def post(self):
vienna_data = self.get_argument('data', default=None)
log = {
'path': self.request.uri,
'ip': self.request.remote_ip,
'tool': 'rnaplot',
'method': self.request.method,
'date': datetime.datetime.now(),
'status': 'running'
}
logs_db['webservices'].insert(log)
rnas, base_pairs = parse_vienna(vienna_data)
rnaplot = Rnaplot()
plot = rnaplot.plot(base_pairs[0], rnas[0])
coords = []
for (index, row) in plot.iterrows():
coords.append([row['x'], row['y']])
logs_db['webservices'].update(
{'_id': log['_id']},
{'$set': {
'status': 'done',
'date': datetime.datetime.now()
}})
self.write(json_encode(coords))
def post(self):
log = {
'_id': str(ObjectId()),
'path': self.request.uri,
'tool': 'rnaplot',
'ip': self.request.remote_ip,
'method': self.request.method,
'date': datetime.datetime.now()
}
logs_db['webservices'].insert(log)
secondary_structure = self.get_argument('secondary_structure', default = None)
api_key = self.get_argument('api_key', default = None)
if not is_registered_user(api_key) or not 'rnaplot' in enabled_algorithms:
self.send_error(status_code=401)
else:
rnas, secondary_structures = parse_vienna(secondary_structure)
self.write(Rnaplot().plot(secondary_structures[0], rnas[0], raw_output = True))
def post(self):
vienna_data = self.get_argument('data', default = None)
log = {
'path': self.request.uri,
'ip': self.request.remote_ip,
'tool': 'rnaplot',
'method': self.request.method,
'date': datetime.datetime.now(),
'status': 'running'
}
logs_db['webservices'].insert(log)
rnas, base_pairs = parse_vienna(vienna_data)
rnaplot = Rnaplot()
plot = rnaplot.plot(base_pairs[0], rnas[0])
coords = []
for (index, row) in plot.iterrows():
coords.append([row['x'], row['y']])
logs_db['webservices'].update({ '_id': log['_id'] }, {'$set': { 'status' : 'done', 'date':datetime.datetime.now()}})
self.write(json_encode(coords))
def post(self):
log = {
'_id': str(ObjectId()),
'path': self.request.uri,
'tool': 'rnaplot',
'ip': self.request.remote_ip,
'method': self.request.method,
'date': datetime.datetime.now(),
'status': 'running'
}
logs_db['webservices'].insert(log)
secondary_structure = self.get_argument('secondary_structure', default = None)
api_key = self.get_argument('api_key', default = None)
if not is_registered_user(api_key) or not 'rnaplot' in enabled_algorithms:
logs_db['webservices'].update({ '_id': log['_id'] }, {'$set': { 'status' : 'error', 'date':datetime.datetime.now()}})
self.send_error(status_code=401)
else:
rnas, secondary_structures = parse_vienna(secondary_structure)
logs_db['webservices'].update({ '_id': log['_id'] }, {'$set': { 'status' : 'done', 'date':datetime.datetime.now()}})
self.write(Rnaplot().plot(secondary_structures[0], rnas[0], raw_output = True))
def on_message(self, message):
message = ujson.loads(message)
if message['header'] == 'new external tool':
for websocket in websockets:
if self == websocket:
external_tools_2_websockets[message['id']] = websocket
elif message['header'] == 'plot 2d':
#rnas, secondary_structures = parse_vienna(message['data'])
#self.write_message( {
# 'header': '2d plot',
# 'data': Rnaplot().plot(secondary_structures[0], rnas[0], raw_output = True)
# })
rnas, secondary_structures = parse_vienna(message['data'])
rna = rnas[0]
base_pairs = secondary_structures[0]
ss = base_pairs_to_secondary_structure(rna, base_pairs)
ss.find_junctions()
coords = Rnaplot().plot(base_pairs, rna)
ss_json = {'rna': {'name': rna.name, 'sequence': rna.sequence}}
helices_descriptions = []
for helix in ss.helices:
helices_descriptions.append(helix)
ss_json['helices'] = helices_descriptions
sstrand_descriptions = []
for sstrand in ss.single_strands:
sstrand_descriptions.append(sstrand)
ss_json['single-strands'] = sstrand_descriptions
tertiary_descriptions = []
for tertiary in ss.tertiary_interactions:
sstrand_descriptions.append(tertiary)
ss_json['single-strands'] = sstrand_descriptions
ss_json['coords'] = []
for index, row in coords.iterrows():
ss_json['coords'].append([int(row['x']), int(row['y'])])
self.write_message({'header': '2d plot', 'data': ss_json})
elif message['header'] == 'server load':
db = mongodb['logs']
now = datetime.datetime.now()
data = []
for i in xrange(1, 61):
counts = {'y': "-%im" % i}
time_range = {
"$gt": now - datetime.timedelta(minutes=i),
"$lte": now - datetime.timedelta(minutes=i - 1)
}
counts['running'] = db['webservices'].find({
"date": time_range,
"status": 'running'
}).count()
counts['error'] = db['webservices'].find({
"date": time_range,
"status": 'error'
}).count()
counts['done'] = db['webservices'].find({
"date": time_range,
"status": 'done'
}).count()
data.append(counts)
answer = {'header': 'server load', 'data': data}
self.write_message(answer, binary=False)
elif message['header'] == 'init booquet':
junction_diameter = 20
rfam = Rfam(use_website=True)
aligned_rnas, species, consensus2D = rfam.get_entry(
rfam_id=message['rfam_id'], nse_labels=0)
print consensus2D
structural_alignment = to_clustalw(consensus2D, aligned_rnas)
booquet_json = consensus2d_to_booquet(
structural_alignment, junction_diameter=junction_diameter)
answer = {'header': 'init booquet'}
answer['booquet_json'] = booquet_json
answer['junction_diameter'] = junction_diameter
self.write_message(answer, binary=False)
def on_message(self, message):
message = ujson.loads(message)
if message['header'] == 'new external tool':
for websocket in websockets:
if self == websocket:
external_tools_2_websockets[message['id']] = websocket
elif message['header'] == 'plot 2d':
#rnas, secondary_structures = parse_vienna(message['data'])
#self.write_message( {
# 'header': '2d plot',
# 'data': Rnaplot().plot(secondary_structures[0], rnas[0], raw_output = True)
# })
rnas, secondary_structures = parse_vienna(message['data'])
rna = rnas[0]
base_pairs = secondary_structures[0]
ss = base_pairs_to_secondary_structure(rna, base_pairs)
ss.find_junctions()
coords = Rnaplot().plot(base_pairs, rna)
ss_json = {
'rna': {
'name': rna.name,
'sequence': rna.sequence
}
}
helices_descriptions = []
for helix in ss.helices:
helices_descriptions.append(helix)
ss_json['helices'] = helices_descriptions
sstrand_descriptions = []
for sstrand in ss.single_strands:
sstrand_descriptions.append(sstrand)
ss_json['single-strands'] = sstrand_descriptions
tertiary_descriptions = []
for tertiary in ss.tertiary_interactions:
sstrand_descriptions.append(tertiary)
ss_json['single-strands'] = sstrand_descriptions
ss_json['coords'] = []
for index, row in coords.iterrows():
ss_json['coords'].append([int(row['x']), int(row['y'])])
self.write_message( {
'header': '2d plot',
'data': ss_json
})
elif message['header'] == 'server load':
db = mongodb['logs']
now = datetime.datetime.now()
data = []
for i in xrange(1, 61):
counts = {'y': "-%im"%
i}
time_range = {
"$gt": now - datetime.timedelta(minutes = i),
"$lte": now - datetime.timedelta(minutes = i-1)
}
counts['running'] = db['webservices'].find({
"date": time_range,
"status": 'running'
}).count()
counts['error'] = db['webservices'].find({
"date": time_range,
"status": 'error'
}).count()
counts['done'] = db['webservices'].find({
"date": time_range,
"status": 'done'
}).count()
data.append(counts)
answer = {
'header': 'server load',
'data': data
}
self.write_message(answer, binary = False)
elif message['header'] == 'init booquet':
junction_diameter = 20
rfam = Rfam(use_website = True)
aligned_rnas, species, consensus2D = rfam.get_entry(rfam_id = message['rfam_id'], nse_labels = 0)
print consensus2D
structural_alignment = to_clustalw(consensus2D, aligned_rnas)
booquet_json = consensus2d_to_booquet(structural_alignment, junction_diameter = junction_diameter)
answer = {'header': 'init booquet'}
answer['booquet_json'] = booquet_json
answer['junction_diameter'] = junction_diameter
self.write_message(answer, binary = False)
def on_message(self, message):
message = ujson.loads(message)
if message['header'] == 'new external tool':
for websocket in websockets:
if self == websocket:
external_tools_2_websockets[message['id']] = websocket
elif message['header'] == 'plot 2d':
#rnas, secondary_structures = parse_vienna(message['data'])
#self.write_message( {
# 'header': '2d plot',
# 'data': Rnaplot().plot(secondary_structures[0], rnas[0], raw_output = True)
# })
rnas, secondary_structures = parse_vienna(message['data'])
rna = rnas[0]
base_pairs = secondary_structures[0]
ss = base_pairs_to_secondary_structure(rna, base_pairs)
ss.find_junctions()
coords = Rnaplot().plot(base_pairs, rna)
ss_json = {
'rna': {
'name': rna.name,
'sequence': rna.sequence
}
}
helices_descriptions = []
for helix in ss.helices:
helices_descriptions.append(helix)
ss_json['helices'] = helices_descriptions
sstrand_descriptions = []
for sstrand in ss.single_strands:
sstrand_descriptions.append(sstrand)
ss_json['single-strands'] = sstrand_descriptions
tertiary_descriptions = []
for tertiary in ss.tertiary_interactions:
sstrand_descriptions.append(tertiary)
ss_json['single-strands'] = sstrand_descriptions
ss_json['coords'] = []
for index, row in coords.iterrows():
ss_json['coords'].append([int(row['x']), int(row['y'])])
self.write_message( {
'header': '2d plot',
'data': ss_json
})
elif message['header'] == 'webservices usage':
db = mongodb['logs']
now = datetime.datetime.now()
data = []
for i in xrange(1, 24):
counts = {'y': "-%ih"%
i}
time_range = {
"$gt": now - datetime.timedelta(hours = i),
"$lte": now - datetime.timedelta(hours = i-1)
}
counts['RNAfold'] = db['webservices'].find({
"date": time_range,
"tool": 'rnafold'
}).count()
counts['RNAsubopt'] = db['webservices'].find({
"date": time_range,
"tool": 'rnasubopt'
}).count()
counts['RNAalifold'] = db['webservices'].find({
"date": time_range,
"tool": 'rnaalifold'
}).count()
counts['Contrafold'] = db['webservices'].find({
"date": time_range,
"tool": 'contrafold'
}).count()
counts['RNAplot'] = db['webservices'].find({
"date": time_range,
"tool": 'rnaplot'
}).count()
counts['Mlocarna'] = db['webservices'].find({
"date": time_range,
"tool": 'mlocarna'
}).count()
counts['RNAVIEW'] = db['webservices'].find({
"date": time_range,
"tool": 'rnaview'
}).count()
data.append(counts)
answer = {
'header': 'webservices usage',
'data': data
}
self.write_message(answer, binary = False)