def test_DateTime(self):
try:
zqc = qc.MzQcFile(version="0.1.0",
creationDate=datetime.now().isoformat(),
runQualities=[],
setQualities=[],
controlledVocabularies=[])
except Exception as error:
raise AssertionError(f"An unexpected exception {error} raised.")
def test_SyntaxCheck():
cvt = qc.CvParameter(cvRef="REF",
accession="TEST:123",
name="testname",
value=99)
infi = qc.InputFile(name="file.raw",
location="file:///dev/null",
fileFormat=qc.CvParameter("MS", "MS:1000584",
"mzML format"),
fileProperties=[
qc.CvParameter(cvRef="MS",
accession="MS:1000747",
name="completion time",
value="2017-12-08-T15:38:57Z")
])
anso = qc.AnalysisSoftware(
cvRef="QC",
accession="QC:9999999",
name="bigwhopqc",
version="1.2.3",
uri="file:///dev/null") # isn't requiring a uri a bit too much?
meta = qc.MetaDataParameters(inputFiles=[infi], analysisSoftware=[anso])
qm = qc.QualityMetric(cvRef="QC",
accession="QC:4000053",
name="RT duration",
value=99)
qm2 = qc.QualityMetric(cvRef="QC",
accession="QC:4000061",
name="Maximal MS2 frequency",
value=999)
qm3 = qc.QualityMetric(cvRef="QC",
accession="QC:4000055",
name="MS1 quantiles RT fraction",
value=9)
rq = qc.RunQuality(metadata=meta, qualityMetrics=[qm, qm2])
sq = qc.SetQuality(metadata=meta, qualityMetrics=[qm3])
cv = qc.ControlledVocabulary(ref="QC", name="QCvocab", uri="www.qc.ml")
cv2 = qc.ControlledVocabulary(ref="REF", name="TEST", uri="www.eff.off")
mzqc = qc.MzQcFile(version="0.0.11",
runQualities=[rq],
setQualities=[sq],
controlledVocabularies=[cv, cv2])
# with open('tests/mzqc_lib_out.mzqc', 'w') as f:
# f.write("{ \"mzQC\": " + qc.JsonSerialisable.ToJson(mzqc) + " }")
syn_check = sy.SyntacticCheck()
syn_check.validate("{ \"mzQC\": " + qc.JsonSerialisable.ToJson(mzqc) +
" }")
def mzqc_assembly(rqs, sqs, out):
# TODO check all the metrics to see which ontologies were used
cv_qc = qc.ControlledVocabulary(
ref="QC",
name="Proteomics Standards Initiative Quality Control Ontology",
version="0.1.0",
uri=
"https://github.com/HUPO-PSI/qcML-development/blob/master/cv/v0_1_0/qc-cv.obo"
)
cv_ms = qc.ControlledVocabulary(
ref="MS",
name="Proteomics Standards Initiative Mass Spectrometry Ontology",
version="4.1.7",
uri="https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo")
return qc.MzQcFile(version="0.1.0",
creationDate=datetime.now().isoformat(),
runQualities=rqs,
setQualities=sqs,
controlledVocabularies=[cv_qc, cv_ms])
anso = qc.AnalysisSoftware(
cvRef="QC",
accession="QC:9999999",
name="bigwhopqc",
version="1.2.3",
uri="file:///dev/null") # isn't requiring a uri a bit too much?
meta = qc.MetaDataParameters(inputFiles=[infi], analysisSoftware=[anso])
qm = qc.QualityMetric(cvRef="QC",
accession="QC:4000053",
name="RT duration",
value=99)
rq = qc.RunQuality(metadata=meta, qualityMetrics=[qm])
sq = qc.SetQuality(metadata=meta, qualityMetrics=[qm])
cv = qc.ControlledVocabulary(ref="REF", name="TEST", uri="www.eff.off")
mzqc = qc.MzQcFile(version="0.0.11",
runQualities=[rq],
setQualities=[sq],
controlledVocabularies=[cv])
class TestSerialisation:
def test_ControlledVocabulary(self):
assert qc.JsonSerialisable.ToJson(cv) == CV
def test_CvParameter(self):
assert qc.JsonSerialisable.ToJson(cvt) == CVT
def test_AnalysisSoftware(self):
assert qc.JsonSerialisable.ToJson(anso) == ANSO
def test_InputFile(self):
assert qc.JsonSerialisable.ToJson(infi) == INFI