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="", gene_id=""):
"""
Endpoint returns sequence for a given gene of a particular species
Response JSON designed to be like current PHP one:
https://bar.utoronto.ca/webservices/bar_araport/get_protein_sequence_by_identifier.php?locus=AT1G01010.1
Species Supported:
- Tomato (ITAG3.2) - e.g. Solyc00g005445.1.1
"""
species = escape(species.lower())
gene_id = escape(gene_id.capitalize())
if species == "tomato":
if BARUtils.is_tomato_gene_valid(gene_id, True):
try:
rows = Tomato32SequenceInfo.query.filter_by(
gene_id=gene_id).all()
if len(rows) == 0:
return (
BARUtils.error_exit(
"There are no data found for the given gene"),
400,
)
else:
return {
"status":
"success",
"result": [{
"length": len(rows[0].full_seq) - 1,
"gene_id": rows[0].gene_id,
"sequence": rows[0].full_seq,
}]
}
except OperationalError:
return BARUtils.error_exit(
"An internal error has occurred"), 500
else:
return BARUtils.error_exit("Invalid gene id"), 400
else:
return BARUtils.error_exit("Invalid species"), 400
def post(self):
"""This end point returns gene isoforms data for a multiple genes for a species.
Only genes/isoforms with pdb structures are returned"""
json_data = request.get_json()
data = {}
# Validate json
try:
json_data = GeneIsoformsSchema().load(json_data)
except ValidationError as err:
return BARUtils.error_exit(err.messages), 400
genes = json_data["genes"]
species = json_data["species"]
# Set species and check gene ID format
if species == "arabidopsis":
database = eplant2_isoforms()
# Check if gene is valid
for gene in genes:
if not BARUtils.is_arabidopsis_gene_valid(gene):
return BARUtils.error_exit("Invalid gene id"), 400
# Query must be run individually for each species
try:
rows = database.query.filter(
eplant2_isoforms.gene.in_(genes)).all()
except OperationalError:
return BARUtils.error_exit(
"An internal error has occurred."), 500
elif species == "poplar":
database = eplant_poplar_isoforms()
for gene in genes:
# Check if gene is valid
if not BARUtils.is_poplar_gene_valid(gene):
return BARUtils.error_exit("Invalid gene id"), 400
try:
rows = database.query.filter(
eplant_poplar_isoforms.gene.in_(genes)).all()
except OperationalError:
return BARUtils.error_exit(
"An internal error has occurred."), 500
elif species == "tomato":
database = eplant_tomato_isoforms()
for gene in genes:
# Check if gene is valid
if not BARUtils.is_tomato_gene_valid(gene, False):
return BARUtils.error_exit("Invalid gene id"), 400
try:
rows = database.query.filter(
eplant_tomato_isoforms.gene.in_(genes)).all()
except OperationalError:
return BARUtils.error_exit(
"An internal error has occurred."), 500
else:
return BARUtils.error_exit("Invalid species"), 400
# If there any isoforms found, return data
if len(rows) > 0:
for row in rows:
if row.gene in data:
data[row.gene].append(row.isoform)
else:
data[row.gene] = []
data[row.gene].append(row.isoform)
return BARUtils.success_exit(data)
else:
return BARUtils.error_exit(
"No data for the given species/genes"), 400