from itertools import groupby
from flask import request, abort
from flask_restx import Resource
from webserver.endpoints import api
from webserver.endpoints.request_models import sequence_post_parameters_annotations, sequence_get_parameters_annotations
from webserver.endpoints.task_interface import get_features
from webserver.endpoints.utils import check_valid_sequence
from webserver.utilities.parsers import (Source, Evidence,
annotations_to_protvista_converter,
SecondaryStructure, Disorder)
ns = api.namespace("annotations", description="Get annotations on the fly.")
def _filter_ontology(annotations, ontology):
if annotations.get(ontology):
first_k = next(goannotations for identifier, goannotations in groupby(
annotations[ontology], lambda x: x["identifier"]))
annotations[ontology] = list(first_k)
def _get_annotations_from_params(params):
sequence = params.get('sequence')
if not sequence or len(sequence) > 2000 or not check_valid_sequence(
sequence):
return abort(400,
"Sequence is too long or contains invalid characters.")
model_name = params.get('model', 'seqvec')
import io
import h5py
from flask import request, send_file, abort
from flask_restx import Resource
from webserver.endpoints import api
from webserver.endpoints.request_models import sequence_post_parameters
from webserver.endpoints.task_interface import get_embedding
from webserver.endpoints.utils import check_valid_sequence
ns = api.namespace("embeddings", description="Calculate embeddings on the fly.")
@ns.route('')
class Embeddings(Resource):
@api.expect(sequence_post_parameters, validate=True)
@api.response(200, "Returns an hdf5 file with one dataset called `sequence` "
"containing the embedding of the supplied sequence.")
@api.response(400, "Invalid input. See return message for details.")
@api.response(505, "Server error")
def post(self):
params = request.json
sequence = params.get('sequence')
if not sequence or len(sequence) > 2000 or not check_valid_sequence(sequence):
return abort(400, "Sequence is too long or contains invalid characters.")
model_name = params.get('model', 'seqvec')
import uuid
from flask import request, send_file, abort
from flask_restx import Resource
from webserver.database import get_file, get_list_of_files
from webserver.endpoints import api
from webserver.endpoints.request_models import (
file_post_parser,
request_status_parser,
request_results_parser,
)
from webserver.endpoints.utils import validate_FASTA_submission
from webserver.tasks.pipeline import run_pipeline
ns = api.namespace("pipeline", description="Run pipeline jobs")
@ns.route('')
class Pipeline(Resource):
@api.expect(file_post_parser, validate=True)
@api.response(200, "Calculated embeddings")
@api.response(400, "Invalid input. See message for details")
@api.response(505, "Server error")
def post(self):
validated_request = validate_FASTA_submission(request)
job_id = uuid.uuid4().hex
pipeline_type = request.form.get('pipeline_type', 'annotations_from_bert')
async_call = run_pipeline.apply_async(args=(job_id, validated_request.sequences, pipeline_type),
task_id=job_id)
from flask import abort
from flask_restx import Resource
from webserver.endpoints import api
from webserver.endpoints.utils import get_queues
ns = api.namespace("status", description="Get the status of the workers.")
_workers = [
'prott5', 'prott5_annotations', 'pipeline', 'colabfold',
'prott5_residue_landscape_annotations'
]
@ns.route('')
class Status(Resource):
@api.response(200, "Returns an object with active workers.")
@api.response(505, "Server error")
def get(self):
queues = get_queues()
active_workers = dict()
for worker in _workers:
active_workers[worker] = worker in queues
return active_workers
@ns.route('/<worker>')
class Status(Resource):
@api.response(
from flask import request
from flask_restx import Resource
from webserver.endpoints import api
from webserver.endpoints.request_models import sequence_get_parameters_structure, sequence_post_parameters_structure
from webserver.endpoints.task_interface import get_structure
from webserver.endpoints.utils import abort, check_valid_sequence
ns = api.namespace("structure", description="Get structure predictions on the fly.")
def _get_structure_from_params(params):
predictor = params.get('predictor', "colabfold")
sequence = params.get('sequence')
if not sequence or len(sequence) > 500 or not check_valid_sequence(sequence):
return abort(400, "Sequence is too long or contains invalid characters.")
if predictor not in {"colabfold"}:
return abort(400, "Invalid predictor specified")
ret = get_structure(predictor, sequence)
return ret
@ns.route('')
class Annotations(Resource):
@api.expect(sequence_get_parameters_structure, validate=True)
@api.response(200, "Annotations in specified format")
@api.response(201, "Created job for structure prediction")
@api.response(202, "Structure prediction request accepted")
@api.response(400, "Invalid input. See return message for details.")
@api.response(505, "Server error")