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repair BMDB SBML test cases and files
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@jcschaff
jcschaff committed Nov 21, 2024
1 parent ff36e74 commit b2830c7
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Showing 12 changed files with 30,061 additions and 2,770 deletions.
13 changes: 2 additions & 11 deletions vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,6 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(151, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.5' for product 'x13' in reaction 'R23') or stoichiometryMath not handled in VCell at this time.
faults.put(154, SBMLTestSuiteTest.FAULT.DELAY); // cause: UnsupportedConstruct: unsupported SBML element 'delay' in expression ' <math><apply><times/><ci> compartment </ci><ci> beta_y </ci><ci> psi </ci><apply><csymbol encoding="text" de
faults.put(155, SBMLTestSuiteTest.FAULT.DELAY); // cause: UnsupportedConstruct: unsupported SBML element 'delay' in expression ' <math><apply><times/><ci> compartment </ci><ci> beta_y </ci><ci> psi </ci><apply><csymbol encoding="text" de
faults.put(175, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(196, SBMLTestSuiteTest.FAULT.DELAY); // cause: UnsupportedConstruct: unsupported SBML element 'delay' in expression ' <math><apply><times/><ci> vM4 </ci><apply><divide/><apply><times/><apply><plus/><cn> 1 </cn><apply><divide/>
faults.put(199, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.5' for reactant 'NADPH' in reaction 'r4') or stoichiometryMath not handled in VCell at this time.
faults.put(206, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.1' for product 's6o' in reaction 'v10') or stoichiometryMath not handled in VCell at this time.
Expand All @@ -108,7 +107,6 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(246, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.001' for product 'Ca_in' in reaction 'vo') or stoichiometryMath not handled in VCell at this time.
faults.put(248, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Unable to create and add rate rule to VC model : 'Capillary.Capillary' is either not found in your model or is not allowed to be used in the current context. Check that you have p
faults.put(256, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'XIAP_ini' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you hav
faults.put(302, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(305, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'V' to model: 'Fw_1st_step' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the
faults.put(319, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.02' for product 'gamma' in reaction 'r3') or stoichiometryMath not handled in VCell at this time.
faults.put(340, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: UnsupportedConstruct: error parsing expression ' <math><apply><gt/><piecewise><piece><apply><minus/><csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time">
Expand Down Expand Up @@ -136,7 +134,6 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(496, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') or stoichiometryMath not handled in VCell at this time.
faults.put(497, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') or stoichiometryMath not handled in VCell at this time.
faults.put(499, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_9' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(520, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(534, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_6' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(535, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_3' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(536, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_80' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
Expand All @@ -145,7 +142,6 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(547, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Compartment_3' to model: 'UNRESOLVED.Size' is either not found in your model or is not allowed to be used in the current context. Check that you ha
faults.put(556, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Unable to create and add rate rule to VC model : 'r0' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the corre
faults.put(562, SBMLTestSuiteTest.FAULT.QUAL_PACKAGE); // cause: Unable to import the SBML file. The model includes elements of SBML extension 'qual', which is required for simulating the model but is not supported.
faults.put(569, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(570, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Unable to create and add rate rule to VC model : 'reaction_4' is either not found in your model or is not allowed to be used in the current context. Check that you have provided t
faults.put(575, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Unable to create and add rate rule to VC model : 'J21' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the corr
faults.put(577, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: UnsupportedConstruct: error parsing expression ' <math><piecewise><piece><cn> 1 </cn><apply><lt/><csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> ti
Expand All @@ -157,16 +153,14 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(599, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_1' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(608, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // cause: UnsupportedConstruct: Non-integer stoichiometry ('0.5' for reactant 'x_18' in reaction 'R_18') or stoichiometryMath not handled in VCell at this time.
faults.put(613, SBMLTestSuiteTest.FAULT.COMP_PACKAGE); // cause: Unable to import the SBML file. The model includes elements of SBML extension 'comp', which is required for simulating the model but is not supported.
faults.put(618, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(627, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_123' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that y
faults.put(628, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_8' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(632, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'k4b' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have pro
faults.put(696, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_16' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(705, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_21' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(706, SBMLTestSuiteTest.FAULT.UNCATEGORIZED); // cause: found more than one SBase match for sid=v, matched [org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@67cc48df, org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@483ac21f]
faults.put(710, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_0_0' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that y
faults.put(731, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(739, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_19' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(731, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Treg_origin_fraction_CD4' to model: 'func_TRegs_Production_from_CD4' faults.put(739, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_19' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(764, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_3' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(775, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: Error adding Lambda function UnsupportedConstruct: error parsing expression ' <math><notanumber/></math>': node type 'notanumber' not supported yet
faults.put(804, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_1' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
Expand All @@ -183,10 +177,8 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(872, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'beta' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have pr
faults.put(908, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_2' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(925, SBMLTestSuiteTest.FAULT.UNCATEGORIZED); // cause: OverallWarning: missing or unexpected value attribute '-Infinity' for SBML object id log_time
faults.put(956, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // should be identified as FBC_PACKAGE
faults.put(961, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'rateOf_re15' to model: 're15' is either not found in your model or is not allowed to be used in the current context. Check that you have provided t
faults.put(969, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_11' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that yo
faults.put(973, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // cause: class org.sbml.jsbml.Constraint cannot be cast to class org.sbml.jsbml.SBMLDocument
faults.put(1005, SBMLTestSuiteTest.FAULT.MATHML_PARSING); // cause: UnsupportedConstruct: error parsing expression ' <math><piecewise><piece><cn> 1 </cn><apply><and/><apply><geq/><piecewise><piece><apply><minus/><csymbol encoding="text" definition
faults.put(1021, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Metabolite_0' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you
faults.put(1026, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context. Check that you have pro
Expand All @@ -196,10 +188,9 @@ public static Map<Integer, SBMLTestSuiteTest.FAULT> knownFaults() {
faults.put(1039, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Compartment_10' to model: 'UNRESOLVED.Size' is either not found in your model or is not allowed to be used in the current context. Check that you h
faults.put(1040, SBMLTestSuiteTest.FAULT.EXPRESSION_BINDING_EXCEPTION); // cause: Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context. Check that you have pro
faults.put(1046, SBMLTestSuiteTest.FAULT.FBC_PACKAGE); // cause: Unable to import the SBML file. The model includes elements of SBML extension 'fbc', which is required for simulating the model but is not supported.
faults.put(1061, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // should be identified as FBC_PACKAGE
faults.put(1062, SBMLTestSuiteTest.FAULT.FBC_PACKAGE); // cause: Unable to import the SBML file. The model includes elements of SBML extension 'fbc', which is required for simulating the model but is not supported.
faults.put(1063, SBMLTestSuiteTest.FAULT.FBC_PACKAGE); // cause: Unable to import the SBML file. The model includes elements of SBML extension 'fbc', which is required for simulating the model but is not supported.
faults.put(1064, SBMLTestSuiteTest.FAULT.CONSTRAINT_CLASS_CAST_EXCEPTION); // should be identified as FBC_PACKAGE
faults.put(1064, SBMLTestSuiteTest.FAULT.NONINTEGER_STOICH); // UnsupportedConstruct: Non-integer stoichiometry ('0.5' for reactant 'M_O2' in reaction 'R_R181') not handled in VCell at this time.
return faults;
}

Expand Down
2 changes: 1 addition & 1 deletion vcell-core/src/test/java/org/vcell/sbml/BMDB_SBML_Files.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ public static int[] getBiomodelDB_curatedModelNumbers() {
// only those Biomodels Database models which are committed to the vcell repo
// Uncomment "includeFilter = n -> true;" to run all tests (must have the other models installed in proper directory).
IntPredicate includeFilter = n -> Arrays.asList(15,48,71,205,264,427,452,453,591,594,595,596,623,643,696,826,952,
956, 302, 175, 618, 569, 973, 520, 731, 1061, 1064
956, 302, 175, 618, 569, 973, 520, 731, 1064
).contains(n);
//IntPredicate includeFilter = n -> true;

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