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fix: read compartment annotations in readYAMLmodel #676

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Merged
edkerk merged 1 commit into from
Jul 17, 2026
Merged

fix: read compartment annotations in readYAMLmodel #676

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29 changes: 26 additions & 3 deletions io/readYAMLmodel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@
'comps',cell(0,0);...
'compNames',cell(0,0);...
'compOutside',cell(0,0);...
'compMiriams',cell(0,0);...
'geneComps',cell(0,0);... %Changed to double in the end.
'geneMiriams',cell(0,0);...
'geneShortNames',cell(0,0);...
Expand Down Expand Up @@ -146,6 +147,7 @@
metMiriams=cell(100000,3); metMirNo=1;
rxnMiriams=cell(100000,3); rxnMirNo=1;
geneMiriams=cell(100000,3); genMirNo=1;
compMiriams=cell(1000,3); compMirNo=1;
subSystems=cell(100000,2); subSysNo=1;
eccodes=cell(100000,2); ecCodeNo=1;
equations=cell(100000,3); equatiNo=1;
Expand Down Expand Up @@ -447,8 +449,22 @@

% import compartments:
if section == 5
model.comps(end+1,1) = {tline_key};
model.compNames(end+1,1) = {tline_value};
switch tline_key
case 'annotation'
readList = 'annotation';
otherwise
% Annotation entries are indented deeper than the
% compartment they belong to, so anything at compartment
% level ends the annotation and starts a new compartment.
if strcmp(readList,'annotation') && ~isempty(regexp(tline_raw,'^ {6,}','once'))
[compMiriams, miriamKey, compMirNo] = gatherAnnotation(pos,compMiriams,tline_key,tline_value,miriamKey,compMirNo);
else
pos = pos + 1;
model.comps(end+1,1) = {tline_key};
model.compNames(end+1,1) = {tline_value};
readList = ''; miriamKey = '';
end
end; continue
end

% import ec reaction info
Expand Down Expand Up @@ -533,6 +549,13 @@
model.geneMiriams{i,1}.value=geneMiriams(locs==i,3);
end
end
if ~isempty(compMiriams)
locs = cell2mat(compMiriams(:,1));
for i=unique(locs)'
model.compMiriams{i,1}.name=compMiriams(locs==i,2);
model.compMiriams{i,1}.value=compMiriams(locs==i,3);
end
end

%Parse subSystems
if ~isempty(subSystems)
Expand Down Expand Up @@ -634,7 +657,7 @@
model = emptyOrFill(model,i{1},1,'genes');
end
% Comps
for i={'compNames'} % Empty strings
for i={'compNames','compMiriams'} % Empty strings
model = emptyOrFill(model,i{1},{''},'comps');
end
for i={'compOutside'} % First comp
Expand Down
17 changes: 17 additions & 0 deletions testing/function_tests/tIO.m
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,23 @@ function writeReadYAMLRoundTrip(testCase)
testCase.verifyEqual(numel(m2.rxns), numel(testCase.model.rxns));
end

function writeReadYAMLPreservesCompartmentAnnotations(testCase)
% Compartment annotations must round-trip, and must not be read
% back as additional compartments.
m = testCase.model;
m.compMiriams = cell(numel(m.comps),1);
m.compMiriams{1}.name = {'go'};
m.compMiriams{1}.value = {'GO:0005737'};
f = [tempname '.yml'];
testCase.addTeardown(@() delete(f));
evalc('writeYAMLmodel(m, f);');
evalc('m2 = readYAMLmodel(f);');
testCase.verifyEqual(m2.comps, m.comps);
testCase.verifyEqual(m2.compNames, m.compNames);
testCase.verifyEqual(m2.compMiriams{1}.name, {'go'});
testCase.verifyEqual(m2.compMiriams{1}.value, {'GO:0005737'});
end

function exportToTabDelimitedWritesFiles(testCase)
d = [tempname filesep];
mkdir(d);
Expand Down