def get(self, fixed_pdb='', moving_pdb=''):
"""This end point returns the superimposition of the moving PDB onto moving PDB in PDB format"""
fixed_pdb = escape(fixed_pdb)
moving_pdb = escape(moving_pdb)
arabidopsis_pdb_path = '/var/www/html/eplant_legacy/java/Phyre2-Models/Phyre2_'
poplar_pdb_path = '/var/www/html/eplant_poplar/pdb/'
phenix_pdb_link = 'https://bar.utoronto.ca/phenix-pdbs/'
phenix_pdb_path = '/var/www/html/phenix-pdbs/'
# Check if genes ids are valid
if BARUtils.is_arabidopsis_gene_valid(fixed_pdb):
fixed_pdb_path = arabidopsis_pdb_path + fixed_pdb.upper() + '.pdb'
elif BARUtils.is_poplar_gene_valid(fixed_pdb):
fixed_pdb_path = poplar_pdb_path + BARUtils.format_poplar(
fixed_pdb) + '.pdb'
else:
return BARUtils.error_exit('Invalid fixed pdb gene id'), 400
if BARUtils.is_arabidopsis_gene_valid(moving_pdb):
moving_pdb_path = arabidopsis_pdb_path + moving_pdb.upper(
) + '.pdb'
elif BARUtils.is_poplar_gene_valid(moving_pdb):
moving_pdb_path = poplar_pdb_path + BARUtils.format_poplar(
moving_pdb) + '.pdb'
else:
return BARUtils.error_exit('Invalid moving pdb gene id'), 400
# Check if model already exists
phenix_file_name = fixed_pdb.upper() + "-" + moving_pdb.upper(
) + "-phenix.pdb"
response = requests.get(phenix_pdb_link + phenix_file_name)
# If not, generate the model
if response.status_code != 200:
subprocess.run([
'phenix.superpose_pdbs',
'file_name=' + phenix_pdb_path + phenix_file_name,
fixed_pdb_path, moving_pdb_path
])
return redirect(phenix_pdb_link + phenix_file_name)
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 test_format_poplar(self):
# Test format
result = BARUtils.format_poplar('potri.019g123900.1')
expected = 'Potri.019G123900.1'
self.assertEqual(result, expected)
