fix: require matching metabolite support in curateModelFromTables

curation/curateModelFromTables.m

@@ -258,8 +258,15 @@
         rxnsToAdd.stoichCoeffs{i}=cell2mat(rxnsToAdd.stoichCoeffs{i});
         %Check if the reaction not already exists, by stoichiometry of its
         %products and reactants
-        modelCoeffs         = transpose(newModel.S(getIndexes(newModel,rxnsToAdd.mets{i},'mets'),:));
+        metIdx              = getIndexes(newModel,rxnsToAdd.mets{i},'mets');
+        modelCoeffs         = transpose(newModel.S(metIdx,:));
         modelCoeffs2        = find(~all(modelCoeffs==0,2));
+        % Only reactions built from exactly these metabolites can be
+        % duplicates. Any model reaction that also involves other
+        % metabolites projects onto the same row of coefficients, but is a
+        % different reaction and must not be overwritten.
+        sameSupport         = full(sum(newModel.S(:,modelCoeffs2)~=0,1))' == numel(metIdx);
+        modelCoeffs2        = modelCoeffs2(sameSupport);
         modelCoeffs         = modelCoeffs(modelCoeffs2,:);
         [~, duplicateRxn]   = intersect(modelCoeffs,rxnsToAdd.stoichCoeffs{i},'rows');
         if ~isempty(duplicateRxn)

testing/function_tests/tCuration.m

@@ -1,12 +1,95 @@
 classdef tCuration < RavenTestCase
 % tCuration  Tests for the table-driven curation functions in curation/.
+%
+%   curateModelFromTables reads its mets/genes/rxns input from tab-delimited
+%   files; the tests below write those files to a temporary directory.
 
     methods (Test)
 
-        function curateModelFromTablesNeedsTableFiles(testCase)
-            % curateModelFromTables reads its mets/genes/rxns input from files
-            % (tab-delimited / Excel); without those it cannot run.
-            testCase.assumeFail('Requires curation input table files.');
+        function curateModelFromTablesKeepsSupersetReaction(testCase)
+            % A model reaction that uses the candidate's metabolites *and*
+            % others is a different reaction, not a duplicate: adding
+            % A + B -> C to a model holding A + B -> C + H must leave the
+            % existing reaction alone and add the candidate separately.
+            model = tCuration.toyModel();
+            [coeffsF, infoF] = tCuration.writeRxnTables(testCase, ...
+                {'A','B','C'}, [-1 -1 1]);
+            evalc(['out = curateModelFromTables(model,''none'',''rxnsCoeffs'',' ...
+                'coeffsF,''rxnsInfo'',infoF);']);
+
+            testCase.verifyNumElements(out.rxns, 2);
+            % The existing reaction keeps its name and its fourth metabolite
+            testCase.verifyEqual(out.rxnNames{1}, 'ATP hydrolysis with proton');
+            testCase.verifyNumElements(find(out.S(:,1)), 4);
+            % The candidate is added as a new reaction
+            testCase.verifyEqual(out.rxnNames{2}, 'newRxn');
+            testCase.verifyNumElements(find(out.S(:,2)), 3);
+        end
+
+        function curateModelFromTablesOverwritesExactDuplicate(testCase)
+            % An exact stoichiometric match is still treated as the same
+            % reaction and has its annotation overwritten.
+            model = tCuration.toyModel();
+            [coeffsF, infoF] = tCuration.writeRxnTables(testCase, ...
+                {'A','B','C','H'}, [-1 -1 1 1]);
+            evalc(['out = curateModelFromTables(model,''none'',''rxnsCoeffs'',' ...
+                'coeffsF,''rxnsInfo'',infoF);']);
+
+            testCase.verifyNumElements(out.rxns, 1);
+            testCase.verifyEqual(out.rxnNames{1}, 'newRxn');
+        end
+
+    end
+
+    methods (Static, Access = private)
+
+        function model = toyModel()
+            % Single reaction: A + B -> C + H, all in one compartment.
+            model = struct();
+            model.id        = 'toy';
+            model.rxns      = {'R1'};
+            model.rxnNames  = {'ATP hydrolysis with proton'};
+            model.mets      = {'m1';'m2';'m3';'m4'};
+            model.metNames  = {'A';'B';'C';'H'};
+            model.comps     = {'c'};
+            model.compNames = {'cytosol'};
+            model.metComps  = [1;1;1;1];
+            model.S         = sparse([-1;-1;1;1]);
+            model.lb        = 0;
+            model.ub        = 1000;
+            model.rev       = 0;
+            model.c         = 0;
+            model.b         = zeros(4,1);
+            model.genes     = {};
+            model.grRules   = {''};
+            model.rxnGeneMat= sparse(1,0);
+            model.metFormulas = {'';'';'';''};
+            model.subSystems  = {{''}};
+            model.eccodes     = {''};
+            model.rxnNotes    = {''};
+            model.rxnReferences = {''};
+            model.rxnConfidenceScores = 0;
+        end
+
+        function [coeffsF, infoF] = writeRxnTables(testCase, metNames, coeffs)
+            % Write a one-reaction rxnsCoeffs/rxnsInfo pair for 'newRxn'.
+            d = tempname; mkdir(d);
+            testCase.addTeardown(@() rmdir(d,'s'));
+            coeffsF = fullfile(d,'coeffs.tsv');
+            infoF   = fullfile(d,'info.tsv');
+
+            fid = fopen(coeffsF,'w');
+            fprintf(fid,'rxnIdx\trxnNames\tmetNames\tcomps\tcoefficient\n');
+            for i=1:numel(metNames)
+                fprintf(fid,'1\tnewRxn\t%s\tc\t%d\n', metNames{i}, coeffs(i));
+            end
+            fclose(fid);
+
+            fid = fopen(infoF,'w');
+            fprintf(fid,['rxnIdx\trxnNames\tgrRules\tlb\tub\trev\tsubSystems\t' ...
+                'eccodes\trxnNotes\trxnReferences\trxnConfidenceScores\n']);
+            fprintf(fid,'1\tnewRxn\t\t0\t1000\t0\t\t\t\t\t\n');
+            fclose(fid);
         end
 
     end