def main (args): """Usage: echo_numl input-filename output-filename """ if len(args) != 3: print(main.__doc__) sys.exit(1) doc = libnuml.readNUML(args[1]); ##if ( doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSNUML_SEV_ERROR) > 0): ## print doc.getErrorLog().toString(); ## else: libnuml.writeNUML(doc, args[2]); return 0;
def main(args): """Usage: echo_numl input-filename output-filename """ if len(args) != 3: print(main.__doc__) sys.exit(1) doc = libnuml.readNUML(args[1]) ##if ( doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSNUML_SEV_ERROR) > 0): ## print doc.getErrorLog().toString(); ## else: libnuml.writeNUML(doc, args[2]) return 0
def add_annotation(input_file, output_file, meta_id, annotation): # type: (str, str, str, str) -> None """ :param input_file: the input numl file :param output_file: the output numl file :param meta_id: the id to which to attach the annotation :param annotation: the annotation """ doc = libnuml.readNUMLFromFile(input_file) assert(isinstance(doc, libnuml.NUMLDocument)) added = add_annotation_for_metaid(doc, meta_id, annotation) if not added: for i in range(doc.getNumResultComponents()): current = doc.getResultComponent(i) assert(isinstance(current, libnuml.ResultComponent)) if add_annotation_for_metaid(current, meta_id, annotation): added = True break libnuml.writeNUML(doc, output_file)
def main (args): """Usage: create_numl output-filename """ if (len(args) != 2): print(main.__doc__) sys.exit(1); # create the document doc = libnuml.NUMLDocument(1, 1); # Header Information encoded in OntologyTerm objects # # No. Term Source Term Id Ontology URI # 1 concentration SBO:0000196 http://www.ebi.ac.uk/sbo/ # 2 metabolite SBO:0000299 http://www.ebi.ac.uk/sbo/ # 3 Time SBO:0000345 http://www.ebi.ac.uk/sbo/ # #--------------------------------------------------------------------------- # # Creates a OntologyTerm object inside OntologyTerms in NUMLDocument object. # #--------------------------------------------------------------------------- oTerm = doc.createOntologyTerm(); oTerm.setId("term1"); oTerm.setTerm("Time"); oTerm.setSourceTermId("SBO:0000345"); oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/"); oTerm = doc.createOntologyTerm(); oTerm.setId("term2"); oTerm.setTerm("metabolite"); oTerm.setSourceTermId("SBO:0000299"); oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/"); oTerm = doc.createOntologyTerm(); oTerm.setId("term3"); oTerm.setTerm("concentration"); oTerm.setSourceTermId("SBO:0000196"); oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/"); #--------------------------------------------------------------------------- # # Creates a ResultComponent object inside ResultComponents in NUMLDocument object. # #--------------------------------------------------------------------------- #The time course data # # Time BL B DLL # 0 0 1.66058 0.0884913 # 20 0.23 1.76058 0.0984913 # rComp = doc.createResultComponent(); rComp.setId("result_comp1"); dimD = rComp.createDimensionDescription(); #1st dimension is the time compDesc = rComp.createCompositeDescription(); compDesc.setName("Time"); compDesc.setIndexType("float"); compDesc.setOntologyTerm("term1"); #2nd dimension is Metabilites subCompDesc = compDesc.createCompositeDescription(); subCompDesc.setName("Metabolites"); subCompDesc.setIndexType("string"); subCompDesc.setOntologyTerm("term2"); # the actual data description of data aDesc= subCompDesc.createAtomicDescription(); aDesc.setName("Concentration"); aDesc.setOntologyTerm("term3"); #encoding the data #row 1 #first column in row 1 compValue = rComp.createCompositeValue(); compValue.setIndexValue("0"); #2nd column in row 1 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("BL"); aValue = subCompValue.createAtomicValue(); aValue.setValue("0"); #3rd column in this row 1 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("B"); aValue = subCompValue.createAtomicValue(); aValue.setValue("1.66058"); #4th column in this row 1 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("DLL"); aValue = subCompValue.createAtomicValue(); aValue.setValue("0.0884913"); #row 2 #first column in row 2 compValue = rComp.createCompositeValue(); compValue.setIndexValue("20"); #2nd column in row 2 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("BL"); aValue = subCompValue.createAtomicValue(); aValue.setValue("0.23"); #3rd column in this row 2 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("B"); aValue = subCompValue.createAtomicValue(); aValue.setValue("1.76058"); #4th column in this row 2 subCompValue = compValue.createCompositeValue(); subCompValue.setIndexValue("DLL"); aValue = subCompValue.createAtomicValue(); aValue.setValue("0.0984913"); # write the document libnuml.writeNUML(doc, args[1]);
t = d.createTupleDescription() t.name = 'Main' a = t.createAtomicDescription() a.name = 'Objective Value' a.value_type= 'float' a = t.createAtomicDescription() a.name = 'Root Mean Square' a.value_type= 'float' a = t.createAtomicDescription() a.name = 'Standard Deviation' a.value_type = 'float' d = r.getDimension() t = d.createTuple() a = t.createAtomicValue() a.value = '12.5015' a = t.createAtomicValue() a.value = '0.158123' a = t.createAtomicValue() a.value = '0.159242' libnuml.writeNUML(doc, 'example5_2.xml')
def main(args): """Usage: create_numl output-filename """ if (len(args) != 2): print(main.__doc__) sys.exit(1) # create the document doc = libnuml.NUMLDocument(1, 1) # Header Information encoded in OntologyTerm objects # # No. Term Source Term Id Ontology URI # 1 concentration SBO:0000196 http://www.ebi.ac.uk/sbo/ # 2 metabolite SBO:0000299 http://www.ebi.ac.uk/sbo/ # 3 Time SBO:0000345 http://www.ebi.ac.uk/sbo/ # #--------------------------------------------------------------------------- # # Creates a OntologyTerm object inside OntologyTerms in NUMLDocument object. # #--------------------------------------------------------------------------- oTerm = doc.createOntologyTerm() oTerm.setId("term1") oTerm.setTerm("Time") oTerm.setSourceTermId("SBO:0000345") oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/") oTerm = doc.createOntologyTerm() oTerm.setId("term2") oTerm.setTerm("metabolite") oTerm.setSourceTermId("SBO:0000299") oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/") oTerm = doc.createOntologyTerm() oTerm.setId("term3") oTerm.setTerm("concentration") oTerm.setSourceTermId("SBO:0000196") oTerm.setOntologyURI("http://www.ebi.ac.uk/sbo/") #--------------------------------------------------------------------------- # # Creates a ResultComponent object inside ResultComponents in NUMLDocument object. # #--------------------------------------------------------------------------- #The time course data # # Time BL B DLL # 0 0 1.66058 0.0884913 # 20 0.23 1.76058 0.0984913 # rComp = doc.createResultComponent() rComp.setId("result_comp1") dimD = rComp.createDimensionDescription() #1st dimension is the time compDesc = rComp.createCompositeDescription() compDesc.setName("Time") compDesc.setIndexType("float") compDesc.setOntologyTerm("term1") #2nd dimension is Metabilites subCompDesc = compDesc.createCompositeDescription() subCompDesc.setName("Metabolites") subCompDesc.setIndexType("string") subCompDesc.setOntologyTerm("term2") # the actual data description of data aDesc = subCompDesc.createAtomicDescription() aDesc.setName("Concentration") aDesc.setOntologyTerm("term3") #encoding the data #row 1 #first column in row 1 compValue = rComp.createCompositeValue() compValue.setIndexValue("0") #2nd column in row 1 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("BL") aValue = subCompValue.createAtomicValue() aValue.setValue("0") #3rd column in this row 1 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("B") aValue = subCompValue.createAtomicValue() aValue.setValue("1.66058") #4th column in this row 1 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("DLL") aValue = subCompValue.createAtomicValue() aValue.setValue("0.0884913") #row 2 #first column in row 2 compValue = rComp.createCompositeValue() compValue.setIndexValue("20") #2nd column in row 2 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("BL") aValue = subCompValue.createAtomicValue() aValue.setValue("0.23") #3rd column in this row 2 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("B") aValue = subCompValue.createAtomicValue() aValue.setValue("1.76058") #4th column in this row 2 subCompValue = compValue.createCompositeValue() subCompValue.setIndexValue("DLL") aValue = subCompValue.createAtomicValue() aValue.setValue("0.0984913") # write the document libnuml.writeNUML(doc, args[1])