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app.py
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297 lines (231 loc) · 9.26 KB
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import functools
import json
import os
import requests
import tempfile
import urllib.request
import zipfile
from flask import Flask, jsonify, make_response, abort, request
from werkzeug.utils import secure_filename
from AppData import AppData
from CommonFunctions import setInDict, getFilenameFromUrl, getFromDict, makeStrPathFromList, \
getOntologyFilePath
from Constants import TRACKS, \
EXPERIMENTS, SAMPLES, TERM_LABEL, \
DOC_ONTOLOGY_VERSIONS_NAMES, FILE_NAME, VERSION_IRI, DOAP_VERSION, \
EDAM_ONTOLOGY, \
SAMPLE_TYPE_MAPPING, BIOSPECIMEN_CLASS_PATH, SAMPLE_TYPE_SUMMARY_PATH, \
EXPERIMENT_TARGET_PATHS, \
TARGET_DETAILS_PATH, TARGET_SUMMARY_PATH, TRACK_FILE_URL_PATH, \
SPECIES_ID_PATH, \
IDENTIFIERS_API_URL, RESOLVED_RESOURCES, NCBI_TAXONOMY_RESOLVER_URL, \
SPECIES_NAME_PATH, SAMPLE_ORGANISM_PART_PATH, SAMPLE_DETAILS_PATH, \
HAS_AUGMENTED_METADATA, SCHEMA_URL_PART1, SCHEMA_URL_PART2
app = Flask(__name__)
ontologies = {}
@app.route('/')
def index():
return 'OK'
@app.errorhandler(400)
def custom400(error):
response = jsonify({'message': error.description})
return make_response(response, 400)
@app.route('/augment', methods=['POST'])
@app.route('/autogenerate', methods=['POST'])
def augment():
if 'data' not in request.files:
abort(400, 'Parameter called data containing fairtracks json data is required')
dataJson = request.files['data']
with tempfile.TemporaryDirectory() as tmpDir:
dataFn = ''
if dataJson:
dataFn = secure_filename(dataJson.filename)
dataJson.save(os.path.join(tmpDir, dataFn))
with open(os.path.join(tmpDir, dataFn)) as dataFile:
data = json.load(dataFile)
appData = AppData(ontologies)
if 'schemas' in request.files:
file = request.files['schemas']
filename = secure_filename(file.filename)
file.save(os.path.join(tmpDir, filename))
with zipfile.ZipFile(os.path.join(tmpDir, filename), 'r') as archive:
archive.extractall(tmpDir)
appData.initApp(data, tmpDir)
else:
appData.initApp(data)
augmentFields(data, appData)
return data
def addOntologyVersions(data, appData):
# Very cumbersome way to support both v1 and v2 names. Should be
# refactored. Also no good error message if no document info property is
# found.
for docInfoName in DOC_ONTOLOGY_VERSIONS_NAMES.keys():
if docInfoName in data:
docInfo = data[docInfoName]
docOntologyVersionsName = DOC_ONTOLOGY_VERSIONS_NAMES[docInfoName]
if docOntologyVersionsName not in docInfo:
docInfo[docOntologyVersionsName] = {}
docOntologyVersions = docInfo[docOntologyVersionsName]
urlAndVersions = []
for url, ontology in appData.getOntologies().items():
fn = getOntologyFilePath(url)
edam = False
if EDAM_ONTOLOGY in url:
edam = True
with open(fn, 'r') as ontoFile:
for line in ontoFile:
if edam:
if DOAP_VERSION in line:
versionNumber = line.split(DOAP_VERSION)[1].split('<')[0]
versionIri = EDAM_ONTOLOGY + 'EDAM_' + versionNumber + '.owl'
urlAndVersions.append((url, versionIri))
break
else:
if VERSION_IRI in line:
versionIri = line.split(VERSION_IRI)[1].split('"')[0]
urlAndVersions.append((url, versionIri))
break
for url, versionIri in urlAndVersions:
docOntologyVersions[url] = versionIri
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) + ')')
@functools.lru_cache(maxsize=50000)
def searchOntologiesForTermId(ontologyUrls, termIdVal, appData):
termLabelVal = ''
for url in ontologyUrls:
ontology = appData.getOntologies()[url]
termLabelSearch = ontology.search(iri=termIdVal)
if termLabelSearch:
termLabelVal = termLabelSearch[0].label[0]
if termLabelVal:
break
return termLabelVal
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 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)
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)
@functools.lru_cache(maxsize=1000)
def getSpeciesNameFromId(speciesId):
providerCode = resolveIdentifier(speciesId)
speciesName = getSpeciesName(speciesId.split('taxonomy:')[1], providerCode)
return speciesName
def resolveIdentifier(speciesId):
url = IDENTIFIERS_API_URL + speciesId
responseJson = requests.get(url).json()
for resource in responseJson['payload'][RESOLVED_RESOURCES]:
if 'providerCode' in resource:
if resource['providerCode'] == 'ncbi':
return resource['providerCode']
def getSpeciesName(speciesId, providerCode):
if providerCode == 'ncbi':
url = NCBI_TAXONOMY_RESOLVER_URL + '&id=' + str(speciesId)
for i in range(3):
try:
responseJson = requests.get(url).json()
speciesName = responseJson['result'][speciesId]['scientificname']
break
except KeyError:
pass
return speciesName
def setAugmentedDataFlag(data):
for docInfoName in HAS_AUGMENTED_METADATA.keys():
if docInfoName in data:
data[docInfoName][HAS_AUGMENTED_METADATA[docInfoName]] = True
def augmentFields(data, appData):
generateTermLabels(data, appData)
addOntologyVersions(data, appData)
addFileName(data)
addSampleSummary(data)
addTargetSummary(data)
addSpeciesName(data)
setAugmentedDataFlag(data)
#print(json.dumps(data))
def initOntologies():
print("initializing ontologies")
i = 1
currentSchemaUrl = ""
with tempfile.TemporaryDirectory() as tmpDir:
while True:
schemaUrl = SCHEMA_URL_PART1 + "v" + str(i) + SCHEMA_URL_PART2
try:
schemaFn, _ = urllib.request.urlretrieve(schemaUrl, os.path.join(tmpDir, 'schema.json'))
currentSchemaUrl = schemaUrl
i += 1
except:
break
data = {}
data["@schema"] = currentSchemaUrl
appData = AppData({})
appData.initApp(data)
return appData.getOntologies()
if __name__ == '__main__':
ontologies = initOntologies()
app.run(host='0.0.0.0')