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Fix for #1330: add spaces after commas for generated IDs. #1348

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Merged
luciansmith merged 1 commit into from
Aug 20, 2026
Merged

Fix for #1330: add spaces after commas for generated IDs. #1348

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112 changes: 110 additions & 2 deletions test/c_api_core/CAPICoreTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ TEST_F(CAPICoreTest, CheckGetEC) {
std::vector<std::string> expectedRxns(
{ "_J0", "_J1" });
std::vector<std::string> expectedIds(
{ "ec(_J0,A)", "ec(_J0,AP)", "ec(_J0,K)", "ec(_J0,Vm1)", "ec(_J0,Km1)", "ec(_J1,A)", "ec(_J1,AP)", "ec(_J1,K)", "ec(_J1,Vm1)", "ec(_J1,Km1)"});
{ "ec(_J0, A)", "ec(_J0, AP)", "ec(_J0, K)", "ec(_J0, Vm1)", "ec(_J0, Km1)", "ec(_J1, A)", "ec(_J1, AP)", "ec(_J1, K)", "ec(_J1, Vm1)", "ec(_J1, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
Expand All @@ -363,7 +363,7 @@ TEST_F(CAPICoreTest, CheckGetUEC) {
std::vector<std::string> expectedRxns(
{ "_J0", "_J1" });
std::vector<std::string> expectedIds(
{ "uec(_J0,A)", "uec(_J0,AP)", "uec(_J0,K)", "uec(_J0,Vm1)", "uec(_J0,Km1)", "uec(_J1,A)", "uec(_J1,AP)", "uec(_J1,K)", "uec(_J1,Vm1)", "uec(_J1,Km1)"});
{ "uec(_J0, A)", "uec(_J0, AP)", "uec(_J0, K)", "uec(_J0, Vm1)", "uec(_J0, Km1)", "uec(_J1, A)", "uec(_J1, AP)", "uec(_J1, K)", "uec(_J1, Vm1)", "uec(_J1, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
Expand All @@ -381,6 +381,114 @@ TEST_F(CAPICoreTest, CheckGetUEC) {
freeRRInstance(rrH);
}

TEST_F(CAPICoreTest, CheckGetFluxControlCoefficientIds) {

RRHandle rrH = createRRInstance();
ASSERT_TRUE(loadSBMLFromFileE(rrH, (cAPICoreModelsDir / path("steadystate.xml")).string().c_str(), true));

RRListPtr actual = getFluxControlCoefficientIds(rrH);
std::vector<std::string> expectedRxns(
{ "_J0", "_J1" });
std::vector<std::string> expectedIds(
{ "cc(_J0, K)", "cc(_J0, Vm1)", "cc(_J0, Km1)", "cc(_J1, K)", "cc(_J1, Vm1)", "cc(_J1, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
RRList* sublist = element->data.lValue;
char* id = sublist->Items[0]->data.sValue;
EXPECT_STREQ(id, expectedRxns[r].c_str());
RRList* subsublist = sublist->Items[1]->data.lValue;
for (int sr=0; sr < subsublist->Count; sr++) {
char* id = subsublist->Items[sr]->data.sValue;
EXPECT_STREQ(id, expectedIds[r*subsublist->Count + sr].c_str());
}
}

freeRRList(actual);
freeRRInstance(rrH);
}

TEST_F(CAPICoreTest, CheckGetUnscaledFluxControlCoefficientIds) {

RRHandle rrH = createRRInstance();
ASSERT_TRUE(loadSBMLFromFileE(rrH, (cAPICoreModelsDir / path("steadystate.xml")).string().c_str(), true));

RRListPtr actual = getUnscaledFluxControlCoefficientIds(rrH);
std::vector<std::string> expectedRxns(
{ "_J0", "_J1" });
std::vector<std::string> expectedIds(
{ "ucc(_J0, K)", "ucc(_J0, Vm1)", "ucc(_J0, Km1)", "ucc(_J1, K)", "ucc(_J1, Vm1)", "ucc(_J1, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
RRList* sublist = element->data.lValue;
char* id = sublist->Items[0]->data.sValue;
EXPECT_STREQ(id, expectedRxns[r].c_str());
RRList* subsublist = sublist->Items[1]->data.lValue;
for (int sr=0; sr < subsublist->Count; sr++) {
char* id = subsublist->Items[sr]->data.sValue;
EXPECT_STREQ(id, expectedIds[r*subsublist->Count + sr].c_str());
}
}

freeRRList(actual);
freeRRInstance(rrH);
}

TEST_F(CAPICoreTest, CheckGetConcentrationControlCoefficientIds) {

RRHandle rrH = createRRInstance();
ASSERT_TRUE(loadSBMLFromFileE(rrH, (cAPICoreModelsDir / path("steadystate.xml")).string().c_str(), true));

RRListPtr actual = getConcentrationControlCoefficientIds(rrH);
std::vector<std::string> expectedSpecies(
{ "A", "AP" });
std::vector<std::string> expectedIds(
{ "cc(A, K)", "cc(A, Vm1)", "cc(A, Km1)", "cc(AP, K)", "cc(AP, Vm1)", "cc(AP, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
RRList* sublist = element->data.lValue;
char* id = sublist->Items[0]->data.sValue;
EXPECT_STREQ(id, expectedSpecies[r].c_str());
RRList* subsublist = sublist->Items[1]->data.lValue;
for (int sr=0; sr < subsublist->Count; sr++) {
char* id = subsublist->Items[sr]->data.sValue;
EXPECT_STREQ(id, expectedIds[r*subsublist->Count + sr].c_str());
}
}

freeRRList(actual);
freeRRInstance(rrH);
}

TEST_F(CAPICoreTest, CheckGetUnscaledConcentrationControlCoefficientIds) {

RRHandle rrH = createRRInstance();
ASSERT_TRUE(loadSBMLFromFileE(rrH, (cAPICoreModelsDir / path("steadystate.xml")).string().c_str(), true));

RRListPtr actual = getUnscaledConcentrationControlCoefficientIds(rrH);
std::vector<std::string> expectedSpecies(
{ "A", "AP" });
std::vector<std::string> expectedIds(
{ "ucc(A, K)", "ucc(A, Vm1)", "ucc(A, Km1)", "ucc(AP, K)", "ucc(AP, Vm1)", "ucc(AP, Km1)"});

for (int r = 0; r < actual->Count; r++) {
RRListItem* element = actual->Items[r];
RRList* sublist = element->data.lValue;
char* id = sublist->Items[0]->data.sValue;
EXPECT_STREQ(id, expectedSpecies[r].c_str());
RRList* subsublist = sublist->Items[1]->data.lValue;
for (int sr=0; sr < subsublist->Count; sr++) {
char* id = subsublist->Items[sr]->data.sValue;
EXPECT_STREQ(id, expectedIds[r*subsublist->Count + sr].c_str());
}
}

freeRRList(actual);
freeRRInstance(rrH);
}

TEST_F(CAPICoreTest, CheckSetTimeCourseSelectionListEx) {

RRHandle rrH = createRRInstance();
Expand Down
40 changes: 20 additions & 20 deletions wrappers/C/rrc_api.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2965,17 +2965,17 @@ static ArrayList RoadRunner_getUnscaledFluxControlCoefficientIds(RoadRunner *rr)

for(int i = 0; i < oParameters.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oParameters[i] + ")");
oInner.push_back("ucc(" + s + ", " + oParameters[i] + ")");
}

for(int i = 0; i < oBoundary.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oBoundary[i] + ")");
oInner.push_back("ucc(" + s + ", " + oBoundary[i] + ")");
}

for(int i = 0; i < oConservation.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oConservation[i] + ")");
oInner.push_back("ucc(" + s + ", " + oConservation[i] + ")");
}

oCCReaction.Add(oInner);
Expand Down Expand Up @@ -3098,17 +3098,17 @@ ArrayList sel_getFluxControlCoefficientIds(RoadRunner* rr)

for(int i = 0; i < oParameters.size(); i++)
{
oInner.add("cc(" + s + "," + oParameters[i] + ")");
oInner.add("cc(" + s + ", " + oParameters[i] + ")");
}

for(int i = 0; i < oBoundary.size(); i++)
{
oInner.add("cc(" + s + "," + oBoundary[i] + ")");
oInner.add("cc(" + s + ", " + oBoundary[i] + ")");
}

for(int i = 0; i < oConservation.size(); i++)
{
oInner.add("cc(" + s + "," + oConservation[i] + ")");
oInner.add("cc(" + s + ", " + oConservation[i] + ")");
}

oCCReaction.Add(oInner);
Expand Down Expand Up @@ -3205,17 +3205,17 @@ ArrayList sel_getConcentrationControlCoefficientIds(RoadRunner* rr)

for(int i = 0; i < oParameters.size(); i++)
{
oInner.add("cc(" + s + "," + oParameters[i] + ")");
oInner.add("cc(" + s + ", " + oParameters[i] + ")");
}

for(int i = 0; i < oBoundary.size(); i++)
{
oInner.add("cc(" + s + "," + oBoundary[i] + ")");
oInner.add("cc(" + s + ", " + oBoundary[i] + ")");
}

for(int i = 0; i < oConservation.size(); i++)
{
oInner.add("cc(" + s + "," + oConservation[i] + ")");
oInner.add("cc(" + s + ", " + oConservation[i] + ")");
}

oCCFloating.Add(oInner);
Expand Down Expand Up @@ -3243,17 +3243,17 @@ ArrayList sel_getUnscaledConcentrationControlCoefficientIds(RoadRunner* rr)

for(int i = 0; i < oParameters.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oParameters[i] + ")");
oInner.push_back("ucc(" + s + ", " + oParameters[i] + ")");
}

for(int i = 0; i < oBoundary.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oBoundary[i] + ")");
oInner.push_back("ucc(" + s + ", " + oBoundary[i] + ")");
}

for(int i = 0; i < oConservation.size(); i++)
{
oInner.push_back("ucc(" + s + "," + oConservation[i] + ")");
oInner.push_back("ucc(" + s + ", " + oConservation[i] + ")");
}

oCCFloating.Add(oInner);
Expand Down Expand Up @@ -3282,22 +3282,22 @@ ArrayList sel_getElasticityCoefficientIds(RoadRunner* rr)

for(int j = 0; j < floatingSpeciesNames.size(); j++)
{
oInner.add(format("ec({0},{1})", reac_name, floatingSpeciesNames[j]));
oInner.add(format("ec({0}, {1})", reac_name, floatingSpeciesNames[j]));
}

for(int j = 0; j < boundarySpeciesNames.size(); j++)
{
oInner.add(format("ec({0},{1})", reac_name, boundarySpeciesNames[j]));
oInner.add(format("ec({0}, {1})", reac_name, boundarySpeciesNames[j]));
}

for(int j = 0; j < globalParameterNames.size(); j++)
{
oInner.add(format("ec({0},{1})", reac_name, globalParameterNames[j]));
oInner.add(format("ec({0}, {1})", reac_name, globalParameterNames[j]));
}

for(int j = 0; j < conservationNames.size(); j++)
{
oInner.add(format("ec({0},{1})", reac_name, conservationNames[j]));
oInner.add(format("ec({0}, {1})", reac_name, conservationNames[j]));
}

oCCReaction.Add(oInner);
Expand Down Expand Up @@ -3327,25 +3327,25 @@ ArrayList sel_getUnscaledElasticityCoefficientIds(RoadRunner* rr)
for(int j = 0; j < oFloating.size(); j++)
{
string variable = oFloating[j];
oInner.add(format("uec({0},{1})", reac_name, variable));
oInner.add(format("uec({0}, {1})", reac_name, variable));
}

for(int j = 0; j < oBoundary.size(); j++)
{
string variable = oBoundary[j];
oInner.add(format("uec({0},{1})", reac_name, variable));
oInner.add(format("uec({0}, {1})", reac_name, variable));
}

for(int j = 0; j < oGlobalParameters.size(); j++)
{
string variable = oGlobalParameters[j];
oInner.add(format("uec({0},{1})", reac_name, variable));
oInner.add(format("uec({0}, {1})", reac_name, variable));
}

for(int j = 0; j < oConservation.size(); j++)
{
string variable = oConservation[j];
oInner.add(format("uec({0},{1})", reac_name, variable));
oInner.add(format("uec({0}, {1})", reac_name, variable));
}

oCCReaction.Add(oInner);
Expand Down
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