def post(self):
"""
Process PathwayCommons paths from-to genes, return INDRA Statements.
Parameters
----------
source : list
A list of HGNC gene symbols that are the sources of paths being
searched for.
Examples: ['BRAF', 'RAF1', 'ARAF']
target : list
A list of HGNC gene symbols that are the targets of paths being
searched for.
Examples: ['MAP2K1', 'MAP2K2']
Returns
-------
statements : list[indra.statements.Statement.to_json()]
A list of extracted INDRA Statements.
"""
args = request.json
source = args.get('source')
target = args.get('target')
bp = biopax.process_pc_pathsfromto(source, target)
return _stmts_from_proc(bp)
def test_pathsfromto():
bp = biopax.process_pc_pathsfromto(['MAP2K1'], ['MAPK1'])
assert_pmids(bp.statements)
assert_source_sub_id(bp.statements)
assert unicode_strs(bp.statements)
num_unique = len({s.get_hash(shallow=False) for s in bp.statements})
assert len(bp.statements) == num_unique
def test_pathsfromto():
bp = biopax.process_pc_pathsfromto(['MAP2K1'], ['MAPK1'])
assert_pmids(bp.statements)
assert_source_sub_id(bp.statements)
assert unicode_strs(bp.statements)
num_unique = len({s.get_hash(shallow=False) for s in bp.statements})
assert len(bp.statements) == num_unique
def biopax_process_pc_pathsfromto():
"""Process PathwayCommons paths from-to genes, return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
source = body.get('source')
target = body.get('target')
bp = biopax.process_pc_pathsfromto(source, target)
return _stmts_from_proc(bp)
def biopax_process_pc_pathsfromto():
"""Process PathwayCommons paths from-to genes, return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
source = body.get('source')
target = body.get('target')
bp = biopax.process_pc_pathsfromto(source, target)
return _stmts_from_proc(bp)
def biopax_process_pc_pathsfromto():
"""Process PathwayCommons paths from-to genes, return INDRA Statements."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
source = body.get('source')
target = body.get('target')
bp = biopax.process_pc_pathsfromto(source, target)
if bp and bp.statements:
stmts = stmts_to_json(bp.statements)
res = {'statements': stmts}
return res
else:
res = {'statements': []}
return res
def test_readme_using_indra5():
from indra.sources import biopax
# Process the neighborhood of BRAF and MAP2K1
biopax_processor = biopax.process_pc_pathsfromto(['BRAF', 'RAF1'],
['MAP2K1', 'MAP2K2'])
assert biopax_processor.statements
def test_pathsfromto():
bp = biopax.process_pc_pathsfromto(['MAP2K1'], ['MAPK1'])
assert_pmids(bp.statements)
assert_source_sub_id(bp.statements)
assert (unicode_strs(bp.statements))
