def main():
app = connexion.App(__name__, specification_dir='./openapi/')
app.app.json_encoder = encoder.JSONEncoder
app.add_api('openapi.yaml',
arguments={'title': 'pathoLogic'},
pythonic_params=True)
# Serve results under /v1/result/PATH
app.app.config['STATIC_URL_PATH'] = os.path.abspath(
os.getenv('BASE_DIR', os.getcwd()))
CORS(app.app) # enable CORS everywhere
# Use dictionary as DB
with app.app.app_context():
get_db()
@app.app.teardown_appcontext
def close_db(e=None):
db = g.pop('db', None)
if db is not None:
pickle.dump(
db,
open(
os.path.join(os.getenv('BASE_DIR', os.getcwd()),
'pathoLogic.db'), 'wb'))
# Create route for nextflow weblog (assembly)
@app.app.route('/v1/nf_assembly/<runid>', methods=['POST'])
def nf_assembly(runid):
req_data = request.get_json()
db = get_db()
db['status_hybridassembly'][runid] = req_data
#print(json.dumps(db['status_assembly'][runid]))
if req_data['event'] == 'process_completed':
for sID in db['runs'][runid]:
db['samples'][sID]['status'] = 'finished'
return 'NF Request received'
# Create route for nextflow weblog (plasmident)
@app.app.route('/v1/nf_plasmident/<runid>', methods=['POST'])
def nf_plasmident(runid):
req_data = request.get_json()
db = get_db()
db['status_plasmident'][runid] = req_data
#print(json.dumps(db['status_plasmident'][runid]))
if req_data['event'] == 'process_completed':
for sID in db['runs'][runid]:
db['samples'][sID]['status'] = 'finished'
return 'NF Request received'
production = os.getenv('PRODUCTION', False)
app.run(port=os.getenv('HTTP_PORT', 8080),
debug=not production,
use_debugger=not production,
use_reloader=not production,
passthrough_errors=not production)
def nf_plasmident(runid):
req_data = request.get_json()
db = get_db()
db['status_plasmident'][runid] = req_data
#print(json.dumps(db['status_plasmident'][runid]))
if req_data['event'] == 'process_completed':
for sID in db['runs'][runid]:
db['samples'][sID]['status'] = 'finished'
return 'NF Request received'
def status_get(): # noqa: E501
"""Get list of all sample statuses
# noqa: E501
:rtype: List[object]
"""
db = get_db()
return [{
'id': sample,
'status': db['samples'][sample]['status']
} for sample in db['samples'].keys()]
def samples_post(user, body=None): # noqa: E501
"""Create new samples
# noqa: E501
:param body:
:type body: dict | bytes
:rtype: Sample
"""
# Create samplepath
samplepath = os.path.join(os.environ.get('BASE_DIR', os.getcwd()),
'samples')
if not os.path.isdir(samplepath):
os.mkdir(samplepath)
# Save config and read files for each sample in new folder
for s in body['samples']:
conf = body['config']
if os.path.isdir(os.path.join(samplepath, s['id'])):
raise BadRequest("Sample with ID: {} exists already.".format(
s['id']))
os.mkdir(os.path.join(samplepath, s['id']))
with open(os.path.join(samplepath, s['id'], "nf_config.json"),
'w') as outfile:
json.dump(conf, outfile)
with open(os.path.join(samplepath, s['id'], "read_locations.tsv"),
'w') as outfile:
if not "path_lr" in s:
raise BadRequest(
"Submitted incomplete sample {}, long run path is missing."
.format(s['id']))
paths = [
join_read_path_with_data_dir(read_path, user) for read_path in
[s['path_lr'],
s.get('path_sr1', ""),
s.get('path_sr2', "")] if len(read_path)
]
outfile.write(s['id'] + '\t' + "\t".join(paths) + '\n')
db = get_db()
db['samples'][s['id']] = {
'user_id': user,
'id': s['id'],
'created': str(datetime.utcnow()),
'last_updated': str(datetime.utcnow()),
'status': "created",
'zip': None
}
return body['samples']
def samples_sample_iddelete(sample_id, user):
# Get current database
db = get_db()
samples = sample_id.split(',')
if not all(map(lambda sample: db['samples'][sample]['user_id'] == user, samples)):
raise BadRequest("You are trying to start a sample for a different user. I am afraid I can't do that, Dave.")
for sID in samples:
sample_folder_path = os.path.join(os.getenv('DATA_DIR', os.getcwd()), user)
if os.path.exists(sample_folder_path):
shutil.rmtree(sample_folder_path) # remove samples from FS
db['samples'].pop(sID) # remove samples from database
return jsonify([{'id': sID} for sID in samples])
def samples_get(user): # noqa: E501
"""List all samples
# noqa: E501
:rtype: List[Sample]
"""
db = get_db()
# filter samples without user id
samples = [
sample for sample in db['samples'].keys()
if 'user_id' in db['samples'][sample]
]
return [
format_sample(db['samples'][sample]) for sample in samples
if db['samples'][sample]['user_id'] == user
]
def result_sample_idget(sample_id): # noqa: E501
"""Lists results for given sample
# noqa: E501
:param sample_id: Comma seperated list of results to return
:type sample_id: List[str]
:rtype: InlineResponse2002
"""
db = get_db()
samples = sample_id.split(',')
sample = [db['samples'][sample] for sample in db['samples'].keys() if sample in samples][0]
return {'id':sample['id'],
'result': {
'statistics_path': 'mystats',
'zip_path': os.path.basename(sample['zip'])
}
}
def samples_sample_idput(sample_id, user): # noqa: E501
"""Starts one or multiple sample via ID
# noqa: E501
:param sample_id:
:type sample_id: List[str]
:rtype: jsonify
"""
# Get current database
db = get_db()
samples = sample_id.split(',')
if not all(map(lambda sample: db['samples'][sample]['user_id'] == user, samples)):
raise BadRequest("You are trying to start a sample for a different user. I am afraid I can't do that, Dave.")
# Set sample status to started
for sID in samples:
db['samples'][sID]['status'] = 'started'
#Try to run all this stuff
# Create run folder
runspath = os.path.join(os.environ.get('BASE_DIR', os.getcwd()), 'runs')
if not os.path.isdir(runspath):
os.mkdir(runspath)
runid = str(uuid.uuid4())
runpath = os.path.join(runspath, runid)
if not os.path.isdir(runpath):
os.mkdir(runpath)
# Get nextflow paths
nfexecutable = os.path.join(os.environ.get('BASE_DIR', os.getcwd()), 'nextflow')
nf_hybridassembly = os.path.join(os.environ.get('BASE_DIR', os.getcwd()), 'hybridassembly', 'main.nf')
nf_plasmident = os.path.join(os.environ.get('BASE_DIR', os.getcwd()), 'plasmIDent', 'main.nf')
# Set sample status to started
for sID in samples:
db['samples'][sID]['status'] = 'started'
# Assign samples to run
db['runs'][runid] = samples
# Copy input and config files to run folder
status = 0
status += os.system("cat " + " ".join([os.path.join(os.environ.get('BASE_DIR', os.getcwd()),
'samples', sID, 'read_locations.tsv') for sID in samples]) +
" >> " + os.path.join(runpath, "read_locations.tsv"))
status += os.system("cp " + os.path.join(os.environ.get('BASE_DIR', os.getcwd()),
'samples', sample_id, "nf_config.json") + " " + os.path.join(runpath,
"nf_config.json"))
# Run Hybrid assembly
call_ha = ("cd " + runpath + " && " + nfexecutable +
" run " + nf_hybridassembly + " -profile app " +
" --outDir " + runpath +
" --input read_locations.tsv " +
"-params-file nf_config.json -with-weblog " +
"http://localhost:"+os.environ.get('HTTP_PORT',"8080")+"/v1/nf_assembly/" + runid)
print(call_ha)
status += os.system("cd " + runpath + " && " + call_ha)
# Run plasmident
call_pi = (nfexecutable + " run " + nf_plasmident + " -profile app " +
" --outDir " + runpath +
" --input file_paths_plasmident.tsv " +
"-params-file nf_config.json -with-weblog "+
"http://localhost:"+os.environ.get('HTTP_PORT',"8080")+"/v1/nf_plasmident/" + runid)
print(call_pi)
status += os.system("cd " + runpath + " && " + call_pi)
if status == 0:
for sID in samples:
# Zip output folders
zip_path = os.path.join(runpath, sID)
zip_name = os.path.join(zip_path, sID + '_pathoLogic_results')
shutil.make_archive(zip_name, 'zip', root_dir=zip_path, base_dir=zip_path)
db['samples'][sID]['zip'] = zip_name + '.zip'
# Store ref to summary statistics file in db
stats_file = os.path.join(runpath, sID, "qc", "qc_summary_" + sID + '.json')
db['samples'][sID]['assembly_stats'] = stats_file
else:
# Set sample status to errored
for sID in samples:
db['samples'][sID]['status'] = 'error'
return jsonify([{'id': sID, 'status': 'error'} for sID in samples])
return jsonify([{'id': sID, 'status': 'started'} for sID in samples])