac'); +0353 fullfile(binDir,'diamond','diamond'); fullfile(binDir,'diamond','diamond.mac'); +0354 fullfile(binDir,'hmmer','hmmbuild'); fullfile(binDir,'hmmer','hmmbuild.mac'); +0355 fullfile(binDir,'hmmer','hmmsearch'); fullfile(binDir,'hmmer','hmmsearch.mac'); +0356 fullfile(binDir,'GLPKmex','glpkcc.mexa64'); fullfile(binDir,'GLPKmex','glpkcc.mexglx'); fullfile(binDir,'GLPKmex','glpkcc.mexmaci64'); fullfile(binDir,'GLPKmex','glpkcc.mexmaca64'); +0357 fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaca64'); +0358 fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaca64'); +0359 fullfile(binDir,'mafft','mafft-linux64','mafft.bat'); +0360 fullfile(binDir,'mafft','mafft-mac','mafft.bat');}; +0361 +0362 for i=1:numel(binList) +0363 [status,cmdout] = system(['chmod +x "' binList{i} '"']); +0364 if status ~= 0 +0365 warning('Failed to make %s executable: %s ',binList{i},strip(cmdout)) +0366 end +0367 end +0368 end +0369 +0370 function printOrange(stringToPrint) +0371 % printOrange +0372 % Duplicate of RAVEN/core/printOrange is also kept here, as this function +0373 % should be able to run before adding RAVEN to the MATLAB path. +0374 try useDesktop = usejava('desktop'); catch, useDesktop = false; end +0375 if useDesktop +0376 fprintf(['[\b' stringToPrint,']\b']) +0377 else +0378 fprintf(stringToPrint) +0379 end +0380 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/testing/unit_tests/importExportTests.html b/doc/testing/unit_tests/importExportTests.html index ed2c527e..9e9df366 100644 --- a/doc/testing/unit_tests/importExportTests.html +++ b/doc/testing/unit_tests/importExportTests.html @@ -42,7 +42,7 @@

    CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

    +
  • function testExcelImport(testCase)
  • function testSBMLImport(testCase)
  • function testYAMLimport(testCase)
  • function testExcelExport(testCase)
  • function testSBMLExport(testCase)
  • function testYAMLexport(testCase)

    • SOURCE CODE ^

    0001 %run this test case with the command
@@ -72,31 +72,52 @@ 
    SOURCE CODE ^end
 0027 
-0028 function testExcelExport(testCase)
+0028 function testYAMLimport(testCase)
 0029 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
-0030 load(fullfile(sourceDir,'testing','unit_tests','test_data','ecoli_textbook.mat'), 'model');
-0031 exportToExcelFormat(model,fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx'));
-0032 %File will not be exactly equal as it contains the current date and time,
-0033 %so md5 or similar would not work. Just check whether file is reasonably
-0034 %sized.
-0035 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx'));         
-0036 filesize = s.bytes;
-0037 verifyTrue(testCase,filesize>17000);
-0038 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx'));
-0039 end
-0040 
-0041 function testSBMLExport(testCase)
-0042 sourceDir=fileparts(fileparts(fileparts(which(mfilename))));
-0043 load(fullfile(sourceDir,'testing','unit_tests','test_data','ecoli_textbook.mat'), 'model');
-0044 evalc('exportModel(model,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.xml''))');
-0045 %File will not be exactly equal as it contains the current date and time,
-0046 %so md5 or similar would not work. Just check whether file is reasonably
-0047 %sized.
-0048 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xml'));         
-0049 filesize = s.bytes;
-0050 verifyTrue(testCase,filesize>18500);
-0051 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xml'));
-0052 end
    +0030 yamlFile=fullfile(sourceDir,'tutorial','empty.yml'); +0031 evalc('model=readYAMLmodel(yamlFile)'); % Repress warnings +0032 load(fullfile(sourceDir,'testing','unit_tests','test_data','importExportResults.mat'), 'modelYAML'); +0033 verifyEqual(testCase,model,modelYAML) +0034 end +0035 +0036 function testExcelExport(testCase) +0037 sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); +0038 load(fullfile(sourceDir,'testing','unit_tests','test_data','ecoli_textbook.mat'), 'model'); +0039 exportToExcelFormat(model,fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx')); +0040 %File will not be exactly equal as it contains the current date and time, +0041 %so md5 or similar would not work. Just check whether file is reasonably +0042 %sized. +0043 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx')); +0044 filesize = s.bytes; +0045 verifyTrue(testCase,filesize>17000); +0046 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xlsx')); +0047 end +0048 +0049 function testSBMLExport(testCase) +0050 sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); +0051 load(fullfile(sourceDir,'testing','unit_tests','test_data','ecoli_textbook.mat'), 'model'); +0052 evalc('exportModel(model,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.xml''))'); +0053 %File will not be exactly equal as it contains the current date and time, +0054 %so md5 or similar would not work. Just check whether file is reasonably +0055 %sized. +0056 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xml')); +0057 filesize = s.bytes; +0058 verifyTrue(testCase,filesize>18500); +0059 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xml')); +0060 end +0061 +0062 function testYAMLexport(testCase) +0063 sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); +0064 load(fullfile(sourceDir,'tutorial','empty.mat'), 'emptyModel'); +0065 evalc('writeYAMLmodel(emptyModel,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.yml''))'); +0066 %File will not be exactly equal as it contains the current date and time, +0067 %so md5 or similar would not work. Just check whether file is reasonably +0068 %sized. +0069 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); +0070 filesize = s.bytes; +0071 verifyTrue(testCase,filesize>1350); +0072 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); +0073 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/installation/checkInstallation.m b/installation/checkInstallation.m index 68b73601..4a1784fa 100755 --- a/installation/checkInstallation.m +++ b/installation/checkInstallation.m @@ -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'); diff --git a/testing/unit_tests/importExportTests.m b/testing/unit_tests/importExportTests.m index f50cb79b..92165374 100755 --- a/testing/unit_tests/importExportTests.m +++ b/testing/unit_tests/importExportTests.m @@ -25,6 +25,14 @@ function testSBMLImport(testCase) verifyEqual(testCase,model,modelSBML) end +function testYAMLimport(testCase) +sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); +yamlFile=fullfile(sourceDir,'tutorial','empty.yml'); +evalc('model=readYAMLmodel(yamlFile)'); % Repress warnings +load(fullfile(sourceDir,'testing','unit_tests','test_data','importExportResults.mat'), 'modelYAML'); +verifyEqual(testCase,model,modelYAML) +end + function testExcelExport(testCase) sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); load(fullfile(sourceDir,'testing','unit_tests','test_data','ecoli_textbook.mat'), 'model'); @@ -50,3 +58,16 @@ function testSBMLExport(testCase) verifyTrue(testCase,filesize>18500); delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.xml')); end + +function testYAMLexport(testCase) +sourceDir=fileparts(fileparts(fileparts(which(mfilename)))); +load(fullfile(sourceDir,'tutorial','empty.mat'), 'emptyModel'); +evalc('writeYAMLmodel(emptyModel,fullfile(sourceDir,''testing'',''unit_tests'',''test_data'',''_test.yml''))'); +%File will not be exactly equal as it contains the current date and time, +%so md5 or similar would not work. Just check whether file is reasonably +%sized. +s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); +filesize = s.bytes; +verifyTrue(testCase,filesize>1350); +delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); +end \ No newline at end of file diff --git a/testing/unit_tests/test_data/importExportResults.mat b/testing/unit_tests/test_data/importExportResults.mat index 0a5df5ef1977e6c2d780509b52c8d408c8d71bf9..83f86ac8cbb213413f9c9f4229228d3f86a94e76 100644 GIT binary patch delta 833 zcmV-H1HSzD3ab&Ycm;nC0000h0{{ScoZVN=Qrj>PmJ^3UJEiHNhaTF|kse^MVQ6na zGL#(n=>Y9aZ@98ZJh7!zmPz2$L!Y7Nz6r0;$LNtqs1(aYHUT>>NoT5wV}Fvq-PLNn zS}y_sem)0aPTc3kRRM9UDQsxhg17?eV*m5@{@%?z6FgJneer+ixj=8k39trT93tlR zxJQYE=a_}+aX9L5eX>Ic1b zZh9_gV}dosZFUs-qYh!@u9&dz@WiSn4SJf*?BGZAd|F4N}o@hcdM;oH1)r zT<^eWA5GP-?_+;W-DRsQjDsG(Q2bU7|3!u`@s8xfVN}47vk38sVI^<%9(hUA<$=HC zZRObiIKz|JUbWYkt<`1g?MMzZioFkUzj-6~wYWscsu*_hnG^YZuaP``Y$*93a_oGS zu~T9ZC@=~!^a$h~43D-y?Hs^9W!}Imt%KDJxzbgGX?W^HRhdaJR^sfx37ls z^=RD{z^s_}Z9+YH{)HL;O59-B>AJK}AU%U&gcudhUh;@YQQQgf8!30*xZ4i%0oEH> zC3$v9-daiC`tA3mh(Gf3)1%D3NUXM^G{5afs3?Cv!rZgd-h@Yw{eigLr!=c`R z#;et1?p=R=s)12XOMG7i>HH@-@+^iRY1dckzL~jS{foRX3w@Gj6yRn3TTweVi~QBL zW~)cfdos?9d-T+lWIe8u8gF#YUT>E1uOXV`ElrpowsO|JkXm<)o0i?O?L*7b z+Y^Pq16gLHF5UCm9j&GWk-twf=?5{p-;4=(PRJ#?&cA^7TuluQQ>2WzOx8JH&OEJB@f> z%;-6j_@v{7Q2ZPyVuDX+o#XP3wPLTVt*rl7=UK00e7Rsc_L)Gp&ji~i&D}Eg{TQRK LXr1#1sfOI`>Z7dS delta 7 OcmZ22_=9Uh1uFmz9|G(E diff --git a/tutorial/empty.mat b/tutorial/empty.mat index 9529981fa53a9e84b643da7dd8c9180df38836be..936aead10021aa4ba5d135f22d305238eecc2904 100644 GIT binary patch delta 770 zcmV+d1O5ER1^Nb%gn#k^004NL-B!N>yJzwi6`Z@x_cz;z3N z4N*5lF+pl|g$=Dd76nIRetAee9M1b$;F)UwEdBxy=tkTKYk$xsgmRY$l*}NTl2~hv zFxTNp#uEs?WMGno3}5IFWx3hD0MTe1XW@|$s$L0I8j`T1^&hh1BwRGg)&orNq07@& z@vM24@WiK#rw+vcbRu{z>0k3w^Q{`vK3#^|3(L%bYHW#f-ru#xNj| z`xqYYf9f8=31y?$r(@-Jp!qeH_|^5v{;vykm>C@=V0OxD7`MlRvV-KhF)u7AGC>)u$RTaRz5r?NatFn`v{ z^Qy*^JYxl3etu20a_cw`djFPqn%@iKl5zG5;ylg7Nim*s<{})1;@V`&&vnVTMfVQO z#g+IS!|uqV69VZOj1$DDxP-O>a)B9lWBlqa>pCc@zwG%O+JBE*o=@W+aq7ymeja68 zQ^WH7J%6PBhl&GB-s?r*=SLvBpCndWs4{;TCTLZDBgdEcOn%aZgH`6Kmf_bx&*@jX zj|^dww^ed}_X_kibK{e^V>>;^>D#vEr^-Bcc6+wd-@O-p)p`D5mCLuDDEt*<5>zew z9wC*#ij7DUhSHo}=4Pq~Mo6T7v7&X!)hyw~~WvKy~JhL87xi4u;e-?_Br?X-q>Adj9tHCYz@XPbeEOQ zH`pQlC3KO__4h+L7Rhp*$KIIvFYq%PGupB!6$D0ECUvA|GJm^+YLVq+HWiw}6HAFD z-z-?zP>D+lW1DNQWwA`>xebrNsCfmh2tqg@>nG~CNbVt&^fCo~gMG_H(b?6`1@A`P=J*|&#Mr?h9@9Jdu!y5iZg^ze2`8>r!^IWSU z)`b#A@0zXly?>PNy?cK+LjA>ZUteo{ZB~3Ch79o{7krj+Jr(@;)9L;Zzmn=ApUSz> zJtMl#1G>~7uHUZl;aWairh<~!bsmr7Jwco_Xvqs(^4_)Ny)StS!t?tj_pyBVtgI;` znjNy98BPy6XUq2M#*7~;<4x7~+5^66eAhfR<$1vT*?(!yYa0)F&I-J0eqB?!|8XAZ z`aV1@?}d58IJ-4*UR!ZWEEZZtu}BiQCY90o(J*e^y~8VU5$`DxU5w>b#^pKBi&#mx zgtlhcrBFJ`#oK?W>sdqpP0!~f_;cTQKApeB@r^P)k2u#O7|-8x`hTuCyy3lG_y7EY z+20dl^G6A_=1-C$UX|ai@DZQmUpfe^lBbTv@33JwYIPqu(2%#)Fu%Js{(6=DAsz(b cFbqdQKy=#Vd9X7K!qLu?@Z0417S{Td&1qpV(EtDd diff --git a/tutorial/empty.yml b/tutorial/empty.yml new file mode 100644 index 00000000..aa0e9684 --- /dev/null +++ b/tutorial/empty.yml @@ -0,0 +1,64 @@ +--- +!!omap +- metaData: + id: "empty" + name: "Empty model structure" + date: "2024-10-17" + note: "For use in the RAVEN workshop" + geckoLight: "false" +- metabolites: + - !!omap + - id: "m1" + - name: "sucrose" + - compartment: "e" + - formula: "C12H22O11" + - !!omap + - id: "m2" + - name: "glucose" + - compartment: "e" + - formula: "C6H12O6" + - !!omap + - id: "m3" + - name: "fructose" + - compartment: "e" + - formula: "C6H12O6" + - !!omap + - id: "m4" + - name: "H2O" + - compartment: "e" + - formula: "H2O" +- reactions: + - !!omap + - id: "r1" + - name: "Breakdown of sucrose (invertase)" + - metabolites: !!omap + - m1: -1 + - m2: 1 + - m3: 1 + - m4: -1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "g1" + - objective_coefficient: 1 +- genes: + - !!omap + - id: "g1" + - name: "g1" +- compartments: !!omap + - e: "extracellular" +- ec-rxns: + - !!omap + - id: "r1" + - kcat: 25 + - source: "standard" + - notes: "This is a test" + - eccodes: "1.2.3.4" + - enzymes: !!omap + - p1: 1 +- ec-enzymes: + - !!omap + - genes: "g1" + - enzymes: "p1" + - mw: 100 + - sequence: "ATCG" + - concs: 150 From 0e45b13ed19d568cc1122bb96931bcc9b03d2eec Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 17 Oct 2024 20:11:04 +0200 Subject: [PATCH 3/5] fix: exportForGit do not test COBRA if not exist --- doc/io/exportForGit.html | 180 ++++++++++++++++++++------------------- io/exportForGit.m | 4 +- 2 files changed, 94 insertions(+), 90 deletions(-) diff --git a/doc/io/exportForGit.html b/doc/io/exportForGit.html index f833f5d1..df04c927 100644 --- a/doc/io/exportForGit.html +++ b/doc/io/exportForGit.html @@ -147,95 +147,97 @@

    SOURCE CODE ^%Get versions or commits of toolboxes: 0072 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag); -0073 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag); -0074 -0075 %Retrieve libSBML version: -0076 [ravenDir,prevDir]=findRAVENroot(); -0077 try % 5.17.0 and newer -0078 libSBMLver=OutputSBML_RAVEN; -0079 libSBMLver=libSBMLver.libSBML_version_string; -0080 catch % before 5.17.0 -0081 fid = fopen('tempModelForLibSBMLversion.xml','w+'); -0082 fclose(fid); -0083 evalc('[~,~,libSBMLver]=TranslateSBML_RAVEN(''tempModelForLibSBMLversion.xml'',0,0)'); -0084 libSBMLver=libSBMLver.libSBML_version_string; -0085 delete('tempModelForLibSBMLversion.xml'); -0086 end -0087 -0088 % Make models folder, no warnings if folder already exists -0089 if subDirs -0090 path=fullfile(path,'model'); -0091 filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'}); -0092 [~,~,~]=mkdir(path); -0093 for i = 1:length(formats) -0094 [~,~,~]=mkdir(fullfile(path,formats{i})); -0095 end -0096 else -0097 filePath=cell(1,5); filePath(:)={path}; -0098 end -0099 -0100 -0101 % Write TXT format -0102 if ismember('txt', formats) -0103 fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w'); -0104 if COBRAtext==true -0105 eqns=constructEquations(model,model.rxns,false,false,false); -0106 eqns=strrep(eqns,' => ',' -> '); -0107 eqns=strrep(eqns,' <=> ',' <=> '); -0108 eqns=regexprep(eqns,'> $','>'); -0109 grRules=regexprep(model.grRules,'\((?!\()','( '); -0110 grRules=regexprep(grRules,'(?<!\))\)',' )'); -0111 else -0112 eqns=constructEquations(model,model.rxns); -0113 grRules=model.grRules; -0114 end -0115 fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n'); -0116 for i = 1:numel(model.rxns) -0117 fprintf(fid, '%s\t', model.rxns{i}); -0118 fprintf(fid, '%s \t', eqns{i}); -0119 fprintf(fid, '%s\t', grRules{i}); -0120 fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i)); -0121 end -0122 fclose(fid); -0123 end -0124 -0125 % Write YML format -0126 if ismember('yml', formats) -0127 writeYAMLmodel(model,fullfile(filePath{2},strcat(prefix,'.yml'))); -0128 end -0129 -0130 % Write MAT format -0131 if ismember('mat', formats) -0132 save(fullfile(filePath{3},strcat(prefix,'.mat')),'model'); -0133 end -0134 -0135 % Write XLSX format -0136 if ismember('xlsx', formats) -0137 exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx'))); -0138 end -0139 -0140 % Write XML format -0141 if ismember('xml', formats) -0142 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),neverPrefixIDs); -0143 end -0144 -0145 %Save file with versions: -0146 fid = fopen(fullfile(path,'dependencies.txt'),'wt'); -0147 fprintf(fid,['MATLAB\t' version '\n']); -0148 fprintf(fid,['libSBML\t' libSBMLver '\n']); -0149 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']); -0150 if ~isempty(COBRAver) -0151 fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']); -0152 end -0153 if isfield(model,'modelVersion') -0154 fields = fieldnames(model.modelVersion); -0155 for i = 1:length(fields) -0156 value = model.modelVersion.(fields{i}); -0157 fprintf(fid,[fields{i} '\t' num2str(value) '\n']); -0158 end -0159 end -0160 fclose(fid); -0161 end +0073 if exist('initCobraToolbox.m','file') +0074 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag); +0075 end +0076 +0077 %Retrieve libSBML version: +0078 [ravenDir,prevDir]=findRAVENroot(); +0079 try % 5.17.0 and newer +0080 libSBMLver=OutputSBML_RAVEN; +0081 libSBMLver=libSBMLver.libSBML_version_string; +0082 catch % before 5.17.0 +0083 fid = fopen('tempModelForLibSBMLversion.xml','w+'); +0084 fclose(fid); +0085 evalc('[~,~,libSBMLver]=TranslateSBML_RAVEN(''tempModelForLibSBMLversion.xml'',0,0)'); +0086 libSBMLver=libSBMLver.libSBML_version_string; +0087 delete('tempModelForLibSBMLversion.xml'); +0088 end +0089 +0090 % Make models folder, no warnings if folder already exists +0091 if subDirs +0092 path=fullfile(path,'model'); +0093 filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'}); +0094 [~,~,~]=mkdir(path); +0095 for i = 1:length(formats) +0096 [~,~,~]=mkdir(fullfile(path,formats{i})); +0097 end +0098 else +0099 filePath=cell(1,5); filePath(:)={path}; +0100 end +0101 +0102 +0103 % Write TXT format +0104 if ismember('txt', formats) +0105 fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w'); +0106 if COBRAtext==true +0107 eqns=constructEquations(model,model.rxns,false,false,false); +0108 eqns=strrep(eqns,' => ',' -> '); +0109 eqns=strrep(eqns,' <=> ',' <=> '); +0110 eqns=regexprep(eqns,'> $','>'); +0111 grRules=regexprep(model.grRules,'\((?!\()','( '); +0112 grRules=regexprep(grRules,'(?<!\))\)',' )'); +0113 else +0114 eqns=constructEquations(model,model.rxns); +0115 grRules=model.grRules; +0116 end +0117 fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n'); +0118 for i = 1:numel(model.rxns) +0119 fprintf(fid, '%s\t', model.rxns{i}); +0120 fprintf(fid, '%s \t', eqns{i}); +0121 fprintf(fid, '%s\t', grRules{i}); +0122 fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i)); +0123 end +0124 fclose(fid); +0125 end +0126 +0127 % Write YML format +0128 if ismember('yml', formats) +0129 writeYAMLmodel(model,fullfile(filePath{2},strcat(prefix,'.yml'))); +0130 end +0131 +0132 % Write MAT format +0133 if ismember('mat', formats) +0134 save(fullfile(filePath{3},strcat(prefix,'.mat')),'model'); +0135 end +0136 +0137 % Write XLSX format +0138 if ismember('xlsx', formats) +0139 exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx'))); +0140 end +0141 +0142 % Write XML format +0143 if ismember('xml', formats) +0144 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),neverPrefixIDs); +0145 end +0146 +0147 %Save file with versions: +0148 fid = fopen(fullfile(path,'dependencies.txt'),'wt'); +0149 fprintf(fid,['MATLAB\t' version '\n']); +0150 fprintf(fid,['libSBML\t' libSBMLver '\n']); +0151 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']); +0152 if ~isempty(COBRAver) +0153 fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']); +0154 end +0155 if isfield(model,'modelVersion') +0156 fields = fieldnames(model.modelVersion); +0157 for i = 1:length(fields) +0158 value = model.modelVersion.(fields{i}); +0159 fprintf(fid,[fields{i} '\t' num2str(value) '\n']); +0160 end +0161 end +0162 fclose(fid); +0163 end
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    \ No newline at end of file diff --git a/io/exportForGit.m b/io/exportForGit.m index 0f04406d..ad5ea1a4 100755 --- a/io/exportForGit.m +++ b/io/exportForGit.m @@ -70,7 +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(); From 58f4ef2fde45e1670a6eda046907d06c743277d3 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 17 Oct 2024 20:12:46 +0200 Subject: [PATCH 4/5] fix: readYAMLmodel correct rxnEnzMat --- doc/io/readYAMLmodel.html | 2 +- io/readYAMLmodel.m | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/io/readYAMLmodel.html b/doc/io/readYAMLmodel.html index a76b6b12..348b94b7 100644 --- a/doc/io/readYAMLmodel.html +++ b/doc/io/readYAMLmodel.html @@ -682,7 +682,7 @@

    SOURCE CODE ^%Parse ec-codes 0631 if ~isempty(ecGecko) diff --git a/io/readYAMLmodel.m b/io/readYAMLmodel.m index 19095d6c..dd5e692f 100755 --- a/io/readYAMLmodel.m +++ b/io/readYAMLmodel.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) From 7a52e32afa8c1a795210612c75780b4bde3b1fc5 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 17 Oct 2024 23:33:22 +0200 Subject: [PATCH 5/5] fix: importExportTests less strict filesize test --- doc/testing/unit_tests/importExportTests.html | 2 +- testing/unit_tests/importExportTests.m | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/testing/unit_tests/importExportTests.html b/doc/testing/unit_tests/importExportTests.html index 9e9df366..6e32b08f 100644 --- a/doc/testing/unit_tests/importExportTests.html +++ b/doc/testing/unit_tests/importExportTests.html @@ -115,7 +115,7 @@

    SOURCE CODE ^%sized. 0069 s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); 0070 filesize = s.bytes; -0071 verifyTrue(testCase,filesize>1350); +0071 verifyTrue(testCase,filesize>1290); 0072 delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); 0073 end
    Generated by m2html © 2005
    diff --git a/testing/unit_tests/importExportTests.m b/testing/unit_tests/importExportTests.m index 92165374..4db6eb9f 100755 --- a/testing/unit_tests/importExportTests.m +++ b/testing/unit_tests/importExportTests.m @@ -68,6 +68,6 @@ function testYAMLexport(testCase) %sized. s = dir(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); filesize = s.bytes; -verifyTrue(testCase,filesize>1350); +verifyTrue(testCase,filesize>1290); delete(fullfile(sourceDir,'testing','unit_tests','test_data','_test.yml')); end \ No newline at end of file