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 get(self, table_id, sample, gene):
"""Returns the value for a given gene and sample. If no sample is given returns all values for that gene"""
if not BARUtils.is_arabidopsis_gene_valid(gene):
return BARUtils.success_exit("Invalid gene ID"), 400
else:
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)
if sample == "":
values = {}
try:
rows = con.execute(
tbl.select(tbl.c.Value).where(tbl.c.Gene == gene))
except SQLAlchemyError:
return BARUtils.error_exit(
"Internal server error"), 500
for row in rows:
values.update({str(row.Sample): float(row.Value)})
else:
values = []
try:
rows = con.execute(
tbl.select(tbl.c.Value).where(
tbl.c.Sample == sample).where(
tbl.c.Gene == gene))
except SQLAlchemyError:
return BARUtils.error_exit(
"Internal server error"), 500
[values.append(row.Value) for row in rows]
return BARUtils.success_exit(values)
else:
return BARUtils.error_exit("Invalid API key")
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 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):
"""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 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 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):
"""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):
"""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 get(self, species='', gene_id=''):
"""This end point provides gene alias given a gene ID."""
aliases = []
# Escape input
species = escape(species)
gene_id = escape(gene_id)
if species == 'arabidopsis':
if BARUtils.is_arabidopsis_gene_valid(gene_id):
try:
rows = AgiAlias.query.filter_by(agi=gene_id).all()
except OperationalError:
return BARUtils.error_exit(
'An internal error has occurred'), 500
[aliases.append(row.alias) for row in rows]
else:
return BARUtils.error_exit('Invalid gene id'), 400
else:
return BARUtils.error_exit('No data for the given species')
# Return results if there are data
if len(aliases) > 0:
return BARUtils.success_exit(aliases)
else:
return BARUtils.error_exit(
'There are no data found for the given gene')
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):
"""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 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='', gene_id=''):
"""This end point provides gene isoforms given a gene ID.
Only genes/isoforms with pdb structures are returned"""
gene_isoforms = []
# Escape input
species = escape(species)
gene_id = escape(gene_id)
if species == 'arabidopsis':
if BARUtils.is_arabidopsis_gene_valid(gene_id):
try:
rows = isoforms.query.filter_by(gene=gene_id).all()
except OperationalError:
return BARUtils.error_exit(
'An internal error has occurred'), 500
[gene_isoforms.append(row.isoform) for row in rows]
# Found isoforms
if len(gene_isoforms) > 0:
return BARUtils.success_exit(gene_isoforms)
else:
return BARUtils.error_exit('Invalid gene id'), 400
elif species == 'poplar':
if BARUtils.is_poplar_gene_valid(gene_id):
# Path is the location of poplar pdb file
if os.environ.get('BAR'):
path = '/DATA/ePlants_Data/eplant_poplar/protein_structures/'
else:
path = os.getcwd(
) + '/data/gene_information/gene_isoforms/'
path += gene_id + '.pdb'
if os.path.exists(path) and os.path.isfile(path):
return BARUtils.success_exit(gene_id)
else:
return BARUtils.error_exit('Invalid gene id'), 400
else:
return BARUtils.error_exit('No data for the given species')
return BARUtils.error_exit(
'There are no data found for the given gene')
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
# Todo: I guess this is work in progress.
if row is None:
return BARUtils.success_exit('Do data found')
else:
if row.uses_left > 0:
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 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 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)
if ApiManagerUtils.send_email():
return BARUtils.success_exit("Data added, email sent")
else:
return BARUtils.success_exit(
"Data added, email failed")
else:
return BARUtils.error_exit("E-mail already in use"), 409
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
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, species="", gene_id=""):
"""This end point provides gene isoforms given a gene ID.
Only genes/isoforms with pdb structures are returned"""
gene_isoforms = []
# Escape input
species = escape(species)
gene_id = escape(gene_id)
# Set the database and check if genes are valid
if species == "arabidopsis":
database = eplant2_isoforms()
if not BARUtils.is_arabidopsis_gene_valid(gene_id):
return BARUtils.error_exit("Invalid gene id"), 400
elif species == "poplar":
database = eplant_poplar_isoforms
if not BARUtils.is_poplar_gene_valid(gene_id):
return BARUtils.error_exit("Invalid gene id"), 400
# Format the gene first
gene_id = BARUtils.format_poplar(gene_id)
elif species == "tomato":
database = eplant_tomato_isoforms
if not BARUtils.is_tomato_gene_valid(gene_id, False):
return BARUtils.error_exit("Invalid gene id"), 400
else:
return BARUtils.error_exit("No data for the given species")
# Now get the data
try:
rows = database.query.filter_by(gene=gene_id).all()
except OperationalError:
return BARUtils.error_exit("An internal error has occurred"), 500
[gene_isoforms.append(row.isoform) for row in rows]
# Found isoforms
if len(gene_isoforms) > 0:
return BARUtils.success_exit(gene_isoforms)
else:
return BARUtils.error_exit(
"There are no data found for the given gene")
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):
"""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
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):
"""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")
species = json["species"]
email = json["email"]
aliases = json["aliases"]
gtf = GTF_DICT[species]
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = {
"geneSummarization.summarizeGenesScript":
"./summarize_genes.R",
"geneSummarization.downloadFilesScript":
"./downloadDriveFiles.py",
"geneSummarization.chrsScript": "./chrs.py",
"geneSummarization.folderId": json["folderId"],
"geneSummarization.credentials": "./data/credentials.json",
"geneSummarization.token": "./data/token.pickle",
"geneSummarization.species": species,
"geneSummarization.gtf": gtf,
"geneSummarization.aliases": str(aliases),
"geneSummarization.id": key,
"geneSummarization.pairedEndScript": "./paired.sh",
"geneSummarization.insertDataScript": "./insertData.py",
"geneSummarization.barEmailScript": "./bar_email.py",
"geneSummarization.errorEmailScript": "./error_email.py",
"geneSummarization.email": email,
}
# Send request to Cromwell
path = os.path.join(SUMMARIZATION_FILES_PATH, "rpkm.wdl")
file = tempfile.TemporaryFile(mode="w+")
file.write(jsonlib.dumps(inputs))
file.seek(0)
files = {
"workflowSource": ("rpkm.wdl", open(path, "rb")),
"workflowInputs": ("rpkm_inputs.json", file.read()),
}
requests.post(CROMWELL_URL + "/api/workflows/v1", files=files)
file.close()
# Return ID for future accessing
return BARUtils.success_exit(key), 200
else:
return BARUtils.error_exit("Invalid API key")
def post(self):
"""Delete a request from the database"""
if request.method == "POST":
response_json = request.get_json()
password = response_json["password"]
if ApiManagerUtils.check_admin_pass(password):
response_json = request.get_json()
table = Requests()
try:
el = table.query.filter_by(
email=response_json["email"]).one()
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
db.session.delete(el)
db.session.commit()
# table.query.filter_by(email=response_json['email']).delete()
return BARUtils.success_exit(True)
else:
return BARUtils.error_exit("Forbidden"), 403
def post(self):
"""This function adds a CSV's data to the database. This is only called by the Cromwell server after receiving the user's file."""
if request.remote_addr != "127.0.0.1":
return BARUtils.error_exit("Forbidden"), 403
if request.method == "POST":
key = request.headers.get("X-Api-Key")
if SummarizationGeneExpressionUtils.decrement_uses(key):
csv = request.get_json()["csv"]
db_id = request.get_json()["uid"]
df = pandas.read_csv(csv)
db_id = db_id.split(".")[0]
df = df.melt(id_vars=["Gene"],
var_name="Sample",
value_name="Value")
db_id = db_id.split("/")[len(db_id.split("/")) - 1]
con = db.get_engine(bind="summarization")
df.to_sql(db_id, con, if_exists="append", index=True)
return BARUtils.success_exit("Success")
else:
return BARUtils.error_exit("Invalid API key")
