diff options
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/entry.py | 7 | ||||
| -rw-r--r-- | qc_app/jobs.py | 19 | ||||
| -rw-r--r-- | qc_app/parse.py | 25 | ||||
| -rw-r--r-- | qc_app/static/js/upload_progress.js | 3 | ||||
| -rw-r--r-- | qc_app/templates/index.html | 17 |
5 files changed, 58 insertions, 13 deletions
diff --git a/qc_app/entry.py b/qc_app/entry.py index 0cd34c5..987fdcd 100644 --- a/qc_app/entry.py +++ b/qc_app/entry.py @@ -104,9 +104,10 @@ def upload_file(): return render_template( "index.html", species=with_db_connection(species)), 400 - return redirect(url_for( - "parse.parse", filename=filename, - filetype=request.form["filetype"])) + return redirect(url_for("parse.parse", + speciesid=request.form["speciesid"], + filename=filename, + filetype=request.form["filetype"])) @entrybp.route("/data-review", methods=["GET"]) def data_review(): diff --git a/qc_app/jobs.py b/qc_app/jobs.py index a8257a3..f5e5173 100644 --- a/qc_app/jobs.py +++ b/qc_app/jobs.py @@ -32,17 +32,24 @@ def initialise_job(# pylint: disable=[too-many-arguments] redis_conn.expire(name=the_job["job_id"], time=timedelta(seconds=ttl_seconds)) return the_job -def build_file_verification_job( - redis_conn: Redis, filepath: str, filetype: str, redisurl: str, +def build_file_verification_job(#pylint: disable=[too-many-arguments] + redis_conn: Redis, + dburi: str, + redisuri: str, + speciesid: int, + filepath: str, + filetype: str, ttl_seconds: int): "Build a file verification job" - job_id = str(uuid4()) + jobid = str(uuid4()) command = [ - sys.executable, "-m", "scripts.validate_file", filetype, filepath, redisurl, - job_id + sys.executable, "-m", "scripts.validate_file", + dburi, redisuri, jobid, + "--redisexpiry", str(ttl_seconds), + str(speciesid), filetype, filepath, ] return initialise_job( - redis_conn, job_id, command, "file-verification", ttl_seconds, { + redis_conn, jobid, command, "file-verification", ttl_seconds, { "filetype": filetype, "filename": os.path.basename(filepath), "percent": 0 }) diff --git a/qc_app/parse.py b/qc_app/parse.py index ceb8fcf..40f7b44 100644 --- a/qc_app/parse.py +++ b/qc_app/parse.py @@ -7,7 +7,10 @@ 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 . import jobs + +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__) @@ -23,8 +26,25 @@ def isduplicateheading(item): 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") + 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") + errors = True + except ValueError: + flash("Invalid speciesid provided. Expected an integer.", + "alert-error") + errors = True + if filename is None: flash("No file provided", "alert-error") errors = True @@ -50,7 +70,8 @@ def parse(): with Redis.from_url(redisurl, decode_responses=True) as rconn: job = jobs.launch_job( jobs.build_file_verification_job( - rconn, filepath, filetype, redisurl, + rconn, app.config["SQL_URI"], redisurl, + speciesid, filepath, filetype, app.config["JOBS_TTL_SECONDS"]), redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors") diff --git a/qc_app/static/js/upload_progress.js b/qc_app/static/js/upload_progress.js index 98a503a..c98c33c 100644 --- a/qc_app/static/js/upload_progress.js +++ b/qc_app/static/js/upload_progress.js @@ -66,6 +66,9 @@ function selected_filetype(radios) { function setup_formdata(form) { var formdata = new FormData(); formdata.append( + "speciesid", + form.querySelector("#select_species01").value) + formdata.append( "qc_text_file", form.querySelector("input[type='file']").files[0]); formdata.append( diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html index a454dd2..358b521 100644 --- a/qc_app/templates/index.html +++ b/qc_app/templates/index.html @@ -1,4 +1,5 @@ {%extends "base.html"%} +{%from "flash_messages.html" import flash_all_messages%} {%block title%}Data Upload{%endblock%} @@ -55,6 +56,18 @@ {%endwith%} <fieldset> + <label for="select_species01">Species</label> + <select id="select_species01" + name="speciesid" + required="required"> + <option value="">Select species</option> + {%for aspecies in species%} + <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> + {%endfor%} + </select> + </fieldset> + + <fieldset> <legend>file type</legend> <input type="radio" name="filetype" value="average" id="filetype_average" @@ -111,8 +124,8 @@ <form method="POST" action="{{url_for('samples.select_species')}}"> <legend class="heading">upload samples</legend> <fieldset> - <label for="select:species">Species</label> - <select id="select:species" name="species_id" required="required"> + <label for="select_species02">Species</label> + <select id="select_species02" name="species_id" required="required"> <option value="">Select species</option> {%for spec in species%} <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> |