def post(self):
"""Saves the given file if the user has a valid API key
"""
if request.method == 'POST':
api_key = request.headers.get('x-api-key')
if api_key is None:
return BARUtils.error_exit('Invalid API key'), 403
elif SummarizationGeneExpressionUtils.decrement_uses(api_key):
now = datetime.now()
dt_string = now.strftime("%d-%m-%Y_%H-%M-%S")
if 'file' in request.files:
file = request.files['file']
extension = ''
if file.content_type == 'text/xml':
extension = '.xml'
elif file.content_type == 'image/svg+xml':
extension = '.svg'
else:
return BARUtils.error_exit('Invalid file type'), 400
filename = os.path.join(DATA_FOLDER, api_key,
dt_string + extension)
file.save(filename)
return BARUtils.success_exit(True)
else:
return BARUtils.error_exit('No file attached'), 400
else:
return BARUtils.error_exit('Invalid API key')
def post(self):
"""This end point returns gene expression data for a single gene and multiple samples."""
json_data = request.get_json()
# Validate json
try:
json_data = RNASeqSchema().load(json_data)
except ValidationError as err:
return BARUtils.error_exit(err.messages), 400
species = json_data['species']
database = json_data['database']
gene_id = json_data['gene_id']
sample_ids = json_data['sample_ids']
results = RNASeqUtils.get_data(species, database, gene_id, sample_ids)
if results['success']:
# Return results if there are data
if len(results['data']) > 0:
return BARUtils.success_exit(results['data'])
else:
return BARUtils.error_exit(
'There are no data found for the given gene')
else:
return BARUtils.error_exit(results['error']), results['error_code']
def post(self):
"""Takes a CSV file containing expression data and inserts the data into the database
"""
if request.method == 'POST':
if 'file' not in request.files:
return BARUtils.error_exit('No file attached'), 400
file = request.files['file']
if file:
filename = secure_filename(file.filename)
key = request.headers.get('X-Api-Key')
file.save(os.path.join(DATA_FOLDER + '/' + key + '/',
filename))
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = """
{
'csvUpload.insertDataScript': './insertData.py',
'csvUpload.id': """ + key + """,
'csvUpload.csv': """ + os.path.join(
DATA_FOLDER, key, filename) + """,
}
"""
path = os.path.join(SUMMARIZATION_FILES_PATH,
'csvUpload.wdl')
files = {
'workflowSource': ('csvUpload.wdl', open(path, 'rb')),
'workflowInputs': ('rpkm_inputs.json', inputs)
}
requests.post(CROMWELL_URL + '/api/workflows/v1',
files=files)
return BARUtils.success_exit(key)
else:
return BARUtils.error_exit('Invalid API key')
def post(self):
"""Returns list of pending requests from the database
"""
if request.method == 'POST':
response_json = request.get_json()
password = response_json['password']
if ApiManagerUtils.check_admin_pass(password):
table = Requests()
values = []
try:
rows = table.query.filter_by().all()
except SQLAlchemyError:
return BARUtils.error_exit('Internal server error'), 500
[
values.append({
'first_name': row.first_name,
'last_name': row.last_name,
'email': row.email,
'telephone': row.telephone,
'contact_type': row.contact_type,
'notes': row.notes
}) for row in rows
]
return BARUtils.success_exit(values)
else:
return BARUtils.error_exit('Forbidden'), 403
def post(self):
"""Takes a CSV file containing expression data and inserts the data into the database"""
if request.method == "POST":
if "file" not in request.files:
return BARUtils.error_exit("No file attached"), 400
file = request.files["file"]
if file:
filename = secure_filename(file.filename)
key = request.headers.get("X-Api-Key")
file.save(os.path.join(DATA_FOLDER, key, filename))
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = ("""
{
"csvUpload.insertDataScript": "./insertData.py",
"csvUpload.id": """ + key + """,
"csvUpload.csv": """ +
os.path.join(DATA_FOLDER, key, filename) + """,
}
""")
path = os.path.join(SUMMARIZATION_FILES_PATH,
"csvUpload.wdl")
files = {
"workflowSource": ("csvUpload.wdl", open(path, "rb")),
"workflowInputs": ("rpkm_inputs.json", inputs),
}
requests.post(CROMWELL_URL + "/api/workflows/v1",
files=files)
return BARUtils.success_exit(key)
else:
return BARUtils.error_exit("Invalid API key")
def post(self):
"""Returns list of pending requests from the database"""
if request.method == "POST":
response_json = request.get_json()
password = response_json["password"]
if ApiManagerUtils.check_admin_pass(password):
table = Requests()
values = []
try:
rows = table.query.filter_by().all()
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
[
values.append({
"first_name": row.first_name,
"last_name": row.last_name,
"email": row.email,
"telephone": row.telephone,
"contact_type": row.contact_type,
"notes": row.notes,
}) for row in rows
]
return BARUtils.success_exit(values)
else:
return BARUtils.error_exit("Forbidden"), 403
def get(self, table_id=""):
"""Checks if a given table exists"""
con = db.get_engine(bind="summarization")
if con.dialect.has_table(con, table_id):
return BARUtils.success_exit(True)
else:
return BARUtils.success_exit(False)
def post(self):
"""Takes a Google Drive folder ID (containing BAM files) and submits them to the Cromwell server for summarization
"""
if request.method == 'POST':
json = request.get_json()
key = request.headers.get('X-Api-Key')
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = """
{
'geneSummarization.gtf': './data/Araport11_GFF3_genes_transposons.201606.gtf',
'geneSummarization.summarizeGenesScript': './summarize_genes.R',
'geneSummarization.downloadFilesScript': './downloadDriveFiles.py',
'geneSummarization.insertDataScript': './insertData.py',
'geneSummarization.credentials': './data/credentials.json',
'geneSummarization.token': './data/token.pickle',
'geneSummarization.aliases': './data/aliases.txt',
'geneSummarization.folderId': """ + json[
'folderId'] + """,
'geneSummarization.id': """ + key + """
}
"""
# Create DB
# Send request to Cromwell
path = os.path.join(SUMMARIZATION_FILES_PATH, 'rpkm.wdl')
files = {
'workflowSource': ('rpkm.wdl', open(path, 'rb')),
'workflowInputs': ('rpkm_inputs.json', inputs)
}
requests.post(CROMWELL_URL + '/api/workflows/v1', files=files)
# Return ID for future accessing
return BARUtils.success_exit(key), 200
else:
return BARUtils.error_exit('Invalid API key')
def get(self, gene_id=""):
"""This end point retrieves publications from ThaleMine given an AGI ID"""
gene_id = escape(gene_id)
# Is data valid
if not BARUtils.is_arabidopsis_gene_valid(gene_id):
return BARUtils.error_exit("Invalid gene id"), 400
query = (
'<query name="" model="genomic" view="Gene.publications.firstAuthor Gene.publications.issue '
"Gene.publications.journal Gene.publications.pages Gene.publications.pubMedId Gene.publications.title "
'Gene.publications.volume Gene.publications.year" longDescription="" '
'sortOrder="Gene.publications.firstAuthor asc"><constraint path="Gene.primaryIdentifier" op="=" value="{'
'}"/></query> ')
query = query.format(gene_id)
# Now query the web service
payload = {"format": "json", "query": query}
resp = requests.post(
"https://bar.utoronto.ca/thalemine/service/query/results",
data=payload,
headers=request_headers,
)
return resp.json()
def test_is_poplar_gene_valid(self):
# Valid gene
result = BARUtils.is_poplar_gene_valid('Potri.019G123900.1')
self.assertTrue(result)
# Invalid gene
result = BARUtils.is_poplar_gene_valid('abc')
self.assertFalse(result)
def post(self):
"""Verify admin password"""
if request.method == "POST":
response_json = request.get_json()
password = response_json["password"]
if ApiManagerUtils.check_admin_pass(password):
return BARUtils.success_exit(True)
else:
return BARUtils.success_exit(False)
def post(self):
"""Verify admin password
"""
if request.method == 'POST':
response_json = request.get_json()
user_key = response_json['key']
if ApiManagerUtils.check_admin_pass(user_key):
return BARUtils.success_exit(True)
else:
return BARUtils.success_exit(False)
def get(self, table_id=""):
"""Returns the list of samples in the table with the given ID"""
con = db.get_engine(bind="summarization")
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(db.select([tbl.c.Sample]).distinct())
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
[values.append(row.Sample) for row in rows]
return BARUtils.success_exit(values)
def test_is_integer(self):
# Valid result
result = BARUtils.is_integer('5')
self.assertTrue(result)
# Valid but too large
result = BARUtils.is_integer('99999999999999')
self.assertFalse(result)
# Invalid
result = BARUtils.is_integer('abc')
self.assertFalse(result)
def test_is_integer(self):
# Valid result
result = BARUtils.is_integer("5")
self.assertTrue(result)
# Valid but too large
result = BARUtils.is_integer("99999999999999")
self.assertFalse(result)
# Invalid
result = BARUtils.is_integer("abc")
self.assertFalse(result)
def test_is_arabidopsis_gene_valid(self):
# Valid gene
result = BARUtils.is_arabidopsis_gene_valid('At1g01010')
self.assertTrue(result)
result = BARUtils.is_arabidopsis_gene_valid('At1g01010.1')
self.assertTrue(result)
# Invalid gene
result = BARUtils.is_arabidopsis_gene_valid('abc')
self.assertFalse(result)
result = BARUtils.is_arabidopsis_gene_valid('At1g01010.11')
self.assertFalse(result)
def test_is_arabidopsis_gene_valid(self):
# Valid gene
result = BARUtils.is_arabidopsis_gene_valid("At1g01010")
self.assertTrue(result)
result = BARUtils.is_arabidopsis_gene_valid("At1g01010.1")
self.assertTrue(result)
# Invalid gene
result = BARUtils.is_arabidopsis_gene_valid("abc")
self.assertFalse(result)
result = BARUtils.is_arabidopsis_gene_valid("At1g01010.11")
self.assertFalse(result)
def get(self, gene_id=''):
""" Endpoint returns annotated SNP poplar data in order of (to match A th API format):
AA pos (zero-indexed), sample id, 'missense_variant','MODERATE', 'MISSENSE', codon/DNA base change,
AA change (DH), pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype
values with single quotes are fixed """
results_json = []
# Escape input
gene_id = escape(gene_id)
if BARUtils.is_poplar_gene_valid(gene_id) is False:
return BARUtils.error_exit('Invalid gene id'), 400
try:
rows = db.session.query(ProteinReference, SnpsToProtein, SnpsReference). \
select_from(ProteinReference). \
join(SnpsToProtein). \
join(SnpsReference). \
filter(ProteinReference.gene_identifier == gene_id).all()
# BAR A Th API format is chr, AA pos (zero-indexed), sample id, 'missense_variant',
# 'MODERATE', 'MISSENSE', codon/DNA base change, AA change (DH),
# pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype
for protein, snpsjoin, snpstbl in rows:
itm_lst = [
snpstbl.chromosome,
# snpstbl.chromosomal_loci,
snpsjoin.aa_pos - 1, # zero index-ed
snpstbl.sample_id,
'missense_variant',
'MODERATE',
'MISSENSE',
str(snpsjoin.transcript_pos) + snpsjoin.ref_DNA + '>' +
snpsjoin.alt_DNA,
snpsjoin.ref_aa + snpsjoin.alt_aa,
None,
re.sub(r".\d$", '', protein.gene_identifier),
'protein_coding',
'CODING',
protein.gene_identifier,
None,
]
results_json.append(itm_lst)
except OperationalError:
return BARUtils.error_exit('An internal error has occurred'), 500
# Return results if there are data
if len(results_json) > 0:
return BARUtils.success_exit(results_json)
else:
return BARUtils.error_exit(
'There are no data found for the given gene')
def get(self, table_id="", user_string=""):
"""Returns all genes that contain a given string as part of their name"""
con = db.get_engine(bind="summarization")
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(
db.select([tbl.c.Gene]).where(
tbl.c.Gene.contains(user_string)).distinct())
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
[values.append(row.Gene) for row in rows]
return BARUtils.success_exit(values)
def get(self, table_id=""):
"""Returns the list of genes in the table with the given ID"""
key = request.headers.get("x-api-key")
if SummarizationGeneExpressionUtils.decrement_uses(key):
con = db.get_engine(bind="summarization")
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
values = []
try:
rows = con.execute(db.select([tbl.c.Gene]).distinct())
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
[values.append(row.Gene) for row in rows]
return BARUtils.success_exit(values)
else:
return BARUtils.error_exit("Invalid API key")
def get(self, table_id=''):
"""Drops the table with the given ID
"""
if request.remote_addr != '127.0.0.1':
return BARUtils.error_exit('Forbidden'), 403
tbl = SummarizationGeneExpressionUtils.get_table_object(table_id)
tbl.drop()
def post(self):
if request.method == 'POST':
response_json = request.get_json()
df = pandas.DataFrame.from_records([response_json])
con = db.get_engine(bind='summarization')
try:
reqs = Requests()
users = Users()
row_req = reqs.query.filter_by(email=df.email[0]).first()
row_users = users.query.filter_by(email=df.email[0]).first()
if row_req is None and row_users is None:
df.to_sql('requests', con, if_exists='append', index=False)
else:
return BARUtils.error_exit('E-mail already in use'), 409
except SQLAlchemyError:
return BARUtils.error_exit('Internal server error'), 500
def post(self):
"""Returns a list of files stored in the user's folder
"""
if request.method == 'POST':
api_key = request.headers.get('x-api-key')
files = []
for file in os.walk(DATA_FOLDER + api_key):
files.append(file[2])
return BARUtils.success_exit(files)
def get(self, file_id):
"""Returns a specific file stored in the user's folder"""
if request.method == "GET":
api_key = request.headers.get("x-api-key")
filename = os.path.join(DATA_FOLDER, api_key, file_id)
if os.path.isfile(filename):
return send_file(filename)
else:
return BARUtils.error_exit("File not found"), 404
def post(self):
"""Returns a list of files stored in the user's folder"""
if request.method == "POST":
api_key = request.headers.get("x-api-key")
files = []
if os.path.exists(os.path.join(DATA_FOLDER, api_key)):
for file in os.walk(os.path.join(DATA_FOLDER, api_key)):
files.append(file[2])
return BARUtils.success_exit(files)
def get(self, species="", database="", gene_id=""):
"""This end point returns RNA-Seq gene expression data"""
# Variables
species = escape(species)
database = escape(database)
gene_id = escape(gene_id)
results = RNASeqUtils.get_data(species, database, gene_id)
if results["success"]:
# Return results if there are data
if len(results["data"]) > 0:
return BARUtils.success_exit(results["data"])
else:
return BARUtils.error_exit(
"There are no data found for the given gene")
else:
return BARUtils.error_exit(results["error"]), results["error_code"]
def post(self):
"""Validates a reCaptcha value using our secret token
"""
if request.method == 'POST':
json = request.get_json()
value = json['response']
key = os.environ.get('CAPTCHA_KEY')
if key:
ret = requests.post(
'https://www.google.com/recaptcha/api/siteverify',
data={
'secret': key,
'response': value
})
return BARUtils.success_exit(ret.text)
else:
return BARUtils.error_exit(
'Forbidden: CAPTCHA key is not found'), 403
def post(self):
"""Validates a reCaptcha value using our secret token"""
if request.method == "POST":
json = request.get_json()
value = json["response"]
key = os.environ.get("CAPTCHA_KEY")
if key:
ret = requests.post(
"https://www.google.com/recaptcha/api/siteverify",
data={
"secret": key,
"response": value
},
)
return BARUtils.success_exit(ret.text)
else:
return BARUtils.error_exit(
"Forbidden: CAPTCHA key is not found"), 403
def get(self, species='', database='', gene_id=''):
"""This end point returns RNA-Seq gene expression data"""
# Variables
species = escape(species)
database = escape(database)
gene_id = escape(gene_id)
results = RNASeqUtils.get_data(species, database, gene_id)
if results['success']:
# Return results if there are data
if len(results['data']) > 0:
return BARUtils.success_exit(results['data'])
else:
return BARUtils.error_exit(
'There are no data found for the given gene')
else:
return BARUtils.error_exit(results['error']), results['error_code']
def post(self):
"""Verify if an API key provided by the user exists in the database"""
if request.method == "POST":
tbl = Users()
json = request.get_json()
key = json["key"]
try:
row = tbl.query.filter_by(api_key=key).first()
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
if row is None:
return BARUtils.error_exit("API key not found"), 404
else:
if row.uses_left > 0:
return BARUtils.success_exit(True)
else:
return BARUtils.error_exit("API key expired"), 401