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fix: read notes maps in readYAMLmodel #12

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Merged
edkerk merged 2 commits into from
Oct 23, 2026
Merged

fix: read notes maps in readYAMLmodel #12

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3815400
fix: readYAMLmodel reads notes maps into the note text
edkerk Oct 19, 2026
0d81bf1
fix: read notes-map lines by indentation, not by key
edkerk Oct 23, 2026
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72 changes: 68 additions & 4 deletions src/io/readYAMLmodel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -195,6 +195,7 @@
end

section = 0;
readList = '';
metMiriams=cell(100000,3); metMirNo=1;
rxnMiriams=cell(100000,3); rxnMirNo=1;
geneMiriams=cell(100000,3); genMirNo=1;
Expand Down Expand Up @@ -346,6 +347,12 @@

% import metabolites:
if section == 2
% The lines of a notes map are indented below the entry's own
% fields; their keys are not entry fields, whatever their name.
if strcmp(readList, 'notes') && ~isempty(regexp(tline_raw, '^ {6,}', 'once'))
model = appendNote(model, 'metNotes', tline_raw, tline_key, tline_value, pos);
continue
end
switch tline_key
case 'id'
pos = pos + 1;
Expand All @@ -364,8 +371,14 @@
model = readFieldValue(model, 'metCharges', tline_value, pos);
readList=''; miriamKey='';
case 'notes'
model = readFieldValue(model, 'metNotes', tline_value, pos);
readList=''; miriamKey='';
% A notes map (other tools' keys, as cobrapy and
% raven-toolbox write them) is read into the note text.
if isempty(tline_value) || strcmp(tline_value, '!!omap')
readList = 'notes';
else
model = readFieldValue(model, 'metNotes', tline_value, pos);
readList=''; miriamKey='';
end
case 'inchis'
model = readFieldValue(model, 'inchis', tline_value, pos);
readList=''; miriamKey='';
Expand Down Expand Up @@ -421,6 +434,12 @@

% import reactions:
if section == 3
% The lines of a notes map are indented below the entry's own
% fields; their keys are not entry fields, whatever their name.
if strcmp(readList, 'notes') && ~isempty(regexp(tline_raw, '^ {6,}', 'once'))
model = appendNote(model, 'rxnNotes', tline_raw, tline_key, tline_value, pos);
continue
end
switch tline_key
case 'id'
pos = pos + 1;
Expand All @@ -445,8 +464,12 @@
% `notes` is the canonical reaction-side key; `rxnNotes`
% is the legacy RAVEN MATLAB key, kept here for
% backward-compatible reads.
model = readFieldValue(model, 'rxnNotes', tline_value, pos);
readList=''; miriamKey='';
if isempty(tline_value) || strcmp(tline_value, '!!omap')
readList = 'notes';
else
model = readFieldValue(model, 'rxnNotes', tline_value, pos);
readList=''; miriamKey='';
end
case 'rxnFrom'
model = readFieldValue(model, 'rxnFrom', tline_value, pos);
readList=''; miriamKey='';
Expand Down Expand Up @@ -878,6 +901,47 @@
model.(fieldName)(pos,1) = {value};
end

function model = appendNote(model, fieldName, raw, key, value, pos)
% One line of a notes map: a 'note' entry adds its value (RAVEN's own note
% text), another entry adds 'key: value', a list item adds its value to the
% entry above it. Entries are separated by '; ', list items by ', '. A
% quoted list item is read whole, as the key detection would split it at
% a ': ' inside the quotes.
item = regexp(raw, '^ +- ([''"])(.*)\1$', 'tokens', 'once');
if ~isempty(item)
key = '';
value = item{2};
end
if strcmp(value, '!!omap')
value = '';
end
text = '';
if numel(model.(fieldName)) >= pos
text = model.(fieldName){pos};
end
if isempty(key)
if isempty(text) || endsWith(text, ':')
text = strtrim([text ' ' value]);
else
text = [text ', ' value];
end
else
if isempty(value)
entry = [key ':'];
elseif strcmp(key, 'note')
entry = value;
else
entry = [key ': ' value];
end
if isempty(text)
text = entry;
else
text = [text '; ' entry];
end
end
model = readFieldValue(model, fieldName, text, pos);
end

function [miriams,miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)
if isempty(key)
key=miriamKey;
Expand Down
39 changes: 39 additions & 0 deletions tests/function_tests/tIO.m
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Original file line number Diff line number Diff line change
Expand Up @@ -294,6 +294,45 @@ function writeReadYAMLPreservesUnknownAnnotationFields(testCase)
testCase.verifyEqual(m2.annotation.geckopyVersion, '0.2.1');
end

function readYAMLmodelReadsNotesMaps(testCase)
% cobrapy and raven-toolbox write other tools' notes as a map
% under "notes"; its entries are read into the note text.
m = testCase.model;
m.metNotes = repmat({''}, numel(m.mets), 1);
m.rxnNotes = repmat({''}, numel(m.rxns), 1);
m.metNotes{1} = 'METPLACEHOLDER';
m.rxnNotes{1} = 'RXNPLACEHOLDER';
f = [tempname '.yml'];
testCase.addTeardown(@() delete(f));
evalc('writeYAMLmodel(m, f);');
txt = fileread(f);
% The metabolite's map has a key named like an entry field and a
% quoted list item with ': ', and is followed by an annotation.
txt = regexprep(txt, '( *)- notes: METPLACEHOLDER', ...
['$1- notes: !!omap\n$1 - enzyme_usage: Enzyme-usage pseudometabolite\n' ...
'$1 - name: other\n$1 - refs:\n$1 - "PMID: 1"\n$1 - b\n' ...
'$1- annotation: !!omap\n$1 - sbo: SBO:0000252']);
% The reaction's map comes before other fields, has keys named
% like entry fields and a list value.
txt = regexprep(txt, '( *)- notes: RXNPLACEHOLDER', ...
['$1- notes: !!omap\n$1 - geckopy_warning: no match for g1\n$1 - id: R99\n' ...
'$1 - name: other\n$1 - refs:\n$1 - a\n$1 - b\n$1 - note: curated\n' ...
'$1- rxnFrom: test']);
fid = fopen(f, 'w'); fwrite(fid, txt); fclose(fid);
evalc('m2 = readYAMLmodel(f);');
testCase.verifyEqual(m2.metNotes{1}, ...
'enzyme_usage: Enzyme-usage pseudometabolite; name: other; refs: PMID: 1, b');
testCase.verifyEqual(m2.metNames, m.metNames);
testCase.verifyTrue(any(strcmp(m2.metMiriams{1}.name, 'sbo')));
testCase.verifyEqual(m2.rxnNotes{1}, ...
'geckopy_warning: no match for g1; id: R99; name: other; refs: a, b; curated');
testCase.verifyEqual(m2.rxns, m.rxns);
testCase.verifyEqual(m2.rxnNames, m.rxnNames);
testCase.verifyEqual(m2.rxnFrom{1}, 'test');
testCase.verifyEqual(numel(m2.mets), numel(m.mets));
testCase.verifyEqual(numel(m2.rxns), numel(m.rxns));
end

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