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fix-add a error report in the import/export cycle #629

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merged 5 commits into from
Jun 16, 2023
Merged

fix-add a error report in the import/export cycle #629

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bfbdd68
fix-add a error report in the import/export cycle
feiranl Jun 12, 2023
182010d
refactor: optimise subsystem reading code
haowang-bioinfo Jun 12, 2023
21f74fb
refactor: simply the extraction of subSystem value
haowang-bioinfo Jun 12, 2023
0cac965
test: revert back testYamlConversion to the original
haowang-bioinfo Jun 13, 2023
e5ee114
fix: typos introduced in #606
haowang-bioinfo Jun 13, 2023
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12 changes: 4 additions & 8 deletions code/io/importYaml.m
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Original file line number Diff line number Diff line change
Expand Up @@ -120,10 +120,6 @@
if ~silentMode
fprintf('\t%d\n', section);
end
if readSubsystems
model.subSystems(end+1,1) = {subSystems}; %last entry from section 3
readSubsystems = false;
end
continue
case '- compartments: !!omap'
section = 5;
Expand Down Expand Up @@ -218,15 +214,15 @@

case 'confidence_score'
model = readFieldValue(model, 'rxnConfidenceScores', tline_value);
if readSubsystems
model.subSystems(end+1,1) = {subSystems};
readSubsystems = false;
end

case 'metabolites'
readEquation = true;
leftEquation = '';
rightEquation = '';
if readSubsystems
model.subSystems(end+1,1) = {subSystems};
readSubsystems = false;
end

otherwise
if readSubsystems
Expand Down
8 changes: 6 additions & 2 deletions code/test/testYamlConversion.m
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Expand Up @@ -22,8 +22,12 @@


% export to yml and then import back
exportYaml(model,'testYamlConversion.yml');
importedHumanGEM = importYaml('testYamlConversion.yml', true);
try
exportYaml(model,'testYamlConversion.yml');
importedHumanGEM = importYaml('testYamlConversion.yml', true);
catch
error('There are problems during the conversion import and export');
end

% remove intermediate Yaml file
delete testYamlConversion.yml;
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4 changes: 2 additions & 2 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -307292,8 +307292,8 @@
- !!omap
- id: "MAR20111"
- name: "MAR20111"
- metabolties: !!omap
- MAM1261m: -1
- metabolites: !!omap
- MAM01261m: -1
- MAM01597m: 1
- MAM02007m: -1
- MAM02040m: -1
Expand Down