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-rw-r--r--uploader/expression_data/parse.py178
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))