diff options
Diffstat (limited to 'uploader/expression_data/parse.py')
| -rw-r--r-- | uploader/expression_data/parse.py | 178 |
1 files changed, 0 insertions, 178 deletions
diff --git a/uploader/expression_data/parse.py b/uploader/expression_data/parse.py deleted file mode 100644 index fc1c3f0..0000000 --- a/uploader/expression_data/parse.py +++ /dev/null @@ -1,178 +0,0 @@ -"""File parsing module""" -import os - -import jsonpickle -from redis import Redis -from flask import flash, request, url_for, redirect, Blueprint, render_template -from flask import current_app as app - -from quality_control.errors import InvalidValue, DuplicateHeading - -from uploader import jobs -from uploader.dbinsert import species_by_id -from uploader.db_utils import with_db_connection -from uploader.authorisation import require_login - -parsebp = Blueprint("parse", __name__) - -def isinvalidvalue(item): - """Check whether item is of type InvalidValue""" - return isinstance(item, InvalidValue) - -def isduplicateheading(item): - """Check whether item is of type DuplicateHeading""" - return isinstance(item, DuplicateHeading) - -@parsebp.route("/parse", methods=["GET"]) -@require_login -def parse(): - """Trigger file parsing""" - errors = False - speciesid = request.args.get("speciesid") - filename = request.args.get("filename") - filetype = request.args.get("filetype") - if speciesid is None: - flash("No species selected", "alert-error error-expr-data") - errors = True - else: - try: - speciesid = int(speciesid) - species = with_db_connection( - lambda con: species_by_id(con, speciesid)) - if not bool(species): - flash("No such species.", "alert-error error-expr-data") - errors = True - except ValueError: - flash("Invalid speciesid provided. Expected an integer.", - "alert-error error-expr-data") - errors = True - - if filename is None: - flash("No file provided", "alert-error error-expr-data") - errors = True - - if filetype is None: - flash("No filetype provided", "alert-error error-expr-data") - errors = True - - if filetype not in ("average", "standard-error"): - flash("Invalid filetype provided", "alert-error error-expr-data") - errors = True - - if filename: - filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename) - if not os.path.exists(filepath): - flash("Selected file does not exist (any longer)", - "alert-error error-expr-data") - errors = True - - if errors: - return redirect(url_for("expression-data.index.upload_file")) - - redisurl = app.config["REDIS_URL"] - with Redis.from_url(redisurl, decode_responses=True) as rconn: - job = jobs.launch_job( - jobs.build_file_verification_job( - rconn, app.config["SQL_URI"], redisurl, - speciesid, filepath, filetype, - app.config["JOBS_TTL_SECONDS"]), - redisurl, - f"{app.config['UPLOAD_FOLDER']}/job_errors") - - return redirect(url_for("expression-data.parse.parse_status", job_id=job["jobid"])) - -@parsebp.route("/status/<job_id>", methods=["GET"]) -def parse_status(job_id: str): - "Retrieve the status of the job" - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: - try: - job = jobs.job(rconn, jobs.jobsnamespace(), job_id) - except jobs.JobNotFound as _exc: - return render_template("no_such_job.html", job_id=job_id), 400 - - error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") - if os.path.exists(error_filename): - stat = os.stat(error_filename) - if stat.st_size > 0: - return redirect(url_for("parse.fail", job_id=job_id)) - - job_id = job["jobid"] - progress = float(job["percent"]) - status = job["status"] - filename = job.get("filename", "uploaded file") - errors = jsonpickle.decode( - job.get("errors", jsonpickle.encode(tuple()))) - if status in ("success", "aborted"): - return redirect(url_for("expression-data.parse.results", job_id=job_id)) - - if status == "parse-error": - return redirect(url_for("parse.fail", job_id=job_id)) - - app.jinja_env.globals.update( - isinvalidvalue=isinvalidvalue, - isduplicateheading=isduplicateheading) - return render_template( - "job_progress.html", - job_id = job_id, - job_status = status, - progress = progress, - message = job.get("message", ""), - job_name = f"Parsing '{filename}'", - errors=errors) - -@parsebp.route("/results/<job_id>", methods=["GET"]) -def results(job_id: str): - """Show results of parsing...""" - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: - job = jobs.job(rconn, jobs.jobsnamespace(), job_id) - - if job: - filename = job["filename"] - errors = jsonpickle.decode(job.get("errors", jsonpickle.encode(tuple()))) - app.jinja_env.globals.update( - isinvalidvalue=isinvalidvalue, - isduplicateheading=isduplicateheading) - return render_template( - "parse_results.html", - errors=errors, - job_name = f"Parsing '{filename}'", - user_aborted = job.get("user_aborted"), - job_id=job["jobid"]) - - return render_template("no_such_job.html", job_id=job_id) - -@parsebp.route("/fail/<job_id>", methods=["GET"]) -def fail(job_id: str): - """Handle parsing failure""" - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: - job = jobs.job(rconn, jobs.jobsnamespace(), job_id) - - if job: - error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") - if os.path.exists(error_filename): - stat = os.stat(error_filename) - if stat.st_size > 0: - return render_template( - "worker_failure.html", job_id=job_id) - - return render_template("parse_failure.html", job=job) - - return render_template("no_such_job.html", job_id=job_id) - -@parsebp.route("/abort", methods=["POST"]) -@require_login -def abort(): - """Handle user request to abort file processing""" - job_id = request.form["job_id"] - - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: - job = jobs.job(rconn, jobs.jobsnamespace(), job_id) - - if job: - rconn.hset(name=jobs.job_key(jobs.jobsnamespace(), job_id), - key="user_aborted", - value=int(True)) - - return redirect(url_for("expression-data.parse.parse_status", job_id=job_id)) |