def addSampleSummary(data):
samples = data[SAMPLES]
for sample in samples:
biospecimenTermId = getFromDict(sample, BIOSPECIMEN_CLASS_PATH)
if biospecimenTermId in SAMPLE_TYPE_MAPPING:
sampleTypeVal = getFromDict(sample, SAMPLE_TYPE_MAPPING[biospecimenTermId])
if TERM_LABEL in sampleTypeVal:
summary = sampleTypeVal[TERM_LABEL]
details = []
try:
organismPart = getFromDict(sample, SAMPLE_ORGANISM_PART_PATH)
if summary != organismPart:
details.append(organismPart)
except KeyError:
pass
try:
sample_details = getFromDict(sample, SAMPLE_DETAILS_PATH)
details.append(sample_details)
except KeyError:
pass
if details:
summary = "{} ({})".format(summary, ', '.join(details))
setInDict(sample, SAMPLE_TYPE_SUMMARY_PATH, summary)
else:
abort(400, 'Unexpected biospecimen_class term_id: ' + biospecimenTermId)
def addTargetSummary(data):
experiments = data[EXPERIMENTS]
val = ''
for exp in experiments:
for path in EXPERIMENT_TARGET_PATHS:
try:
val = getFromDict(exp, path)
break
except KeyError:
continue
if val:
details = ''
try:
details = getFromDict(exp, TARGET_DETAILS_PATH)
except KeyError:
pass
if details:
val += ' (' + details + ')'
setInDict(exp, TARGET_SUMMARY_PATH, val)
def generateTermLabels(data, appData):
for category in data:
if not isinstance(data[category], list):
continue
for item in data[category]:
for path, ontologyUrls in appData.getPathsWithOntologyUrls():
if path[0] != category:
continue
try:
termIdVal = getFromDict(item, path[1:])
except KeyError:
continue
termLabelVal = searchOntologiesForTermId(tuple(ontologyUrls), termIdVal, appData)
if termLabelVal:
setInDict(item, path[1:-1] + [TERM_LABEL], termLabelVal)
else:
abort(400, 'Item ' + termIdVal + ' not found in ontologies ' + str(ontologyUrls)
+ ' (path in json: ' + makeStrPathFromList(path, category) + ')')
def addSpeciesName(data):
samples = data[SAMPLES]
for sample in samples:
speciesId = getFromDict(sample, SPECIES_ID_PATH)
speciesName = getSpeciesNameFromId(speciesId)
setInDict(sample, SPECIES_NAME_PATH, speciesName)
def addFileName(data):
tracks = data[TRACKS]
for track in tracks:
fileUrl = getFromDict(track, TRACK_FILE_URL_PATH)
fileName = getFilenameFromUrl(fileUrl)
setInDict(track, TRACK_FILE_URL_PATH[:-1] + [FILE_NAME], fileName)