def search(args):
"""
args contains a dict with one or key:values
locus is AGI identifier and is mandatory
"""
locus = args["locus"].upper()
dedupe = args["dedupe"]
"""
Make the request to the remote service
"""
response = tools.do_request(locus)
"""
Iterate through the results
Foreach record from the remote service, build the response json
Print this json to stdout followed by a record separator "---"
ADAMA takes care of serializing these results
"""
nodes = []
edges = []
proteins = {}
for result in response.iter_lines():
fields = result.strip().split("\t")
id_a = (tools.getProteinXref(fields[0]))[0]
id_b = (tools.getProteinXref(fields[1]))[0]
locus_a = tools.getLocus(fields[4])
locus_b = tools.getLocus(fields[5])
# handle nodes
if not proteins.has_key(id_a["id"]):
nodes.append(tools.createNodeRecord(id_a, locus_a))
proteins[id_a["id"]] = 1
if not proteins.has_key(id_b["id"]):
nodes.append(tools.createNodeRecord(id_b, locus_b))
proteins[id_b["id"]] = 1
# handle edges
edge = tools.createEdgeRecord(fields)
if dedupe:
if not tools.isEdgeDuplicate(edges, edge):
edges.append(edge)
else:
edges.append(edge)
elements = {"nodes": nodes, "edges": edges}
return "application/json", json.dumps(elements)
def search(args):
"""
args contains a dict with one or key:values
locus is AGI identifier and is mandatory
"""
locus = args['locus'].upper()
"""
Make the request to the remote service
"""
response = tools.do_request(locus)
"""
Iterate through the results
Foreach record from the remote service, build the response json
Print this json to stdout followed by a record separator "---"
ADAMA takes care of serializing these results
"""
for result in response.iter_lines():
fields = result.strip().split('\t')
record = {
'locus': locus,
'class': 'locus_property',
'source_text_description': 'Molecular Interactions',
'interaction_record': {
'unique_identifier_for_interactor_a': tools.getProteinXref(fields[0]),
'unique_identifier_for_interactor_b': tools.getProteinXref(fields[1]),
'alt_identifier_for_interactor_a': tools.getValue(fields[2]),
'alt_identifier_for_interactor_b': tools.getValue(fields[3]),
'aliases_for_a': tools.getValue(fields[4]),
'aliases_for_b': tools.getValue(fields[5]),
'interaction_detection_methods': tools.getDescriptionValueXref(fields[6]),
'first_author': fields[7],
'publication_identifier': tools.getValueXref(fields[8]),
'ncbi_tax_identifier_for_interactor_a': tools.getDescriptionValueXref(fields[9]),
'ncbi_tax_identifier_for_interactor_b': tools.getDescriptionValueXref(fields[10]),
'interaction_types': tools.getDescriptionValueXref(fields[11]),
'source_databases': tools.getDescriptionValueXref(fields[12]),
'interaction_identifiers_in_source': tools.getInteractionXref(fields[13]),
'confidence_score': tools.getRawValue(fields[14])
}
}
print json.dumps(record, indent=2)
print '---'
