diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 169 |
1 files changed, 153 insertions, 16 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 2cf0ca0..23bc682 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,4 +1,6 @@ """Views handling ('classical') phenotypes."""# pylint: disable=[too-many-lines] +import io +import csv import sys import uuid import json @@ -21,12 +23,14 @@ from gn_libs import jobs as gnlibs_jobs from gn_libs.jobs.jobs import JobNotFound from gn_libs.mysqldb import database_connection +from werkzeug.datastructures import Headers from flask import (flash, request, jsonify, redirect, Blueprint, - current_app as app) + current_app as app, + Response as FlaskResponse) from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe @@ -522,6 +526,65 @@ def job_status( @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/job/<uuid:job_id>/download-errors", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def download_errors( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs):# pylint: disable=[unused-argument] + """Download the list of errors as a CSV file.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + _prefix_ = jobs.jobsnamespace() + _jobid_ = job['jobid'] + def __generate_chunks__(): + _errors_ = ( + json.loads(error) + for key in rconn.keys( + f"{_prefix_}:{str(_jobid_)}:*:errors:*") + for error in rconn.lrange(key, 0, -1)) + _chunk_no_ = 0 + _all_errors_printed_ = False + while not _all_errors_printed_: + _chunk_ = [] + try: + for _ in range(0, 1000): + _chunk_.append(next(_errors_)) + except StopIteration: + _all_errors_printed_ = True + if len(_chunk_) <= 0: + raise + + _out_ = io.StringIO() + _writer_ = csv.DictWriter(_out_, fieldnames=tuple(_chunk_[0].keys())) + if _chunk_no_ == 0: + _writer_.writeheader() + _writer_.writerows(_chunk_) + _chunk_no_ += 1 + yield _out_.getvalue() + if _all_errors_printed_: + return + + headers = Headers() + headers.set("Content-Disposition", + "attachment", + filename=f"{job['job-type']}_{job['jobid']}.csv") + return FlaskResponse( + __generate_chunks__(), mimetype="text/csv", headers=headers) + except jobs.JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/job/<uuid:job_id>/review", methods=["GET"]) @require_login @@ -612,6 +675,12 @@ def load_phenotypes_success_handler(job): job_id=job["job_id"])) +def proceed_to_job_status(job): + """A generic 'job success' handler for asynchronous phenotype jobs.""" + app.logger.debug("The new job: %s", job) + return redirect(url_for("background-jobs.job_status", job_id=job["job_id"])) + + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/load-data-to-database", @@ -654,11 +723,6 @@ def load_data_to_database( def __handle_error__(resp): return render_template("http-error.html", *resp.json()) - def __handle_success__(load_job): - app.logger.debug("The phenotypes loading job: %s", load_job) - return redirect(url_for( - "background-jobs.job_status", job_id=load_job["job_id"])) - return request_token( token_uri=urljoin(oauth2client.authserver_uri(), "auth/token"), @@ -689,7 +753,7 @@ def load_data_to_database( Path(f"{uploads_dir(app)}/job_errors"), worker_manager="gn_libs.jobs.launcher", loglevel=_loglevel) - ).either(__handle_error__, __handle_success__) + ).either(__handle_error__, proceed_to_job_status) def update_phenotype_metadata(conn, metadata: dict): @@ -1158,6 +1222,12 @@ def rerun_qtlreaper_success_handler(job): return return_to_dataset_view_handler(job, "QTLReaper ran successfully!") +def delete_phenotypes_success_handler(job): + """Handle success running the 'delete-phenotypes' script.""" + return return_to_dataset_view_handler( + job, "Phenotypes deleted successfully.") + + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/delete", @@ -1167,14 +1237,29 @@ def rerun_qtlreaper_success_handler(job): species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", redirect_uri="species.populations.phenotypes.list_datasets") -def delete_phenotypes(# pylint: disable=[unused-argument] +def delete_phenotypes(# pylint: disable=[unused-argument, too-many-locals] species: dict, population: dict, dataset: dict, **kwargs ): """Delete the specified phenotype data.""" - with database_connection(app.config["SQL_URI"]) as conn: + _dataset_page = redirect(url_for( + "species.populations.phenotypes.view_dataset", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"])) + + def __handle_error__(resp): + flash( + "Error retrieving authorisation token. Phenotype deletion " + "failed. Please try again later.", + "alert alert-danger") + return _dataset_page + + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + with (database_connection(app.config["SQL_URI"]) as conn, + sqlite3.connection(_jobs_db) as jobsconn): form = request.form xref_ids = tuple(int(item) for item in set(form.getlist("xref_ids"))) @@ -1186,16 +1271,68 @@ def delete_phenotypes(# pylint: disable=[unused-argument] population_id=population["Id"], dataset_id=dataset["Id"])) case "delete": - # delete everything - # python3 -m scripts.phenotypes.delete_phenotypes <mariadburi> <authdburi> <speciesid> <populationid> - # - # delete selected phenotypes - # python3 -m scripts.phenotypes.delete_phenotypes <mariadburi> <authdburi> <speciesid> <populationid> --xref-ids-file=/path/to/file.txt - return "Would actually delete the data!" + _loglevel = logging.getLevelName( + app.logger.getEffectiveLevel()).lower() + if form.get("confirm_delete_all_phenotypes", "") == "on": + _cmd = ["--delete-all"] + else: + # setup phenotypes xref_ids file + _xref_ids_file = Path( + app.config["SCRATCH_DIRECTORY"], + f"delete-phenotypes-{uuid.uuid4()}.txt") + with _xref_ids_file.open(mode="w", encoding="utf8") as ptr: + ptr.write("\n".join(str(_id) for _id in xref_ids)) + + _cmd = ["--xref_ids_file", str(_xref_ids_file)] + + _job_id = uuid.uuid4() + return request_token( + token_uri=urljoin( + oauth2client.authserver_uri(), "auth/token"), + user_id=session.user_details()["user_id"] + ).then( + lambda token: gnlibs_jobs.initialise_job( + jobsconn, + _job_id, + [ + sys.executable, + "-u", + "-m", + "scripts.phenotypes.delete_phenotypes", + "--log-level", _loglevel, + app.config["SQL_URI"], + str(species["SpeciesId"]), + str(population["Id"]), + str(dataset["Id"]), + app.config["AUTH_SERVER_URL"], + token["access_token"]] + _cmd, + "delete-phenotypes", + extra_meta={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "success_handler": ( + "uploader.phenotypes.views." + "delete_phenotypes_success_handler") + }, + external_id=session.logged_in_user_id()) + ).then( + lambda _job: gnlibs_jobs.launch_job( + _job, + _jobs_db, + Path(f"{uploads_dir(app)}/job_errors"), + worker_manager="gn_libs.jobs.launcher", + loglevel=_loglevel) + ).either(__handle_error__, proceed_to_job_status) case _: + _phenos: tuple[dict, ...] = tuple() + if len(xref_ids) > 0: + _phenos = dataset_phenotypes( + conn, population["Id"], dataset["Id"], xref_ids=xref_ids) + return render_template( "phenotypes/confirm-delete-phenotypes.html", species=species, population=population, dataset=dataset, - phenotypes=xref_ids) + phenotypes=_phenos) |