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 get_table_object(table_name):
metadata = db.MetaData()
table_object = db.Table(
table_name,
metadata,
autoload=True,
autoload_with=db.get_engine(bind="summarization"),
)
return table_object
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, 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 decrement_uses(key):
"""Subtracts 1 from the uses_left column of the user whose key matches the given string
:param key: The user's API key
"""
if SummarizationGeneExpressionUtils.validate_api_key(key):
tbl = SummarizationGeneExpressionUtils.get_table_object("users")
con = db.get_engine(bind="summarization")
try:
con.execute(
db.update(tbl).where(tbl.c.api_key == key).values(
uses_left=(tbl.c.uses_left - 1)))
db.session.commit()
except SQLAlchemyError as e:
error = str(e.__dict__["orig"])
return error
return True
else:
return False
def validate_api_key(key):
"""Checks if a given API key is in the Users database
:param key: The API key to be checked
"""
tbl = SummarizationGeneExpressionUtils.get_table_object("users")
con = db.get_engine(bind="summarization")
try:
row = con.execute(
db.select([tbl.c.uses_left
]).where(tbl.c.api_key == key)).first()
except SQLAlchemyError as e:
error = str(e.__dict__["orig"])
return error
if row is None:
return False
else:
if row.uses_left > 0:
return True
else:
return False
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")
def get(self):
"""Get a user's details from the server"""
if request.method == "GET":
key = request.headers.get("X-Api-Key")
tbl = SummarizationGeneExpressionUtils.get_table_object("users")
con = db.get_engine(bind="summarization")
values = []
try:
rows = con.execute(db.select("*").where(tbl.c.api_key == key))
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
[
values.append([
row.first_name,
row.last_name,
row.email,
row.telephone,
row.contact_type,
]) 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 post(self):
"""Approve a request from the database and add it to the Users table"""
if request.method == "POST":
response_json = request.get_json()
email = response_json["email"]
password = response_json["password"]
if ApiManagerUtils.check_admin_pass(password):
table = Requests()
values = []
try:
rows = table.query.filter_by(email=email).all()
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
key = uuid.uuid4().hex
[
values.append({
"first_name": row.first_name,
"last_name": row.last_name,
"email": row.email,
"telephone": row.telephone,
"contact_type": row.contact_type,
"date_added": datetime.now(),
"status": "user",
"api_key": key,
"uses_left": 25,
}) for row in rows
]
df = pandas.DataFrame.from_records([values[0]])
con = db.get_engine(bind="summarization")
try:
df.to_sql("users", con, if_exists="append", index=False)
el = table.query.filter_by(email=email).one()
db.session.delete(el)
except SQLAlchemyError:
return BARUtils.error_exit("Internal server error"), 500
return BARUtils.success_exit(key)
else:
return BARUtils.error_exit("Forbidden"), 403