"""File parsing module""" import os from rq import get_current_job from flask import ( request, url_for, redirect, Blueprint, render_template, current_app as app) from . import jobs from quality_control.errors import ParseError from quality_control.parsing import ( FileType, parse_file, strain_names, parse_strains) parsebp = Blueprint("parse", __name__) def queued_parse(filepath, filetype): job = get_current_job() job.meta["filename"] = os.path.basename(filepath) job.meta["status"] = "in-progress" job.save_meta() filesize = os.stat(filepath).st_size try: parsed = parse_file( filepath, filetype, strain_names(parse_strains("strains.csv"))) for line, curr_size in parsed: job.meta["progress"] = (curr_size/filesize) * 100 job.meta["status"] = f"Parsed {curr_size} bytes" job.save_meta() os.remove(filepath) job.meta["progress"] = 100 job.meta["status"] = "success" job.meta["results"] = {"message": "no errors found"} job.save_meta() except ParseError as pe: pe_dict = pe.args[0] job.meta["status"] = "parse-error" job.meta["results"] = { "filename": filename, "filetype": filetype, "position": pe_dict["position"] } job.save_meta() @parsebp.route("/parse", methods=["GET"]) def parse(): """Trigger file parsing""" # TODO: Maybe implement external process to parse the files errors = False filename = request.args.get("filename") filetype = request.args.get("filetype") if filename is None: flash("No file provided", "alert-error") errors = True if filetype is None: flash("No filetype provided", "alert-error") errors = True filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename) if not os.path.exists(filepath): flash("Selected file does not exist (any longer)", "alert-danger") errors = True if errors: return redirect(url_for("entry.index")) filetype = ( FileType.AVERAGE if filetype == "average" else FileType.STANDARD_ERROR) job = jobs.enqueue_job("qc_app.parse.queued_parse", filepath, filetype) job.meta["filename"] = filename job.save_meta() return redirect(url_for("parse.parse_status", job_id=job.get_id())) @parsebp.route("/status/", methods=["GET"]) def parse_status(job_id): job = jobs.job(job_id) if job: job_id = job.get_id() progress = job.meta.get("progress", 0) status = job.meta["status"] filename = job.meta.get("filename", "uploaded file") if status == "success": return redirect(url_for("parse.results", job_id=job_id)) if status == "parse-error": return redirect(url_for("parse.fail", job_id=job_id)) return render_template( "job_progress.html", job_id = job_id, job_status = status, progress = progress, job_name = f"Parsing '{filename}'") return render_template("no_such_job.html", job_id=job_id) @parsebp.route("/results/", methods=["GET"]) def results(job_id): """Indicates success if parsing the file is successful""" return "STUB: Parse success!!!" @parsebp.route("/fail", methods=["GET"]) def fail(): """Indicates success if parsing the file is successful""" return "STUB: Parse Failure!!!"