def derived_from_file(filename, depth):
'''search specified attributes and labels, custom query as POST'''
if request.method == 'GET': #get filenames relations at depth
msg = ''
if filename:
msg += 'Searching for {}'.format(filename)
if depth:
try:
depth = int(depth) #make sure depth is int
except ValueError:
logger.error('Depth provided was not int')
raise
msg += ' at depth {}'.format(depth)
logger.info(msg)
with cpool.get_session() as session: #get session from driver
statement = 'MATCH (n {name:{filename}})<-[:DERIVED_FROM*1..'
if depth:
statement += '{}'.format(depth)
statement += ']-(m) return distinct m' #give me unique nodes
return_me = []
logger.debug(statement) #if necessary
for r in session.run(statement, {'filename': filename}):
logger.info(r[0].properties) #testing
return_me.append(r[0].properties) #format this later
return jsonify(return_me), 200 #maybe 204 if empty... think still 200
def all_nodes():
'''Get All Nodes'''
if request.method == 'GET': #get filenames relations at depth
with cpool.get_session() as session: #get session from driver
statement = 'MATCH (n)'
statement += ' return distinct n' #give me unique nodes
return_me = []
logger.debug(statement) #if necessary
seen = {}
for r in session.run(statement):
logger.info(r[0].properties) #testing
return_me.append(r[0].properties) #format this later
return jsonify({'data': return_me
}), 200 #maybe 204 if empty... think still 200
def parents_by_name(query):
'''Get All parents for a given node'''
if request.method == 'GET': #get filenames relations at depth
with cpool.get_session() as session: #get session from driver
statement = 'MATCH (n {name:{filename}})-[:CHILD_OF]->(m)'
statement += ' return distinct m' #give me unique nodes
return_me = []
logger.debug(statement) #if necessary
seen = {}
for r in session.run(statement, {'filename': query}):
logger.info(r[0].properties) #testing
return_me.append(r[0].properties) #format this later
return jsonify({'data': return_me
}), 200 #maybe 204 if empty... think still 200
def parents_by_name_post():
'''Get All parents for a given node by passing a list'''
if request.method == 'POST': #get filenames relations at depth
return_me = []
posted_data = request.get_json(force=True)
if not posted_data:
return 'You must post a list called data containing filenames', 400
for d in posted_data:
with cpool.get_session() as session: #get session from driver
statement = 'MATCH (n {name:{filename}})-[:CHILD_OF]->(m)'
statement += ' return distinct m' #give me unique nodes
# return_me = []
logger.debug(statement) #if necessary
# seen = {}
my_obj = {d: {'parents': []}}
for r in session.run(statement, {'filename': d}):
logger.info(r[0].properties) #testing
my_obj[d]['parents'].append(
r[0].properties) #attach parent
return_me.append(my_obj)
return jsonify({'data': return_me}), 200 #maybe 204 if empty...
def taxonomoy_list(genus):
'''search specified attributes and labels, custom query as POST'''
if request.method == 'GET': #get filenames relations at depth
msg = ''
with cpool.get_session() as session: #get session from driver
statement = 'MATCH (n:fasta'
if genus:
genus = genus.lower()
statement += ':{}'.format(genus)
statement += ') return n' #give me unique nodes
return_me = []
logger.debug(statement) #if necessary
seen = {}
for r in session.run(statement):
target = r[0].properties['genus']
if genus:
target = r[0].properties['species']
if target in seen:
continue
seen[target] = 1
logger.info(target) #testing
return_me.append(target) #format this later
return jsonify({'data': return_me
}), 200 #maybe 204 if empty... think still 200
def visualize_paths(filename):
'''Get all data from parent assembly for visualization
returns a list of url and name tuples
'''
if request.method == 'GET': # get fasta and then get all others
msg = ''
count = 0
if filename:
msg += 'Searching for {}'.format(filename)
logger.info(msg)
with cpool.get_session() as session: # get session from driver
statement = 'MATCH (n {name:{filename}})-[:DERIVED_FROM*1..'
statement += ']->(m:fasta) return distinct m' # give me unique nodes
return_me = []
logger.debug(statement) # if necessary
for r in session.run(statement, {'filename': filename}):
if count == 1:
logger.warning('Multiple fasta for {}'.format(filename))
count += 1
logger.info(r[0].properties) # testing
return_me.append(r[0].properties) # get dictionary
if not return_me:
statement = 'MATCH (n:fasta {name:{filename}}) return n'
return_me = []
for r in session.run(statement, {'filename': filename}):
return_me.append(r[0].properties)
if not return_me:
logger.error('No fasta found for {}'.format(filename))
return jsonify([]), 200
fasta = return_me[0]['name']
statement = 'MATCH p=(n {name:{filename}})-[:DERIVED_FROM*1..]-(m) return distinct m;' # should be one line fix later
return_me = []
for r in session.run(statement, {'filename': fasta}):
return_me.append(r[0].properties) # get dictionary
return jsonify(return_me), 200 # maybe 204 if empty... think still 200