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])
