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Diffstat (limited to 'uploader/expression_data/rqtl2.py')
| -rw-r--r-- | uploader/expression_data/rqtl2.py | 1175 |
1 files changed, 0 insertions, 1175 deletions
diff --git a/uploader/expression_data/rqtl2.py b/uploader/expression_data/rqtl2.py deleted file mode 100644 index a855699..0000000 --- a/uploader/expression_data/rqtl2.py +++ /dev/null @@ -1,1175 +0,0 @@ -"""Module to handle uploading of R/qtl2 bundles."""#pylint: disable=[too-many-lines] -import sys -import json -import traceback -from pathlib import Path -from datetime import date -from uuid import UUID, uuid4 -from functools import partial -from zipfile import ZipFile, is_zipfile -from typing import Union, Callable, Optional - -import MySQLdb as mdb -from redis import Redis -from MySQLdb.cursors import DictCursor -from werkzeug.utils import secure_filename -from flask import ( - flash, - escape, - request, - jsonify, - url_for, - redirect, - Response, - Blueprint, - render_template, - current_app as app) - -from r_qtl import r_qtl2 - -from uploader import jobs -from uploader.files import save_file, fullpath -from uploader.dbinsert import species as all_species -from uploader.db_utils import with_db_connection, database_connection - -from uploader.authorisation import require_login -from uploader.db.platforms import platform_by_id, platforms_by_species -from uploader.db.averaging import averaging_methods, averaging_method_by_id -from uploader.db.tissues import all_tissues, tissue_by_id, create_new_tissue -from uploader.population.models import (save_population, - populations_by_species, - population_by_species_and_id) -from uploader.species.models import species_by_id -from uploader.db.datasets import ( - geno_dataset_by_id, - geno_datasets_by_species_and_population, - - probeset_study_by_id, - probeset_create_study, - probeset_dataset_by_id, - probeset_create_dataset, - probeset_datasets_by_study, - probeset_studies_by_species_and_population) - -rqtl2 = Blueprint("rqtl2", __name__) - - -@rqtl2.route("/", methods=["GET", "POST"]) -@rqtl2.route("/select-species", methods=["GET", "POST"]) -@require_login -def select_species(): - """Select the species.""" - if request.method == "GET": - return render_template("rqtl2/index.html", species=with_db_connection(all_species)) - - species_id = request.form.get("species_id") - species = with_db_connection( - lambda conn: species_by_id(conn, species_id)) - if bool(species): - return redirect(url_for( - "expression-data.rqtl2.select_population", species_id=species_id)) - flash("Invalid species or no species selected!", "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_species")) - - -@rqtl2.route("/upload/species/<int:species_id>/select-population", - methods=["GET", "POST"]) -@require_login -def select_population(species_id: int): - """Select/Create the population to organise data under.""" - with database_connection(app.config["SQL_URI"]) as conn: - species = species_by_id(conn, species_id) - if not bool(species): - flash("Invalid species selected!", "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_species")) - - if request.method == "GET": - return render_template( - "rqtl2/select-population.html", - species=species, - populations=populations_by_species(conn, species_id)) - - population = population_by_species_and_id( - conn, species["SpeciesId"], request.form.get("inbredset_id")) - if not bool(population): - flash("Invalid Population!", "alert-error error-rqtl2") - return redirect( - url_for("expression-data.rqtl2.select_population", pgsrc="error"), - code=307) - - return redirect(url_for("expression-data.rqtl2.upload_rqtl2_bundle", - species_id=species["SpeciesId"], - population_id=population["InbredSetId"])) - - -@rqtl2.route("/upload/species/<int:species_id>/create-population", - methods=["POST"]) -@require_login -def create_population(species_id: int): - """Create a new population for the given species.""" - population_page = redirect(url_for("expression-data.rqtl2.select_population", - species_id=species_id)) - with database_connection(app.config["SQL_URI"]) as conn: - species = species_by_id(conn, species_id) - population_name = request.form.get("inbredset_name", "").strip() - population_fullname = request.form.get("inbredset_fullname", "").strip() - if not bool(species): - flash("Invalid species!", "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_species")) - if not bool(population_name): - flash("Invalid Population Name!", "alert-error error-rqtl2") - return population_page - if not bool(population_fullname): - flash("Invalid Population Full Name!", "alert-error error-rqtl2") - return population_page - new_population = save_population(conn, { - "SpeciesId": species["SpeciesId"], - "Name": population_name, - "InbredSetName": population_fullname, - "FullName": population_fullname, - "Family": request.form.get("inbredset_family") or None, - "Description": request.form.get("description") or None - }) - - flash("Population created successfully.", "alert-success") - return redirect( - url_for("expression-data.rqtl2.upload_rqtl2_bundle", - species_id=species_id, - population_id=new_population["population_id"], - pgsrc="create-population"), - code=307) - - -class __RequestError__(Exception): #pylint: disable=[invalid-name] - """Internal class to avoid pylint's `too-many-return-statements` error.""" - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle"), - methods=["GET", "POST"]) -@require_login -def upload_rqtl2_bundle(species_id: int, population_id: int): - """Allow upload of R/qtl2 bundle.""" - with database_connection(app.config["SQL_URI"]) as conn: - species = species_by_id(conn, species_id) - population = population_by_species_and_id( - conn, species["SpeciesId"], population_id) - if not bool(species): - flash("Invalid species!", "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_species")) - if not bool(population): - flash("Invalid Population!", "alert-error error-rqtl2") - return redirect( - url_for("expression-data.rqtl2.select_population", pgsrc="error"), - code=307) - if request.method == "GET" or ( - request.method == "POST" - and bool(request.args.get("pgsrc"))): - return render_template("rqtl2/upload-rqtl2-bundle-step-01.html", - species=species, - population=population) - - try: - app.logger.debug("Files in the form: %s", request.files) - the_file = save_file(request.files["rqtl2_bundle_file"], - Path(app.config["UPLOAD_FOLDER"])) - except AssertionError: - app.logger.debug(traceback.format_exc()) - flash("Please provide a valid R/qtl2 zip bundle.", - "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.upload_rqtl2_bundle", - species_id=species_id, - population_id=population_id)) - - if not is_zipfile(str(the_file)): - app.logger.debug("The file is not a zip file.") - raise __RequestError__("Invalid file! Expected a zip file.") - - jobid = trigger_rqtl2_bundle_qc( - species_id, - population_id, - the_file, - request.files["rqtl2_bundle_file"].filename)#type: ignore[arg-type] - return redirect(url_for( - "expression-data.rqtl2.rqtl2_bundle_qc_status", jobid=jobid)) - - -def trigger_rqtl2_bundle_qc( - species_id: int, - population_id: int, - rqtl2bundle: Path, - originalfilename: str -) -> UUID: - """Trigger QC on the R/qtl2 bundle.""" - redisuri = app.config["REDIS_URL"] - with Redis.from_url(redisuri, decode_responses=True) as rconn: - jobid = uuid4() - redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"] - jobs.launch_job( - jobs.initialise_job( - rconn, - jobs.jobsnamespace(), - str(jobid), - [sys.executable, "-m", "scripts.qc_on_rqtl2_bundle", - app.config["SQL_URI"], app.config["REDIS_URL"], - jobs.jobsnamespace(), str(jobid), str(species_id), - str(population_id), "--redisexpiry", - str(redis_ttl_seconds)], - "rqtl2-bundle-qc-job", - redis_ttl_seconds, - {"job-metadata": json.dumps({ - "speciesid": species_id, - "populationid": population_id, - "rqtl2-bundle-file": str(rqtl2bundle.absolute()), - "original-filename": originalfilename})}), - redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") - return jobid - - -def chunk_name(uploadfilename: str, chunkno: int) -> str: - """Generate chunk name from original filename and chunk number""" - if uploadfilename == "": - raise ValueError("Name cannot be empty!") - if chunkno < 1: - raise ValueError("Chunk number must be greater than zero") - return f"{secure_filename(uploadfilename)}_part_{chunkno:05d}" - - -def chunks_directory(uniqueidentifier: str) -> Path: - """Compute the directory where chunks are temporarily stored.""" - if uniqueidentifier == "": - raise ValueError("Unique identifier cannot be empty!") - return Path(app.config["UPLOAD_FOLDER"], f"tempdir_{uniqueidentifier}") - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle-chunked"), - methods=["GET"]) -@require_login -def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"] - species_id: int, - population_id: int -): - """ - Extension to the `upload_rqtl2_bundle` endpoint above that provides a way - for testing whether all the chunks have been uploaded and to assist with - resuming a failed expression-data. - """ - fileid = request.args.get("resumableIdentifier", type=str) or "" - filename = request.args.get("resumableFilename", type=str) or "" - chunk = request.args.get("resumableChunkNumber", type=int) or 0 - if not(fileid or filename or chunk): - return jsonify({ - "message": "At least one required query parameter is missing.", - "error": "BadRequest", - "statuscode": 400 - }), 400 - - if Path(chunks_directory(fileid), - chunk_name(filename, chunk)).exists(): - return "OK" - - return jsonify({ - "message": f"Chunk {chunk} was not found.", - "error": "NotFound", - "statuscode": 404 - }), 404 - - -def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path: - """Merge the chunks into a single file.""" - with open(targetfile, "ab") as _target: - for chunkfile in chunkpaths: - with open(chunkfile, "rb") as _chunkdata: - _target.write(_chunkdata.read()) - - chunkfile.unlink() - return targetfile - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle-chunked"), - methods=["POST"]) -@require_login -def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int): - """ - Extension to the `upload_rqtl2_bundle` endpoint above that allows large - files to be uploaded in chunks. - - This should hopefully speed up uploads, and if done right, even enable - resumable uploads - """ - _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0 - _chunk = request.form.get("resumableChunkNumber", default=1, type=int) - _uploadfilename = request.form.get( - "resumableFilename", default="", type=str) or "" - _fileid = request.form.get( - "resumableIdentifier", default="", type=str) or "" - _targetfile = Path(app.config["UPLOAD_FOLDER"], _fileid) - - if _targetfile.exists(): - return jsonify({ - "message": ( - "A file with a similar unique identifier has previously been " - "uploaded and possibly is/has being/been processed."), - "error": "BadRequest", - "statuscode": 400 - }), 400 - - try: - # save chunk data - chunks_directory(_fileid).mkdir(exist_ok=True, parents=True) - request.files["file"].save(Path(chunks_directory(_fileid), - chunk_name(_uploadfilename, _chunk))) - - # Check whether upload is complete - chunkpaths = tuple( - Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk)) - for _achunk in range(1, _totalchunks+1)) - if all(_file.exists() for _file in chunkpaths): - # merge_files and clean up chunks - __merge_chunks__(_targetfile, chunkpaths) - chunks_directory(_fileid).rmdir() - jobid = trigger_rqtl2_bundle_qc( - species_id, population_id, _targetfile, _uploadfilename) - return url_for( - "expression-data.rqtl2.rqtl2_bundle_qc_status", jobid=jobid) - except Exception as exc:# pylint: disable=[broad-except] - msg = "Error processing uploaded file chunks." - app.logger.error(msg, exc_info=True, stack_info=True) - return jsonify({ - "message": msg, - "error": type(exc).__name__, - "error-description": " ".join(str(arg) for arg in exc.args), - "error-trace": traceback.format_exception(exc) - }), 500 - - return "OK" - - -@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>", - methods=["GET", "POST"]) -@require_login -def rqtl2_bundle_qc_status(jobid: UUID): - """Check the status of the QC jobs.""" - with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, - database_connection(app.config["SQL_URI"]) as dbconn): - try: - thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid) - messagelistname = thejob.get("log-messagelist") - logmessages = (rconn.lrange(messagelistname, 0, -1) - if bool(messagelistname) else []) - jobstatus = thejob["status"] - if jobstatus == "error": - return render_template("rqtl2/rqtl2-qc-job-error.html", - job=thejob, - errorsgeneric=json.loads( - thejob.get("errors-generic", "[]")), - errorsgeno=json.loads( - thejob.get("errors-geno", "[]")), - errorspheno=json.loads( - thejob.get("errors-pheno", "[]")), - errorsphenose=json.loads( - thejob.get("errors-phenose", "[]")), - errorsphenocovar=json.loads( - thejob.get("errors-phenocovar", "[]")), - messages=logmessages) - if jobstatus == "success": - jobmeta = json.loads(thejob["job-metadata"]) - species = species_by_id(dbconn, jobmeta["speciesid"]) - return render_template( - "rqtl2/rqtl2-qc-job-results.html", - species=species, - population=population_by_species_and_id( - dbconn, species["SpeciesId"], jobmeta["populationid"]), - rqtl2bundle=Path(jobmeta["rqtl2-bundle-file"]).name, - rqtl2bundleorig=jobmeta["original-filename"]) - - def compute_percentage(thejob, filetype) -> Union[str, None]: - if f"{filetype}-linecount" in thejob: - return "100" - if f"{filetype}-filesize" in thejob: - percent = ((int(thejob.get(f"{filetype}-checked", 0)) - / - int(thejob.get(f"{filetype}-filesize", 1))) - * 100) - return f"{percent:.2f}" - return None - - return render_template( - "rqtl2/rqtl2-qc-job-status.html", - job=thejob, - geno_percent=compute_percentage(thejob, "geno"), - pheno_percent=compute_percentage(thejob, "pheno"), - phenose_percent=compute_percentage(thejob, "phenose"), - messages=logmessages) - except jobs.JobNotFound: - return render_template("rqtl2/no-such-job.html", jobid=jobid) - - -def redirect_on_error(flaskroute, **kwargs): - """Utility to redirect on error""" - return redirect(url_for(flaskroute, **kwargs, pgsrc="error"), - code=(307 if request.method == "POST" else 302)) - - -def check_species(conn: mdb.Connection, formargs: dict) -> Optional[ - tuple[str, Response]]: - """ - Check whether the 'species_id' value is provided, and whether a - corresponding species exists in the database. - - Maybe give the function a better name...""" - speciespage = redirect_on_error("expression-data.rqtl2.select_species") - if "species_id" not in formargs: - return "You MUST provide the Species identifier.", speciespage - - if not bool(species_by_id(conn, formargs["species_id"])): - return "No species with the provided identifier exists.", speciespage - - return None - - -def check_population(conn: mdb.Connection, - formargs: dict, - species_id) -> Optional[tuple[str, Response]]: - """ - Check whether the 'population_id' value is provided, and whether a - corresponding population exists in the database. - - Maybe give the function a better name...""" - poppage = redirect_on_error( - "expression-data.rqtl2.select_species", species_id=species_id) - if "population_id" not in formargs: - return "You MUST provide the Population identifier.", poppage - - if not bool(population_by_species_and_id( - conn, species_id, formargs["population_id"])): - return "No population with the provided identifier exists.", poppage - - return None - - -def check_r_qtl2_bundle(formargs: dict, - species_id, - population_id) -> Optional[tuple[str, Response]]: - """Check for the existence of the R/qtl2 bundle.""" - fileuploadpage = redirect_on_error("expression-data.rqtl2.upload_rqtl2_bundle", - species_id=species_id, - population_id=population_id) - if not "rqtl2_bundle_file" in formargs: - return ( - "You MUST provide a R/qtl2 zip bundle for expression-data.", fileuploadpage) - - if not Path(fullpath(formargs["rqtl2_bundle_file"])).exists(): - return "No R/qtl2 bundle with the given name exists.", fileuploadpage - - return None - - -def check_geno_dataset(conn: mdb.Connection, - formargs: dict, - species_id, - population_id) -> Optional[tuple[str, Response]]: - """Check for the Genotype dataset.""" - genodsetpg = redirect_on_error("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id) - if not bool(formargs.get("geno-dataset-id")): - return ( - "You MUST provide a valid Genotype dataset identifier", genodsetpg) - - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s", - (formargs["geno-dataset-id"],)) - results = cursor.fetchall() - if not bool(results): - return ("No genotype dataset with the provided identifier exists.", - genodsetpg) - if len(results) > 1: - return ( - "Data corruption: More than one genotype dataset with the same " - "identifier.", - genodsetpg) - - return None - -def check_tissue( - conn: mdb.Connection,formargs: dict) -> Optional[tuple[str, Response]]: - """Check for tissue/organ/biological material.""" - selectdsetpg = redirect_on_error("expression-data.rqtl2.select_dataset_info", - species_id=formargs["species_id"], - population_id=formargs["population_id"]) - if not bool(formargs.get("tissueid", "").strip()): - return ("No tissue/organ/biological material provided.", selectdsetpg) - - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM Tissue WHERE Id=%s", - (formargs["tissueid"],)) - results = cursor.fetchall() - if not bool(results): - return ("No tissue/organ with the provided identifier exists.", - selectdsetpg) - - if len(results) > 1: - return ( - "Data corruption: More than one tissue/organ with the same " - "identifier.", - selectdsetpg) - - return None - - -def check_probe_study(conn: mdb.Connection, - formargs: dict, - species_id, - population_id) -> Optional[tuple[str, Response]]: - """Check for the ProbeSet study.""" - dsetinfopg = redirect_on_error("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id) - if not bool(formargs.get("probe-study-id")): - return "No probeset study was selected!", dsetinfopg - - if not bool(probeset_study_by_id(conn, formargs["probe-study-id"])): - return ("No probeset study with the provided identifier exists", - dsetinfopg) - - return None - - -def check_probe_dataset(conn: mdb.Connection, - formargs: dict, - species_id, - population_id) -> Optional[tuple[str, Response]]: - """Check for the ProbeSet dataset.""" - dsetinfopg = redirect_on_error("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id) - if not bool(formargs.get("probe-dataset-id")): - return "No probeset dataset was selected!", dsetinfopg - - if not bool(probeset_dataset_by_id(conn, formargs["probe-dataset-id"])): - return ("No probeset dataset with the provided identifier exists", - dsetinfopg) - - return None - - -def with_errors(endpointthunk: Callable, *checkfns): - """Run 'endpointthunk' with error checking.""" - formargs = {**dict(request.args), **dict(request.form)} - errors = tuple(item for item in (_fn(formargs=formargs) for _fn in checkfns) - if item is not None) - if len(errors) > 0: - flash(errors[0][0], "alert-error error-rqtl2") - return errors[0][1] - - return endpointthunk() - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/select-geno-dataset"), - methods=["POST"]) -@require_login -def select_geno_dataset(species_id: int, population_id: int): - """Select from existing geno datasets.""" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - geno_dset = geno_datasets_by_species_and_population( - conn, species_id, population_id) - if not bool(geno_dset): - flash("No genotype dataset was provided!", - "alert-error error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_geno_dataset", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - - flash("Genotype accepted", "alert-success error-rqtl2") - return redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="expression-data.rqtl2.select_geno_dataset"), - code=307) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/create-geno-dataset"), - methods=["POST"]) -@require_login -def create_geno_dataset(species_id: int, population_id: int): - """Create a new geno dataset.""" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - sgeno_page = redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset" - if not bool(request.form.get("dataset-name")): - flash("You must provide the dataset name", errorclasses) - return sgeno_page - if not bool(request.form.get("dataset-fullname")): - flash("You must provide the dataset full name", errorclasses) - return sgeno_page - public = 2 if request.form.get("dataset-public") == "on" else 0 - - with conn.cursor(cursorclass=DictCursor) as cursor: - datasetname = request.form["dataset-name"] - new_dataset = { - "name": datasetname, - "fname": request.form.get("dataset-fullname"), - "sname": request.form.get("dataset-shortname") or datasetname, - "today": date.today().isoformat(), - "pub": public, - "isetid": population_id - } - cursor.execute("SELECT * FROM GenoFreeze WHERE Name=%s", - (datasetname,)) - results = cursor.fetchall() - if bool(results): - flash( - f"A genotype dataset with name '{escape(datasetname)}' " - "already exists.", - errorclasses) - return redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="error"), - code=307) - cursor.execute( - "INSERT INTO GenoFreeze(" - "Name, FullName, ShortName, CreateTime, public, InbredSetId" - ") " - "VALUES(" - "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s" - ")", - new_dataset) - flash("Created dataset successfully.", "alert-success") - return render_template( - "rqtl2/create-geno-dataset-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset={**new_dataset, "id": cursor.lastrowid}) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, conn=conn, species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/select-tissue"), - methods=["POST"]) -@require_login -def select_tissue(species_id: int, population_id: int): - """Select from existing tissues.""" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - if not bool(request.form.get("tissueid", "").strip()): - flash("Invalid tissue selection!", - "alert-error error-select-tissue error-rqtl2") - - return redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="expression-data.rqtl2.select_geno_dataset"), - code=307) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id)) - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/create-tissue"), - methods=["POST"]) -@require_login -def create_tissue(species_id: int, population_id: int): - """Add new tissue, organ or biological material to the system.""" - form = request.form - datasetinfopage = redirect( - url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id, - pgsrc="expression-data.rqtl2.select_geno_dataset"), - code=307) - with database_connection(app.config["SQL_URI"]) as conn: - tissuename = form.get("tissuename", "").strip() - tissueshortname = form.get("tissueshortname", "").strip() - if not bool(tissuename): - flash("Organ/Tissue name MUST be provided.", - "alert-error error-create-tissue error-rqtl2") - return datasetinfopage - - if not bool(tissueshortname): - flash("Organ/Tissue short name MUST be provided.", - "alert-error error-create-tissue error-rqtl2") - return datasetinfopage - - try: - tissue = create_new_tissue(conn, tissuename, tissueshortname) - flash("Tissue created successfully!", "alert-success") - return render_template( - "rqtl2/create-tissue-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset=geno_dataset_by_id( - conn, - int(request.form["geno-dataset-id"])), - tissue=tissue) - except mdb.IntegrityError as _ierr: - flash("Tissue/Organ with that short name already exists!", - "alert-error error-create-tissue error-rqtl2") - return datasetinfopage - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/select-probeset-study"), - methods=["POST"]) -@require_login -def select_probeset_study(species_id: int, population_id: int): - """Select or create a probeset study.""" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - summary_page = redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): - flash("Invalid study selected!", "alert-error error-rqtl2") - return summary_page - - return summary_page - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_tissue, conn=conn), - partial(check_probe_study, - conn=conn, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/select-probeset-dataset"), - methods=["POST"]) -@require_login -def select_probeset_dataset(species_id: int, population_id: int): - """Select or create a probeset dataset.""" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - summary_page = redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): - flash("Invalid study selected!", "alert-error error-rqtl2") - return summary_page - - return summary_page - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_tissue, conn=conn), - partial(check_probe_study, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_probe_dataset, - conn=conn, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/create-probeset-study"), - methods=["POST"]) -@require_login -def create_probeset_study(species_id: int, population_id: int): - """Create a new probeset study.""" - errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-study" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - form = request.form - dataset_info_page = redirect( - url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - - if not (bool(form.get("platformid")) and - bool(platform_by_id(conn, int(form["platformid"])))): - flash("Invalid platform selected.", errorclasses) - return dataset_info_page - - if not (bool(form.get("tissueid")) and - bool(tissue_by_id(conn, int(form["tissueid"])))): - flash("Invalid tissue selected.", errorclasses) - return dataset_info_page - - studyname = form["studyname"] - try: - study = probeset_create_study( - conn, population_id, int(form["platformid"]), int(form["tissueid"]), - studyname, form.get("studyfullname") or "", - form.get("studyshortname") or "") - except mdb.IntegrityError as _ierr: - flash(f"ProbeSet study with name '{escape(studyname)}' already " - "exists.", - errorclasses) - return dataset_info_page - return render_template( - "rqtl2/create-probe-study-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset=geno_dataset_by_id( - conn, - int(request.form["geno-dataset-id"])), - study=study) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_tissue, conn=conn)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/create-probeset-dataset"), - methods=["POST"]) -@require_login -def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements] - """Create a new probeset dataset.""" - errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-dataset" - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__():#pylint: disable=[too-many-return-statements] - form = request.form - summary_page = redirect(url_for("expression-data.rqtl2.select_dataset_info", - species_id=species_id, - population_id=population_id), - code=307) - if not bool(form.get("averageid")): - flash("Averaging method not selected!", errorclasses) - return summary_page - if not bool(form.get("datasetname")): - flash("Dataset name not provided!", errorclasses) - return summary_page - if not bool(form.get("datasetfullname")): - flash("Dataset full name not provided!", errorclasses) - return summary_page - - tissue = tissue_by_id(conn, form.get("tissueid", "").strip()) - - study = probeset_study_by_id(conn, int(form["probe-study-id"])) - if not bool(study): - flash("Invalid ProbeSet study provided!", errorclasses) - return summary_page - - avgmethod = averaging_method_by_id(conn, int(form["averageid"])) - if not bool(avgmethod): - flash("Invalid averaging method provided!", errorclasses) - return summary_page - - try: - dset = probeset_create_dataset(conn, - int(form["probe-study-id"]), - int(form["averageid"]), - form["datasetname"], - form["datasetfullname"], - form["datasetshortname"], - form["datasetpublic"] == "on", - form.get( - "datasetdatascale", "log2")) - except mdb.IntegrityError as _ierr: - app.logger.debug("Possible integrity error: %s", traceback.format_exc()) - flash(("IntegrityError: The data you provided has some errors: " - f"{_ierr.args}"), - errorclasses) - return summary_page - except Exception as _exc:# pylint: disable=[broad-except] - app.logger.debug("Error creating ProbeSet dataset: %s", - traceback.format_exc()) - flash(("There was a problem creating your dataset. Please try " - "again."), - errorclasses) - return summary_page - return render_template( - "rqtl2/create-probe-dataset-success.html", - species=species_by_id(conn, species_id), - population=population_by_species_and_id( - conn, species_id, population_id), - rqtl2_bundle_file=request.form["rqtl2_bundle_file"], - geno_dataset=geno_dataset_by_id( - conn, - int(request.form["geno-dataset-id"])), - tissue=tissue, - study=study, - avgmethod=avgmethod, - dataset=dset) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_tissue, conn=conn), - partial(check_probe_study, - conn=conn, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/dataset-info"), - methods=["POST"]) -@require_login -def select_dataset_info(species_id: int, population_id: int): - """ - If `geno` files exist in the R/qtl2 bundle, prompt user to provide the - dataset the genotypes belong to. - """ - form = request.form - with database_connection(app.config["SQL_URI"]) as conn: - def __thunk__(): - species = species_by_id(conn, species_id) - population = population_by_species_and_id( - conn, species_id, population_id) - thefile = fullpath(form["rqtl2_bundle_file"]) - with ZipFile(str(thefile), "r") as zfile: - cdata = r_qtl2.control_data(zfile) - - geno_dataset = geno_dataset_by_id( - conn,form.get("geno-dataset-id", "").strip()) - if "geno" in cdata and not bool(form.get("geno-dataset-id")): - return render_template( - "rqtl2/select-geno-dataset.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - datasets=geno_datasets_by_species_and_population( - conn, species_id, population_id)) - - tissue = tissue_by_id(conn, form.get("tissueid", "").strip()) - if "pheno" in cdata and not bool(tissue): - return render_template( - "rqtl2/select-tissue.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - studies=probeset_studies_by_species_and_population( - conn, species_id, population_id), - platforms=platforms_by_species(conn, species_id), - tissues=all_tissues(conn)) - - probeset_study = probeset_study_by_id( - conn, form.get("probe-study-id", "").strip()) - if "pheno" in cdata and not bool(probeset_study): - return render_template( - "rqtl2/select-probeset-study-id.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - studies=probeset_studies_by_species_and_population( - conn, species_id, population_id), - platforms=platforms_by_species(conn, species_id), - tissue=tissue) - probeset_study = probeset_study_by_id( - conn, int(form["probe-study-id"])) - - probeset_dataset = probeset_dataset_by_id( - conn, form.get("probe-dataset-id", "").strip()) - if "pheno" in cdata and not bool(probeset_dataset): - return render_template( - "rqtl2/select-probeset-dataset.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - probe_study=probeset_study, - tissue=tissue, - datasets=probeset_datasets_by_study( - conn, int(form["probe-study-id"])), - avgmethods=averaging_methods(conn)) - - return render_template("rqtl2/summary-info.html", - species=species, - population=population, - rqtl2_bundle_file=thefile.name, - geno_dataset=geno_dataset, - tissue=tissue, - probe_study=probeset_study, - probe_dataset=probeset_dataset) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" - "/rqtl2-bundle/confirm-bundle-details"), - methods=["POST"]) -@require_login -def confirm_bundle_details(species_id: int, population_id: int): - """Confirm the details and trigger R/qtl2 bundle processing...""" - redisuri = app.config["REDIS_URL"] - with (database_connection(app.config["SQL_URI"]) as conn, - Redis.from_url(redisuri, decode_responses=True) as rconn): - def __thunk__(): - redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"] - jobid = str(uuid4()) - _job = jobs.launch_job( - jobs.initialise_job( - rconn, - jobs.jobsnamespace(), - jobid, - [ - sys.executable, "-m", "scripts.process_rqtl2_bundle", - app.config["SQL_URI"], app.config["REDIS_URL"], - jobs.jobsnamespace(), jobid, "--redisexpiry", - str(redis_ttl_seconds)], - "R/qtl2 Bundle Upload", - redis_ttl_seconds, - { - "bundle-metadata": json.dumps({ - "speciesid": species_id, - "populationid": population_id, - "rqtl2-bundle-file": str(fullpath( - request.form["rqtl2_bundle_file"])), - "geno-dataset-id": request.form.get( - "geno-dataset-id", ""), - "probe-study-id": request.form.get( - "probe-study-id", ""), - "probe-dataset-id": request.form.get( - "probe-dataset-id", ""), - **({ - "platformid": probeset_study_by_id( - conn, - int(request.form["probe-study-id"]))["ChipId"] - } if bool(request.form.get("probe-study-id")) else {}) - }) - }), - redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") - - return redirect(url_for("expression-data.rqtl2.rqtl2_processing_status", - jobid=jobid)) - - return with_errors(__thunk__, - partial(check_species, conn=conn), - partial(check_population, - conn=conn, - species_id=species_id), - partial(check_r_qtl2_bundle, - species_id=species_id, - population_id=population_id), - partial(check_geno_dataset, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_probe_study, - conn=conn, - species_id=species_id, - population_id=population_id), - partial(check_probe_dataset, - conn=conn, - species_id=species_id, - population_id=population_id)) - - -@rqtl2.route("/status/<uuid:jobid>") -def rqtl2_processing_status(jobid: UUID): - """Retrieve the status of the job processing the uploaded R/qtl2 bundle.""" - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: - try: - thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid) - - messagelistname = thejob.get("log-messagelist") - logmessages = (rconn.lrange(messagelistname, 0, -1) - if bool(messagelistname) else []) - - if thejob["status"] == "error": - return render_template( - "rqtl2/rqtl2-job-error.html", job=thejob, messages=logmessages) - if thejob["status"] == "success": - return render_template("rqtl2/rqtl2-job-results.html", - job=thejob, - messages=logmessages) - - return render_template( - "rqtl2/rqtl2-job-status.html", job=thejob, messages=logmessages) - except jobs.JobNotFound as _exc: - return render_template("rqtl2/no-such-job.html", jobid=jobid) |