diff options
18 files changed, 606 insertions, 515 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index 1af159b..9fdb383 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -12,7 +12,6 @@ from uploader.oauth2.client import user_logged_in, authserver_authorise_uri from . import session from .base_routes import base from .species import speciesbp -from .dbinsert import dbinsertbp from .oauth2.views import oauth2 from .expression_data import exprdatabp from .errors import register_error_handlers @@ -85,8 +84,6 @@ def create_app(): app.register_blueprint(base, url_prefix="/") app.register_blueprint(oauth2, url_prefix="/oauth2") app.register_blueprint(speciesbp, url_prefix="/species") - app.register_blueprint(dbinsertbp, url_prefix="/dbinsert") - app.register_blueprint(exprdatabp, url_prefix="/expression-data") register_error_handlers(app) return app diff --git a/uploader/expression_data/__init__.py b/uploader/expression_data/__init__.py index 206a764..fc8bd41 100644 --- a/uploader/expression_data/__init__.py +++ b/uploader/expression_data/__init__.py @@ -1,11 +1,2 @@ """Package handling upload of files.""" -from flask import Blueprint - -from .rqtl2 import rqtl2 -from .index import indexbp -from .parse import parsebp - -exprdatabp = Blueprint("expression-data", __name__) -exprdatabp.register_blueprint(indexbp, url_prefix="/") -exprdatabp.register_blueprint(rqtl2, url_prefix="/rqtl2") -exprdatabp.register_blueprint(parsebp, url_prefix="/parse") +from .views import exprdatabp diff --git a/uploader/dbinsert.py b/uploader/expression_data/dbinsert.py index 2116031..2116031 100644 --- a/uploader/dbinsert.py +++ b/uploader/expression_data/dbinsert.py diff --git a/uploader/expression_data/index.py b/uploader/expression_data/index.py deleted file mode 100644 index db23136..0000000 --- a/uploader/expression_data/index.py +++ /dev/null @@ -1,125 +0,0 @@ -"""Entry-point module""" -import os -import mimetypes -from typing import Tuple -from zipfile import ZipFile, is_zipfile - -from werkzeug.utils import secure_filename -from flask import ( - flash, - request, - url_for, - redirect, - Blueprint, - render_template, - current_app as app) - -from uploader.species.models import all_species as species -from uploader.authorisation import require_login -from uploader.db_utils import with_db_connection - -indexbp = Blueprint("index", __name__) - - -def errors(rqst) -> Tuple[str, ...]: - """Return a tuple of the errors found in the request `rqst`. If no error is - found, then an empty tuple is returned.""" - def __filetype_error__(): - return ( - ("Invalid file type provided.",) - if rqst.form.get("filetype") not in ("average", "standard-error") - else tuple()) - - def __file_missing_error__(): - return ( - ("No file was uploaded.",) - if ("qc_text_file" not in rqst.files or - rqst.files["qc_text_file"].filename == "") - else tuple()) - - def __file_mimetype_error__(): - text_file = rqst.files["qc_text_file"] - return ( - ( - ("Invalid file! Expected a tab-separated-values file, or a zip " - "file of the a tab-separated-values file."),) - if text_file.mimetype not in ( - "text/plain", "text/tab-separated-values", - "application/zip") - else tuple()) - - return ( - __filetype_error__() + - (__file_missing_error__() or __file_mimetype_error__())) - -def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]: - """Check the uploaded zip file for errors.""" - zfile_errors: Tuple[str, ...] = tuple() - if is_zipfile(filepath): - with ZipFile(filepath, "r") as zfile: - infolist = zfile.infolist() - if len(infolist) != 1: - zfile_errors = zfile_errors + ( - ("Expected exactly one (1) member file within the uploaded zip " - f"file. Got {len(infolist)} member files."),) - if len(infolist) == 1 and infolist[0].is_dir(): - zfile_errors = zfile_errors + ( - ("Expected a member text file in the uploaded zip file. Got a " - "directory/folder."),) - - if len(infolist) == 1 and not infolist[0].is_dir(): - zfile.extract(infolist[0], path=upload_dir) - mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}") - if mime[0] != "text/tab-separated-values": - zfile_errors = zfile_errors + ( - ("Expected the member text file in the uploaded zip file to" - " be a tab-separated file."),) - - return zfile_errors - - -@indexbp.route("/", methods=["GET"]) -@require_login -def index(): - """Display the expression data index page.""" - return render_template("expression-data/index.html") - - -@indexbp.route("/upload", methods=["GET", "POST"]) -@require_login -def upload_file(): - """Enables uploading the files""" - if request.method == "GET": - return render_template( - "select_species.html", species=with_db_connection(species)) - - upload_dir = app.config["UPLOAD_FOLDER"] - request_errors = errors(request) - if request_errors: - for error in request_errors: - flash(error, "alert-danger error-expr-data") - return redirect(url_for("expression-data.index.upload_file")) - - filename = secure_filename(request.files["qc_text_file"].filename) - if not os.path.exists(upload_dir): - os.mkdir(upload_dir) - - filepath = os.path.join(upload_dir, filename) - request.files["qc_text_file"].save(os.path.join(upload_dir, filename)) - - zip_errors = zip_file_errors(filepath, upload_dir) - if zip_errors: - for error in zip_errors: - flash(error, "alert-danger error-expr-data") - return redirect(url_for("expression-data.index.upload_file")) - - return redirect(url_for("expression-data.parse.parse", - speciesid=request.form["speciesid"], - filename=filename, - filetype=request.form["filetype"])) - -@indexbp.route("/data-review", methods=["GET"]) -@require_login -def data_review(): - """Provide some help on data expectations to the user.""" - return render_template("data_review.html") 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)) diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py new file mode 100644 index 0000000..6900c51 --- /dev/null +++ b/uploader/expression_data/views.py @@ -0,0 +1,384 @@ +"""Views for expression data""" +import os +import uuid +import mimetypes +from typing import Tuple +from zipfile import ZipFile, is_zipfile + +import jsonpickle +from redis import Redis +from werkzeug.utils import secure_filename +from flask import (flash, + request, + url_for, + redirect, + Blueprint, + current_app as app) + +from quality_control.errors import InvalidValue, DuplicateHeading + +from uploader import jobs +from uploader.ui import make_template_renderer +from uploader.authorisation import require_login +from uploader.species.models import all_species, species_by_id +from uploader.db_utils import with_db_connection, database_connection +from uploader.datautils import safe_int, order_by_family, enumerate_sequence +from uploader.population.models import (populations_by_species, + population_by_species_and_id) + +exprdatabp = Blueprint("expression-data", __name__) +render_template = make_template_renderer("expression-data") + +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) + + +def errors(rqst) -> Tuple[str, ...]: + """Return a tuple of the errors found in the request `rqst`. If no error is + found, then an empty tuple is returned.""" + def __filetype_error__(): + return ( + ("Invalid file type provided.",) + if rqst.form.get("filetype") not in ("average", "standard-error") + else tuple()) + + def __file_missing_error__(): + return ( + ("No file was uploaded.",) + if ("qc_text_file" not in rqst.files or + rqst.files["qc_text_file"].filename == "") + else tuple()) + + def __file_mimetype_error__(): + text_file = rqst.files["qc_text_file"] + return ( + ( + ("Invalid file! Expected a tab-separated-values file, or a zip " + "file of the a tab-separated-values file."),) + if text_file.mimetype not in ( + "text/plain", "text/tab-separated-values", + "application/zip") + else tuple()) + + return ( + __filetype_error__() + + (__file_missing_error__() or __file_mimetype_error__())) + + +def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]: + """Check the uploaded zip file for errors.""" + zfile_errors: Tuple[str, ...] = tuple() + if is_zipfile(filepath): + with ZipFile(filepath, "r") as zfile: + infolist = zfile.infolist() + if len(infolist) != 1: + zfile_errors = zfile_errors + ( + ("Expected exactly one (1) member file within the uploaded zip " + f"file. Got {len(infolist)} member files."),) + if len(infolist) == 1 and infolist[0].is_dir(): + zfile_errors = zfile_errors + ( + ("Expected a member text file in the uploaded zip file. Got a " + "directory/folder."),) + + if len(infolist) == 1 and not infolist[0].is_dir(): + zfile.extract(infolist[0], path=upload_dir) + mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}") + if mime[0] != "text/tab-separated-values": + zfile_errors = zfile_errors + ( + ("Expected the member text file in the uploaded zip file to" + " be a tab-separated file."),) + + return zfile_errors + + +@exprdatabp.route("populations/expression-data", methods=["GET"]) +@require_login +def index(): + """Display the expression data index page.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("species_id")): + return render_template("expression-data/index.html", + species=order_by_family(all_species(conn)), + activelink="genotypes") + species = species_by_id(conn, request.args.get("species_id")) + if not bool(species): + flash(f"Could not find species with ID '{request.args.get('species_id')}'!", + "alert-danger") + return redirect(url_for("species.populations.expression-data.index")) + return redirect(url_for("species.populations.expression-data.select_population", + species_id=species["SpeciesId"])) + return render_template() + + +@exprdatabp.route("<int:species_id>/populations/expression-data/select-population", + methods=["GET"]) +@require_login +def select_population(species_id: int): + """Select the expression data's population.""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("Invalid species provided!", "alert-danger") + return redirect(url_for("species.populations.expression-data.index")) + + if not bool(request.args.get("population_id")): + return render_template("expression-data/select-population.html", + species=species, + populations=order_by_family( + populations_by_species(conn, species_id), + order_key="FamilyOrder"), + activelink="genotypes") + + population = population_by_species_and_id( + conn, species_id, request.args.get("population_id")) + if not bool(population): + flash("Invalid population selected!", "alert-danger") + return redirect(url_for( + "species.populations.expression-data.select_population", + species_id=species_id)) + + return redirect(url_for("species.populations.expression-data.upload_file", + species_id=species_id, + population_id=population["Id"])) + + +@exprdatabp.route("<int:species_id>/populations/<int:population_id>/" + "expression-data/upload", + methods=["GET", "POST"]) +@require_login +def upload_file(species_id: int, population_id: int): + """Enables uploading the files""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + population = population_by_species_and_id(conn, species_id, population_id) + if request.method == "GET": + return render_template("expression-data/select-file.html", + species=species, + population=population) + + upload_dir = app.config["UPLOAD_FOLDER"] + request_errors = errors(request) + if request_errors: + for error in request_errors: + flash(error, "alert-danger error-expr-data") + return redirect(url_for("species.populations.expression-data.upload_file")) + + filename = secure_filename(request.files["qc_text_file"].filename) + if not os.path.exists(upload_dir): + os.mkdir(upload_dir) + + filepath = os.path.join(upload_dir, filename) + request.files["qc_text_file"].save(os.path.join(upload_dir, filename)) + + zip_errors = zip_file_errors(filepath, upload_dir) + if zip_errors: + for error in zip_errors: + flash(error, "alert-danger error-expr-data") + return redirect(url_for("species.populations.expression-data.index.upload_file")) + + return redirect(url_for("species.populations.expression-data.parse_file", + species_id=species_id, + population_id=population_id, + filename=filename, + filetype=request.form["filetype"])) + + +@exprdatabp.route("/data-review", methods=["GET"]) +@require_login +def data_review(): + """Provide some help on data expectations to the user.""" + return render_template("expression-data/data-review.html") + + +@exprdatabp.route( + "<int:species_id>/populations/<int:population_id>/expression-data/parse", + methods=["GET"]) +@require_login +def parse_file(species_id: int, population_id: int): + """Trigger file parsing""" + errors = False + filename = request.args.get("filename") + filetype = request.args.get("filetype") + + species = with_db_connection(lambda con: species_by_id(con, species_id)) + if not bool(species): + flash("No such species.", "alert-danger") + errors = True + + if filename is None: + flash("No file provided", "alert-danger") + errors = True + + if filetype is None: + flash("No filetype provided", "alert-danger") + errors = True + + if filetype not in ("average", "standard-error"): + flash("Invalid filetype provided", "alert-danger") + 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-danger") + errors = True + + if errors: + return redirect(url_for("species.populations.expression-data.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, + species_id, filepath, filetype, + app.config["JOBS_TTL_SECONDS"]), + redisurl, + f"{app.config['UPLOAD_FOLDER']}/job_errors") + + return redirect(url_for("species.populations.expression-data.parse_status", + species_id=species_id, + population_id=population_id, + job_id=job["jobid"])) + + +@exprdatabp.route( + "<int:species_id>/populations/<int:population_id>/expression-data/parse/" + "status/<uuid:job_id>", + methods=["GET"]) +@require_login +def parse_status(species_id: int, population_id: int, 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("species.populations.expression-data.results", + species_id=species_id, + population_id=population_id, + job_id=job_id)) + + if status == "parse-error": + return redirect(url_for("species.populations.expression-data.fail", job_id=job_id)) + + app.jinja_env.globals.update( + isinvalidvalue=isinvalidvalue, + isduplicateheading=isduplicateheading) + return render_template( + "expression-data/job-progress.html", + job_id = job_id, + job_status = status, + progress = progress, + message = job.get("message", ""), + job_name = f"Parsing '{filename}'", + errors=errors, + species=with_db_connection( + lambda conn: species_by_id(conn, species_id)), + population=with_db_connection( + lambda conn: population_by_species_and_id( + conn, species_id, population_id))) + + +@exprdatabp.route( + "<int:species_id>/populations/<int:population_id>/expression-data/parse/" + "<uuid:job_id>/results", + methods=["GET"]) +@require_login +def results(species_id: int, population_id: int, job_id: uuid.UUID): + """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( + "expression-data/parse-results.html", + errors=errors, + job_name = f"Parsing '{filename}'", + user_aborted = job.get("user_aborted"), + job_id=job["jobid"], + species=with_db_connection( + lambda conn: species_by_id(conn, species_id)), + population=with_db_connection( + lambda conn: population_by_species_and_id( + conn, species_id, population_id))) + + return render_template("expression-data/no-such-job.html", job_id=job_id) + + +@exprdatabp.route( + "<int:species_id>/populations/<int:population_id>/expression-data/parse/" + "<uuid:job_id>/fail", + methods=["GET"]) +@require_login +def fail(species_id: int, population_id: int, 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("expression-data/no-such-job.html", + **with_db_connection(lambda conn: { + "species_id": species_by_id(conn, species_id), + "population_id": population_by_species_and_id( + conn, species_id, population_id)}), + job_id=job_id) + + +@exprdatabp.route( + "<int:species_id>/populations/<int:population_id>/expression-data/parse/" + "abort", + methods=["POST"]) +@require_login +def abort(species_id: int, population_id: int): + """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("species.populations.expression-data.parse_status", + species_id=species_id, + population_id=population_id, + job_id=job_id)) diff --git a/uploader/population/views.py b/uploader/population/views.py index 39a5762..631f0be 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -18,6 +18,7 @@ from uploader.oauth2.client import oauth2_post from uploader.ui import make_template_renderer from uploader.authorisation import require_login from uploader.genotypes.views import genotypesbp +from uploader.expression_data.views import exprdatabp from uploader.db_utils import database_connection from uploader.datautils import enumerate_sequence from uploader.species.models import (all_species, @@ -34,6 +35,7 @@ __active_link__ = "populations" popbp = Blueprint("populations", __name__) popbp.register_blueprint(samplesbp, url_prefix="/") popbp.register_blueprint(genotypesbp, url_prefix="/") +popbp.register_blueprint(exprdatabp, url_prefix="/") render_template = make_template_renderer("populations") diff --git a/uploader/templates/expression-data/base.html b/uploader/templates/expression-data/base.html new file mode 100644 index 0000000..d63fd7e --- /dev/null +++ b/uploader/templates/expression-data/base.html @@ -0,0 +1,13 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="expression-data"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.expression-data.index')}}"> + Expression Data</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/data_review.html b/uploader/templates/expression-data/data-review.html index 4e5c586..c985b03 100644 --- a/uploader/templates/data_review.html +++ b/uploader/templates/expression-data/data-review.html @@ -26,7 +26,7 @@ <small class="text-muted"> If you encounter an error saying your sample(s)/case(s) do not exist in the GeneNetwork database, then you will have to use the - <a href="{{url_for('expression-data.samples.select_species')}}" + <a href="{{url_for('species.populations.samples.index')}}" title="Upload samples/cases feature">Upload Samples/Cases</a> option on this system to upload them. </small> @@ -70,8 +70,8 @@ column</li> <li>The values of each field <strong>ARE NOT</strong> quoted.</li> <li>Here is an - <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv"> - example file</a> with a single data row.</li> + <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv" + target="_blank">example file</a> with a single data row.</li> </ul> </li> <li>.txt files: Content has the same format as .tsv file above</li> diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html index ed5d8dd..9ba3582 100644 --- a/uploader/templates/expression-data/index.html +++ b/uploader/templates/expression-data/index.html @@ -1,5 +1,6 @@ -{%extends "base.html"%} +{%extends "expression-data/base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} {%block title%}Expression Data{%endblock%} @@ -10,86 +11,23 @@ <a href="{{url_for('base.index')}}">Home</a> </li> <li class="breadcrumb-item active"> - <a href="{{url_for('expression-data.index.index')}}">Expression Data</a> + <a href="{{url_for('species.populations.expression-data.index')}}" + title="Upload expression data."> + Expression Data</a> </li> {%endblock%} {%block contents%} <div class="row"> - {{flash_all_messages()}} - - <h1 class="heading">data upload</h1> - - <div class="explainer"> - <p>Each of the sections below gives you a different option for data expression-data. - Please read the documentation for each section carefully to understand what - each section is about.</p> - </div> -</div> - -<div class="row"> - <h2 class="heading">R/qtl2 Bundles</h2> - - <div class="explainer"> - <p>This feature combines and extends the two upload methods below. Instead of - uploading one item at a time, the R/qtl2 bundle you upload can contain both - the genotypes data (samples/individuals/cases and their data) and the - expression data.</p> - <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither - of the methods below can handle.</p> - - <a href="{{url_for('expression-data.rqtl2.select_species')}}" - title="Upload a zip bundle of R/qtl2 files"> - <button class="btn btn-primary">upload R/qtl2 bundle</button></a> - </div> -</div> - - -<div class="row"> <h2 class="heading">Expression Data</h2> + {{flash_all_messages()}} - <div class="explainer"> - <p>This feature enables you to upload expression data. It expects the data to - be in <strong>tab-separated values (TSV)</strong> files. The data should be - a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a - list of the <em>phenotypes</em> and the first row is a list of - <em>samples/cases</em>.</p> - - <p>If you haven't done so please go to this page to learn the requirements for - file formats and helpful suggestions to enter your data in a fast and easy - way.</p> - - <ol> - <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies - with our system requirements. ( - <a href="{{url_for('expression-data.index.data_review')}}#data-concerns" - title="Details for the data expectations.">Help</a> - )</li> - <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept - <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> - files (<a href="{{url_for('expression-data.index.data_review')}}#file-types" - title="Details for the data expectations.">Help</a>)</li> - </ol> - </div> - - <a href="{{url_for('expression-data.index.upload_file')}}" - title="Upload your expression data" - class="btn btn-primary">upload expression data</a> + <p>This section allows you to enter the expression data for your experiment. + You will need to select the species that your data concerns below.</p> </div> <div class="row"> - <h2 class="heading">samples/cases</h2> - - <div class="explainer"> - <p>For the expression data above, you need the samples/cases in your file to - already exist in the GeneNetwork database. If there are any samples that do - not already exist the upload of the expression data will fail.</p> - <p>This section gives you the opportunity to upload any missing samples</p> - </div> - - <a href="{{url_for('expression-data.samples.select_species')}}" - title="Upload samples/cases/individuals for your data" - class="btn btn-primary">upload Samples/Cases</a> + {{select_species_form(url_for("species.populations.expression-data.index"), + species)}} </div> - {%endblock%} diff --git a/uploader/templates/job_progress.html b/uploader/templates/expression-data/job-progress.html index 2feaa89..ef264e1 100644 --- a/uploader/templates/job_progress.html +++ b/uploader/templates/expression-data/job-progress.html @@ -1,5 +1,6 @@ {%extends "base.html"%} {%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} {%block extrameta%} <meta http-equiv="refresh" content="5"> @@ -11,7 +12,9 @@ <h1 class="heading">{{job_name}}</h2> <div class="row"> - <form action="{{url_for('expression-data.parse.abort')}}" method="POST"> + <form action="{{url_for('species.populations.expression-data.abort', + species_id=species.SpeciesId, + population_id=population.Id)}}" method="POST"> <legend class="heading">Status</legend> <div class="form-group"> <label for="job_status" class="form-label">status:</label> @@ -38,3 +41,7 @@ </div> {%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/no_such_job.html b/uploader/templates/expression-data/no-such-job.html index 874d047..d22c429 100644 --- a/uploader/templates/no_such_job.html +++ b/uploader/templates/expression-data/no-such-job.html @@ -1,7 +1,8 @@ {%extends "base.html"%} {%block extrameta%} -<meta http-equiv="refresh" content="5;url={{url_for('expression-data.index.upload_file')}}"> +<meta http-equiv="refresh" + content="5;url={{url_for('species.populations.expression-data.index.upload_file')}}"> {%endblock%} {%block title%}No Such Job{%endblock%} diff --git a/uploader/templates/parse_failure.html b/uploader/templates/expression-data/parse-failure.html index 31f6be8..31f6be8 100644 --- a/uploader/templates/parse_failure.html +++ b/uploader/templates/expression-data/parse-failure.html diff --git a/uploader/templates/expression-data/parse-results.html b/uploader/templates/expression-data/parse-results.html new file mode 100644 index 0000000..03a23e2 --- /dev/null +++ b/uploader/templates/expression-data/parse-results.html @@ -0,0 +1,39 @@ +{%extends "base.html"%} +{%from "errors_display.html" import errors_display%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Parse Results{%endblock%} + +{%block contents%} + +<div class="row"> + <h2 class="heading">{{job_name}}: parse results</h2> + + {%if user_aborted%} + <span class="alert-warning">Job aborted by the user</span> + {%endif%} + + {{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} + + {%if errors | length == 0 and not user_aborted %} + <form method="post" action="{{url_for('dbinsert.select_platform')}}"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + <input type="submit" value="update database" class="btn btn-primary" /> + </form> + {%endif%} + + {%if errors | length > 0 or user_aborted %} + <br /> + <a href="{{url_for('species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Back to index page." + class="btn btn-primary">Go back</a> + + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/expression-data/select-file.html b/uploader/templates/expression-data/select-file.html new file mode 100644 index 0000000..4ca461e --- /dev/null +++ b/uploader/templates/expression-data/select-file.html @@ -0,0 +1,115 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "upload_progress_indicator.html" import upload_progress_indicator%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Expression Data — Upload Data{%endblock%} + +{%block pagetitle%}Expression Data — Upload Data{%endblock%} + +{%block contents%} +{{upload_progress_indicator()}} + +<div class="row"> + <h2 class="heading">Upload Expression Data</h2> + + <p>This feature enables you to upload expression data. It expects the data to + be in <strong>tab-separated values (TSV)</strong> files. The data should be + a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a + list of the <em>phenotypes</em> and the first row is a list of + <em>samples/cases</em>.</p> + + <p>If you haven't done so please go to this page to learn the requirements for + file formats and helpful suggestions to enter your data in a fast and easy + way.</p> + + <ol> + <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies + with our system requirements. ( + <a href="{{url_for('species.populations.expression-data.data_review')}}#data-concerns" + title="Details for the data expectations.">Help</a> + )</li> + <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept + <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> + files (<a href="{{url_for('species.populations.expression-data.data_review')}}#file-types" + title="Details for the data expectations.">Help</a>)</li> + </ol> +</div> + +<div class="row"> + <form action="{{url_for( + 'species.populations.expression-data.upload_file', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST" + enctype="multipart/form-data" + id="frm-upload-expression-data"> + {{flash_messages("error-expr-data")}} + + <div class="form-group"> + <legend class="heading">File Type</legend> + + <div class="radio"> + <label for="filetype_average" class="form-check-label"> + <input type="radio" name="filetype" value="average" id="filetype_average" + required="required" class="form-check-input" /> + Average</label> + <p class="form-text text-muted"> + <small>The averages data …</small></p> + </div> + + <div class="radio"> + <label for="filetype_standard_error" class="form-check-label"> + <input type="radio" name="filetype" value="standard-error" + id="filetype_standard_error" required="required" + class="form-check-input" /> + Standard Error + </label> + <p class="form-text text-muted"> + <small>The standard errors computed from the averages …</small></p> + </div> + </div> + + <div class="form-group"> + <span id="no-file-error" class="alert-danger" style="display: none;"> + No file selected + </span> + <label for="file_upload" class="form-label">Select File</label> + <input type="file" name="qc_text_file" id="file_upload" + accept="text/plain, text/tab-separated-values, application/zip" + class="form-control"/> + <p class="form-text text-muted"> + <small>Select the file to upload.</small></p> + </div> + + <button type="submit" + class="btn btn-primary" + data-toggle="modal" + data-target="#upload-progress-indicator">upload file</button> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/upload_progress.js"></script> +<script type="text/javascript"> + function setup_formdata(form) { + var formdata = new FormData(); + formdata.append( + "qc_text_file", + form.querySelector("input[type='file']").files[0]); + formdata.append( + "filetype", + selected_filetype( + Array.from(form.querySelectorAll("input[type='radio']")))); + return formdata; + } + + setup_upload_handlers( + "frm-upload-expression-data", make_data_uploader(setup_formdata)); +</script> +{%endblock%} diff --git a/uploader/templates/expression-data/select-population.html b/uploader/templates/expression-data/select-population.html new file mode 100644 index 0000000..8555e27 --- /dev/null +++ b/uploader/templates/expression-data/select-population.html @@ -0,0 +1,29 @@ +{%extends "expression-data/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Expression Data{%endblock%} + +{%block pagetitle%}Expression Data{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>You have selected the species. Now you need to select the population that + the expression data belongs to.</p> +</div> + +<div class="row"> + {{select_population_form(url_for( + "species.populations.expression-data.select_population", + species_id=species.SpeciesId), + populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/parse_results.html b/uploader/templates/parse_results.html deleted file mode 100644 index 46fbaaf..0000000 --- a/uploader/templates/parse_results.html +++ /dev/null @@ -1,30 +0,0 @@ -{%extends "base.html"%} -{%from "errors_display.html" import errors_display%} - -{%block title%}Parse Results{%endblock%} - -{%block contents%} -<h1 class="heading">{{job_name}}: parse results</h2> - -{%if user_aborted%} -<span class="alert-warning">Job aborted by the user</span> -{%endif%} - -{{errors_display(errors, "No errors found in the file", "We found the following errors", True)}} - -{%if errors | length == 0 and not user_aborted %} -<form method="post" action="{{url_for('dbinsert.select_platform')}}"> - <input type="hidden" name="job_id" value="{{job_id}}" /> - <input type="submit" value="update database" class="btn btn-primary" /> -</form> -{%endif%} - -{%if errors | length > 0 or user_aborted %} -<br /> -<a href="{{url_for('expression-data.index.upload_file')}}" title="Back to index page." - class="btn btn-primary"> - Go back -</a> -{%endif%} - -{%endblock%} diff --git a/uploader/templates/select_species.html b/uploader/templates/select_species.html deleted file mode 100644 index 1642401..0000000 --- a/uploader/templates/select_species.html +++ /dev/null @@ -1,92 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} -{%from "upload_progress_indicator.html" import upload_progress_indicator%} - -{%block title%}expression data: select species{%endblock%} - -{%block contents%} -{{upload_progress_indicator()}} - -<h2 class="heading">expression data: select species</h2> - -<div class="row"> - <form action="{{url_for('expression-data.index.upload_file')}}" - method="POST" - enctype="multipart/form-data" - id="frm-upload-expression-data"> - <legend class="heading">upload expression data</legend> - {{flash_messages("error-expr-data")}} - - <div class="form-group"> - <label for="select_species01" class="form-label">Species</label> - <select id="select_species01" - name="speciesid" - required="required" - class="form-control"> - <option value="">Select species</option> - {%for aspecies in species%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> - {%endfor%} - </select> - </div> - - <div class="form-group"> - <legend class="heading">file type</legend> - - <div class="form-check"> - <input type="radio" name="filetype" value="average" id="filetype_average" - required="required" class="form-check-input" /> - <label for="filetype_average" class="form-check-label">average</label> - </div> - - <div class="form-check"> - <input type="radio" name="filetype" value="standard-error" - id="filetype_standard_error" required="required" - class="form-check-input" /> - <label for="filetype_standard_error" class="form-check-label"> - standard error - </label> - </div> - </div> - - <div class="form-group"> - <span id="no-file-error" class="alert-danger" style="display: none;"> - No file selected - </span> - <label for="file_upload" class="form-label">select file</label> - <input type="file" name="qc_text_file" id="file_upload" - accept="text/plain, text/tab-separated-values, application/zip" - class="form-control"/> - </div> - - <button type="submit" - class="btn btn-primary" - data-toggle="modal" - data-target="#upload-progress-indicator">upload file</button> - </form> -</div> -{%endblock%} - - -{%block javascript%} -<script type="text/javascript" src="static/js/upload_progress.js"></script> -<script type="text/javascript"> - 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( - "filetype", - selected_filetype( - Array.from(form.querySelectorAll("input[type='radio']")))); - return formdata; - } - - setup_upload_handlers( - "frm-upload-expression-data", make_data_uploader(setup_formdata)); -</script> -{%endblock%} |