Rename module: qc_app --> uploader

1 files changed, 0 insertions, 175 deletions

diff --git a/qc_app/parse.py b/qc_app/parse.py
deleted file mode 100644
index d20f6f0..0000000
--- a/qc_app/parse.py
+++ /dev/null
@@ -1,175 +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 qc_app import jobs
-from qc_app.dbinsert import species_by_id
-from qc_app.db_utils import with_db_connection
-
-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"])
-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("entry.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("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("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"])
-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("parse.parse_status", job_id=job_id))