diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 62 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes.html | 2 |
2 files changed, 61 insertions, 3 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 5f6e4a6..02e8078 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,6 +1,11 @@ """Views handling ('classical') phenotypes.""" +import sys +import uuid +import json +from pathlib import Path from functools import wraps +from redis import Redis from requests.models import Response from MySQLdb.cursors import DictCursor from flask import (flash, @@ -11,6 +16,12 @@ from flask import (flash, render_template, current_app as app) +# from r_qtl import r_qtl2 as rqtl2 +from r_qtl import r_qtl2_qc as rqc +from r_qtl import exceptions as rqe + +from uploader import jobs +from uploader.files import save_file#, fullpath from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login from uploader.db_utils import database_connection @@ -299,12 +310,59 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= redirect_uri="species.populations.phenotypes.list_datasets") def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# pylint: disable=[unused-argument, too-many-locals] """Add one or more phenotypes to the dataset.""" - with (database_connection(app.config["SQL_URI"]) as conn, - conn.cursor(cursorclass=DictCursor) as cursor): + add_phenos_uri = redirect(url_for( + "species.populations.phenotypes.add_phenotypes", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"])) + _redisuri = app.config["REDIS_URL"] + _sqluri = app.config["SQL_URI"] + with (Redis.from_url(_redisuri, decode_responses=True) as rconn, + # database_connection(_sqluri) as conn, + # conn.cursor(cursorclass=DictCursor) as cursor + ): if request.method == "GET": return render_template("phenotypes/add-phenotypes.html", species=species, population=population, dataset=dataset, activelink="add-phenotypes") + + try: + ## Handle huge files here... + phenobundle = save_file(request.files["phenotypes-bundle"], + Path(app.config["UPLOAD_FOLDER"])) + rqc.validate_bundle(phenobundle) + except AssertionError as _aerr: + app.logger.debug("File upload error!", exc_info=True) + flash("Expected a zipped bundle of files with phenotypes' " + "information.", + "alert-danger") + return add_phenos_uri + except rqe.RQTLError as rqtlerr: + app.logger.debug("Bundle validation error!", exc_info=True) + flash("R/qtl2 Error: " + " ".join(rqtlerr.args), "alert-danger") + return add_phenos_uri + + _jobid = uuid.uuid4() + _namespace = jobs.jobsnamespace() + _ttl_seconds = app.config["JOBS_TTL_SECONDS"] + _job = jobs.initialise_job( + rconn, + _namespace, + str(_jobid), + [sys.executable, "-m", "scripts.rqtl2.phenotypes_qc", _sqluri, + _redisuri, _namespace, str(_jobid), str(species["SpeciesId"]), + str(population["Id"]), str(dataset["Id"]), "--redisexpiry", + str(_ttl_seconds)], "phenotype_qc", _ttl_seconds, + {"job-metadata": json.dumps({ + "speciesid": species["SpeciesId"], + "populationid": population["Id"], + "datasetid": dataset["Id"], + "bundle": str(phenobundle.absolute())})}) + # jobs.launch_job( + # _job, + # redisuri, + # f"{app.config['UPLOAD_FOLDER']}/job_errors") + raise NotImplementedError("Please implement this...") diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html index 8ad6999..196bc69 100644 --- a/uploader/templates/phenotypes/add-phenotypes.html +++ b/uploader/templates/phenotypes/add-phenotypes.html @@ -57,7 +57,7 @@ <div class="form-group"> <input type="submit" value="upload phenotypes" - class="not-implemented btn btn-primary" /> + class="btn btn-primary" /> </div> </form> </div> |