diff options
Diffstat (limited to 'uploader')
127 files changed, 6925 insertions, 1869 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index 1af159b..cae531b 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -11,8 +11,8 @@ from uploader.oauth2.client import user_logged_in, authserver_authorise_uri from . import session from .base_routes import base +from .files.views import files from .species import speciesbp -from .dbinsert import dbinsertbp from .oauth2.views import oauth2 from .expression_data import exprdatabp from .errors import register_error_handlers @@ -83,10 +83,9 @@ def create_app(): # setup blueprints app.register_blueprint(base, url_prefix="/") + app.register_blueprint(files, url_prefix="/files") 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/authorisation.py b/uploader/authorisation.py index ee8fe97..a283980 100644 --- a/uploader/authorisation.py +++ b/uploader/authorisation.py @@ -18,7 +18,7 @@ def require_login(function): """Check that the user is logged in and their token is valid.""" def __clear_session__(_no_token): session.clear_session_info() - flash("You need to be logged in.", "alert-danger") + flash("You need to be signed in.", "alert-danger big-alert") return redirect("/") return session.user_token().either( diff --git a/uploader/base_routes.py b/uploader/base_routes.py index 88247b2..326086f 100644 --- a/uploader/base_routes.py +++ b/uploader/base_routes.py @@ -1,15 +1,16 @@ """Basic routes required for all pages""" import os +from urllib.parse import urljoin -from flask import ( - Blueprint, - render_template, - current_app as app, - send_from_directory) +from flask import (Blueprint, + current_app as app, + send_from_directory) +from uploader.ui import make_template_renderer from uploader.oauth2.client import user_logged_in base = Blueprint("base", __name__) +render_template = make_template_renderer("home") @base.route("/favicon.ico", methods=["GET"]) @@ -23,7 +24,9 @@ def favicon(): @base.route("/", methods=["GET"]) def index(): """Load the landing page""" - return render_template("index.html" if user_logged_in() else "login.html") + return render_template("index.html" if user_logged_in() else "login.html", + gn2server_intro=urljoin(app.config["GN2_SERVER_URL"], + "/intro")) def appenv(): """Get app's guix environment path.""" @@ -43,6 +46,13 @@ def jquery(filename): appenv(), f"share/genenetwork2/javascript/jquery/{filename}") +@base.route("/datatables/<path:filename>") +def datatables(filename): + """Fetch DataTables files.""" + return send_from_directory( + appenv(), f"share/genenetwork2/javascript/DataTables/{filename}") + + @base.route("/node-modules/<path:filename>") def node_modules(filename): """Fetch node-js modules.""" diff --git a/uploader/check_connections.py b/uploader/check_connections.py index 2561e55..c9b9aa3 100644 --- a/uploader/check_connections.py +++ b/uploader/check_connections.py @@ -4,8 +4,7 @@ import traceback import redis import MySQLdb - -from uploader.db_utils import database_connection +from gn_libs.mysqldb import database_connection def check_redis(uri: str): "Check the redis connection" diff --git a/uploader/datautils.py b/uploader/datautils.py index 2ee079d..46a55c4 100644 --- a/uploader/datautils.py +++ b/uploader/datautils.py @@ -1,7 +1,7 @@ """Generic data utilities: Rename module.""" import math -from typing import Sequence from functools import reduce +from typing import Union, Sequence def enumerate_sequence(seq: Sequence[dict], start:int = 1) -> Sequence[dict]: """Enumerate sequence beginning at 1""" @@ -28,7 +28,7 @@ def order_by_family(items: tuple[dict, ...], key=lambda item: item[0][0]) -def safe_int(val: str) -> int: +def safe_int(val: Union[str, int, float]) -> int: """ Convert val into an integer: if val cannot be converted, return a zero. """ diff --git a/uploader/db/platforms.py b/uploader/db/platforms.py deleted file mode 100644 index cb527a7..0000000 --- a/uploader/db/platforms.py +++ /dev/null @@ -1,25 +0,0 @@ -"""Handle db interactions for platforms.""" -from typing import Optional - -import MySQLdb as mdb -from MySQLdb.cursors import DictCursor - -def platforms_by_species( - conn: mdb.Connection, speciesid: int) -> tuple[dict, ...]: - """Retrieve platforms by the species""" - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s " - "ORDER BY GeneChipName ASC", - (speciesid,)) - return tuple(dict(row) for row in cursor.fetchall()) - -def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]: - """Retrieve a platform by its ID""" - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM GeneChip WHERE Id=%s", - (platformid,)) - result = cursor.fetchone() - if bool(result): - return dict(result) - - return None diff --git a/uploader/db_utils.py b/uploader/db_utils.py index d31e2c2..d9d521e 100644 --- a/uploader/db_utils.py +++ b/uploader/db_utils.py @@ -1,54 +1,20 @@ """module contains all db related stuff""" -import logging -import traceback -import contextlib -from urllib.parse import urlparse -from typing import Any, Tuple, Iterator, Callable +from typing import Any, Callable import MySQLdb as mdb from redis import Redis -from MySQLdb.cursors import Cursor from flask import current_app as app +from gn_libs.mysqldb import database_connection -def parse_db_url(db_url) -> Tuple: - """ - Parse SQL_URI configuration variable. - """ - parsed_db = urlparse(db_url) - return (parsed_db.hostname, parsed_db.username, - parsed_db.password, parsed_db.path[1:], parsed_db.port) - - -@contextlib.contextmanager -def database_connection(db_url: str) -> Iterator[mdb.Connection]: - """function to create db connector""" - host, user, passwd, db_name, db_port = parse_db_url(db_url) - connection = mdb.connect( - host, user, passwd, db_name, port=(db_port or 3306)) - try: - yield connection - connection.commit() - except mdb.Error as _mdb_err: - logging.error(traceback.format_exc()) - connection.rollback() - finally: - connection.close() def with_db_connection(func: Callable[[mdb.Connection], Any]) -> Any: """Call `func` with a MySQDdb database connection.""" with database_connection(app.config["SQL_URI"]) as conn: return func(conn) + def with_redis_connection(func: Callable[[Redis], Any]) -> Any: """Call `func` with a redis connection.""" redisuri = app.config["REDIS_URL"] with Redis.from_url(redisuri, decode_responses=True) as rconn: return func(rconn) - - -def debug_query(cursor: Cursor): - """Debug the actual query run with MySQLdb""" - for attr in ("_executed", "statement", "_last_executed"): - if hasattr(cursor, attr): - logging.debug("MySQLdb QUERY: %s", getattr(cursor, attr)) - break diff --git a/uploader/default_settings.py b/uploader/default_settings.py index 26fe665..1acb247 100644 --- a/uploader/default_settings.py +++ b/uploader/default_settings.py @@ -2,15 +2,12 @@ The default configuration file. The values here should be overridden in the actual configuration file used for the production and staging systems. """ - -import os - -LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING") +LOG_LEVEL = "WARNING" SECRET_KEY = b"<Please! Please! Please! Change This!>" UPLOAD_FOLDER = "/tmp/qc_app_files" REDIS_URL = "redis://" JOBS_TTL_SECONDS = 1209600 # 14 days -GNQC_REDIS_PREFIX="GNQC" +GNQC_REDIS_PREFIX="gn-uploader" SQL_URI = "" GN2_SERVER_URL = "https://genenetwork.org/" 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..6d8ce80 100644 --- a/uploader/dbinsert.py +++ b/uploader/expression_data/dbinsert.py @@ -7,16 +7,17 @@ from datetime import datetime from redis import Redis from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from flask import ( flash, request, url_for, Blueprint, redirect, render_template, current_app as app) +from uploader import jobs from uploader.authorisation import require_login +from uploader.db_utils import with_db_connection from uploader.population.models import populations_by_species -from uploader.db_utils import with_db_connection, database_connection -from uploader.species.models import species_by_id, all_species as species - -from . import jobs +from uploader.species.models import all_species, species_by_id +from uploader.platforms.models import platform_by_species_and_id dbinsertbp = Blueprint("dbinsert", __name__) @@ -49,14 +50,6 @@ def genechips(): return {} -def platform_by_id(genechipid:int) -> Union[dict, None]: - "Retrieve the gene platform by id" - with database_connection(app.config["SQL_URI"]) as conn: - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute( - "SELECT * FROM GeneChip WHERE GeneChipId=%s", - (genechipid,)) - return cursor.fetchone() def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple: "Retrieve the studies by the related species and gene platform" @@ -108,7 +101,7 @@ def select_platform(): return render_template( "select_platform.html", filename=filename, filetype=job["filetype"], totallines=int(job["currentline"]), - default_species=default_species, species=species(conn), + default_species=default_species, species=all_species(conn), genechips=gchips[default_species], genechips_data=json.dumps(gchips)) return render_error(f"File '{filename}' no longer exists.") @@ -327,37 +320,38 @@ def selected_keys(original: dict, keys: tuple) -> dict: @require_login def final_confirmation(): "Preview the data before triggering entry into the database" - form = request.form - try: - assert form.get("filename"), "filename" - assert form.get("filetype"), "filetype" - assert form.get("species"), "species" - assert form.get("genechipid"), "platform" - assert form.get("studyid"), "study" - assert form.get("datasetid"), "dataset" - - speciesid = form["species"] - genechipid = form["genechipid"] - studyid = form["studyid"] - datasetid=form["datasetid"] - return render_template( - "final_confirmation.html", filename=form["filename"], - filetype=form["filetype"], totallines=form["totallines"], - species=speciesid, genechipid=genechipid, studyid=studyid, - datasetid=datasetid, the_species=selected_keys( - with_db_connection(lambda conn: species_by_id(conn, speciesid)), - ("SpeciesName", "Name", "MenuName")), - platform=selected_keys( - platform_by_id(genechipid), - ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")), - study=selected_keys( - study_by_id(studyid), ("Name", "FullName", "ShortName")), - dataset=selected_keys( - dataset_by_id(datasetid), - ("AvgMethodName", "Name", "Name2", "FullName", "ShortName", - "DataScale"))) - except AssertionError as aserr: - return render_error(f"Missing data: {aserr.args[0]}") + with database_connection(app.config["SQL_URI"]) as conn: + form = request.form + try: + assert form.get("filename"), "filename" + assert form.get("filetype"), "filetype" + assert form.get("species"), "species" + assert form.get("genechipid"), "platform" + assert form.get("studyid"), "study" + assert form.get("datasetid"), "dataset" + + speciesid = form["species"] + genechipid = form["genechipid"] + studyid = form["studyid"] + datasetid=form["datasetid"] + return render_template( + "final_confirmation.html", filename=form["filename"], + filetype=form["filetype"], totallines=form["totallines"], + species=speciesid, genechipid=genechipid, studyid=studyid, + datasetid=datasetid, the_species=selected_keys( + with_db_connection(lambda conn: species_by_id(conn, speciesid)), + ("SpeciesName", "Name", "MenuName")), + platform=selected_keys( + platform_by_species_and_id(conn, speciesid, genechipid), + ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")), + study=selected_keys( + study_by_id(studyid), ("Name", "FullName", "ShortName")), + dataset=selected_keys( + dataset_by_id(datasetid), + ("AvgMethodName", "Name", "Name2", "FullName", "ShortName", + "DataScale"))) + except AssertionError as aserr: + return render_error(f"Missing data: {aserr.args[0]}") @dbinsertbp.route("/insert-data", methods=["POST"]) @require_login 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..7629f3e --- /dev/null +++ b/uploader/expression_data/views.py @@ -0,0 +1,385 @@ +"""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 gn_libs.mysqldb import database_connection +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.datautils import order_by_family +from uploader.ui import make_template_renderer +from uploader.authorisation import require_login +from uploader.db_utils import with_db_connection +from uploader.species.models import all_species, species_by_id +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="expression-data") + species = species_by_id(conn, request.args.get("species_id")) + if not bool(species): + flash("Could not find species selected!", "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"])) + + +@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("No such species!", "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="expression-data") + + population = population_by_species_and_id( + conn, species_id, request.args.get("population_id")) + if not bool(population): + flash("No such population!", "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)# type: ignore[arg-type] + 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,# type: ignore[arg-type] + 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/files/__init__.py b/uploader/files/__init__.py new file mode 100644 index 0000000..53c3176 --- /dev/null +++ b/uploader/files/__init__.py @@ -0,0 +1,5 @@ +"""General files and chunks utilities.""" +from .chunks import chunked_binary_read +from .functions import (fullpath, + save_file, + sha256_digest_over_file) diff --git a/uploader/files/chunks.py b/uploader/files/chunks.py new file mode 100644 index 0000000..c4360b5 --- /dev/null +++ b/uploader/files/chunks.py @@ -0,0 +1,32 @@ +"""Functions dealing with chunking of files.""" +from pathlib import Path +from typing import Iterator + +from flask import current_app as app +from werkzeug.utils import secure_filename + + +def chunked_binary_read(filepath: Path, chunksize: int = 2048) -> Iterator: + """Read a file in binary mode in chunks.""" + with open(filepath, "rb") as inputfile: + while True: + data = inputfile.read(chunksize) + if data != b"": + yield data + continue + break + +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}") diff --git a/uploader/files.py b/uploader/files/functions.py index b163612..7b9f06b 100644 --- a/uploader/files.py +++ b/uploader/files/functions.py @@ -2,17 +2,23 @@ import hashlib from pathlib import Path from datetime import datetime + from flask import current_app from werkzeug.utils import secure_filename from werkzeug.datastructures import FileStorage -def save_file(fileobj: FileStorage, upload_dir: Path) -> Path: +from .chunks import chunked_binary_read + +def save_file(fileobj: FileStorage, upload_dir: Path, hashed: bool = True) -> Path: """Save the uploaded file and return the path.""" assert bool(fileobj), "Invalid file object!" - hashed_name = hashlib.sha512( - f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8") - ).hexdigest() + hashed_name = ( + hashlib.sha512( + f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8") + ).hexdigest() + if hashed else + fileobj.filename) filename = Path(secure_filename(hashed_name)) # type: ignore[arg-type] if not upload_dir.exists(): upload_dir.mkdir() @@ -21,6 +27,16 @@ def save_file(fileobj: FileStorage, upload_dir: Path) -> Path: fileobj.save(filepath) return filepath + def fullpath(filename: str): """Get a file's full path. This makes use of `flask.current_app`.""" return Path(current_app.config["UPLOAD_FOLDER"], filename).absolute() + + +def sha256_digest_over_file(filepath: Path) -> str: + """Compute the sha256 digest over a file's contents.""" + filehash = hashlib.sha256() + for chunk in chunked_binary_read(filepath): + filehash.update(chunk) + + return filehash.hexdigest() diff --git a/uploader/files/views.py b/uploader/files/views.py new file mode 100644 index 0000000..8d81654 --- /dev/null +++ b/uploader/files/views.py @@ -0,0 +1,116 @@ +"""Module for generic files endpoints.""" +import traceback +from pathlib import Path + +from flask import request, jsonify, Blueprint, current_app as app + +from .chunks import chunk_name, chunks_directory + +files = Blueprint("files", __name__) + +def target_file(fileid: str) -> Path: + """Compute the full path for the target file.""" + return Path(app.config["UPLOAD_FOLDER"], fileid) + + +@files.route("/upload/resumable", methods=["GET"]) +def resumable_upload_get(): + """Used for checking whether **ALL** chunks have been uploaded.""" + 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 the complete target file exists, return 200 for all chunks. + _targetfile = target_file(fileid) + if _targetfile.exists(): + return jsonify({ + "uploaded-file": _targetfile.name, + "original-name": filename, + "chunk": chunk, + "message": "The complete file already exists.", + "statuscode": 200 + }), 200 + + if Path(chunks_directory(fileid), + chunk_name(filename, chunk)).exists(): + return jsonify({ + "chunk": chunk, + "message": f"Chunk {chunk} exists.", + "statuscode": 200 + }), 200 + + 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 + + +@files.route("/upload/resumable", methods=["POST"]) +def resumable_upload_post(): + """Do the actual chunks upload here.""" + _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 = target_file(_fileid) + + if _targetfile.exists(): + return jsonify({ + "uploaded-file": _targetfile.name, + "original-name": _uploadfilename, + "message": "File was uploaded successfully!", + "statuscode": 200 + }), 200 + + try: + 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() + return jsonify({ + "uploaded-file": _targetfile.name, + "original-name": _uploadfilename, + "message": "File was uploaded successfully!", + "statuscode": 200 + }), 200 + return jsonify({ + "message": f"Chunk {int(_chunk)} uploaded successfully.", + "statuscode": 201 + }), 201 + 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 diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py new file mode 100644 index 0000000..4c3e634 --- /dev/null +++ b/uploader/genotypes/models.py @@ -0,0 +1,102 @@ +"""Functions for handling genotypes.""" +from typing import Optional +from datetime import datetime + +import MySQLdb as mdb +from MySQLdb.cursors import Cursor, DictCursor +from flask import current_app as app + +from gn_libs.mysqldb import debug_query + +def genocode_by_population( + conn: mdb.Connection, population_id: int) -> tuple[dict, ...]: + """Get the allele/genotype codes.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM GenoCode WHERE InbredSetId=%s", + (population_id,)) + return tuple(dict(item) for item in cursor.fetchall()) + + +def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int: + """Find the total count of the genotype markers for a species.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT COUNT(Name) AS markers_count FROM Geno WHERE SpeciesId=%s", + (species_id,)) + return int(cursor.fetchone()["markers_count"]) + + +def genotype_markers( + conn: mdb.Connection, + species_id: int, + offset: int = 0, + limit: Optional[int] = None +) -> tuple[dict, ...]: + """Retrieve markers from the database.""" + _query = "SELECT * FROM Geno WHERE SpeciesId=%s" + if bool(limit) and limit > 0:# type: ignore[operator] + _query = _query + f" LIMIT {limit} OFFSET {offset}" + + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, (species_id,)) + debug_query(cursor, app.logger) + return tuple(dict(row) for row in cursor.fetchall()) + + +def genotype_dataset( + conn: mdb.Connection, + species_id: int, + population_id: int, + dataset_id: Optional[int] = None +) -> Optional[dict]: + """Retrieve genotype datasets from the database. + + Apparently, you should only ever have one genotype dataset for a population. + """ + _query = ( + "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset " + "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf " + "ON iset.Id=gf.InbredSetId " + "WHERE s.Id=%s AND iset.Id=%s") + _params = (species_id, population_id) + if bool(dataset_id): + _query = _query + " AND gf.Id=%s" + _params = _params + (dataset_id,)# type: ignore[assignment] + + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, _params) + debug_query(cursor, app.logger) + result = cursor.fetchone() + if bool(result): + return dict(result) + return None + + +def save_new_dataset( + cursor: Cursor, + population_id: int, + name: str, + fullname: str, + shortname: str +) -> dict: + """Save a new genotype dataset into the database.""" + params = { + "InbredSetId": population_id, + "Name": name, + "FullName": fullname, + "ShortName": shortname, + "CreateTime": datetime.now().date().isoformat(), + "public": 2, + "confidentiality": 0, + "AuthorisedUsers": None + } + cursor.execute( + "INSERT INTO GenoFreeze(" + "Name, FullName, ShortName, CreateTime, public, InbredSetId, " + "confidentiality, AuthorisedUsers" + ") VALUES (" + "%(Name)s, %(FullName)s, %(ShortName)s, %(CreateTime)s, %(public)s, " + "%(InbredSetId)s, %(confidentiality)s, %(AuthorisedUsers)s" + ")", + params) + return {**params, "Id": cursor.lastrowid} diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 885e008..5105730 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,4 +1,6 @@ """Views for the genotypes.""" +from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from flask import (flash, request, url_for, @@ -7,14 +9,24 @@ from flask import (flash, render_template, current_app as app) -from uploader.datautils import order_by_family +from uploader.ui import make_template_renderer +from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login -from uploader.db_utils import database_connection from uploader.species.models import all_species, species_by_id +from uploader.monadic_requests import make_either_error_handler +from uploader.request_checks import with_species, with_population +from uploader.datautils import safe_int, order_by_family, enumerate_sequence from uploader.population.models import (populations_by_species, population_by_species_and_id) +from .models import (genotype_markers, + genotype_dataset, + save_new_dataset, + genotype_markers_count, + genocode_by_population) + genotypesbp = Blueprint("genotypes", __name__) +render_template = make_template_renderer("genotypes") @genotypesbp.route("populations/genotypes", methods=["GET"]) @require_login @@ -23,8 +35,15 @@ def index(): with database_connection(app.config["SQL_URI"]) as conn: if not bool(request.args.get("species_id")): return render_template("genotypes/index.html", - species=order_by_family(all_species(conn)), + species=all_species(conn), activelink="genotypes") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.genotypes.select_population")) + 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')}'!", @@ -37,22 +56,24 @@ def index(): @genotypesbp.route("/<int:species_id>/populations/genotypes/select-population", methods=["GET"]) @require_login -def select_population(species_id: int): +@with_species(redirect_uri="species.populations.genotypes.index") +def select_population(species: dict, species_id: int): """Select the population under which the genotypes go.""" 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.genotypes.index")) - if not bool(request.args.get("population_id")): return render_template("genotypes/select-population.html", species=species, - populations=order_by_family( - populations_by_species(conn, species_id), - order_key="FamilyOrder"), + populations=populations_by_species( + conn, species_id), activelink="genotypes") + population_id = request.args["population_id"] + if population_id == "CREATE-POPULATION": + return redirect(url_for( + "species.populations.create_population", + species_id=species["SpeciesId"], + return_to="species.populations.samples.list_genotypes")) + population = population_by_species_and_id( conn, species_id, request.args.get("population_id")) if not bool(population): @@ -70,6 +91,135 @@ def select_population(species_id: int): "/<int:species_id>/populations/<int:population_id>/genotypes", methods=["GET"]) @require_login -def list_genotypes(species_id: int, population_id: int): +@with_population(species_redirect_uri="species.populations.genotypes.index", + redirect_uri="species.populations.genotypes.select_population") +def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """List genotype details for species and population.""" - return f"Would list geno info for population {population_id} from species {species_id}" + with database_connection(app.config["SQL_URI"]) as conn: + return render_template("genotypes/list-genotypes.html", + species=species, + population=population, + genocode=genocode_by_population( + conn, population["Id"]), + total_markers=genotype_markers_count( + conn, species["SpeciesId"]), + dataset=genotype_dataset(conn, + species["SpeciesId"], + population["Id"]), + activelink="list-genotypes") + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/list-markers", + methods=["GET"]) +@require_login +@with_population(species_redirect_uri="species.populations.genotypes.index", + redirect_uri="species.populations.genotypes.select_population") +def list_markers( + species: dict, + population: dict, + **kwargs +):# pylint: disable=[unused-argument] + """List a species' genetic markers.""" + with database_connection(app.config["SQL_URI"]) as conn: + start_from = max(safe_int(request.args.get("start_from") or 0), 0) + count = safe_int(request.args.get("count") or 20) + return render_template("genotypes/list-markers.html", + species=species, + population=population, + total_markers=genotype_markers_count( + conn, species["SpeciesId"]), + start_from=start_from, + count=count, + markers=enumerate_sequence( + genotype_markers(conn, + species["SpeciesId"], + offset=start_from, + limit=count), + start=start_from+1), + activelink="list-markers") + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "<int:dataset_id>/view", + methods=["GET"]) +@require_login +def view_dataset(species_id: int, population_id: int, dataset_id: int): + """View details regarding a specific dataset.""" + 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.genotypes.index")) + + population = population_by_species_and_id( + conn, species_id, population_id) + if not bool(population): + flash("Invalid population selected!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.select_population", + species_id=species_id)) + + dataset = genotype_dataset(conn, species_id, population_id, dataset_id) + if not bool(dataset): + flash("Could not find such a dataset!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.list_genotypes", + species_id=species_id, + population_id=population_id)) + + return render_template("genotypes/view-dataset.html", + species=species, + population=population, + dataset=dataset, + activelink="view-dataset") + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "create", + methods=["GET", "POST"]) +@require_login +@with_population(species_redirect_uri="species.populations.genotypes.index", + redirect_uri="species.populations.genotypes.select_population") +def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Create a genotype dataset.""" + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-dataset") + + form = request.form + new_dataset = save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"]) + + def __success__(_success): + flash("Successfully created genotype dataset.", "alert-success") + return redirect(url_for( + "species.populations.genotypes.list_genotypes", + species_id=species["SpeciesId"], + population_id=population["Id"])) + + return oauth2_post( + "auth/resource/genotypes/create", + json={ + **dict(request.form), + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": new_dataset["Id"], + "dataset_name": form["geno-dataset-name"], + "dataset_fullname": form["geno-dataset-fullname"], + "dataset_shortname": form["geno-dataset-shortname"], + "public": "on" + } + ).either( + make_either_error_handler( + "There was an error creating the genotype dataset."), + __success__) diff --git a/uploader/input_validation.py b/uploader/input_validation.py index 9abe742..627c69e 100644 --- a/uploader/input_validation.py +++ b/uploader/input_validation.py @@ -1,14 +1,19 @@ """Input validation utilities""" +import re +import json +import base64 from typing import Any def is_empty_string(value: str) -> bool: """Check whether as string is empty""" return (isinstance(value, str) and value.strip() == "") + def is_empty_input(value: Any) -> bool: """Check whether user provided an empty value.""" return (value is None or is_empty_string(value)) + def is_integer_input(value: Any) -> bool: """ Check whether user provided a value that can be parsed into an integer. @@ -25,3 +30,42 @@ def is_integer_input(value: Any) -> bool: __is_int__(value, 10) or __is_int__(value, 8) or __is_int__(value, 16)))) + + +def is_valid_representative_name(repr_name: str) -> bool: + """ + Check whether the given representative name is a valid according to our rules. + + Parameters + ---------- + repr_name: a string of characters. + + Checks For + ---------- + * The name MUST start with an alphabet [a-zA-Z] + * The name MUST end with an alphabet [a-zA-Z] or number [0-9] + * The name MUST be composed of alphabets [a-zA-Z], numbers [0-9], + underscores (_) and/or hyphens (-). + + Returns + ------- + Boolean indicating whether or not the name is valid. + """ + pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$") + return bool(pattern.match(repr_name)) + + +def encode_errors(errors: tuple[tuple[str, str], ...], form) -> bytes: + """Encode form errors into base64 string.""" + return base64.b64encode( + json.dumps({ + "errors": dict(errors), + "original_formdata": dict(form) + }).encode("utf8")) + + +def decode_errors(errorstr) -> dict[str, dict]: + """Decode errors from base64 string""" + if not bool(errorstr): + return {"errors": {}, "original_formdata": {}} + return json.loads(base64.b64decode(errorstr.encode("utf8")).decode("utf8")) diff --git a/uploader/jobs.py b/uploader/jobs.py index 21889da..e86ee05 100644 --- a/uploader/jobs.py +++ b/uploader/jobs.py @@ -1,6 +1,8 @@ """Handle jobs""" import os import sys +import uuid +import json import shlex import subprocess from uuid import UUID, uuid4 @@ -10,7 +12,9 @@ from typing import Union, Optional from redis import Redis from flask import current_app as app -JOBS_PREFIX = "JOBS" +from functional_tools import take + +JOBS_PREFIX = "jobs" class JobNotFound(Exception): """Raised if we try to retrieve a non-existent job.""" @@ -128,3 +132,33 @@ def update_stdout_stderr(rconn: Redis, contents = thejob.get(stream, '') new_contents = contents + bytes_read.decode("utf-8") rconn.hset(name=job_key(rprefix, jobid), key=stream, value=new_contents) + + +def job_errors( + rconn: Redis, + prefix: str, + job_id: Union[str, uuid.UUID], + count: int = 100 +) -> list: + """Fetch job errors""" + return take( + ( + json.loads(error) + for key in rconn.keys(f"{prefix}:{str(job_id)}:*:errors:*") + for error in rconn.lrange(key, 0, -1)), + count) + + +def job_files_metadata( + rconn: Redis, + prefix: str, + job_id: Union[str, uuid.UUID] +) -> dict: + """Get the metadata for specific job file.""" + return { + key.split(":")[-1]: { + **rconn.hgetall(key), + "filetype": key.split(":")[-3] + } + for key in rconn.keys(f"{prefix}:{str(job_id)}:*:metadata*") + } diff --git a/uploader/monadic_requests.py b/uploader/monadic_requests.py index aa34951..c492df5 100644 --- a/uploader/monadic_requests.py +++ b/uploader/monadic_requests.py @@ -5,13 +5,12 @@ from typing import Union, Optional, Callable import requests from requests.models import Response from pymonad.either import Left, Right, Either -from flask import ( - flash, - request, - redirect, - render_template, - current_app as app, - escape as flask_escape) +from flask import (flash, + request, + redirect, + render_template, + current_app as app, + escape as flask_escape) # HTML Status codes indicating a successful request. SUCCESS_CODES = (200, 201, 202, 203, 204, 205, 206, 207, 208, 226) @@ -84,3 +83,22 @@ def post(url, data=None, json=None, **kwargs) -> Either: return Left(resp) except requests.exceptions.RequestException as exc: return Left(exc) + + +def make_either_error_handler(msg): + """Make generic error handler for pymonads Either objects.""" + def __fail__(error): + if issubclass(type(error), Exception): + app.logger.debug("\n\n%s (Exception)\n\n", msg, exc_info=True) + raise error + if issubclass(type(error), Response): + try: + _data = error.json() + except Exception as _exc: + raise Exception(error.content) from _exc + raise Exception(_data) + + app.logger.debug("\n\n%s\n\n", msg) + raise Exception(error) + + return __fail__ diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py index 70a32ff..1efa299 100644 --- a/uploader/oauth2/client.py +++ b/uploader/oauth2/client.py @@ -112,7 +112,8 @@ def oauth2_client(): try: jwt = JsonWebToken(["RS256"]).decode( token["access_token"], key=jwk) - return datetime.now().timestamp() > jwt["exp"] + if bool(jwt.get("exp")): + return datetime.now().timestamp() > jwt["exp"] except BadSignatureError as _bse: pass @@ -191,7 +192,7 @@ def oauth2_get(url, **kwargs) -> Either: return Right(resp.json()) return Left(resp) except Exception as exc:#pylint: disable=[broad-except] - app.logger.error("Error retriving data from auth server: (GET %s)", + app.logger.error("Error retrieving data from auth server: (GET %s)", _uri, exc_info=True) return Left(exc) @@ -223,7 +224,7 @@ def oauth2_post(url, data=None, json=None, **kwargs):#pylint: disable=[redefined return Right(resp.json()) return Left(resp) except Exception as exc:#pylint: disable=[broad-except] - app.logger.error("Error retriving data from auth server: (POST %s)", + app.logger.error("Error retrieving data from auth server: (POST %s)", _uri, exc_info=True) return Left(exc) diff --git a/uploader/oauth2/views.py b/uploader/oauth2/views.py index 61037f3..a7211cb 100644 --- a/uploader/oauth2/views.py +++ b/uploader/oauth2/views.py @@ -116,7 +116,7 @@ def logout(): _user = session_info["user"] _user_str = f"{_user['name']} ({_user['email']})" session.clear_session_info() - flash("Successfully logged out.", "alert-success") + flash("Successfully signed out.", "alert-success") return redirect("/") if user_logged_in(): diff --git a/uploader/phenotypes/__init__.py b/uploader/phenotypes/__init__.py new file mode 100644 index 0000000..c17d32c --- /dev/null +++ b/uploader/phenotypes/__init__.py @@ -0,0 +1,2 @@ +"""Package for handling ('classical') phenotype data""" +from .views import phenotypesbp diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py new file mode 100644 index 0000000..e1ec0c9 --- /dev/null +++ b/uploader/phenotypes/models.py @@ -0,0 +1,256 @@ +"""Database and utility functions for phenotypes.""" +from typing import Optional +from functools import reduce +from datetime import datetime + +import MySQLdb as mdb +from MySQLdb.cursors import Cursor, DictCursor +from flask import current_app as app + +from gn_libs.mysqldb import debug_query + +def datasets_by_population( + conn: mdb.Connection, + species_id: int, + population_id: int +) -> tuple[dict, ...]: + """Retrieve all of a population's phenotype studies.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT s.SpeciesId, pf.* FROM Species AS s " + "INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId " + "INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId " + "WHERE s.Id=%s AND iset.Id=%s;", + (species_id, population_id)) + return tuple(dict(row) for row in cursor.fetchall()) + + +def dataset_by_id(conn: mdb.Connection, + species_id: int, + population_id: int, + dataset_id: int) -> dict: + """Fetch dataset details by identifier""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT s.SpeciesId, pf.* FROM Species AS s " + "INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId " + "INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId " + "WHERE s.Id=%s AND iset.Id=%s AND pf.Id=%s", + (species_id, population_id, dataset_id)) + return dict(cursor.fetchone()) + + +def phenotypes_count(conn: mdb.Connection, + population_id: int, + dataset_id: int) -> int: + """Count the number of phenotypes in the dataset.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT COUNT(*) AS total_phenos FROM Phenotype AS pheno " + "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " + "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId " + "WHERE pxr.InbredSetId=%s AND pf.Id=%s", + (population_id, dataset_id)) + return int(cursor.fetchone()["total_phenos"]) + + +def phenotype_publication_data(conn, phenotype_id) -> Optional[dict]: + """Retrieve the publication data for a phenotype if it exists.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT DISTINCT pxr.PhenotypeId, pub.* FROM PublishXRef AS pxr " + "INNER JOIN Publication as pub ON pxr.PublicationId=pub.Id " + "WHERE pxr.PhenotypeId=%s", + (phenotype_id,)) + res = cursor.fetchone() + if res is None: + return res + return dict(res) + + +def dataset_phenotypes(conn: mdb.Connection, + population_id: int, + dataset_id: int, + offset: int = 0, + limit: Optional[int] = None) -> tuple[dict, ...]: + """Fetch the actual phenotypes.""" + _query = ( + "SELECT pheno.*, pxr.Id AS xref_id, ist.InbredSetCode FROM Phenotype AS pheno " + "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " + "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId " + "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id " + "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, (population_id, dataset_id)) + debug_query(cursor, app.logger) + return tuple(dict(row) for row in cursor.fetchall()) + + +def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids): + """Fetch standard-error values (if they exist) for a phenotype.""" + paramstr = ", ".join(["(%s, %s)"] * len(dataids_and_strainids)) + flat = tuple(item for sublist in dataids_and_strainids for item in sublist) + cursor.execute("SELECT * FROM PublishSE WHERE (DataId, StrainId) IN " + f"({paramstr})", + flat) + debug_query(cursor, app.logger) + _se = { + (row["DataId"], row["StrainId"]): { + "DataId": row["DataId"], + "StrainId": row["StrainId"], + "error": row["error"] + } + for row in cursor.fetchall() + } + + cursor.execute("SELECT * FROM NStrain WHERE (DataId, StrainId) IN " + f"({paramstr})", + flat) + debug_query(cursor, app.logger) + _n = { + (row["DataId"], row["StrainId"]): { + "DataId": row["DataId"], + "StrainId": row["StrainId"], + "count": row["count"] + } + for row in cursor.fetchall() + } + + keys = set(tuple(_se.keys()) + tuple(_n.keys())) + return { + key: {"xref_id": xref_id, **_se.get(key,{}), **_n.get(key,{})} + for key in keys + } + +def __organise_by_phenotype__(pheno, row): + """Organise disparate data rows into phenotype 'objects'.""" + _pheno = pheno.get(row["Id"]) + return { + **pheno, + row["Id"]: { + "Id": row["Id"], + "Pre_publication_description": row["Pre_publication_description"], + "Post_publication_description": row["Post_publication_description"], + "Original_description": row["Original_description"], + "Units": row["Units"], + "Pre_publication_abbreviation": row["Pre_publication_abbreviation"], + "Post_publication_abbreviation": row["Post_publication_abbreviation"], + "xref_id": row["pxr.Id"], + "data": { + **(_pheno["data"] if bool(_pheno) else {}), + (row["DataId"], row["StrainId"]): { + "DataId": row["DataId"], + "StrainId": row["StrainId"], + "mean": row["mean"], + "Locus": row["Locus"], + "LRS": row["LRS"], + "additive": row["additive"], + "Sequence": row["Sequence"], + "comments": row["comments"], + "value": row["value"], + "StrainName": row["Name"], + "StrainName2": row["Name2"], + "StrainSymbol": row["Symbol"], + "StrainAlias": row["Alias"] + } + } + } + } + + +def __merge_pheno_data_and_se__(data, sedata) -> dict: + """Merge phenotype data with the standard errors.""" + return { + key: {**value, **sedata.get(key, {})} + for key, value in data.items() + } + + +def phenotype_by_id( + conn: mdb.Connection, + species_id: int, + population_id: int, + dataset_id: int, + xref_id +) -> Optional[dict]: + """Fetch a specific phenotype.""" + _dataquery = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " + "FROM Phenotype AS pheno " + "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " + "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " + "INNER JOIN Strain AS str ON pd.StrainId=str.Id " + "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId " + "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId " + "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId " + "WHERE " + "(str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_dataquery, + (species_id, population_id, dataset_id, xref_id)) + _pheno: dict = reduce(__organise_by_phenotype__, cursor.fetchall(), {}) + if bool(_pheno) and len(_pheno.keys()) == 1: + _pheno = tuple(_pheno.values())[0] + return { + **_pheno, + "data": tuple(__merge_pheno_data_and_se__( + _pheno["data"], + __phenotype_se__( + cursor, xref_id, tuple(_pheno["data"].keys())) + ).values()) + } + if bool(_pheno) and len(_pheno.keys()) > 1: + raise Exception( + "We found more than one phenotype with the same identifier!") + + return None + + +def phenotypes_data(conn: mdb.Connection, + population_id: int, + dataset_id: int, + offset: int = 0, + limit: Optional[int] = None) -> tuple[dict, ...]: + """Fetch the data for the phenotypes.""" + # — Phenotype -> PublishXRef -> PublishData -> Strain -> StrainXRef -> PublishFreeze + _query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " + "FROM Phenotype AS pheno " + "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " + "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " + "INNER JOIN Strain AS str ON pd.StrainId=str.Id " + "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId " + "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId " + "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId " + "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, (population_id, dataset_id)) + debug_query(cursor, app.logger) + return tuple(dict(row) for row in cursor.fetchall()) + + +def save_new_dataset(cursor: Cursor, + population_id: int, + dataset_name: str, + dataset_fullname: str, + dataset_shortname: str) -> dict: + """Create a new phenotype dataset.""" + params = { + "population_id": population_id, + "dataset_name": dataset_name, + "dataset_fullname": dataset_fullname, + "dataset_shortname": dataset_shortname, + "created": datetime.now().date().isoformat(), + "public": 2, + "confidentiality": 0, + "users": None + } + cursor.execute( + "INSERT INTO PublishFreeze(Name, FullName, ShortName, CreateTime, " + "public, InbredSetId, confidentiality, AuthorisedUsers) " + "VALUES(%(dataset_name)s, %(dataset_fullname)s, %(dataset_shortname)s, " + "%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, " + "%(users)s)", + params) + debug_query(cursor, app.logger) + return {**params, "Id": cursor.lastrowid} diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py new file mode 100644 index 0000000..bcbb3a9 --- /dev/null +++ b/uploader/phenotypes/views.py @@ -0,0 +1,864 @@ +"""Views handling ('classical') phenotypes.""" +import sys +import uuid +import json +import datetime +from typing import Any +from pathlib import Path +from zipfile import ZipFile +from functools import wraps, reduce +from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING + +from redis import Redis +from pymonad.either import Left +from requests.models import Response +from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection +from flask import (flash, + request, + url_for, + jsonify, + redirect, + Blueprint, + current_app as app) + +# from r_qtl import r_qtl2 as rqtl2 +from r_qtl import r_qtl2_qc as rqc +from r_qtl import exceptions as rqe + +from uploader import jobs +from uploader.files import save_file#, fullpath +from uploader.ui import make_template_renderer +from uploader.oauth2.client import oauth2_post +from uploader.authorisation import require_login +from uploader.species.models import all_species, species_by_id +from uploader.monadic_requests import make_either_error_handler +from uploader.request_checks import with_species, with_population +from uploader.datautils import safe_int, order_by_family, enumerate_sequence +from uploader.population.models import (populations_by_species, + population_by_species_and_id) +from uploader.input_validation import (encode_errors, + decode_errors, + is_valid_representative_name) + +from .models import (dataset_by_id, + phenotype_by_id, + phenotypes_count, + save_new_dataset, + dataset_phenotypes, + datasets_by_population, + phenotype_publication_data) + +phenotypesbp = Blueprint("phenotypes", __name__) +render_template = make_template_renderer("phenotypes") + +_FAMILIES_WITH_SE_AND_N_ = ( + "Reference Populations (replicate average, SE, N)",) + +@phenotypesbp.route("/phenotypes", methods=["GET"]) +@require_login +def index(): + """Direct entry-point for phenotypes data handling.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("species_id")): + return render_template("phenotypes/index.html", + species=all_species(conn), + activelink="phenotypes") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.phenotypes.select_population")) + + species = species_by_id(conn, species_id) + if not bool(species): + flash("No such species!", "alert-danger") + return redirect(url_for("species.populations.phenotypes.index")) + return redirect(url_for("species.populations.phenotypes.select_population", + species_id=species["SpeciesId"])) + + +@phenotypesbp.route("<int:species_id>/phenotypes/select-population", + methods=["GET"]) +@require_login +@with_species(redirect_uri="species.populations.phenotypes.index") +def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument] + """Select the population for your phenotypes.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("population_id")): + return render_template("phenotypes/select-population.html", + species=species, + populations=populations_by_species( + conn, species["SpeciesId"]), + activelink="phenotypes") + + population_id = request.args["population_id"] + if population_id == "CREATE-POPULATION": + return redirect(url_for( + "species.populations.create_population", + species_id=species["SpeciesId"], + return_to="species.populations.phenotypes.list_datasets")) + population = population_by_species_and_id( + conn, species["SpeciesId"], int(population_id)) + if not bool(population): + flash("No such population found!", "alert-danger") + return redirect(url_for( + "species.populations.phenotypes.select_population", + species_id=species["SpeciesId"])) + + return redirect(url_for("species.populations.phenotypes.list_datasets", + species_id=species["SpeciesId"], + population_id=population["Id"])) + + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets", + methods=["GET"]) +@require_login +@with_population(species_redirect_uri="species.populations.phenotypes.index", + redirect_uri="species.populations.phenotypes.select_population") +def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """List available phenotype datasets.""" + with database_connection(app.config["SQL_URI"]) as conn: + datasets = datasets_by_population( + conn, species["SpeciesId"], population["Id"]) + if len(datasets) == 1: + return redirect(url_for( + "species.populations.phenotypes.view_dataset", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=datasets[0]["Id"])) + return render_template("phenotypes/list-datasets.html", + species=species, + population=population, + datasets=datasets, + activelink="list-datasets") + + +def with_dataset( + species_redirect_uri: str, + population_redirect_uri: str, + redirect_uri: str +): + """Ensure the dataset actually exists.""" + def __decorator__(func): + @wraps(func) + @with_population(species_redirect_uri, population_redirect_uri) + def __with_dataset__(**kwargs): + try: + _spcid = int(kwargs["species_id"]) + _popid = int(kwargs["population_id"]) + _dsetid = int(kwargs.get("dataset_id")) + select_dataset_uri = redirect(url_for( + redirect_uri, species_id=_spcid, population_id=_popid)) + if not bool(_dsetid): + flash("You need to select a valid 'dataset_id' value.", + "alert-danger") + return select_dataset_uri + with database_connection(app.config["SQL_URI"]) as conn: + dataset = dataset_by_id(conn, _spcid, _popid, _dsetid) + if not bool(dataset): + flash("You must select a valid dataset.", + "alert-danger") + return select_dataset_uri + except ValueError as _verr: + app.logger.debug( + "Exception converting 'dataset_id' to integer: %s", + kwargs.get("dataset_id"), + exc_info=True) + flash("Expected 'dataset_id' value to be an integer." + "alert-danger") + return select_dataset_uri + return func(dataset=dataset, **kwargs) + return __with_dataset__ + return __decorator__ + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/view", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def view_dataset(# pylint: disable=[unused-argument] + species: dict, population: dict, dataset: dict, **kwargs): + """View a specific dataset""" + with database_connection(app.config["SQL_URI"]) as conn: + dataset = dataset_by_id( + conn, species["SpeciesId"], population["Id"], dataset["Id"]) + if not bool(dataset): + flash("Could not find such a phenotype dataset!", "alert-danger") + return redirect(url_for( + "species.populations.phenotypes.list_datasets", + species_id=species["SpeciesId"], + population_id=population["Id"])) + + start_at = max(safe_int(request.args.get("start_at") or 0), 0) + count = int(request.args.get("count") or 20) + return render_template("phenotypes/view-dataset.html", + species=species, + population=population, + dataset=dataset, + phenotype_count=phenotypes_count( + conn, population["Id"], dataset["Id"]), + phenotypes=enumerate_sequence( + dataset_phenotypes( + conn, + population["Id"], + dataset["Id"])), + start_from=start_at, + count=count, + activelink="view-dataset") + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/phenotype/<xref_id>", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def view_phenotype(# pylint: disable=[unused-argument] + species: dict, + population: dict, + dataset: dict, + xref_id: int, + **kwargs +): + """View an individual phenotype from the dataset.""" + def __render__(privileges): + phenotype = phenotype_by_id(conn, + species["SpeciesId"], + population["Id"], + dataset["Id"], + xref_id) + def __non_empty__(value) -> bool: + if isinstance(value, str): + return value.strip() != "" + return bool(value) + + return render_template( + "phenotypes/view-phenotype.html", + species=species, + population=population, + dataset=dataset, + xref_id=xref_id, + phenotype=phenotype, + has_se=any(bool(item.get("error")) for item in phenotype["data"]), + publish_data={ + key.replace("_", " "): val + for key,val in + (phenotype_publication_data(conn, phenotype["Id"]) or {}).items() + if (key in ("PubMed_ID", "Authors", "Title", "Journal") + and __non_empty__(val)) + }, + privileges=(privileges + ### For demo! Do not commit this part + + ("group:resource:edit-resource", + "group:resource:delete-resource",) + ### END: For demo! Do not commit this part + ), + activelink="view-phenotype") + + def __fail__(error): + if isinstance(error, Response) and error.json() == "No linked resource!": + return __render__(tuple()) + return make_either_error_handler( + "There was an error fetching the roles and privileges.")(error) + + with database_connection(app.config["SQL_URI"]) as conn: + return oauth2_post( + "/auth/resource/phenotypes/individual/linked-resource", + json={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "xref_id": xref_id + } + ).then( + lambda resource: tuple( + privilege["privilege_id"] for role in resource["roles"] + for privilege in role["privileges"]) + ).then(__render__).either(__fail__, lambda resp: resp) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets/create", + methods=["GET", "POST"]) +@require_login +@with_population( + species_redirect_uri="species.populations.phenotypes.index", + redirect_uri="species.populations.phenotypes.select_population") +def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Create a new phenotype dataset.""" + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + if request.method == "GET": + return render_template("phenotypes/create-dataset.html", + activelink="create-dataset", + species=species, + population=population, + **decode_errors( + request.args.get("error_values", ""))) + + form = request.form + _errors: tuple[tuple[str, str], ...] = tuple() + if not is_valid_representative_name( + (form.get("dataset-name") or "").strip()): + _errors = _errors + (("dataset-name", "Invalid dataset name."),) + + if not bool((form.get("dataset-fullname") or "").strip()): + _errors = _errors + (("dataset-fullname", + "You must provide a value for 'Full Name'."),) + + if bool(_errors) > 0: + return redirect(url_for( + "species.populations.phenotypes.create_dataset", + species_id=species["SpeciesId"], + population_id=population["Id"], + error_values=encode_errors(_errors, form))) + + dataset_shortname = ( + form["dataset-shortname"] or form["dataset-name"]).strip() + _pheno_dataset = save_new_dataset( + cursor, + population["Id"], + form["dataset-name"].strip(), + form["dataset-fullname"].strip(), + dataset_shortname) + return redirect(url_for("species.populations.phenotypes.list_datasets", + species_id=species["SpeciesId"], + population_id=population["Id"])) + + +def process_phenotypes_rqtl2_bundle(error_uri): + """Process phenotypes from the uploaded R/qtl2 bundle.""" + _redisuri = app.config["REDIS_URL"] + _sqluri = app.config["SQL_URI"] + try: + ## Handle huge files here... + phenobundle = save_file(request.files["phenotypes-bundle"], + Path(app.config["UPLOAD_FOLDER"])) + rqc.validate_bundle(phenobundle) + return phenobundle + except AssertionError as _aerr: + app.logger.debug("File upload error!", exc_info=True) + flash("Expected a zipped bundle of files with phenotypes' " + "information.", + "alert-danger") + return error_uri + except rqe.RQTLError as rqtlerr: + app.logger.debug("Bundle validation error!", exc_info=True) + flash("R/qtl2 Error: " + " ".join(rqtlerr.args), "alert-danger") + return error_uri + + +def process_phenotypes_individual_files(error_uri): + """Process the uploaded individual files.""" + form = request.form + cdata = { + "sep": form["file-separator"], + "comment.char": form["file-comment-character"], + "na.strings": form["file-na"].split(" "), + } + bundlepath = Path(app.config["UPLOAD_FOLDER"], + f"{str(uuid.uuid4()).replace('-', '')}.zip") + with ZipFile(bundlepath,mode="w") as zfile: + for rqtlkey, formkey in (("phenocovar", "phenotype-descriptions"), + ("pheno", "phenotype-data"), + ("phenose", "phenotype-se"), + ("phenonum", "phenotype-n")): + if form.get("resumable-upload", False): + # Chunked upload of large files was used + filedata = json.loads(form[formkey]) + zfile.write( + Path(app.config["UPLOAD_FOLDER"], filedata["uploaded-file"]), + arcname=filedata["original-name"]) + cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]] + else: + # TODO: Check this path: fix any bugs. + _sentfile = request.files[formkey] + if not bool(_sentfile): + flash(f"Expected file ('{formkey}') was not provided.", + "alert-danger") + return error_uri + + filepath = save_file( + _sentfile, Path(app.config["UPLOAD_FOLDER"]), hashed=False) + zfile.write( + Path(app.config["UPLOAD_FOLDER"], filepath), + arcname=filepath.name) + cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name] + + zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2)) + + return bundlepath + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/add-phenotypes", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# pylint: disable=[unused-argument, too-many-locals] + """Add one or more phenotypes to the dataset.""" + use_bundle = request.args.get("use_bundle", "").lower() == "true" + add_phenos_uri = redirect(url_for( + "species.populations.phenotypes.add_phenotypes", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"])) + _redisuri = app.config["REDIS_URL"] + _sqluri = app.config["SQL_URI"] + with (Redis.from_url(_redisuri, decode_responses=True) as rconn, + # database_connection(_sqluri) as conn, + # conn.cursor(cursorclass=DictCursor) as cursor + ): + if request.method == "GET": + today = datetime.date.today() + return render_template( + ("phenotypes/add-phenotypes-with-rqtl2-bundle.html" + if use_bundle else "phenotypes/add-phenotypes-raw-files.html"), + species=species, + population=population, + dataset=dataset, + monthnames=( + "January", "February", "March", "April", + "May", "June", "July", "August", + "September", "October", "November", + "December"), + current_month=today.strftime("%B"), + current_year=int(today.strftime("%Y")), + families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_, + use_bundle=use_bundle, + activelink="add-phenotypes") + + phenobundle = (process_phenotypes_rqtl2_bundle(add_phenos_uri) + if use_bundle else + process_phenotypes_individual_files(add_phenos_uri)) + + _jobid = uuid.uuid4() + _namespace = jobs.jobsnamespace() + _ttl_seconds = app.config["JOBS_TTL_SECONDS"] + _job = jobs.launch_job( + jobs.initialise_job( + rconn, + _namespace, + str(_jobid), + [sys.executable, "-m", "scripts.rqtl2.phenotypes_qc", _sqluri, + _redisuri, _namespace, str(_jobid), str(species["SpeciesId"]), + str(population["Id"]), + # str(dataset["Id"]), + str(phenobundle), + "--loglevel", + { + INFO: "INFO", + ERROR: "ERROR", + DEBUG: "DEBUG", + FATAL: "FATAL", + CRITICAL: "CRITICAL", + WARNING: "WARNING" + }[app.logger.getEffectiveLevel()], + "--redisexpiry", + str(_ttl_seconds)], "phenotype_qc", _ttl_seconds, + {"job-metadata": json.dumps({ + "speciesid": species["SpeciesId"], + "populationid": population["Id"], + "datasetid": dataset["Id"], + "bundle": str(phenobundle.absolute())})}), + _redisuri, + f"{app.config['UPLOAD_FOLDER']}/job_errors") + + app.logger.debug("JOB DETAILS: %s", _job) + jobstatusuri = url_for("species.populations.phenotypes.job_status", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"], + job_id=str(_job["jobid"])) + return ((jsonify({ + "redirect-to": jobstatusuri, + "statuscode": 200, + "message": ("Follow the 'redirect-to' URI to see the state " + "of the quality-control job started for your " + "uploaded files.") + }), 200) + if request.form.get("resumable-upload", False) else + redirect(jobstatusuri)) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/job/<uuid:job_id>", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def job_status( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs +):# pylint: disable=[unused-argument] + """Retrieve current status of a particular phenotype QC job.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + except jobs.JobNotFound as _jnf: + job = None + return render_template("phenotypes/job-status.html", + species=species, + population=population, + dataset=dataset, + job_id=job_id, + job=job, + errors=jobs.job_errors( + rconn, jobs.jobsnamespace(), job['jobid']), + metadata=jobs.job_files_metadata( + rconn, jobs.jobsnamespace(), job['jobid']), + activelink="add-phenotypes") + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/job/<uuid:job_id>/review", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def review_job_data( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs +):# pylint: disable=[unused-argument] + """Review data one more time before entering it into the database.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + except jobs.JobNotFound as _jnf: + job = None + + def __metadata_by_type__(by_type, item): + filetype = item[1]["filetype"] + return { + **by_type, + filetype: (by_type.get(filetype, tuple()) + + ({"filename": item[0], **item[1]},)) + } + metadata: dict[str, Any] = reduce( + __metadata_by_type__, + (jobs.job_files_metadata( + rconn, jobs.jobsnamespace(), job['jobid']) + if job else {}).items(), + {}) + + def __desc__(filetype): + match filetype: + case "phenocovar": + desc = "phenotypes" + case "pheno": + desc = "phenotypes data" + case "phenose": + desc = "phenotypes standard-errors" + case "phenonum": + desc = "phenotypes samples" + case _: + desc = f"unknown file type '{filetype}'." + + return desc + + def __summarise__(filetype, files): + return { + "filetype": filetype, + "number-of-files": len(files), + "total-data-rows": sum( + int(afile["linecount"]) - 1 for afile in files), + "description": __desc__(filetype) + } + + summary = { + filetype: __summarise__(filetype, meta) + for filetype,meta in metadata.items() + } + return render_template("phenotypes/review-job-data.html", + species=species, + population=population, + dataset=dataset, + job_id=job_id, + job=job, + summary=summary, + activelink="add-phenotypes") + + +def update_phenotype_metadata(conn, metadata: dict): + """Update a phenotype's basic metadata values.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM Phenotype WHERE Id=%(phenotype-id)s", + metadata) + res = { + **{ + _key: _val for _key,_val in { + key.lower().replace("_", "-"): value + for key, value in (cursor.fetchone() or {}).items() + }.items() + if _key in metadata.keys() + }, + "phenotype-id": metadata.get("phenotype-id") + } + if res == metadata: + return False + + cursor.execute( + "UPDATE Phenotype SET " + "Pre_publication_description=%(pre-publication-description)s, " + "Post_publication_description=%(post-publication-description)s, " + "Original_description=%(original-description)s, " + "Units=%(units)s, " + "Pre_publication_abbreviation=%(pre-publication-abbreviation)s, " + "Post_publication_abbreviation=%(post-publication-abbreviation)s " + "WHERE Id=%(phenotype-id)s", + metadata) + return cursor.rowcount + + +def update_phenotype_values(conn, values): + """Update a phenotype's data values.""" + with conn.cursor() as cursor: + cursor.executemany( + "UPDATE PublishData SET value=%(new)s " + "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in values if item["new"] is not None)) + cursor.executemany( + "DELETE FROM PublishData " + "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in values if item["new"] is None)) + return len(values) + return 0 + + +def update_phenotype_se(conn, serrs): + """Update a phenotype's standard-error values.""" + with conn.cursor() as cursor: + cursor.executemany( + "INSERT INTO PublishSE(DataId, StrainId, error) " + "VALUES(%(data_id)s, %(strain_id)s, %(new)s) " + "ON DUPLICATE KEY UPDATE error=VALUES(error)", + tuple(item for item in serrs if item["new"] is not None)) + cursor.executemany( + "DELETE FROM PublishSE " + "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in serrs if item["new"] is None)) + return len(serrs) + return 0 + + +def update_phenotype_n(conn, counts): + """Update a phenotype's strain counts.""" + with conn.cursor() as cursor: + cursor.executemany( + "INSERT INTO NStrain(DataId, StrainId, count) " + "VALUES(%(data_id)s, %(strain_id)s, %(new)s) " + "ON DUPLICATE KEY UPDATE count=VALUES(count)", + tuple(item for item in counts if item["new"] is not None)) + cursor.executemany( + "DELETE FROM NStrain " + "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s", + tuple(item for item in counts if item["new"] is None)) + return len(counts) + + return 0 + + +def update_phenotype_data(conn, data: dict): + """Update the numeric data for a phenotype.""" + def __organise_by_dataid_and_strainid__(acc, current): + _key, dataid, strainid = current[0].split("::") + _keysrc, _keytype = _key.split("-") + newkey = f"{dataid}::{strainid}" + newitem = acc.get(newkey, {}) + newitem[_keysrc] = newitem.get(_keysrc, {}) + newitem[_keysrc][_keytype] = current[1] + return {**acc, newkey: newitem} + + def __separate_items__(acc, row): + key, val = row + return ({ + **acc[0], + key: { + **val["value"], + "changed?": (not val["value"]["new"] == val["value"]["original"]) + } + }, { + **acc[1], + key: { + **val["se"], + "changed?": (not val["se"]["new"] == val["se"]["original"]) + } + },{ + **acc[2], + key: { + **val["n"], + "changed?": (not val["n"]["new"] == val["n"]["original"]) + } + }) + + values, serrs, counts = tuple( + tuple({ + "data_id": row[0].split("::")[0], + "strain_id": row[0].split("::")[1], + "new": row[1]["new"] + } for row in item) + for item in ( + filter(lambda val: val[1]["changed?"], item.items())# type: ignore[arg-type] + for item in reduce(# type: ignore[var-annotated] + __separate_items__, + reduce(__organise_by_dataid_and_strainid__, + data.items(), + {}).items(), + ({}, {}, {})))) + + return (update_phenotype_values(conn, values), + update_phenotype_se(conn, serrs), + update_phenotype_n(conn, counts)) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/phenotype/<int:xref_id>/edit", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def edit_phenotype_data(# pylint: disable=[unused-argument] + species: dict, + population: dict, + dataset: dict, + xref_id: int, + **kwargs +): + """Edit the data for a particular phenotype.""" + def __render__(**kwargs): + processed_kwargs = { + **kwargs, + "privileges": (kwargs.get("privileges", tuple()) + ### For demo! Do not commit this part + + ("group:resource:edit-resource", + "group:resource:delete-resource",) + ### END: For demo! Do not commit this part + ) + } + return render_template( + "phenotypes/edit-phenotype.html", + species=species, + population=population, + dataset=dataset, + xref_id=xref_id, + families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_, + **processed_kwargs, + activelink="edit-phenotype") + + with database_connection(app.config["SQL_URI"]) as conn: + if request.method == "GET": + def __fetch_phenotype__(privileges): + phenotype = phenotype_by_id(conn, + species["SpeciesId"], + population["Id"], + dataset["Id"], + xref_id) + if phenotype is None: + msg = ("Could not find the phenotype with cross-reference ID" + f" '{xref_id}' from dataset '{dataset['FullName']}' " + f" from the '{population['FullName']}' population of " + f" species '{species['FullName']}'.") + return Left({"privileges": privileges, "phenotype-error": msg}) + return {"privileges": privileges, "phenotype": phenotype} + + def __fetch_publication_data__(**kwargs): + pheno = kwargs["phenotype"] + return { + **kwargs, + "publication_data": phenotype_publication_data( + conn, pheno["Id"]) + } + + def __fail__(failure_object): + # process the object + return __render__(failure_object=failure_object) + + return oauth2_post( + "/auth/resource/phenotypes/individual/linked-resource", + json={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "xref_id": xref_id + } + ).then( + lambda resource: tuple( + privilege["privilege_id"] for role in resource["roles"] + for privilege in role["privileges"]) + ).then( + __fetch_phenotype__ + ).then( + lambda args: __fetch_publication_data__(**args) + ).either(__fail__, lambda args: __render__(**args)) + + ## POST + _change = False + match request.form.get("submit", "invalid-action"): + case "update basic metadata": + _change = update_phenotype_metadata(conn, { + key: value.strip() if bool(value.strip()) else None + for key, value in request.form.items() + if key not in ("submit",) + }) + msg = "Basic metadata was updated successfully." + case "update data": + _update = update_phenotype_data(conn, { + key: value.strip() if bool(value.strip()) else None + for key, value in request.form.items() + if key not in ("submit",) + }) + msg = (f"{_update[0]} value rows, {_update[1]} standard-error " + f"rows and {_update[2]} 'N' rows were updated.") + _change = any(item != 0 for item in _update) + case "update publication": + flash("NOT IMPLEMENTED: Would update publication data.", "alert-success") + case _: + flash("Invalid phenotype editing action.", "alert-danger") + + if _change: + flash(msg, "alert-success") + return redirect(url_for( + "species.populations.phenotypes.view_phenotype", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"], + xref_id=xref_id)) + + flash("No change was made by the user.", "alert-info") + return redirect(url_for( + "species.populations.phenotypes.edit_phenotype_data", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"], + xref_id=xref_id)) diff --git a/uploader/platforms/__init__.py b/uploader/platforms/__init__.py new file mode 100644 index 0000000..8cb89c9 --- /dev/null +++ b/uploader/platforms/__init__.py @@ -0,0 +1,2 @@ +"""Module to handle management of genetic platforms.""" +from .views import platformsbp diff --git a/uploader/platforms/models.py b/uploader/platforms/models.py new file mode 100644 index 0000000..a859371 --- /dev/null +++ b/uploader/platforms/models.py @@ -0,0 +1,95 @@ +"""Handle db interactions for platforms.""" +from typing import Optional + +import MySQLdb as mdb +from MySQLdb.cursors import Cursor, DictCursor + +def platforms_by_species( + conn: mdb.Connection, + speciesid: int, + offset: int = 0, + limit: Optional[int] = None +) -> tuple[dict, ...]: + """Retrieve platforms by the species""" + _query = ("SELECT * FROM GeneChip WHERE SpeciesId=%s " + "ORDER BY GeneChipName ASC") + if bool(limit) and limit > 0:# type: ignore[operator] + _query = f"{_query} LIMIT {limit} OFFSET {offset}" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, (speciesid,)) + return tuple(dict(row) for row in cursor.fetchall()) + + +def species_platforms_count(conn: mdb.Connection, species_id: int) -> int: + """Get the number of platforms in the database for a particular species.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT COUNT(GeneChipName) AS count FROM GeneChip " + "WHERE SpeciesId=%s", + (species_id,)) + return int(cursor.fetchone()["count"]) + + +def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]: + """Retrieve a platform by its ID""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM GeneChip WHERE Id=%s", + (platformid,)) + result = cursor.fetchone() + if bool(result): + return dict(result) + + return None + + +def platform_by_species_and_id( + conn: mdb.Connection, species_id: int, platformid: int +) -> Optional[dict]: + """Retrieve a platform by its species and ID""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s AND Id=%s", + (species_id, platformid)) + result = cursor.fetchone()#pylint: disable=[duplicate-code] + if bool(result): + return dict(result) + + return None + + +def save_new_platform(# pylint: disable=[too-many-arguments] + cursor: Cursor, + species_id: int, + geo_platform: str, + platform_name: str, + platform_shortname: str, + platform_title: str, + go_tree_value: Optional[str] +) -> dict: + """Save a new platform to the database.""" + params = { + "species_id": species_id, + "GeoPlatform": geo_platform, + "GeneChipName": platform_name, + "Name": platform_shortname, + "Title": platform_title, + "GO_tree_value": go_tree_value + } + cursor.execute("SELECT SpeciesId, GeoPlatform FROM GeneChip") + assert (species_id, geo_platform) not in ( + (row["SpeciesId"], row["GeoPlatform"]) for row in cursor.fetchall()) + cursor.execute( + "INSERT INTO " + "GeneChip(SpeciesId, GeneChipName, Name, GeoPlatform, Title, GO_tree_value) " + "VALUES(" + "%(species_id)s, %(GeneChipName)s, %(Name)s, %(GeoPlatform)s, " + "%(Title)s, %(GO_tree_value)s" + ")", + params) + new_id = cursor.lastrowid + cursor.execute("UPDATE GeneChip SET GeneChipId=%s WHERE Id=%s", + (new_id, new_id)) + return { + **params, + "Id": new_id, + "GeneChipId": new_id + } diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py new file mode 100644 index 0000000..114c1a9 --- /dev/null +++ b/uploader/platforms/views.py @@ -0,0 +1,118 @@ +"""The endpoints for the platforms""" +from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection +from flask import ( + flash, + request, + url_for, + redirect, + Blueprint, + current_app as app) + +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.datautils import safe_int, order_by_family, enumerate_sequence + +from .models import (save_new_platform, + platforms_by_species, + species_platforms_count) + +platformsbp = Blueprint("platforms", __name__) +render_template = make_template_renderer("platforms") + +@platformsbp.route("platforms", methods=["GET"]) +@require_login +def index(): + """Entry-point to the platforms feature.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("species_id")): + return render_template( + "platforms/index.html", + species=all_species(conn), + activelink="platforms") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.platforms.list_platforms")) + + species = species_by_id(conn, request.args["species_id"]) + if not bool(species): + flash("No species selected.", "alert-danger") + return redirect(url_for("species.platforms.index")) + + return redirect(url_for("species.platforms.list_platforms", + species_id=species["SpeciesId"])) + + +@platformsbp.route("<int:species_id>/platforms", methods=["GET"]) +@require_login +def list_platforms(species_id: int): + """List all the available genetic sequencing platforms.""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("No species provided.", "alert-danger") + return redirect(url_for("species.platforms.index")) + + start_from = max(safe_int(request.args.get("start_from") or 0), 0) + count = safe_int(request.args.get("count") or 20) + return render_template( + "platforms/list-platforms.html", + species=species, + platforms=enumerate_sequence( + platforms_by_species(conn, + species_id, + offset=start_from, + limit=count), + start=start_from+1), + start_from=start_from, + count=count, + total_platforms=species_platforms_count(conn, species_id), + activelink="list-platforms") + + +@platformsbp.route("<int:species_id>/platforms/create", methods=["GET", "POST"]) +@require_login +def create_platform(species_id: int): + """Create a new genetic sequencing platform.""" + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + species = species_by_id(conn, species_id) + if not bool(species): + flash("No species provided.", "alert-danger") + return redirect(url_for("species.platforms.index")) + + if request.method == "GET": + return render_template( + "platforms/create-platform.html", + species=species, + activelink="create-platform") + + try: + form = request.form + _new_platform = save_new_platform( + cursor, + species_id, + form["geo-platform"], + form["platform-name"], + form["platform-shortname"], + form["platform-title"], + form.get("go-tree-value") or None) + except KeyError as _kerr: + flash(f"Required value for field {_kerr.args[0]} was not provided.", + "alert-danger") + return redirect(url_for("species.platforms.create_platform", + species_id=species_id)) + except AssertionError as _aerr: + flash(f"Platform with GeoPlatform value of '{form['geo-platform']}'" + f" already exists for species '{species['FullName']}'.", + "alert-danger") + return redirect(url_for("species.platforms.create_platform", + species_id=species_id)) + + flash("Platform created successfully", "alert-success") + return redirect(url_for("species.platforms.list_platforms", + species_id=species_id)) diff --git a/uploader/population/models.py b/uploader/population/models.py index c6c77ae..d78a821 100644 --- a/uploader/population/models.py +++ b/uploader/population/models.py @@ -46,29 +46,41 @@ def population_genetic_types(conn) -> tuple: def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dict: """Save the population details to the db.""" - #TODO: Handle FamilyOrder here + cursor.execute("SELECT DISTINCT(Family), FamilyOrder FROM InbredSet " + "WHERE Family IS NOT NULL AND Family != '' " + "AND FamilyOrder IS NOT NULL " + "ORDER BY FamilyOrder ASC") + _families = { + row["Family"]: int(row["FamilyOrder"]) + for row in cursor.fetchall() + } + params = { + "MenuOrderId": 0, + "InbredSetId": 0, + "public": 2, + **population_details, + "FamilyOrder": _families.get( + population_details["Family"], + max((0,) + tuple(_families.values()))+1) + } cursor.execute( "INSERT INTO InbredSet(" "InbredSetId, InbredSetName, Name, SpeciesId, FullName, " - "public, MappingMethodId, GeneticType, Family, MenuOrderId, " - "InbredSetCode, Description" + "public, MappingMethodId, GeneticType, Family, FamilyOrder," + " MenuOrderId, InbredSetCode, Description" ") " "VALUES (" "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, " "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, " - "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s" + "%(Family)s, %(FamilyOrder)s, %(MenuOrderId)s, %(InbredSetCode)s, " + "%(Description)s" ")", - { - "MenuOrderId": 0, - "InbredSetId": 0, - "public": 2, - **population_details - }) + params) new_id = cursor.lastrowid cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s", (new_id, new_id)) return { - **population_details, + **params, "Id": new_id, "InbredSetId": new_id, "population_id": new_id diff --git a/uploader/expression_data/rqtl2.py b/uploader/population/rqtl2.py index a855699..044cdd4 100644 --- a/uploader/expression_data/rqtl2.py +++ b/uploader/population/rqtl2.py @@ -3,7 +3,6 @@ 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 @@ -12,12 +11,11 @@ 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 gn_libs.mysqldb import database_connection from flask import ( flash, escape, request, - jsonify, url_for, redirect, Response, @@ -29,15 +27,14 @@ 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.species.models import all_species +from uploader.db_utils import with_db_connection from uploader.authorisation import require_login -from uploader.db.platforms import platform_by_id, platforms_by_species +from uploader.platforms.models 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, +from uploader.population.models import (populations_by_species, population_by_species_and_id) from uploader.species.models import species_by_id from uploader.db.datasets import ( @@ -60,19 +57,21 @@ rqtl2 = Blueprint("rqtl2", __name__) def select_species(): """Select the species.""" if request.method == "GET": - return render_template("rqtl2/index.html", species=with_db_connection(all_species)) + return render_template("expression-data/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)) + "species.populations.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", +@rqtl2.route("<int:species_id>/expression-data/rqtl2/select-population", methods=["GET", "POST"]) @require_login def select_population(species_id: int): @@ -85,7 +84,7 @@ def select_population(species_id: int): if request.method == "GET": return render_template( - "rqtl2/select-population.html", + "expression-data/rqtl2/select-population.html", species=species, populations=populations_by_species(conn, species_id)) @@ -102,44 +101,6 @@ def select_population(species_id: int): 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.""" @@ -165,9 +126,10 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): 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) + return render_template( + "expression-data/rqtl2/upload-rqtl2-bundle-step-01.html", + species=species, + population=population) try: app.logger.debug("Files in the form: %s", request.files) @@ -227,127 +189,6 @@ def trigger_rqtl2_bundle_qc( 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 @@ -362,24 +203,25 @@ def rqtl2_bundle_qc_status(jobid: UUID): 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) + return render_template( + "expression-data/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", + "expression-data/rqtl2/rqtl2-qc-job-results.html", species=species, population=population_by_species_and_id( dbconn, species["SpeciesId"], jobmeta["populationid"]), @@ -398,14 +240,14 @@ def rqtl2_bundle_qc_status(jobid: UUID): return None return render_template( - "rqtl2/rqtl2-qc-job-status.html", + "expression-data/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) + return render_template("expression-data/rqtl2/no-such-job.html", jobid=jobid) def redirect_on_error(flaskroute, **kwargs): @@ -609,76 +451,6 @@ def select_geno_dataset(species_id: int, population_id: int): @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 @@ -739,7 +511,7 @@ def create_tissue(species_id: int, population_id: int): tissue = create_new_tissue(conn, tissuename, tissueshortname) flash("Tissue created successfully!", "alert-success") return render_template( - "rqtl2/create-tissue-success.html", + "expression-data/rqtl2/create-tissue-success.html", species=species_by_id(conn, species_id), population=population_by_species_and_id( conn, species_id, population_id), @@ -869,7 +641,7 @@ def create_probeset_study(species_id: int, population_id: int): errorclasses) return dataset_info_page return render_template( - "rqtl2/create-probe-study-success.html", + "expression-data/rqtl2/create-probe-study-success.html", species=species_by_id(conn, species_id), population=population_by_species_and_id( conn, species_id, population_id), @@ -954,7 +726,7 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl errorclasses) return summary_page return render_template( - "rqtl2/create-probe-dataset-success.html", + "expression-data/rqtl2/create-probe-dataset-success.html", species=species_by_id(conn, species_id), population=population_by_species_and_id( conn, species_id, population_id), @@ -1009,7 +781,7 @@ def select_dataset_info(species_id: int, population_id: int): 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", + "expression-data/rqtl2/select-geno-dataset.html", species=species, population=population, rqtl2_bundle_file=thefile.name, @@ -1019,7 +791,7 @@ def select_dataset_info(species_id: int, population_id: int): tissue = tissue_by_id(conn, form.get("tissueid", "").strip()) if "pheno" in cdata and not bool(tissue): return render_template( - "rqtl2/select-tissue.html", + "expression-data/rqtl2/select-tissue.html", species=species, population=population, rqtl2_bundle_file=thefile.name, @@ -1033,7 +805,7 @@ def select_dataset_info(species_id: int, population_id: int): 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", + "expression-data/rqtl2/select-probeset-study-id.html", species=species, population=population, rqtl2_bundle_file=thefile.name, @@ -1049,7 +821,7 @@ def select_dataset_info(species_id: int, population_id: int): conn, form.get("probe-dataset-id", "").strip()) if "pheno" in cdata and not bool(probeset_dataset): return render_template( - "rqtl2/select-probeset-dataset.html", + "expression-data/rqtl2/select-probeset-dataset.html", species=species, population=population, rqtl2_bundle_file=thefile.name, @@ -1060,7 +832,7 @@ def select_dataset_info(species_id: int, population_id: int): conn, int(form["probe-study-id"])), avgmethods=averaging_methods(conn)) - return render_template("rqtl2/summary-info.html", + return render_template("expression-data/rqtl2/summary-info.html", species=species, population=population, rqtl2_bundle_file=thefile.name, @@ -1163,13 +935,19 @@ def rqtl2_processing_status(jobid: UUID): if thejob["status"] == "error": return render_template( - "rqtl2/rqtl2-job-error.html", job=thejob, messages=logmessages) + "expression-data/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( + "expression-data/rqtl2/rqtl2-job-results.html", + job=thejob, + messages=logmessages) return render_template( - "rqtl2/rqtl2-job-status.html", job=thejob, messages=logmessages) + "expression-data/rqtl2/rqtl2-job-status.html", + job=thejob, + messages=logmessages) except jobs.JobNotFound as _exc: - return render_template("rqtl2/no-such-job.html", jobid=jobid) + return render_template("expression-data/rqtl2/no-such-job.html", + jobid=jobid) diff --git a/uploader/population/views.py b/uploader/population/views.py index 39a5762..f42e547 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -1,12 +1,11 @@ """Views dealing with populations/inbredsets""" -import re import json import base64 -import traceback -from requests.models import Response from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from flask import (flash, + escape, request, url_for, redirect, @@ -18,8 +17,11 @@ 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.db_utils import database_connection from uploader.datautils import enumerate_sequence +from uploader.phenotypes.views import phenotypesbp +from uploader.expression_data.views import exprdatabp +from uploader.monadic_requests import make_either_error_handler +from uploader.input_validation import is_valid_representative_name from uploader.species.models import (all_species, species_by_id, order_species_by_family) @@ -34,6 +36,8 @@ __active_link__ = "populations" popbp = Blueprint("populations", __name__) popbp.register_blueprint(samplesbp, url_prefix="/") popbp.register_blueprint(genotypesbp, url_prefix="/") +popbp.register_blueprint(phenotypesbp, url_prefix="/") +popbp.register_blueprint(exprdatabp, url_prefix="/") render_template = make_template_renderer("populations") @@ -45,7 +49,15 @@ def index(): if not bool(request.args.get("species_id")): return render_template( "populations/index.html", - species=order_species_by_family(all_species(conn))) + species=all_species(conn), + activelink="populations") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.list_species_populations")) + species = species_by_id(conn, request.args.get("species_id")) if not bool(species): flash("Invalid species identifier provided!", "alert-danger") @@ -70,29 +82,6 @@ def list_species_populations(species_id: int): activelink="list-populations") -def valid_population_name(population_name: str) -> bool: - """ - Check whether the given name is a valid population name. - - Parameters - ---------- - population_name: a string of characters. - - Checks For - ---------- - * The name MUST start with an alphabet [a-zA-Z] - * The name MUST end with an alphabet [a-zA-Z] or number [0-9] - * The name MUST be composed of alphabets [a-zA-Z], numbers [0-9], - underscores (_) and/or hyphens (-). - - Returns - ------- - Boolean indicating whether or not the name is valid. - """ - pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$") - return bool(pattern.match(population_name)) - - @popbp.route("/<int:species_id>/populations/create", methods=["GET", "POST"]) @require_login def create_population(species_id: int): @@ -121,6 +110,7 @@ def create_population(species_id: int): {"id": "2", "value": "GEMMA"}, {"id": "3", "value": "R/qtl"}, {"id": "4", "value": "GEMMA, PLINK"}), + return_to=(request.args.get("return_to") or ""), activelink="create-population", **error_values) @@ -136,7 +126,7 @@ def create_population(species_id: int): errors = errors + (("population_name", "You must provide a name for the population!"),) - if not valid_population_name(population_name): + if not is_valid_representative_name(population_name): errors = errors + (( "population_name", "The population name can only contain letters, numbers, " @@ -170,24 +160,16 @@ def create_population(species_id: int): "GeneticType": request.form.get("population_genetic_type") or None }) - def __handle_error__(error): - error_format = ( - "\n\nThere was an error creating the population:\n\t%s\n\n") - if issubclass(type(error), Exception): - app.logger.debug(error_format, traceback.format_exc()) - raise error - if issubclass(type(error), Response): - try: - _data = error.json() - except Exception as _exc: - raise Exception(error.content) from _exc - raise Exception(_data) - - app.logger.debug(error_format, error) - raise Exception(error) - def __flash_success__(_success): - flash("Successfully created resource.", "alert-success") + flash("Successfully created population " + f"{escape(new_population['FullName'])}.", + "alert-success") + return_to = request.form.get("return_to") or "" + if return_to: + return redirect(url_for( + return_to, + species_id=species["SpeciesId"], + population_id=new_population["InbredSetId"])) return redirect(url_for( "species.populations.view_population", species_id=species["SpeciesId"], @@ -202,7 +184,10 @@ def create_population(species_id: int): "population_id": new_population["Id"], "public": "on" } - ).either(__handle_error__, __flash_success__) + ).either( + make_either_error_handler( + "There was an error creating the population"), + __flash_success__) @popbp.route("/<int:species_id>/populations/<int:population_id>", diff --git a/uploader/request_checks.py b/uploader/request_checks.py new file mode 100644 index 0000000..f1d8027 --- /dev/null +++ b/uploader/request_checks.py @@ -0,0 +1,75 @@ +"""Functions to perform common checks. + +These are useful for reusability, and hence maintainability of the code. +""" +from functools import wraps + +from gn_libs.mysqldb import database_connection +from flask import flash, url_for, redirect, current_app as app + +from uploader.species.models import species_by_id +from uploader.population.models import population_by_species_and_id + +def with_species(redirect_uri: str): + """Ensure the species actually exists.""" + def __decorator__(function): + @wraps(function) + def __with_species__(**kwargs): + try: + species_id = int(kwargs.get("species_id")) + if not bool(species_id): + flash("Expected species_id value to be present!", + "alert-danger") + return redirect(url_for(redirect_uri)) + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("Could not find species with that ID", + "alert-danger") + return redirect(url_for(redirect_uri)) + except ValueError as _verr: + app.logger.debug( + "Exception converting value to integer: %s", + kwargs.get("species_id"), + exc_info=True) + flash("Expected an integer for 'species_id' value.", + "alert-danger") + return redirect(url_for(redirect_uri)) + return function(**{**kwargs, "species": species}) + return __with_species__ + return __decorator__ + + +def with_population(species_redirect_uri: str, redirect_uri: str): + """Ensure the population actually exists.""" + def __decorator__(function): + @wraps(function) + @with_species(redirect_uri=species_redirect_uri) + def __with_population__(**kwargs): + try: + species_id = int(kwargs["species_id"]) + population_id = int(kwargs.get("population_id")) + select_population_uri = redirect(url_for( + redirect_uri, species_id=species_id)) + if not bool(population_id): + flash("Expected population_id value to be present!", + "alert-danger") + return select_population_uri + with database_connection(app.config["SQL_URI"]) as conn: + population = population_by_species_and_id( + conn, species_id, population_id) + if not bool(population): + flash("Could not find population with that ID", + "alert-danger") + return select_population_uri + except ValueError as _verr: + app.logger.debug( + "Exception converting value to integer: %s", + kwargs.get("population_id"), + exc_info=True) + flash("Expected an integer for 'population_id' value.", + "alert-danger") + return select_population_uri + return function(**{**kwargs, "population": population}) + return __with_population__ + return __decorator__ diff --git a/uploader/samples/__init__.py b/uploader/samples/__init__.py new file mode 100644 index 0000000..1bd6d2d --- /dev/null +++ b/uploader/samples/__init__.py @@ -0,0 +1 @@ +"""Samples package. Handle samples uploads and editing.""" diff --git a/uploader/samples/views.py b/uploader/samples/views.py index fd3c601..95a6f8c 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -3,40 +3,34 @@ import os import sys import uuid from pathlib import Path -from typing import Iterator -import MySQLdb as mdb from redis import Redis -from MySQLdb.cursors import DictCursor -from flask import ( - flash, - request, - url_for, - redirect, - Blueprint, - render_template, - current_app as app) +from flask import (flash, + request, + url_for, + redirect, + Blueprint, + current_app as app) from uploader import jobs from uploader.files import save_file +from uploader.ui import make_template_renderer from uploader.authorisation import require_login +from uploader.request_checks import with_population from uploader.input_validation import is_integer_input -from uploader.datautils import order_by_family, enumerate_sequence -from uploader.db_utils import ( - with_db_connection, - database_connection, - with_redis_connection) +from uploader.datautils import safe_int, order_by_family, enumerate_sequence +from uploader.population.models import population_by_id, populations_by_species +from uploader.db_utils import (with_db_connection, + database_connection, + with_redis_connection) from uploader.species.models import (all_species, species_by_id, order_species_by_family) -from uploader.population.models import(save_population, - population_by_id, - populations_by_species, - population_by_species_and_id) from .models import samples_by_species_and_population samplesbp = Blueprint("samples", __name__) +render_template = make_template_renderer("samples") @samplesbp.route("/samples", methods=["GET"]) @require_login @@ -46,8 +40,15 @@ def index(): if not bool(request.args.get("species_id")): return render_template( "samples/index.html", - species=order_species_by_family(all_species(conn)), + species=all_species(conn), activelink="samples") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.samples.select_population")) + species = species_by_id(conn, request.args.get("species_id")) if not bool(species): flash("No such species!", "alert-danger") @@ -69,13 +70,18 @@ def select_population(species_id: int): if not bool(request.args.get("population_id")): return render_template("samples/select-population.html", species=species, - populations=order_by_family( - populations_by_species( - conn, - species_id), - order_key="FamilyOrder"), + populations=populations_by_species( + conn, + species_id), activelink="samples") + population_id = request.args["population_id"] + if population_id == "CREATE-POPULATION": + return redirect(url_for( + "species.populations.create_population", + species_id=species["SpeciesId"], + return_to="species.populations.samples.list_samples")) + population = population_by_id(conn, request.args.get("population_id")) if not bool(population): flash("Population not found!", "alert-danger") @@ -110,9 +116,7 @@ def list_samples(species_id: int, population_id: int): all_samples = enumerate_sequence(samples_by_species_and_population( conn, species_id, population_id)) total_samples = len(all_samples) - offset = int(request.args.get("from") or 0) - if offset < 0: - offset = 0 + offset = max(safe_int(request.args.get("from") or 0), 0) count = int(request.args.get("count") or 20) return render_template("samples/list-samples.html", species=species, @@ -233,53 +237,41 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "upload-samples/status/<uuid:job_id>", methods=["GET"]) @require_login -def upload_status(species_id: int, population_id: int, job_id: uuid.UUID): +@with_population(species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] """Check on the status of a samples upload job.""" - with database_connection(app.config["SQL_URI"]) as conn: - species = species_by_id(conn, species_id) - if not bool(species): - flash("You must provide a valid species.", "alert-danger") - return redirect(url_for("species.populations.samples.index")) + job = with_redis_connection(lambda rconn: jobs.job( + rconn, jobs.jobsnamespace(), job_id)) + if job: + status = job["status"] + if status == "success": + return render_template("samples/upload-success.html", + job=job, + species=species, + population=population,) - population = population_by_species_and_id( - conn, species_id, population_id) - if not bool(population): - flash("You must provide a valid population.", "alert-danger") + if status == "error": return redirect(url_for( - "species.populations.samples.select_population", - species_id=species_id)) + "species.populations.samples.upload_failure", job_id=job_id)) - job = with_redis_connection(lambda rconn: jobs.job( - rconn, jobs.jobsnamespace(), job_id)) - if job: - status = job["status"] - if status == "success": - return render_template("samples/upload-success.html", - job=job, - species=species, - population=population,) - - if status == "error": + error_filename = Path(jobs.error_filename( + job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) + if error_filename.exists(): + stat = os.stat(error_filename) + if stat.st_size > 0: return redirect(url_for( - "species.populations.samples.upload_failure", job_id=job_id)) + "samples.upload_failure", job_id=job_id)) - error_filename = Path(jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) - if error_filename.exists(): - stat = os.stat(error_filename) - if stat.st_size > 0: - return redirect(url_for( - "samples.upload_failure", job_id=job_id)) - - return render_template("samples/upload-progress.html", - species=species, - population=population, - job=job) # maybe also handle this? - - return render_template("no_such_job.html", - job_id=job_id, + return render_template("samples/upload-progress.html", species=species, - population=population), 400 + population=population, + job=job) # maybe also handle this? + + return render_template("no_such_job.html", + job_id=job_id, + species=species, + population=population), 400 @samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"]) @require_login diff --git a/uploader/species/models.py b/uploader/species/models.py index 51f941c..9477aa8 100644 --- a/uploader/species/models.py +++ b/uploader/species/models.py @@ -58,7 +58,8 @@ def save_species(conn: mdb.Connection, common_name: The species' common name. scientific_name; The species' scientific name. """ - genus, species_name = scientific_name.split(" ") + genus, *species_name = scientific_name.split(" ") + species_name = " ".join(species_name) families = species_families(conn) with conn.cursor() as cursor: cursor.execute("SELECT MAX(OrderId) FROM Species") @@ -68,7 +69,7 @@ def save_species(conn: mdb.Connection, "menu_name": f"{common_name} ({genus[0]}. {species_name.lower()})", "scientific_name": scientific_name, "family": family, - "family_order": families[family], + "family_order": families.get(family, 999999), "taxon_id": taxon_id, "species_order": cursor.fetchone()[0] + 5 } @@ -116,7 +117,8 @@ def update_species(# pylint: disable=[too-many-arguments] species_order: The ordering of this species in relation to others """ with conn.cursor(cursorclass=DictCursor) as cursor: - genus, species_name = scientific_name.split(" ") + genus, *species_name = scientific_name.split(" ") + species_name = " ".join(species_name) species = { "species_id": species_id, "common_name": common_name, diff --git a/uploader/species/views.py b/uploader/species/views.py index 08d3728..f0798d6 100644 --- a/uploader/species/views.py +++ b/uploader/species/views.py @@ -1,6 +1,8 @@ """Endpoints handling species.""" from pymonad.either import Left, Right, Either +from gn_libs.mysqldb import database_connection from flask import (flash, + escape, request, url_for, redirect, @@ -8,8 +10,8 @@ from flask import (flash, current_app as app) from uploader.population import popbp +from uploader.platforms import platformsbp from uploader.ui import make_template_renderer -from uploader.db_utils import database_connection from uploader.oauth2.client import oauth2_get, oauth2_post from uploader.authorisation import require_login, require_token from uploader.datautils import order_by_family, enumerate_sequence @@ -23,10 +25,12 @@ from .models import (all_species, speciesbp = Blueprint("species", __name__) speciesbp.register_blueprint(popbp, url_prefix="/") +speciesbp.register_blueprint(platformsbp, url_prefix="/") render_template = make_template_renderer("species") @speciesbp.route("/", methods=["GET"]) +@require_login def list_species(): """List and display all the species in the database.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -59,6 +63,8 @@ def create_species(): if request.method == "GET": return render_template("species/create-species.html", families=species_families(conn), + return_to=( + request.args.get("return_to") or ""), activelink="create-species") error = False @@ -76,7 +82,7 @@ def create_species(): error = True parts = tuple(name.strip() for name in scientific_name.split(" ")) - if len(parts) != 2 or not all(bool(name) for name in parts): + if (len(parts) != 2 and len(parts) != 3) or not all(bool(name) for name in parts): flash("The scientific name you provided is invalid.", "alert-danger") error = True @@ -110,7 +116,14 @@ def create_species(): species = save_species( conn, common_name, scientific_name, family, taxon_id) - flash("Species saved successfully!", "alert-success") + flash( + f"You have successfully added species '{species['scientific_name']} " + f"({species['common_name']})'.", + "alert-success") + + return_to = request.form.get("return_to").strip() + if return_to: + return redirect(url_for(return_to, species_id=species["species_id"])) return redirect(url_for("species.view_species", species_id=species["species_id"])) diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css index 30d5808..35c0627 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -1,116 +1,154 @@ +* { + box-sizing: border-box; +} + body { margin: 0.7em; - box-sizing: border-box; display: grid; - grid-template-columns: 1fr 6fr; - grid-template-rows: 5em 100%; + grid-template-columns: 1fr 9fr; grid-gap: 20px; - font-family: Georgia, Garamond, serif; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-style: normal; + font-size: 20px; } #header { - grid-column: 1/3; - width: 100%; - /* background: cyan; */ - padding-top: 0.5em; - border-radius: 0.5em; + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 3; + /* Define layout for the children elements */ + display: grid; + grid-template-columns: 8fr 2fr; + + /* Content styling */ background-color: #336699; - border-color: #080808; color: #FFFFFF; - background-image: none; + border-radius: 3px; + min-height: 30px; } -#header .header { - font-size: 2em; - display: inline-block; - text-align: start; -} +#header #header-text { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; -#header .header-nav { - display: inline-block; - color: #FFFFFF; + /* Content styling */ + padding-left: 1em; } -#header .header-nav li { - border-width: 1px; - border-color: #FFFFFF; - vertical-align: middle; - margin: 0.2em; +#header #header-nav { + /* Place it in the parent element */ + grid-column-start: 2; + grid-column-end: 3; } -#header .header-nav a { +#header #header-nav .nav li a { + /* Content styling */ color: #FFFFFF; - text-decoration: none; + background: #4477AA; + border: solid 5px #336699; + border-radius: 5px; + font-size: 0.7em; + text-align: center; + padding: 1px 7px; } #nav-sidebar { - grid-column: 1/2; - /* background: #e5e5ff; */ - padding-top: 0.5em; - border-radius: 0.5em; - font-size: 1.2em; + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; } -#main { - grid-column: 2/3; - width: 100%; - /* background: gray; */ +#nav-sidebar .nav li a:hover { border-radius: 0.5em; } -.pagetitle { - padding-top: 0.5em; - /* background: pink; */ +#nav-sidebar .nav .activemenu { + border-style: solid; border-radius: 0.5em; - /* background-color: #6699CC; */ - /* background-color: #77AADD; */ + border-color: #AAAAAA; + background-color: #EFEFEF; +} + +#main { + /* Place it in the parent element */ + grid-column-start: 2; + grid-column-end: 3; + + /* Define layout for the children elements */ + display: grid; + grid-template-columns: 1fr; + grid-template-rows: 4em 100%; + grid-gap: 1em; +} + +#main #pagetitle { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 3; + + /* Content-styling */ + border-radius: 3px; background-color: #88BBEE; } -.pagetitle h1 { - text-align: start; +#main #pagetitle .title { + font-size: 1.4em; text-transform: capitalize; - padding-left: 0.25em; + padding-left: 0.5em; +} + +#main #all-content { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 3; + + /* Define layout for the children elements */ + display: grid; + grid-template-columns: 7fr 3fr; /* For a maximum screen width of 1366 pixels */ + grid-gap: 1.5em; +} + +#main #all-content .row { + margin: 0 2px; } -.pagetitle .breadcrumb { +#main #all-content #main-content { + background: #FFFFFF; + max-width: 950px; +} + +#pagetitle .breadcrumb { background: none; + text-transform: capitalize; + font-size: 0.75em; } -.pagetitle .breadcrumb .active a { +#pagetitle .breadcrumb .active a { color: #333333; } -.pagetitle .breadcrumb a { +#pagetitle .breadcrumb a { color: #666666; } -.main-content { - font-size: 1.275em; -} - -.breadcrumb { +.heading { + border-bottom: solid #EEBB88; text-transform: capitalize; } -dd { - margin-left: 3em; - font-size: 0.88em; - padding-bottom: 1em; +.subheading { + padding: 1em 0 0.1em 0.5em; + border-bottom: solid #88BBEE; + text-transform: capitalize; } -input[type="submit"] { - text-transform: capitalize; +input[type="search"] { + border-radius: 5px; } -.card { - margin-top: 0.3em; - border-width: 1px; - border-style: solid; - border-radius: 0.3em; - border-color: #AAAAAA; - padding: 0.5em; +.btn { + text-transform: Capitalize; } diff --git a/uploader/static/js/files.js b/uploader/static/js/files.js new file mode 100644 index 0000000..9d6bca1 --- /dev/null +++ b/uploader/static/js/files.js @@ -0,0 +1,118 @@ +var readFirstNLines = (thefile, count, process_content_fns) => { + var reader = new FileReader(); + if(typeof thefile !== "undefined" && thefile !== null) { + reader.addEventListener("load", (event) => { + var content = event + .target + .result + .split("\n") + .slice(0, count) + .map((line) => {return line.trim("\r");}); + process_content_fns.forEach((fn) => {fn(content);}); + }); + reader.readAsText(thefile); + } +}; +var read_first_n_lines = readFirstNLines; + + +var readBinaryFile = (file) => { + return new Promise((resolve, reject) => { + var _reader = new FileReader(); + _reader.onload = (event) => {resolve(_reader.result);}; + _reader.readAsArrayBuffer(file); + }); +}; + + +var Uint8ArrayToHex = (arr) => { + var toHex = (val) => { + _hex = val.toString(16); + if(_hex.length < 2) { + return "0" + val; + } + return _hex; + }; + _hexstr = "" + arr.forEach((val) => {_hexstr += toHex(val)}); + return _hexstr +}; + + +var computeFileChecksum = (file) => { + return readBinaryFile(file) + .then((content) => { + return window.crypto.subtle.digest( + "SHA-256", new Uint8Array(content)); + }).then((digest) => { + return Uint8ArrayToHex(new Uint8Array(digest)) + }); +}; + + +var defaultResumableHandler = (event) => { + throw new Error("Please provide a valid event handler!"); +}; + +var addHandler = (resumable, handlername, handler) => { + if(resumable.support) { + resumable.on(handlername, (handler || defaultResumableHandler)); + } + return resumable; +}; + + +var makeResumableHandler = (handlername) => { + return (resumable, handler) => { + return addHandler(resumable, handlername, handler); + }; +}; + + +var fileSuccessHandler = makeResumableHandler("fileSuccess"); +var fileProgressHandler = makeResumableHandler("fileProgress"); +var fileAddedHandler = makeResumableHandler("fileAdded"); +var filesAddedHandler = makeResumableHandler("filesAdded"); +var filesRetryHandler = makeResumableHandler("filesRetry"); +var filesErrorHandler = makeResumableHandler("filesError"); +var uploadStartHandler = makeResumableHandler("uploadStart"); +var completeHandler = makeResumableHandler("complete"); +var progressHandler = makeResumableHandler("progress"); +var errorHandler = makeResumableHandler("error"); + + +var markResumableDragAndDropElement = (resumable, fileinput, droparea, browsebutton) => { + if(resumable.support) { + //Hide file input element and display drag&drop UI + add_class(fileinput, "hidden"); + remove_class(droparea, "hidden"); + + // Define UI elements for browse and drag&drop + resumable.assignDrop(droparea); + resumable.assignBrowse(browsebutton); + } + + return resumable; +}; + + +var makeResumableElement = (targeturi, fileinput, droparea, uploadbutton, filetype) => { + var resumable = Resumable({ + target: targeturi, + fileType: filetype, + maxFiles: 1, + forceChunkSize: true, + generateUniqueIdentifier: (file, event) => { + return computeFileChecksum(file).then((checksum) => { + var _relativePath = (file.webkitRelativePath + || file.relativePath + || file.fileName + || file.name); + return checksum + "-" + _relativePath.replace( + /[^a-zA-Z0-9_-]/img, ""); + }); + } + }); + + return resumable; +}; diff --git a/uploader/static/js/misc.js b/uploader/static/js/misc.js new file mode 100644 index 0000000..cf7b39e --- /dev/null +++ b/uploader/static/js/misc.js @@ -0,0 +1,6 @@ +"Miscellaneous functions and event-handlers" + +$(".not-implemented").click((event) => { + event.preventDefault(); + alert("This feature is not implemented yet. Please bear with us."); +}); diff --git a/uploader/static/js/populations.js b/uploader/static/js/populations.js new file mode 100644 index 0000000..ded9b10 --- /dev/null +++ b/uploader/static/js/populations.js @@ -0,0 +1,40 @@ +var populationDataTable = (populationdata) => { + var lengthMenu = [10, 25, 50, 100, 1000]; + if(populationdata.length > 1000) { + lengthMenu.push(populationdata.length) + } + $("#tbl-select-population").DataTable({ + responsive: true, + lengthMenu: lengthMenu, + language: { + processing: "Processing… Please wait.", + loadingRecords: "Loading population — Please wait.", + lengthMenu: "Show _MENU_ populations", + info: "Showing _START_ to _END_ of _TOTAL_ populations" + }, + data: populationdata, + columns: [ + { + data: (apopulation) => { + return `<input type="radio" name="population_id"` + + `id="rdo_population_id_${apopulation.InbredSetId}" ` + + `value="${apopulation.InbredSetId}">`; + } + }, + { + data: (apopulation) => { + return `<label for="rdo_population_id_${apopulation.InbredSetId}" ` + + `class="control-label" style="font-weight: 1;">` + + `${apopulation.FullName} (${apopulation.InbredSetName})` + + `</label>`; + } + } + ] + }); +}; + + +$(() => { + populationDataTable(JSON.parse( + $("#tbl-select-population").attr("data-populations-list"))); +}); diff --git a/uploader/static/js/species.js b/uploader/static/js/species.js new file mode 100644 index 0000000..b070725 --- /dev/null +++ b/uploader/static/js/species.js @@ -0,0 +1,39 @@ +var speciesDataTable = (speciesdata) => { + var lengthMenu = [10, 25, 50, 100, 1000]; + if(speciesdata.length > 1000) { + lengthMenu.push(speciesdata.length) + } + $("#tbl-select-species").DataTable({ + responsive: true, + lengthMenu: lengthMenu, + language: { + processing: "Processing… Please wait.", + loadingRecords: "Loading species — Please wait.", + lengthMenu: "Show _MENU_ species", + info: "Showing _START_ to _END_ of _TOTAL_ species" + }, + data: speciesdata, + columns: [ + { + data: (aspecies) => { + return `<input type="radio" name="species_id"` + + `id="rdo_species_id_${aspecies.SpeciesId}" ` + + `value="${aspecies.SpeciesId}">`; + } + }, + { + data: (aspecies) => { + return `<label for="rdo_species_id_${aspecies.SpeciesId}" ` + + `class="control-label" style="font-weight: 1;">` + + `${aspecies.FullName} (${aspecies.SpeciesName})` + + `</label>`; + } + } + ] + }); +}; + +$(() => { + speciesDataTable(JSON.parse( + $("#tbl-select-species").attr("data-species-list"))); +}); diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 3af14ef..5eca445 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -8,7 +8,7 @@ <meta name="viewport" content="width=device-width, initial-scale=1.0" /> {%block extrameta%}{%endblock%} - <title>GN Uploader: {%block title%}{%endblock%}</title> + <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> <link rel="stylesheet" type="text/css" href="{{url_for('base.bootstrap', @@ -17,78 +17,110 @@ href="{{url_for('base.bootstrap', filename='css/bootstrap-theme.min.css')}}" /> <link rel="stylesheet" type="text/css" href="/static/css/styles.css" /> + <link rel="stylesheet" + href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" /> {%block css%}{%endblock%} </head> <body> - <header id="header" class="container-fluid"> - <div class="row"> - <span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span> - <nav class="header-nav col-lg-3"> - <ul class="nav justify-content-end"> - <li class="btn"> - {%if user_logged_in()%} - <a href="{{url_for('oauth2.logout')}}" - title="Log out of the system">{{user_email()}} — Log Out</a> - {%else%} - <a href="{{authserver_authorise_uri()}}" - title="Log in to the system">Log In</a> - {%endif%} - </li> - </ul> - </nav> + <header id="header"> + <span id="header-text">GeneNetwork</span> + <nav id="header-nav"> + <ul class="nav justify-content-end"> + <li> + {%if user_logged_in()%} + <a href="{{url_for('oauth2.logout')}}" + title="Log out of the system"> + <span class="glyphicon glyphicon-user"></span> + Sign Out</a> + {%else%} + <a href="{{authserver_authorise_uri()}}" + title="Log in to the system">Sign In</a> + {%endif%} + </li> + </ul> + </nav> </header> - <aside id="nav-sidebar" class="container-fluid"> + <aside id="nav-sidebar"> <ul class="nav flex-column"> - <li><a href="/" >Home</a></li> - <li><a href="{{url_for('species.list_species')}}" - title="View and manage species information.">Species</a></li> - <li><a href="{{url_for('species.populations.index')}}" - title="View and manage species populations.">Populations</a></li> - <li><a href="{{url_for('species.populations.genotypes.index')}}" - title="Upload Genotype data.">Genotype Data</a></li> - <li><a href="{{url_for('species.populations.samples.index')}}" - title="Upload population samples.">Samples</a></li> - <li><a href="{{url_for('expression-data.index.index')}}" - title="Upload expression data.">Expression Data</a></li> - <li><a href="#" - title="Upload phenotype data.">Phenotype Data</a></li> - <li><a href="#" - title="Upload individual data.">Individual Data</a></li> - <li><a href="#" - title="Upload RNA-Seq data.">RNA-Seq Data</a></li> + <li {%if activemenu=="home"%}class="activemenu"{%endif%}> + <a href="/" >Home</a></li> + <li {%if activemenu=="species"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.list_species')}}" + title="View and manage species information.">Species</a></li> + <li {%if activemenu=="platforms"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.platforms.index')}}" + title="View and manage species platforms.">Sequencing Platforms</a></li> + <li {%if activemenu=="populations"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.index')}}" + title="View and manage species populations.">Populations</a></li> + <li {%if activemenu=="samples"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.samples.index')}}" + title="Upload population samples.">Samples</a></li> + <li {%if activemenu=="genotypes"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.genotypes.index')}}" + title="Upload Genotype data.">Genotype Data</a></li> + <!-- + TODO: Maybe include menus here for managing studies and dataset or + maybe have the studies/datasets managed under their respective + sections, e.g. "Publish*" studies/datasets under the "Phenotypes" + section, "ProbeSet*" studies/datasets under the "Expression Data" + sections, etc. + --> + <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.phenotypes.index')}}" + title="Upload phenotype data.">Phenotype Data</a></li> + <!-- + <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> + <a href="{{url_for('species.populations.expression-data.index')}}" + title="Upload expression data." + class="not-implemented">Expression Data</a></li> + <li {%if activemenu=="individuals"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload individual data.">Individual Data</a></li> + <li {%if activemenu=="rna-seq"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="Upload RNA-Seq data.">RNA-Seq Data</a></li> + <li {%if activemenu=="async-jobs"%}class="activemenu"{%endif%}> + <a href="#" + class="not-implemented" + title="View and manage the backgroud jobs you have running"> + Background Jobs</a></li> + --> </ul> </aside> - <main id="main" class="main container-fluid"> + <main id="main" class="main"> - <div class="pagetitle row"> - <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1> - <nav> - <ol class="breadcrumb"> - <li {%if activelink is not defined or activelink=="home"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('base.index')}}">Home</a> - </li> - {%block lvl1_breadcrumbs%}{%endblock%} - </ol> - </nav> + <div id="pagetitle" class="pagetitle"> + <span class="title">Data Upload and Quality Control: {%block pagetitle%}{%endblock%}</span> + <!-- + <nav> + <ol class="breadcrumb"> + <li {%if activelink is not defined or activelink=="home"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('base.index')}}">Home</a> + </li> + {%block lvl1_breadcrumbs%}{%endblock%} + </ol> + </nav> + --> </div> - <div class="row"> - <div class="container-fluid"> - <div class="col-md-8 main-content"> - {%block contents%}{%endblock%} - </div> - <div class="sidebar-content col-md-4"> - {%block sidebarcontents%}{%endblock%} - </div> + <div id="all-content"> + <div id="main-content"> + {%block contents%}{%endblock%} + </div> + <div id="sidebar-content"> + {%block sidebarcontents%}{%endblock%} </div> </div> </main> @@ -98,8 +130,10 @@ filename='jquery.min.js')}}"></script> <script src="{{url_for('base.bootstrap', filename='js/bootstrap.min.js')}}"></script> + <script type="text/javascript" src="/static/js/misc.js"></script> + <script type="text/javascript" + src="{{url_for('base.datatables', + filename='js/jquery.dataTables.js')}}"></script> {%block javascript%}{%endblock%} - </body> - </html> diff --git a/uploader/templates/cli-output.html b/uploader/templates/cli-output.html index 33fb73b..64b1a9a 100644 --- a/uploader/templates/cli-output.html +++ b/uploader/templates/cli-output.html @@ -1,7 +1,7 @@ {%macro cli_output(job, stream)%} -<h4>{{stream | upper}} Output</h4> -<div class="cli-output"> +<h4 class="subheading">{{stream | upper}} Output</h4> +<div class="cli-output" style="max-height: 10em; overflow: auto;"> <pre>{{job.get(stream, "")}}</pre> </div> 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/genotypes/base.html b/uploader/templates/genotypes/base.html index 1b274bf..7d61312 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -6,7 +6,18 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + {%if dataset is defined and dataset is mapping%} + {{dataset.Name}} + {%else%} + Genotypes + {%endif%}</a> + {%else%} <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> + {%endif%} </li> {%block lvl4_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..10331c1 --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,82 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-geno-create-dataset" + method="POST" + action="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + <legend>Create a new Genotype Dataset</legend> + + <div class="form-group"> + <label for="txt-geno-dataset-name" class="form-label">Name</label> + <input type="text" + id="txt-geno-dataset-name" + name="geno-dataset-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a short representative, but constrained name for the genotype + dataset.<br /> + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt-geno-dataset-fullname" + name="geno-dataset-fullname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a longer, more descriptive name for your dataset.</p></small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-shortname" + class="form-label">Short Name</label> + <input type="text" + id="txt-geno-dataset-shortname" + name="geno-dataset-shortname" + class="form-control" /> + <small class="form-text text-muted"> + <p>A short name for your dataset. If you leave this field blank, the + short name will be set to the same value as the + "<strong>Name</strong>" field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create dataset" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html index 9ffea73..b50ebc5 100644 --- a/uploader/templates/genotypes/index.html +++ b/uploader/templates/genotypes/index.html @@ -25,12 +25,8 @@ {{select_species_form(url_for("species.populations.genotypes.index"), species)}} </div> +{%endblock%} -<div class="row"> - <h3>Some Important Concepts to Consider/Remember</h3> - <ul> - <li>Reference vs. Non-reference alleles</li> - <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> - </ul> -</div> +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> {%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html new file mode 100644 index 0000000..0f074fd --- /dev/null +++ b/uploader/templates/genotypes/list-genotypes.html @@ -0,0 +1,149 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-genotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}">List genotypes</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genetic Markers</h2> + <p>There are a total of {{total_markers}} currently registered genetic markers + for the "{{species.FullName}}" species. You can click + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View genetic markers for species '{{species.FullName}}"> + this link to view the genetic markers + </a>. + </p> +</div> + +<div class="row"> + <h2>Genotype Encoding</h2> + <p> + The genotype encoding used for the "{{population.FullName}}" population from + the "{{species.FullName}}" species is as shown in the table below. + </p> + <table class="table"> + + <thead> + <tr> + <th>Allele Type</th> + <th>Allele Symbol</th> + <th>Allele Value</th> + </tr> + </thead> + + <tbody> + {%for row in genocode%} + <tr> + <td>{{row.AlleleType}}</td> + <td>{{row.AlleleSymbol}}</td> + <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td> + </tr> + {%else%} + <tr> + <td colspan="7" class="text-info"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no explicit genotype encoding defined for this population. + </td> + </tr> + {%endfor%} + </tbody> + </table> + + {%if genocode | length < 1%} + <a href="#add-genotype-encoding" + title="Add a genotype encoding system for this population" + class="btn btn-primary not-implemented"> + add genotype encoding + </a> + {%endif%} +</div> + +<div class="row text-danger"> + <h3>Some Important Concepts to Consider/Remember</h3> + <ul> + <li>Reference vs. Non-reference alleles</li> + <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> + </ul> + <h3>Possible references</h3> + <ul> + <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> + <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> + </ul> +</div> + +<div class="row"> + <h2>Genotype Datasets</h2> + + <p>The genotype data is organised under various genotype datasets. You can + click on the link for the relevant dataset to view a little more information + about it.</p> + + {%if dataset is not none%} + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td><a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="View details regarding and manage dataset '{{dataset.FullName}}'"> + {{dataset.FullName}}</a></td> + </tr> + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no genotype dataset defined for this population. + </p> + <p> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." + class="btn btn-primary"> + create new genotype dataset</a></p> + {%endif%} +</div> +<div class="row text-warning"> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset. If there is more than one, the system apparently + fails in unpredictable ways. + </p> + <p>Fix this to allow multiple datasets, each with a different assembly from + all the rest.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html new file mode 100644 index 0000000..a705ae3 --- /dev/null +++ b/uploader/templates/genotypes/list-markers.html @@ -0,0 +1,105 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Genotypes: List Markers{%endblock%} + +{%block pagetitle%}Genotypes: List Markers{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-markers"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id)}}">List markers</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +{%if markers | length > 0%} +<div class="row"> + <p> + There are a total of {{total_markers}} genotype markers for this species. + </p> + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying markers {{start_from+1}} to {{start_from+count if start_from+count < total_markers else total_markers}} of + {{total_markers}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_markers%} + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species.SpeciesId, + population_id=population.Id, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + <table class="table"> + <thead> + <tr> + <th title="">#</th> + <th title="">Marker Name</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of the marker in megabasepairs"> + Location (Mb)</th> + <th title="">Source</th> + <th title="">Source2</th> + </thead> + + <tbody> + {%for marker in markers%} + <tr> + <td>{{marker.sequence_number}}</td> + <td>{{marker.Marker_Name}}</td> + <td>{{marker.Chr}}</td> + <td>{{marker.Mb}}</td> + <td>{{marker.Source}}</td> + <td>{{marker.Source2}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%else%} +<div class="row"> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This species does not currently have any genetic markers uploaded, therefore, + there is nothing to display here. + </p> + <p> + <a href="#add-genetic-markers-for-species-{{species.SpeciesId}}" + title="Add genetic markers for this species" + class="btn btn-primary"> + add genetic markers + </a> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html index 7c81943..acdd063 100644 --- a/uploader/templates/genotypes/select-population.html +++ b/uploader/templates/genotypes/select-population.html @@ -12,20 +12,14 @@ {{flash_all_messages()}} <div class="row"> - <p> - You have indicated that you intend to upload the genotypes for species - '{{species.FullName}}'. We now just require the population for your - experiment/study, and you should be good to go. - </p> -</div> - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", - species_id=species.SpeciesId), - populations)}} + {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}} </div> {%endblock%} {%block sidebarcontents%} {{display_species_card(species)}} {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html new file mode 100644 index 0000000..e7ceb36 --- /dev/null +++ b/uploader/templates/genotypes/view-dataset.html @@ -0,0 +1,61 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes: View Dataset{%endblock%} + +{%block pagetitle%}Genotypes: View Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">view dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Dataset Details</h2> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row text-warning"> + <h2>Assembly Details</h2> + + <p>Maybe include the assembly details here if found to be necessary.</p> +</div> + +<div class="row"> + <h2>Genotype Data</h2> + + <p class="text-danger"> + Provide link to enable uploading of genotype data here.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/index.html b/uploader/templates/index.html index e3f5af4..aa1414e 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -5,23 +5,103 @@ {%block pagetitle%}Home{%endblock%} -{%block breadcrumb%} -<li class="breadcrumb-item active"> - <a href="{{url_for('base.index')}}">Home</a> -</li> -{%endblock%} - {%block contents%} <div class="row"> {{flash_all_messages()}} <div class="explainer"> - <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p> + <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control + System</strong>.</p> + <p>This tool helps you prepare and upload research data to GeneNetwork for + analysis.</p> - <p>Click on the menu items on the left to select the kind of data you want to upload.</p> + <h2 class="heading">Getting Started</h2> + <p>The sections below explain the features of the system. Review this guide + to learn how to use the system.</p> {%block extrapageinfo%}{%endblock%} + + <h3 class="subheading">Species</h3> + + <p>GeneNetwork supports genetic studies across multiple species (e.g. mice + [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . + Here you can:</p> + <ul> + <li>View all species that are currently supported</li> + <li>Add new species not yet in the system</li> + </ul> + + <h3 class="subheading">Populations</h3> + + <p>A "population" refers to a specific subgroup within a species that you’re + studying (e.g., BXD mice). Here you can:</p> + <ul> + <li>View the populations that exist for a selected species</li> + <li>Add new populations of study for a selected species</li> + </ul> + + <h3 class="subheading">Samples</h3> + + <p>Manage individual specimens or cases used in your experiments. These + include:</p> + + <ul> + <li>Experimental subjects</li> + <li>Data sources (e.g., tissue samples, clinical cases)</li> + <li>Strain means (instead of entering multiple BXD1 individuals, for + example, the mean would be entered for a single BXD1 strain)</li> + </ul> + + + <h3 class="subheading">Genotype Data</h3> + + <p>Upload and review genetic markers and allele encodings for your + population. Key details:</p> + + <ul> + <li>Markers are species-level (e.g., mouse SNP databases).</li> + <li>Allele data is population-specific (tied to your experimental + samples).</li> + </ul> + + <p><strong>Requirement</strong>: Samples must already have been registered + in the system before uploading genotype data.</p> + + <h3 class="subheading">Phenotype Data</h3> + + <p>Phenotypes are the visible traits or features of a living thing. For + example, phenotypes include:</p> + + <ul> + <li>Weight</li> + <li>Height</li> + <li>Color (such as the color of fur or eyes)</li> + </ul> + + <p>This part of the system will allow you to upload and manage the values + for different phenotypes from various samples in your studies.</p> + + <!-- + + <h3 class="subheading">Expression Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h3 class="subheading">Individual Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h3 class="subheading">RNA-Seq Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> </div> + --> </div> {%endblock%} diff --git a/uploader/templates/login.html b/uploader/templates/login.html index bbca42f..e76c644 100644 --- a/uploader/templates/login.html +++ b/uploader/templates/login.html @@ -5,7 +5,8 @@ {%block pagetitle%}log in{%endblock%} {%block extrapageinfo%} -<p> - You <strong>do need to be logged in</strong> to upload data onto this system. - Please do that by clicking the "Log In" button at the top of the page.</p> +<p class="text-dark"> + You <strong>need to + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system">sign in</a></strong> to use this system.</p> {%endblock%} diff --git a/uploader/templates/macro-table-pagination.html b/uploader/templates/macro-table-pagination.html new file mode 100644 index 0000000..292c531 --- /dev/null +++ b/uploader/templates/macro-table-pagination.html @@ -0,0 +1,26 @@ +{%macro table_pagination(start_at, page_count, total_count, base_uri, name)%} +{%set ns = namespace(forward_uri=base_uri, back_uri=base_uri)%} +{%set ns.forward_uri="brr"%} + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_at > 0%} + <a href="{{base_uri + + '?start_at='+((start_at-page_count)|string) + + '&count='+(page_count|string)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying {{name}} {{start_at+1}} to {{start_at+page_count if start_at+page_count < total_count else total_count}} of {{total_count}}</div> + <div class="col-md-2" style="text-align: end;"> + {%if start_at + page_count < total_count%} + <a href="{{base_uri + + '?start_at='+((start_at+page_count)|string) + + '&count='+(page_count|string)}}"> + Next<span class="glyphicon glyphicon-forward"></span></a> + {%endif%} + </div> + </div> +{%endmacro%} 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/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html new file mode 100644 index 0000000..97b55f2 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -0,0 +1,331 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-add-phenotypes" + method="POST" + enctype="multipart/form-data" + action="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=use_bundle)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> + <legend>Add New Phenotypes</legend> + + <div class="form-text help-block"> + {%block frm_add_phenotypes_documentation%}{%endblock%} + <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> + </div> + + {%block frm_add_phenotypes_elements%}{%endblock%} + + <div class="checkbox"> + <label> + <input id="chk-published" type="checkbox" name="published?" /> + These phenotypes are published</label> + </div> + + <fieldset id="fldset-publication-info" class="hidden"> + <legend>Publication Information</legend> + <div class="form-group"> + <label for="txt-pubmed-id" class="form-label">Pubmed ID</label> + <div class="input-group"> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-search-pubmed-id" class="btn btn-info">Search</button> + </span> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger hidden"> + </span><br /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID above and click "Search" to search + for some (or all) of the publication details requested below. + </span> + </div> + + <div class="form-group"> + <label for="txt-publication-authors" class="form-label">Authors</label> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors in the following format …</span> + </div> + + <div class="form-group"> + <label for="txt-publication-title" class="form-label"> + Publication Title</label> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-abstract" class="form-label"> + Publication Abstract</label> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-journal" class="form-label">Journal</label> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> + + <div class="form-group"> + <label for="txt-publication-volume" class="form-label">Volume</label> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> + + <div class="form-group"> + <label for="txt-publication-pages" class="form-label">Pages</label> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> + + <div class="form-group"> + <label for="select-publication-month" class="form-label"> + Publication Month</label> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="form-label">Publication Year</label> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + </fieldset> + + <div class="form-group"> + <input type="submit" + value="upload phenotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + {%block page_documentation%}{%endblock%} +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + var remove_class = (element, classvalue) => { + new_classes = (element.attr("class") || "").split(" ").map((val) => { + return val.trim(); + }).filter((val) => { + return ((val !== classvalue) && + (val !== "")) + }).join(" "); + + if(new_classes === "") { + element.removeAttr("class"); + } else { + element.attr("class", new_classes); + } + }; + + var add_class = (element, classvalue) => { + remove_class(element, classvalue); + element.attr("class", (element.attr("class") || "") + " " + classvalue); + }; + + $("#chk-published").on("click", (event) => { + pub_details = $("#fldset-publication-info") + if(event.target.checked) { + // display the publication details + remove_class(pub_details, "hidden"); + } else { + // hide the publication details + add_class(pub_details, "hidden"); + } + }); + + var extract_details = (pubmed_id, details) => { + var months = { + "jan": "January", + "feb": "February", + "mar": "March", + "apr": "April", + "may": "May", + "jun": "June", + "jul": "July", + "aug": "August", + "sep": "September", + "oct": "October", + "nov": "November", + "dec": "December" + }; + var _date = details[pubmed_id].pubdate.split(" "); + return { + "authors": details[pubmed_id].authors.map((authobj) => { + return authobj.name; + }), + "title": details[pubmed_id].title, + "journal": details[pubmed_id].fulljournalname, + "volume": details[pubmed_id].volume, + "pages": details[pubmed_id].pages, + "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan", + "year": _date[0], + }; + }; + + var update_publication_details = (details) => { + Object.entries(details).forEach((entry) => {; + switch(entry[0]) { + case "authors": + $("#txt-publication-authors").val(entry[1].join(", ")); + break; + case "month": + $("#select-publication-month") + .children("option") + .each((index, child) => { + child.selected = child.value == entry[1].toLowerCase(); + }); + default: + $("#txt-publication-" + entry[0]).val(entry[1]); + break; + } + }); + }; + + var fetch_publication_abstract = (pubmed_id, pub_details) => { + $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", + { + "method": "GET", + "data": { + "db": "pubmed", + "id": pubmed_id, + "rettype": "abstract", + "retmode": "xml" + }, + "success": (data, textStatus, jqXHR) => { + update_publication_details({ + ...pub_details, + ...{ + "abstract": Array.from(data + .getElementsByTagName( + "Abstract")[0] + .children) + .map((elt) => {return elt.textContent.trim();}) + .join("\r\n") + }}); + }, + "error": (jqXHR, textStatus, errorThrown) => {}, + "complete": (jqXHR, textStatus) => {}, + "dataType": "xml" + }); + }; + + var fetch_publication_details = (pubmed_id, complete_thunks) => { + error_display = $("#search-pubmed-id-error"); + error_display.text(""); + add_class(error_display, "hidden"); + $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", + { + "method": "GET", + "data": {"db": "pubmed", "id": pubmed_id, "format": "json"}, + "success": (data, textStatus, jqXHR) => { + // process and update publication details + hasError = ( + Object.hasOwn(data, "error") || + Object.hasOwn(data.result[pubmed_id], "error")); + if(hasError) { + error_display.text( + "There was an error fetching a publication with " + + "the given PubMed ID! The error received " + + "was: '" + ( + data.error || + data.result[pubmed_id].error) + + "'. Please check ID you provided and try " + + "again."); + remove_class(error_display, "hidden"); + } else { + fetch_publication_abstract( + pubmed_id, + extract_details(pubmed_id, data.result)); + } + }, + "error": (jqXHR, textStatus, errorThrown) => {}, + "complete": () => { + complete_thunks.forEach((thunk) => {thunk()}); + }, + "dataType": "json" + }); + }; + + $("#btn-search-pubmed-id").on("click", (event) => { + event.preventDefault(); + var search_button = event.target; + var pubmed_id = $("#txt-pubmed-id").val().trim(); + remove_class($("#txt-pubmed-id").parent(), "has-error"); + if(pubmed_id == "") { + add_class($("#txt-pubmed-id").parent(), "has-error"); + return false; + } + + search_button.disabled = true; + // Fetch publication details + fetch_publication_details(pubmed_id, + [() => {search_button.disabled = false;}]); + return false; + }); +</script> + +{%block more_javascript%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html new file mode 100644 index 0000000..7f8d8b0 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -0,0 +1,732 @@ +{%extends "phenotypes/add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} +{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} +{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block frm_add_phenotypes_documentation%} +<p>This page will allow you to upload all the separate files that make up your + phenotypes. Here, you will have to upload each separate file individually. If + you want instead to upload all your files as a single ZIP file, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + use_bundle=true)}}" + title="">click here</a>.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<fieldset id="fldset-file-metadata"> + <legend>File(s) Metadata</legend> + <div class="form-group"> + <label for="txt-file-separator" class="form-label">File Separator</label> + <div class="input-group"> + <input id="txt-file-separator" + name="file-separator" + type="text" + value="	" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + Provide the character that separates the fields in your file(s). It should + be the same character for all files (if more than one is provided).<br /> + A tab character will be assumed if you leave this field blank. See + <a href="#docs-file-separator" + title="Documentation for file-separator characters"> + documentation for more information</a>. + </span> + </div> + + <div class="form-group"> + <label for="txt-file-comment-character" class="form-label">File Comment-Character</label> + <div class="input-group"> + <input id="txt-file-comment-character" + name="file-comment-character" + type="text" + value="#" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-comment-character" class="btn btn-info"> + Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies that lines that begin with the character provided will be + considered comment lines and ignored in their entirety. See + <a href="#docs-file-comment-character" + title="Documentation for comment characters"> + documentation for more information</a>. + </span> + </div> + + <div class="form-group"> + <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label> + <div class="input-group"> + <input id="txt-file-na" + name="file-na" + type="text" + value="- NA N/A" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button> + </span> + </div> + <span class="form-text text-muted"> + This specifies strings in your file indicate that there is no value for a + particular cell (a cell is where a column and row intersect). Provide a + space-separated list of strings if you have more than one way of + indicating no values. See + <a href="#docs-file-na" title="Documentation for no-value fields"> + documentation for more information</a>.</span> + </div> +</fieldset> + +<fieldset id="fldset-data-files"> + <legend>Data File(s)</legend> + + <div class="form-group non-resumable-elements"> + <label for="finput-phenotype-descriptions" class="form-label"> + Phenotype Descriptions</label> + <input id="finput-phenotype-descriptions" + name="phenotype-descriptions" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-desc" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype descriptions, + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-descriptions", + "phenotype descriptions", + '<p>You can drop a CSV file that contains the phenotype descriptions here, + or you can click the "Browse" button (below and to the right) to select it + from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + "Phenotypes Descriptions" documentation</a> section below.</p>')}} + + + <div class="form-group non-resumable-elements"> + <label for="finput-phenotype-data" class="form-label">Phenotype Data</label> + <input id="finput-phenotype-data" + name="phenotype-data" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-data" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the phenotype data. See + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + the documentation for the expected format of the file</a>.</span> + </div> + + {{display_resumable_elements( + "resumable-phenotype-data", + "phenotype data", + '<p>You can drop a CSV file that contains the phenotype data here, + or you can click the "Browse" button (below and to the right) to select it + from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} + + {%if population.Family in families_with_se_and_n%} + <div class="form-group non-resumable-elements"> + <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label> + <input id="finput-phenotype-se" + name="phenotype-se" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-se" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the standard errors for the phenotypes, + computed from the data above.</span> + </div> + {{display_resumable_elements( + "resumable-phenotype-se", + "standard errors", + '<p>You can drop a CSV file that contains the computed standard-errors data + here, or you can click the "Browse" button (below and to the right) to + select it from your computer.</p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} + + + <div class="form-group non-resumable-elements"> + <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label> + <input id="finput-phenotype-n" + name="phenotype-n" + class="form-control" + type="file" + data-preview-table="tbl-preview-pheno-n" + required="required" /> + <span class="form-text text-muted"> + Provide a file that contains only the number of samples/individuals used in + the computation of the standard errors above.</span> + </div> + {{display_resumable_elements( + "resumable-phenotype-n", + "number of samples/individuals", + '<p>You can drop a CSV file that contains the number of samples/individuals + used in computation of the standard-errors here, or you can click the + "Browse" button (below and to the right) to select it from your computer. + </p> + <p>The CSV file must conform to some standards, as documented in the + <a href="#docs-file-phenotype-n" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below.</p>')}} +</fieldset> +{%endif%} +{%endblock%} + + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="docs-help">Help</h2> + <h3 class="subheading">Common Features</h3> + <p>The following are the common expectations for <strong>ALL</strong> the + files provided in the form above: + <ul> + <li>The file <strong>MUST</strong> be character-separated values (CSV) + text file</li> + <li>The first row in the file <strong>MUST</strong> be a heading row, and + will be composed of the list identifiers for all of + samples/individuals/cases involved in your study.</li> + <li>The first column of data in the file <strong>MUST</strong> be the + identifiers for all of the phenotypes you wish to upload.</li> + </ul> + </p> + + <p>If you do not specify the separator character, then we will assume a + <strong>TAB</strong> character was used as your separator.</p> + + <p>We also assume you might include comments lines in your files. In that + case, if you do not specify what character denotes that a line in your files + is a comment line, we will assume the <strong>#</strong> character.<br /> + A comment <strong>MUST ALWAYS</strong> begin at the start of the line marked + with the comment character specified.</p> + + <h3 class="subheading" id="docs-file-metadata">File Metadata</h3> + <p>We request some details about your files to help us parse and process the + files correctly. The details we collect are:</p> + <dl> + <dt id="docs-file-separator">File separator</dt> + <dd>The files you provide should be character-separated value (CSV) files. + We need to know what character you used to separate the values in your + file. Some common ones are the Tab character, the comma, etc.<br /> + Providing that information makes it possible for the system to parse and + process your files correctly.<br> + <strong>NOTE:</strong> All the files you upload MUST use the same + separator.</dd> + + <dt id="docs-file-comment-character">Comment character</dt> + <dd>We support use of comment lines in your files. We only support one type + of comment style, the <em>line comment</em>.<br /> + This mean the comment begins at the start of the line, and the end of that + line indicates the end of that comment. If you have a really long comment, + then you need to break it across multiple lines, marking each line a + comment line.<br /> + The "comment character" is the character at the start of the line that + indicates that the line is a line comment.</dd> + + <dt id="docs-file-na">No-Value indicator(s)</dt> + <dd>Data in the real world is messy, and in some cases, entirely absent. You + need to indicate, in your files, that a particular field did not have a + value, and once you do that, you then need to let the system know how you + mark such fields. Common ways of indicating "empty values" are, leaving + the field blank, using a character such as '-', or using strings like + "NA", "N/A", "NULL", etc.<br /> + Providing this information will help with parsing and processing such + no-value fields the correct way.</dd> + </dl> + + <h3 class="subheading" id="docs-file-phenotype-description"> + file: Phenotypes Descriptions</h3> + <p>The data in this file is a matrix of <em>phenotypes × metadata-fields</em>. + Please note we use the term "metadata-fields" above loosely, due to lack of + a good word for this.</p> + <p>The file <strong>MUST</strong> have columns in this order: + <dl> + <dt>Phenotype Identifiers</dt> + <dd>These are the names/identifiers for your phenotypes. These + names/identifiers are the same ones you will have in all the other files you are + uploading.</dd> + + <dt>Descriptions</dt> + <dd>Each phenotype will need a description. Good description are necessary + to inform other people of what the data is about. Good description are + hard to construct, so we provide + <a href="https://info.genenetwork.org/faq.php#q-22" + title="How to write phenotype descriptions"> + advice on describing your phenotypes.</a></dd> + + <dt>Units</dt> + <dd>Each phenotype will need units for the measurements taken. If there are + none, then indicate the field is a no-value field.</dd> + </dl></p> + <p>You can add more columns after those three if you want to, but these 3 + <strong>MUST</strong> be present.</p> + <p>The file would, for example, look like the following:</p> + <code>id,description,units,…<br /> + pheno10001|Central nervous system, behavior, cognition; …|mg|…<br /> + pheno10002|Aging, metabolism, central nervous system: …|mg|…<br /> + â‹®<br /></code> + + <p><strong>Note 01</strong>: The first usable row is the heading row.</p> + <p><strong>Note 02: </strong>This example demonstrates a subtle issue that + could make your CSV file invalid — the choice of your field separator + character.<br > + In the example above, we use the pipe character (<code>|</code>) as our + field separator. This is because, if we follow the advice on how to write + good descriptions, then we cannot use the comma as our separator – if + we did, then our CSV file would be invalid because the system would have no + way to tell the difference between the comma as a field separator, and the + comma as a way to separate the "general category and ontology terms".</p> + + <h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3> + <span id="docs-file-phenotype-data"></span> + <span id="docs-file-phenotype-se"></span> + <span id="docs-file-phenotype-n"></span> + <p>The data is a matrix of <em>phenotypes × individuals</em>, e.g.</p> + <code> + # num-cases: 2549 + # num-phenos: 13 + id,IND001,IND002,IND003,IND004,…<br /> + pheno10001,61.400002,54.099998,483,49.799999,…<br /> + pheno10002,49,50.099998,403,45.5,…<br /> + pheno10003,62.5,53.299999,501,62.900002,…<br /> + pheno10004,53.099998,55.099998,403,NA,…<br /> + â‹®<br /></code> + + <p>where <code>IND001,IND002,IND003,IND004,…</code> are the + samples/individuals/cases in your study, and + <code>pheno10001,pheno10002,pheno10004,pheno10004,…</code> are the + identifiers for your phenotypes.</p> + <p>The lines beginning with the "<em>#</em>" symbol (i.e. + <code># num-cases: 2549</code> and <code># num-phenos: 13</code> are comment + lines and will be ignored</p> + <p>In this example, the comma (,) is used as the file separator.</p> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_preview_table("tbl-preview-pheno-desc", "descriptions")}} +{{display_preview_table("tbl-preview-pheno-data", "data")}} +{%if population.Family in families_with_se_and_n%} +{{display_preview_table("tbl-preview-pheno-se", "standard errors")}} +{{display_preview_table("tbl-preview-pheno-n", "number of samples")}} +{%endif%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block more_javascript%} +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script type="text/javascript" src="/static/js/files.js"></script> + +<script type="text/javascript"> + $("#btn-reset-file-separator").on("click", (event) => { + event.preventDefault(); + $("#txt-file-separator").val("\t"); + $("#txt-file-separator").trigger("change"); + }); + $("#btn-reset-file-comment-character").on("click", (event) => { + event.preventDefault(); + $("#txt-file-comment-character").val("#"); + $("#txt-file-comment-character").trigger("change"); + }); + $("#btn-reset-file-na").on("click", (event) => { + event.preventDefault(); + $("#txt-file-na").val("- NA N/A"); + $("#txt-file-na").trigger("change"); + }); + + var update_preview = (table, filedata, formdata, numrows) => { + table.find("thead tr").remove() + table.find(".data-row").remove(); + var linenum = 0; + var tableheader = table.find("thead"); + var tablebody = table.find("tbody"); + var numheadings = 0; + var navalues = formdata + .na_strings + .split(" ") + .map((v) => {return v.trim();}) + .filter((v) => {return Boolean(v);}); + filedata.forEach((line) => { + if(line.startsWith(formdata.comment_char) || linenum >= numrows) { + return false; + } + var row = $("<tr></tr>"); + line.split(formdata.separator) + .map((field) => { + var value = field.trim(); + if(navalues.includes(value)) { + return "⋘NULâ‹™"; + } + return value; + }) + .filter((field) => { + return (field !== "" && field != undefined && field != null); + }) + .forEach((field) => { + if(linenum == 0) { + numheadings += 1; + var tablefield = $("<th></th>"); + tablefield.text(field); + row.append(tablefield); + } else { + add_class(row, "data-row"); + var tablefield = $("<td></td>"); + tablefield.text(field); + row.append(tablefield); + } + }); + + if(linenum == 0) { + tableheader.append(row); + } else { + tablebody.append(row); + } + linenum += 1; + }); + + if(table.find("tbody tr.data-row").length > 0) { + add_class(table.find(".data-row-template"), "hidden"); + } else { + remove_class(table.find(".data-row-template"), "hidden"); + } + }; + + var makePreviewUpdater = (preview_table) => { + return (data) => { + update_preview( + preview_table, + data, + filesMetadata(), + PREVIEW_ROWS); + }; + }; + + var preview_tables_to_elements_map = { + "#tbl-preview-pheno-desc": "#finput-phenotype-descriptions", + "#tbl-preview-pheno-data": "#finput-phenotype-data", + "#tbl-preview-pheno-se": "#finput-phenotype-se", + "#tbl-preview-pheno-n": "#finput-phenotype-n" + }; + + var filesMetadata = () => { + return { + "separator": $("#txt-file-separator").val(), + "comment_char": $( + "#txt-file-comment-character").val(), + "na_strings": $("#txt-file-na").val() + } + }; + + var PREVIEW_ROWS = 5; + + var handler_update_previews = (event) => { + Object.entries(preview_tables_to_elements_map).forEach((mapentry) => { + var preview_table = $(mapentry[0]); + var file_input = $(mapentry[1]); + if(file_input.length === 1) { + readFirstNLines( + file_input[0].files[0], + 10, + [makePreviewUpdater(preview_table)]); + } + }); + }; + + [ + "#txt-file-separator", + "#txt-file-comment-character", + "#txt-file-na" + ].forEach((elementid) => { + $(elementid).on("change", handler_update_previews); + }); + + [ + "#finput-phenotype-descriptions", + "#finput-phenotype-data", + "#finput-phenotype-se", + "#finput-phenotype-n" + ].forEach((elementid) => { + $(elementid).on("change", (event) => { + readFirstNLines( + event.target.files[0], + 10, + [makePreviewUpdater( + $("#" + event.target.getAttribute("data-preview-table")))]); + }); + }); + + + var resumableDisplayFiles = (display_area, files) => { + files.forEach((file) => { + display_area.find(".file-display").remove(); + var display_element = display_area + .find(".file-display-template") + .clone(); + remove_class(display_element, "hidden"); + remove_class(display_element, "file-display-template"); + add_class(display_element, "file-display"); + display_element.find(".filename").text(file.name + || file.fileName + || file.relativePath + || file.webkitRelativePath); + display_element.find(".filesize").text( + (file.size / (1024*1024)).toFixed(2) + "MB"); + display_element.find(".fileuniqueid").text(file.uniqueIdentifier); + display_element.find(".filemimetype").text(file.file.type); + display_area.append(display_element); + }); + }; + + + var indicateProgress = (resumable, progress_bar) => { + return () => {/*Has no event!*/ + var progress = (resumable.progress() * 100).toFixed(2); + var pbar = progress_bar.find(".progress-bar"); + remove_class(progress_bar, "hidden"); + pbar.css("width", progress+"%"); + pbar.attr("aria-valuenow", progress); + pbar.text("Uploading: " + progress + "%"); + }; + }; + + var retryUpload = (retry_button, cancel_button) => { + retry_button.on("click", (event) => { + resumable.files.forEach((file) => {file.retry();}); + add_class(retry_button, "hidden"); + remove_class(cancel_button, "hidden"); + add_class(browse_button, "hidden"); + }); + }; + + var cancelUpload = (cancel_button, retry_button) => { + cancel_button.on("click", (event) => { + resumable.files.forEach((file) => { + if(file.isUploading()) { + file.abort(); + } + }); + add_class(cancel_button, "hidden"); + remove_class(retry_button, "hidden"); + remove_class(browse_button, "hidden"); + }); + }; + + + var startUpload = (browse_button, retry_button, cancel_button) => { + return (event) => { + remove_class(cancel_button, "hidden"); + add_class(retry_button, "hidden"); + add_class(browse_button, "hidden"); + }; + }; + + var processForm = (form) => { + var formdata = new FormData(form); + uploaded_files.forEach((msg) => { + formdata.delete(msg["file-input-name"]); + formdata.append(msg["file-input-name"], JSON.stringify({ + "uploaded-file": msg["uploaded-file"], + "original-name": msg["original-name"] + })); + }); + formdata.append("resumable-upload", "true"); + return formdata; + } + + var uploaded_files = new Set(); + var submitForm = (new_file) => { + uploaded_files.add(new_file); + if(uploaded_files.size === resumables.length) { + var form = $("#frm-add-phenotypes"); + if(form.length !== 1) { + // TODO: Handle error somehow? + alert("Could not find form!!!"); + return false; + } + + $.ajax({ + "url": form.attr("action"), + "type": "POST", + "data": processForm(form[0]), + "processData": false, + "contentType": false, + "success": (data, textstatus, jqxhr) => { + // TODO: Redirect to endpoint that should come as part of the + // success/error message. + console.log("SUCCESS DATA: ", data); + console.log("SUCCESS STATUS: ", textstatus); + console.log("SUCCESS jqXHR: ", jqxhr); + window.location.assign(window.location.origin + data["redirect-to"]); + }, + }); + return false; + } + return false; + }; + + var uploadSuccess = (file_input_name) => { + return (file, message) => { + submitForm({...JSON.parse(message), "file-input-name": file_input_name}); + }; + }; + + + var uploadError = () => { + return (message, file) => { + $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled"); + console.log("THE FILE:", file); + console.log("THE ERROR MESSAGE:", message); + }; + }; + + + + var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id) => { + var the_form = $("#" + form_id); + var file_input = $("#" + file_input_id); + var submit_button = the_form.find("input[type=submit]"); + if(file_input.length != 1) { + return false; + } + var r = errorHandler( + fileSuccessHandler( + uploadStartHandler( + filesAddedHandler( + markResumableDragAndDropElement( + makeResumableElement( + the_form.attr("data-resumable-target"), + file_input.parent(), + $("#" + resumable_element_id), + submit_button, + ["csv", "tsv"]), + file_input.parent(), + $("#" + resumable_element_id), + $("#" + resumable_element_id + "-browse-button")), + (files) => { + // TODO: Also trigger preview! + resumableDisplayFiles( + $("#" + resumable_element_id + "-selected-files"), files); + files.forEach((file) => { + readFirstNLines( + file.file, + 10, + [makePreviewUpdater( + $("#" + preview_table_id))]) + }); + }), + startUpload($("#" + resumable_element_id + "-browse-button"), + $("#" + resumable_element_id + "-retry-button"), + $("#" + resumable_element_id + "-cancel-button"))), + uploadSuccess(file_input.attr("name"))), + uploadError()); + + /** Setup progress indicator **/ + progressHandler( + r, + indicateProgress(r, $("#" + resumable_element_id + "-progress-bar"))); + + return r; + }; + + var resumables = [ + ["frm-add-phenotypes", "finput-phenotype-descriptions", "resumable-phenotype-descriptions", "tbl-preview-pheno-desc"], + ["frm-add-phenotypes", "finput-phenotype-data", "resumable-phenotype-data", "tbl-preview-pheno-data"], + ["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"], + ["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"], + ].map((row) => { + return makeResumableObject(row[0], row[1], row[2], row[3]); + }).filter((val) => { + return Boolean(val); + }); + + $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { + event.preventDefault(); + // TODO: Check all the relevant files exist + // TODO: Verify that files are not duplicated + var filenames = []; + var nondupfiles = []; + resumables.forEach((r) => { + var fname = r.files[0].file.name; + filenames.push(fname); + if(!nondupfiles.includes(fname)) { + nondupfiles.push(fname); + } + }); + + // Check that all files were provided + if(resumables.length !== filenames.length) { + window.alert("You MUST provide all the files requested."); + event.target.removeAttribute("disabled"); + return false; + } + + // Check that there are no duplicate files + var duplicates = Object.entries(filenames.reduce( + (acc, curr, idx, arr) => { + acc[curr] = (acc[curr] || 0) + 1; + return acc; + }, + {})).filter((entry) => {return entry[1] !== 1;}); + if(duplicates.length > 0) { + var msg = "The file(s):\r\n"; + msg = msg + duplicates.reduce( + (msgstr, afile) => { + return msgstr + " • " + afile[0] + "\r\n"; + }, + ""); + msg = msg + "is(are) duplicated. Please fix and try again."; + window.alert(msg); + event.target.removeAttribute("disabled"); + return false; + } + // TODO: Check all fields + // Start the uploads. + event.target.setAttribute("disabled", "disabled"); + resumables.forEach((r) => {r.upload();}); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html new file mode 100644 index 0000000..898fc0c --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -0,0 +1,207 @@ +{%extends "phenotypes/add-phenotypes-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">Add Phenotypes</a> +</li> +{%endblock%} + +{%block frm_add_phenotypes_documentation%} +<p>Select the zip file bundle containing information on the phenotypes you + wish to upload, then click the "Upload Phenotypes" button below to + upload the data.</p> +<p>If you wish to upload the files individually instead, + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="">click here</a>.</p> +<p>See the <a href="#section-file-formats">File Formats</a> section below + to get an understanding of what is expected of the bundle files you + upload.</p> +{%endblock%} + +{%block frm_add_phenotypes_elements%} +<div class="form-group"> + <label for="finput-phenotypes-bundle" class="form-label"> + Phenotypes Bundle</label> + <input type="file" + id="finput-phenotypes-bundle" + name="phenotypes-bundle" + accept="application/zip, .zip" + required="required" + class="form-control" /> +</div> +{%endblock%} + +{%block page_documentation%} +<div class="row"> + <h2 class="heading" id="section-file-formats">File Formats</h2> + <p>We accept an extended form of the + <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files" + title="R/qtl2 software input file format documentation"> + input files' format used with the R/qtl2 software</a> as a single ZIP + file</p> + <p>The files that are used for this feature are: + <ul> + <li>the <em>control</em> file</li> + <li><em>pheno</em> file(s)</li> + <li><em>phenocovar</em> file(s)</li> + <li><em>phenose</em> files(s)</li> + </ul> + </p> + <p>Other files within the bundle will be ignored, for this feature.</p> + <p>The following section will detail the expectations for each of the + different file types within the uploaded ZIP file bundle for phenotypes:</p> + + <h3 class="subheading">Control File</h3> + <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts + as the control file. This file can be: + <ul> + <li>a <em>JSON</em> file, or</li> + <li>a <em>YAML</em> file.</li> + </ul> + </p> + + <p>The control file is useful for defining things about the bundle such as:</p> + <ul> + <li>The field separator value (default: <code>sep: ','</code>). There can + only ever be one field separator and it <strong>MUST</strong> be the same + one for <strong>ALL</strong> files in the bundle.</li> + <li>The comment character (default: <code>comment.char: '#'</code>). Any + line that starts with this character will be considered a comment line and + be ignored in its entirety.</li> + <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You + can specify more than one code to indicate missing values, e.g. + <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li> + </ul> + + <h3 class="subheading"><em>pheno</em> File(s)</h3> + <p>These files are the main data files. You must have at least one of these + files in your bundle for it to be valid for this step.</p> + <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as + below:<br /> + <code> + id,10001,10002,10003,10004,…<br /> + BXD1,61.400002,54.099998,483,49.799999,…<br /> + BXD2,49,50.099998,403,45.5,…<br /> + BXD5,62.5,53.299999,501,62.900002,…<br /> + BXD6,53.099998,55.099998,403,NA,…<br /> + â‹®<br /></code> + </p> + <p>If the <code>pheno_transposed</code> value is set to <code>True</code>, + then the data will be a <em>phenotypes × individuals</em> matrix as in the + example below:<br /> + <code> + id,BXD1,BXD2,BXD5,BXD6,…<br /> + 10001,61.400002,49,62.5,53.099998,…<br /> + 10002,54.099998,50.099998,53.299999,55.099998,…<br /> + 10003,483,403,501,403,…<br /> + 10004,49.799999,45.5,62.900002,NA,…<br /> + â‹® + </code> + </p> + + + <h3 class="subheading"><em>phenocovar</em> File(s)</h3> + <p>At least one phenotypes metadata file with the metadata values such as + descriptions, PubMed Identifier, publication titles (if present), etc.</p> + <p>The data in this/these file(s) is a matrix of + <em>phenotypes × phenotypes-covariates</em>. The first column is always the + phenotype names/identifiers — same as in the R/qtl2 format.</p> + <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p> + <p>This file <strong>MUST</strong> be present in the bundle, and have data for + the bundle to be considered valid by our system for this step.<br /> + In addition to that, the following are the fields that <strong>must be + present</strong>, and + have values, in the file before the file is considered valid: + <ul> + <li><em>description</em>: A description for each phenotype. Useful + for users to know what the phenotype is about.</li> + <li><em>units</em>: The units of measurement for the phenotype, + e.g. milligrams for brain weight, centimetres/millimetres for + tail-length, etc.</li> + </ul></p> + + <p>The following <em>optional</em> fields can also be provided: + <ul> + <li><em>pubmedid</em>: A PubMed Identifier for the publication where + the phenotype is published. If this field is not provided, the system will + assume your phenotype is not published.</li> + </ul> + </p> + <p>These files will be marked up in the control file with the + <code>phenocovar</code> key, as in the examples below: + <ol> + <li>JSON: single file<br /> + <code>{<br /> + â‹®,<br /> + "phenocovar": "your_covariates_file.csv",<br /> + â‹®<br /> + } + </code> + </li> + <li>JSON: multiple files<br /> + <code>{<br /> + â‹®,<br /> + "phenocovar": [<br /> + "covariates_file_01.csv",<br /> + "covariates_file_01.csv",<br /> + â‹®<br /> + ],<br /> + â‹®<br /> + } + </code> + </li> + <li>YAML: single file or<br /> + <code> + â‹®<br /> + phenocovar: your_covariates_file.csv<br /> + â‹® + </code> + </li> + <li>YAML: multiple files<br /> + <code> + â‹®<br /> + phenocovar:<br /> + - covariates_file_01.csv<br /> + - covariates_file_02.csv<br /> + - covariates_file_03.csv<br /> + …<br /> + â‹® + </code> + </li> + </ol> + </p> + + <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3> + <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are + not supported by the original R/qtl2 file format</p> + <p>We use these files to upload the standard errors (<em>phenose</em>) when + the data file (<em>pheno</em>) is average data. In that case, the + <em>phenonum</em> file(s) contains the number of individuals that were + involved when computing the averages.</p> + <p>Both types of files are matrices of <em>individuals × phenotypes</em> by + default. Like the related <em>pheno</em> files, if + <code>pheno_transposed: True</code>, then the file will be a matrix of + <em>phenotypes × individuals</em>.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html new file mode 100644 index 0000000..adbc012 --- /dev/null +++ b/uploader/templates/phenotypes/base.html @@ -0,0 +1,19 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + {%if dataset is mapping%} + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a> + {%else%} + <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a> + {%endif%} +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html new file mode 100644 index 0000000..8e45491 --- /dev/null +++ b/uploader/templates/phenotypes/create-dataset.html @@ -0,0 +1,108 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Create a new phenotype dataset.</p> +</div> + +<div class="row"> + <form id="frm-create-pheno-dataset" + action="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-name">Name</label> + {%if errors["dataset-name"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-name"]}}</p></small> + {%endif%} + <input type="text" + name="dataset-name" + id="txt-dataset-name" + value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}" + {%if errors["dataset-name"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A short representative name for the dataset.</p> + <p>Recommended: Use the population code and append "Publish" at the end. + <br />This field will only accept names composed of + letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-fullname">Full Name</label> + {%if errors["dataset-fullname"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-fullname"]}}</p></small> + {%endif%} + <input id="txt-dataset-fullname" + name="dataset-fullname" + type="text" + value="{{original_formdata.get('dataset-fullname', '')}}" + {%if errors["dataset-fullname"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A longer, descriptive name for the dataset. The name is meant for use + by humans, and therefore, it should be clear what the dataset contains + from the name.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-shortname">Short Name</label> + <input id="txt-dataset-shortname" + name="dataset-shortname" + type="text" + class="form-control" + value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" /> + <small class="form-text text-muted"> + <p>An optional, short name for the dataset. <br /> + If this is not provided, it will default to the value provided for the + <strong>Name</strong> field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create phenotype dataset" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html new file mode 100644 index 0000000..32c903f --- /dev/null +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -0,0 +1,332 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="edit-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">edit phenotype data</h2> + <p>The forms provided in this page help you update the data for the + phenotypes, and the publication information for the phenotype, + respectively.</p> +</div> + +<div class="row"> + <h3 class="subheading">Basic metadata</h3> + <form name="frm-phenotype-basic-metadata" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" /> + <div class="form-group"> + <label for="txt-pre-publication-description" + class="control-label col-sm-2">Pre-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-description" + name="pre-publication-description" + class="form-control" + value="{{phenotype['Pre_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-pre-publication-abbreviation" + class="control-label col-sm-2">Pre-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-abbreviation" + name="pre-publication-abbreviation" + class="form-control" + value="{{phenotype['Pre_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-description" + class="control-label col-sm-2">Post-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-description" + name="post-publication-description" + class="form-control" + value="{{phenotype['Post_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-abbreviation" + class="control-label col-sm-2">Post-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-abbreviation" + name="post-publication-abbreviation" + class="form-control" + value="{{phenotype['Post_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-original-description" + class="control-label col-sm-2">Original Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-original-description" + name="original-description" + class="form-control" + value="{{phenotype['Original_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-units" + class="control-label col-sm-2">units</label> + <div class="col-sm-10"> + <input type="text" + id="txt-units" + name="units" + class="form-control" + required="required" + value="{{phenotype['Units']}}" /> + </div> + </div> + + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update basic metadata"> + </div> + </div> + </form> +</div> + + +<div class="row"> + <h3 class="subheading">phenotype data</h3> + <form id="frm-edit-phenotype-data" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <div style="max-height: 23.37em;overflow-y: scroll;"> + <table class="table table-striped table-responsive table-form-table"> + <thead style="position: sticky; top: 0;"> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if population.Family in families_with_se_and_n%} + <th>Standard-Error</th> + <th>Number of Samples</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td> + <input type="text" + name="value-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" + class="form-control" /> + <input type="hidden" + name="value-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" /></td> + {%if population.Family in families_with_se_and_n%} + <td> + <input type="text" + name="se-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" + data-original-value="{{item.error or ''}}" + class="form-control" /> + <input type="hidden" + name="se-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" /></td> + <td> + <input type="text" + name="n-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" + data-original-value="{{item.count or "-"}}" + class="form-control" /> + <input type="hidden" + name="n-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" /></td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update data" /> + </div> + </div> + </form> +</div> + + +<div class="row"> + <h3 class="subheading">publication information</h3> + <p>Use the form below to update the publication information for this + phenotype.</p> + <form id="frm-edit-phenotype-pub-data" + class="form-horizontal" + method="POST" + action="#"> + <div class="form-group"> + <label for="txt-pubmed-id" class="control-label col-sm-2">Pubmed ID</label> + <div class="col-sm-10"> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-authors" class="control-label col-sm-2">Authors</label> + <div class="col-sm-10"> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-title" class="control-label col-sm-2"> + Publication Title</label> + <div class="col-sm-10"> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-abstract" class="control-label col-sm-2"> + Publication Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-journal" class="control-label col-sm-2">Journal</label> + <div class="col-sm-10"> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-volume" class="control-label col-sm-2">Volume</label> + <div class="col-sm-10"> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-pages" class="control-label col-sm-2">Pages</label> + <div class="col-sm-10"> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> + </div> + + <div class="form-group"> + <label for="select-publication-month" class="control-label col-sm-2"> + Publication Month</label> + <div class="col-sm-10"> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="control-label col-sm-2">Publication Year</label> + <div class="col-sm-10"> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary not-implemented" + value="update publication" /> + </div> + </div> + </form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html new file mode 100644 index 0000000..689c28e --- /dev/null +++ b/uploader/templates/phenotypes/index.html @@ -0,0 +1,21 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {{select_species_form(url_for("species.populations.phenotypes.index"), species)}} +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html new file mode 100644 index 0000000..12963c1 --- /dev/null +++ b/uploader/templates/phenotypes/job-status.html @@ -0,0 +1,155 @@ +{%extends "phenotypes/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block extrameta%} +{%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} +<meta http-equiv="refresh" content="5" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<h4 class="subheading">Progress</h4> +<div class="row" style="overflow:scroll;"> + <p><strong>Process Status:</strong> {{job.status}}</p> + {%if metadata%} + <table class="table table-responsive"> + <thead> + <tr> + <th>File</th> + <th>Status</th> + <th>Lines Processed</th> + <th>Total Errors</th> + </tr> + </thead> + + <tbody> + {%for file,meta in metadata.items()%} + <tr> + <td>{{file}}</td> + <td>{{meta.status}}</td> + <td>{{meta.linecount}}</td> + <td>{{meta["total-errors"]}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {%if job.status in ("completed:success", "success")%} + <p> + {%if errors | length == 0%} + <a href="{{url_for('species.populations.phenotypes.review_job_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" + class="btn btn-primary" + title="Continue to process data">Continue</a> + {%else%} + <span class="text-muted" + disabled="disabled" + style="border: solid 2px;border-radius: 5px;padding: 0.3em;"> + Cannot continue due to errors. Please fix the errors first. + </span> + {%endif%} + </p> + {%endif%} +</div> + +<h4 class="subheading">Errors</h4> +<div class="row" style="max-height: 20em; overflow: scroll;"> + {%if errors | length == 0 %} + <p class="text-info"> + <span class="glyphicon glyphicon-info-sign"></span> + No errors found so far + </p> + {%else%} + <table class="table table-responsive"> + <thead style="position: sticky; top: 0; background: white;"> + <tr> + <th>File</th> + <th>Row</th> + <th>Column</th> + <th>Value</th> + <th>Message</th> + </tr> + </thead> + + <tbody style="font-size: 0.9em;"> + {%for error in errors%} + <tr> + <td>{{error.filename}}</td> + <td>{{error.rowtitle}}</td> + <td>{{error.coltitle}}</td> + <td>{%if error.cellvalue | length > 25%} + {{error.cellvalue[0:24]}}… + {%else%} + {{error.cellvalue}} + {%endif%} + </td> + <td> + {%if error.message | length > 250 %} + {{error.message[0:249]}}… + {%else%} + {{error.message}} + {%endif%} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} +</div> + +<div class="row"> + {{cli_output(job, "stdout")}} +</div> + +<div class="row"> + {{cli_output(job, "stderr")}} +</div> + +{%else%} +<div class="row"> + <h3 class="text-danger">No Such Job</h3> + <p>Could not find a job with the ID: {{job_id}}</p> + <p> + Please go back to + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="'{{dataset.Name}}' dataset page"> + the '{{dataset.Name}}' dataset page</a> + to upload new phenotypes or edit existing ones.</p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html new file mode 100644 index 0000000..2cf2c7f --- /dev/null +++ b/uploader/templates/phenotypes/list-datasets.html @@ -0,0 +1,68 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-datasets"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}">List Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {%if datasets | length > 0%} + <p>The dataset(s) available for this population is/are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + {%for dataset in datasets%} + <tr> + <td><a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p>Phenotypes need to go into a dataset. We do not currently have a dataset + for species <strong>'{{species["FullName"]}} ({{species["Name"]}})'</strong> + phenotypes.</p> + + <p>Do, please, create a new dataset by clicking on the "Create Dataset" button + below and following the prompts/instructions.</p> + <p><a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + class="btn btn-primary" + title="Create a new phenotype dataset.">create dataset</a></p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html new file mode 100644 index 0000000..11b108b --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -0,0 +1,31 @@ +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%macro display_pheno_dataset_card(species, population, dataset)%} +{{display_population_card(species, population)}} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Phenotypes' Dataset</h5> + <div class="card-text"> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{dataset.Name}}</td> + </tr> + + <tr> + <td>Full Name</td> + <td>{{dataset.FullName}}</td> + </tr> + + <tr> + <td>Short Name</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html new file mode 100644 index 0000000..f54c53e --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -0,0 +1,21 @@ +{%macro display_preview_table(tableid, filetype)%} +<div class="card" style="max-width: 676px;"> + <div class="card-body"> + <h5 class="card-title">Phenotypes '{{filetype | title}}' File Preview</h5> + <div class="card-text" style="overflow: scroll;"> + <table id="{{tableid}}" class="table table-condensed table-responsive"> + <thead> + <tr> + </tr> + <tbody> + <tr> + <td class="data-row-template text-info"> + Provide a phenotype '{{filetype | lower}}' file to preview. + </td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html new file mode 100644 index 0000000..b0bf1b5 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html @@ -0,0 +1,60 @@ +{%macro display_resumable_elements(id, title, help)%} +<div id="{{id}}" + class="resumable-elements hidden" + style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;"> + <strong style="line-height: 1.2em;">{{title | title}}</strong> + + <span class="form-text text-muted">{{help | safe}}</span> + + <div id="{{id}}-selected-files" + class="resumable-selected-files" + style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"> + <div class="panel panel-info file-display-template hidden"> + <div class="panel-heading filename">The Filename Goes Here!</div> + <div class="panel-body"> + <ul> + <li> + <strong>Name</strong>: + <span class="filename">the file's name</span></li> + + <li><strong>Size</strong>: <span class="filesize">0 MB</span></li> + + <li> + <strong>Unique Identifier</strong>: + <span class="fileuniqueid">brrr</span></li> + + <li> + <strong>Mime</strong>: + <span class="filemimetype">text/csv</span></li> + </ul> + </div> + </div> + </div> + + <a id="{{id}}-browse-button" + class="resumable-browse-button btn btn-info" + href="#" + style="margin-left: 80%;">Browse</a> + + <div id="{{id}}-progress-bar" class="progress hidden"> + <div class="progress-bar" + role="progress-bar" + aria-valuenow="60" + aria-valuemin="0" + aria-valuemax="100" + style="width: 0%;"> + Uploading: 60% + </div> + </div> + + <div id="{{id}}-cancel-resume-buttons"> + <a id="{{id}}-resume-button" + class="resumable-resume-button btn btn-info hidden" + href="#">resume upload</a> + + <a id="{{id}}-cancel-button" + class="resumable-cancel-button btn btn-danger hidden" + href="#">cancel upload</a> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html new file mode 100644 index 0000000..7bc8c62 --- /dev/null +++ b/uploader/templates/phenotypes/review-job-data.html @@ -0,0 +1,101 @@ +{%extends "phenotypes/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block extrameta%} +{%if not job%} +<meta http-equiv="refresh" + content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<div class="row"> + <h3 class="heading">Data Review</h3> + <p>The “<strong>{{dataset.FullName}}</strong>” dataset from the + “<strong>{{population.FullName}}</strong>” population of the + species “<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>” + will be updated as follows:</p> + + {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} + {%if summary.get(ftype, False)%} + <ul> + <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed + adding {%if ftype == "phenocovar"%}(possibly){%endif%} + {{summary[ftype]["total-data-rows"]}} new + {%if ftype == "phenocovar"%} + phenotypes + {%else%} + {{summary[ftype]["description"]}} rows + {%endif%} + to the database. + </li> + </ul> + {%endif%} + {%endfor%} + + <a href="#" class="not-implemented btn btn-primary">continue</a> +</div> +{%else%} +<div class="row"> + <h4 class="subheading">Invalid Job</h3> + <p class="text-danger"> + Could not find a job with the ID: <strong>{{job_id}}.</p> + <p>You will be redirected in + <span id="countdown-element" class="text-info">20</span> second(s)</p> + <p class="text-muted"> + <small> + If you are not redirected, please + <a href="{{url_for( + 'species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">click here</a> to continue + </small> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(document).ready(function() { + var countdown = 20; + var countdown_element = $("#countdown-element"); + if(countdown_element.length === 1) { + intv = window.setInterval(function() { + countdown = countdown - 1; + countdown_element.html(countdown); + }, 1000); + } + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/select-population.html b/uploader/templates/phenotypes/select-population.html new file mode 100644 index 0000000..cea0806 --- /dev/null +++ b/uploader/templates/phenotypes/select-population.html @@ -0,0 +1,31 @@ +{%extends "phenotypes/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%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + + +<div class="row"> + {{select_population_form(url_for("species.populations.phenotypes.select_population", species_id=species.SpeciesId), species, populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +<script type="text/javascript"> + $(function() { + populationDataTable(JSON.parse($("#tbl-select-population").attr("data-populations-list"))); + }); + </script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html new file mode 100644 index 0000000..c896214 --- /dev/null +++ b/uploader/templates/phenotypes/view-dataset.html @@ -0,0 +1,123 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>The basic dataset details are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row"> + <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a></p> +</div> + +<div class="row"> + <h2>Phenotype Data</h2> + + <p>Click on any of the phenotypes in the table below to view and edit that + phenotype's data.</p> + <p>Use the search to filter through all the phenotypes and find specific + phenotypes of interest.</p> + + <table id="tbl-phenotypes-list" class="table compact stripe"> + <thead> + <tr> + <th></th> + <th>Record</th> + <th>Description</th> + </tr> + </thead> + + <tbody></tbody> + </table> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var data = {{phenotypes | tojson}}; + $("#tbl-phenotypes-list").DataTable({ + responsive: true, + lengthMenu: [10, 25, 50, 100, 1000, data.length], + language: { + processing: "Processing results… Please wait.", + loadingRecord: "Loading phenotypes — Please wait.", + info: "_START_ to _END_ of _TOTAL_ phenotypes", + lengthMenu: "Show _MENU_ phenotypes", + }, + data: data, + columns: [ + {data: "sequence_number"}, + { + data: function(pheno) { + var spcs_id = {{species.SpeciesId}}; + var pop_id = {{population.Id}}; + var dtst_id = {{dataset.Id}}; + return `<a href="/species/${spcs_id}` + + `/populations/${pop_id}` + + `/phenotypes/datasets/${dtst_id}` + + `/phenotype/${pheno.xref_id}` + + `" target="_blank">` + + `${pheno.InbredSetCode}_${pheno.xref_id}` + + `</a>`; + } + }, + {data: function(pheno) { + return (pheno.Post_publication_description || + pheno.Original_description || + pheno.Pre_publication_description); + }} + ] + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html new file mode 100644 index 0000000..21ac501 --- /dev/null +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -0,0 +1,135 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-phenotype"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_phenotype', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}">View Phenotype</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> + + <table class="table"> + <tbody> + <tr> + <td><strong>Phenotype</strong></td> + <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} + </tr> + <tr> + <td><strong>Database</strong></td> + <td>{{dataset.FullName}}</td> + </tr> + <tr> + <td><strong>Units</strong></td> + <td>{{phenotype.Units}}</td> + </tr> + {%for key,value in publish_data.items()%} + <tr> + <td><strong>{{key}}</strong></td> + <td>{{value}}</td> + </tr> + {%else%} + <tr> + <td colspan="2" class="text-muted"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + No publication data found. + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> +</div> + +{%if "group:resource:edit-resource" in privileges +or "group:resource:delete-resource" in privileges%} +<div class="row"> + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary">Edit</a> + {%endif%} + </div> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <a href="#" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + disabled="disabled">delete</a> + {%endif%} + </div> + </div> +</div> +{%endif%} + +<div class="row"> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Phenotype Data</strong></div> + {%if "group:resource:view-resource" in privileges%} + <table class="table"> + <thead> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if has_se%} + <th>SE</th> + <th>N</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td>{{item.value}}</td> + {%if has_se%} + <td>{{item.error or "-"}}</td> + <td>{{item.count or "-"}}</td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + You do not currently have privileges to view this phenotype in greater + detail. + </p> + {%endif%} + </div> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html new file mode 100644 index 0000000..dac965f --- /dev/null +++ b/uploader/templates/platforms/base.html @@ -0,0 +1,13 @@ +{%extends "species/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="platforms"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.platforms.index')}}"> + Sequencing Platforms</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html new file mode 100644 index 0000000..0866d5e --- /dev/null +++ b/uploader/templates/platforms/create-platform.html @@ -0,0 +1,124 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — Create Platforms{%endblock%} + +{%block pagetitle%}Platforms — Create Platforms{%endblock%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="create-platform"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}">create platform</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Create New Platform</h2> + + <p>You can create a new genetic sequencing platform below.</p> +</div> + +<div class="row"> + <form id="frm-create-platform" + method="POST" + action="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}"> + + <div class="form-group"> + <label for="txt-geo-platform" class="form-label">GEO Platform</label> + <input type="text" + id="txt-geo-platform" + name="geo-platform" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is the platform's + <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Platforms for '{{species.FullName}}' on NCBI"> + accession value on NCBI</a>. If you do not know the value, click the + link and search on NCBI for species '{{species.FullName}}'.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-name" class="form-label">Platform Name</label> + <input type="text" + id="txt-platform-name" + name="platform-name" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is name of the genetic sequencing platform.</p></small> + </div> + + <div class="form-group"> + <label for="txt-platform-shortname" class="form-label"> + Platform Short Name</label> + <input type="text" + id="txt-platform-shortname" + name="platform-shortname" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>Use the following conventions for this field: + <ol> + <li>Start with a 4-letter vendor code, e.g. "Affy" for "Affymetrix", "Illu" for "Illumina", etc.</li> + <li>Append an underscore to the 4-letter vendor code</li> + <li>Use the name of the array given by the vendor, e.g. U74AV2, MOE430A, etc.</li> + </ol> + </p> + </small> + </div> + + <div class="form-group"> + <label for="txt-platform-title" class="form-label">Platform Title</label> + <input type="text" + id="txt-platform-title" + name="platform-title" + required="required" + class="form-control" /> + <small class="form-text text-muted"> + <p>The full platform title. Sometimes, this is the same as the Platform + Name above.</p></small> + </div> + + <div class="form-group"> + <label for="txt-go-tree-value" class="form-label">GO Tree Value</label> + <input type="text" + id="txt-go-tree-value" + name="go-tree-value" + class="form-control" /> + <small class="form-text text-muted"> + <p>This is a Chip identification value useful for analysis with the + <strong> + <a href="https://www.geneweaver.org/" + title="Go to the GeneWeaver site." + target="_blank">GeneWeaver</a></strong> + and + <strong> + <a href="https://www.webgestalt.org/" + title="Go to the WEB-based GEne SeT AnaLysis Toolkit site." + target="_blank">WebGestalt</a></strong> + tools.<br /> + This can be left blank for custom platforms.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + value="create new platform" + class="btn btn-primary" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html new file mode 100644 index 0000000..555b444 --- /dev/null +++ b/uploader/templates/platforms/index.html @@ -0,0 +1,25 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Platforms{%endblock%} + +{%block pagetitle%}Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>In this section, you will be able to view and manage the sequencing + platforms that are currently supported by GeneNetwork.</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.platforms.index"), species)}} +</div> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html new file mode 100644 index 0000000..a6bcfdc --- /dev/null +++ b/uploader/templates/platforms/list-platforms.html @@ -0,0 +1,93 @@ +{%extends "platforms/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Platforms — List Platforms{%endblock%} + +{%block pagetitle%}Platforms — List Platforms{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>View the list of the genetic sequencing platforms that are currently + supported by GeneNetwork.</p> + <p>If you cannot find the platform you wish to use, you can add it by clicking + the "New Platform" button below.</p> + <p><a href="{{url_for('species.platforms.create_platform', + species_id=species.SpeciesId)}}" + title="Create a new genetic sequencing platform for species {{species.FullName}}" + class="btn btn-primary">Create Platform</a></p> +</div> + +<div class="row"> + <h2>Supported Platforms</h2> + {%if platforms is defined and platforms | length > 0%} + <p>There are {{total_platforms}} platforms supported by GeneNetwork</p> + + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%if start_from > 0%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from-count, + count=count)}}"> + <span class="glyphicon glyphicon-backward"></span> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying platforms {{start_from+1}} to {{start_from+count if start_from+count < total_platforms else total_platforms}} of + {{total_platforms}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%if start_from + count < total_platforms%} + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + start_from=start_from+count, + count=count)}}"> + Next + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + + <table class="table"> + <thead> + <tr> + <th></th> + <th>Platform Name</th> + <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" + title="Gene Expression Omnibus: Platforms section" + target="_blank">GEO Platform</a></th> + <th>Title</th> + </tr> + </thead> + + <tbody> + {%for platform in platforms%} + <tr> + <td>{{platform.sequence_number}}</td> + <td>{{platform.GeneChipName}}</td> + <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{platform.GeoPlatform}}" + title="View platform on the Gene Expression Omnibus" + target="_blank">{{platform.GeoPlatform}}</a></td> + <td>{{platform.Title}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There are no platforms supported at this time!</p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html index d763fc1..9db8083 100644 --- a/uploader/templates/populations/base.html +++ b/uploader/templates/populations/base.html @@ -6,7 +6,13 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if population is mapping%} + <a href="{{url_for('species.populations.view_population', + species_id=species.SpeciesId, + population_id=population.Id)}}">{{population.Name}}</a> + {%else%} <a href="{{url_for('species.populations.index')}}">Populations</a> + {%endif%} </li> {%block lvl3_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index b05ce37..c0c4f45 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -37,12 +37,15 @@ <div class="row"> <form method="POST" action="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}"> + species_id=species.SpeciesId, + return_to=return_to)}}"> <legend>Create Population</legend> {{flash_all_messages()}} + <input type="hidden" name="return_to" value="{{return_to}}"> + <div {%if errors.population_fullname%} class="form-group has-error" {%else%} @@ -107,9 +110,12 @@ value="{{error_values.population_code or ''}}" class="form-control" /> <small class="form-text text-muted"> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - What is this field is for? Confirm with Arthur and the rest. + <p class="form-text text-muted"> + This is a 3-character code for your population, that is prepended to + the phenotype identifiers. e.g. For the "BXD Family" population, the + code is "BXD" and therefore, the phenotype identifiers for the + population look like the following examples: <em>BXD_10148</em>, + <em>BXD_10180</em>, <em>BXD_10197</em>, etc. </p> </small> </div> diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html index 4354e02..d2bee77 100644 --- a/uploader/templates/populations/index.html +++ b/uploader/templates/populations/index.html @@ -22,3 +22,7 @@ {{select_species_form(url_for("species.populations.index"), species)}} </div> {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index 7c7145f..f780e94 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -51,7 +51,7 @@ <caption>Populations for {{species.FullName}}</caption> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Full Name</th> <th>Description</th> diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index e68f8e3..16b477f 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -7,25 +7,34 @@ <div class="card-body"> <h5 class="card-title">Population</h5> <div class="card-text"> - <dl> - <dt>Name</dt> - <dd>{{population.Name}}</dd> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{population.Name}}</td> + </tr> - <dt>Full Name</dt> - <dd>{{population.FullName}}</dd> + <tr> + <td>Full Name</td> + <td>{{population.FullName}}</td> + </tr> - <dt>Code</dt> - <dd>{{population.InbredSetCode}}</dd> + <tr> + <td>Code</td> + <td>{{population.InbredSetCode}}</td> + </tr> - <dt>Genetic Type</dt> - <dd>{{population.GeneticType}}</dd> + <tr> + <td>Genetic Type</td> + <td>{{population.GeneticType}}</td> + </tr> - <dt>Family</dt> - <dd>{{population.Family}}</dd> - - <dt>Description</dt> - <dd>{{population.Description or "-"}}</dd> - </dl> + <tr> + <td>Family</td> + <td>{{population.Family}}</td> + </tr> + </tbody> + </table> </div> </div> </div> diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html index af4fd3a..14b0510 100644 --- a/uploader/templates/populations/macro-select-population.html +++ b/uploader/templates/populations/macro-select-population.html @@ -1,30 +1,52 @@ -{%macro select_population_form(form_action, populations)%} -<form method="GET" action="{{form_action}}"> - <legend>Select Population</legend> - - <div class="form-group"> - <label for="select-population" class="form-label">Select Population</label> - <select id="select-population" - name="population_id" - class="form-control" - required="required"> - <option value="">Select Population</option> - {%for family in populations%} - <optgroup {%if family[0][1] is not none%} - label="{{family[0][1]}}" - {%else%} - label="Undefined" - {%endif%}> - {%for population in family[1]%} - <option value="{{population.Id}}">{{population.FullName}}</option> - {%endfor%} - </optgroup> - {%endfor%} - </select> +{%from "macro-step-indicator.html" import step_indicator%} + +{%macro select_population_form(form_action, species, populations)%} +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("2")}} What population do you want to work with?</h2> + + {%if populations | length != 0%} + + <p class="form-text">Search for, and select the population from the table + below and click "Continue"</p> + + <div class="radio"> + <label class="control-label" for="rdo-cant-find-population"> + <input type="radio" id="rdo-cant-find-population" + name="population_id" value="CREATE-POPULATION" /> + I cannot find the population I want — create it! + </label> + </div> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> + </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-population" class="table compact stripe" + data-populations-list='{{populations | tojson}}'> + <thead> + <tr> + <th></th> + <th>Population</th> + </tr> + </thead> + + <tbody></tbody> + </table> </div> - <div class="form-group"> - <input type="submit" value="Select" class="btn btn-primary" /> + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).<br /> + Click "Continue" to create the first!</p> + <input type="hidden" name="population_id" value="CREATE-POPULATION" /> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> </div> + {%endif%} + </form> {%endmacro%} diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html index d6fe154..d6fe154 100644 --- a/uploader/templates/rqtl2/create-tissue-success.html +++ b/uploader/templates/populations/rqtl2/create-tissue-success.html diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html new file mode 100644 index 0000000..ec6ffb8 --- /dev/null +++ b/uploader/templates/populations/rqtl2/index.html @@ -0,0 +1,54 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Data Upload{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 data upload</h1> + +<h2>R/qtl2 Upload</h2> + +<div class="row"> + <form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}" + id="frm-rqtl2-upload"> + <legend class="heading">upload R/qtl2 bundle</legend> + {{flash_messages("error-rqtl2")}} + + <div class="form-group"> + <label for="select:species" class="form-label">Species</label> + <select id="select:species" + name="species_id" + required="required" + class="form-control"> + <option value="">Select species</option> + {%for spec in species%} + <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + Data that you upload to the system should belong to a know species. + Here you can select the species that you wish to upload data for. + </small> + </div> + + <input type="submit" class="btn btn-primary" value="submit" /> + </form> +</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> +{%endblock%} diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html index b17004f..b17004f 100644 --- a/uploader/templates/rqtl2/no-such-job.html +++ b/uploader/templates/populations/rqtl2/no-such-job.html diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html index 9817518..9817518 100644 --- a/uploader/templates/rqtl2/rqtl2-job-error.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-error.html diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html index 4ecd415..4ecd415 100644 --- a/uploader/templates/rqtl2/rqtl2-job-results.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-results.html diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html index e896f88..e896f88 100644 --- a/uploader/templates/rqtl2/rqtl2-job-status.html +++ b/uploader/templates/populations/rqtl2/rqtl2-job-status.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html index 90e8887..90e8887 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html index b3c3a8f..b3c3a8f 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html index f4a6266..f4a6266 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-status.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html index f126835..f126835 100644 --- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html +++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html new file mode 100644 index 0000000..3233abc --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html @@ -0,0 +1,69 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Select Genotypes Dataset</h2> + +<div class="row"> + <p>Your R/qtl2 files bundle could contain a "geno" specification. You will + therefore need to select from one of the existing Genotype datasets or + create a new one.</p> + <p>This is the dataset where your data will be organised under.</p> +</div> + +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('expression-data.rqtl2.select_geno_dataset', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">select from existing genotype datasets</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + {{flash_messages("error-rqtl2-select-geno-dataset")}} + + <div class="form-group"> + <legend>Datasets</legend> + <label for="select:geno-datasets" class="form-label">Dataset</label> + <select id="select:geno-datasets" + name="geno-dataset-id" + required="required" + {%if datasets | length == 0%} + disabled="disabled" + {%endif%} + class="form-control" + aria-describedby="help-geno-dataset-select-dataset"> + <option value="">Select dataset</option> + {%for dset in datasets%} + <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> + {%endfor%} + </select> + <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> + Select from the existing genotype datasets for species + {{species.SpeciesName}} ({{species.FullName}}). + </span> + </div> + + <button type="submit" class="btn btn-primary">select dataset</button> + </form> +</div> + +<div class="row"> + <p>If the genotype dataset you need does not currently exist for your dataset, + go the <a href="{{url_for( + 'species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Create a new genotypes dataset for {{species.FullName}}"> + genotypes page to create the genotype dataset</a></p> +</div> + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html new file mode 100644 index 0000000..ded425f --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-population.html @@ -0,0 +1,57 @@ +{%extends "expression-data/index.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%block title%}Select Grouping/Population{%endblock%} + +{%block contents%} +<h1 class="heading">Select grouping/population</h1> + +<div class="row"> + <p>The data is organised in a hierarchical form, beginning with + <em>species</em> at the very top. Under <em>species</em> the data is + organised by <em>population</em>, sometimes referred to as <em>grouping</em>. + (In some really old documents/systems, you might see this referred to as + <em>InbredSet</em>.)</p> + <p>In this section, you get to define what population your data is to be + organised by.</p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.rqtl2.select_population', + species_id=species.SpeciesId)}}"> + <legend class="heading">select grouping/population</legend> + {{flash_messages("error-select-population")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + + <div class="form-group"> + <label for="select:inbredset" class="form-label">population</label> + <select id="select:inbredset" + name="inbredset_id" + required="required" + class="form-control"> + <option value="">Select a grouping/population</option> + {%for pop in populations%} + <option value="{{pop.InbredSetId}}"> + {{pop.InbredSetName}} ({{pop.FullName}})</option> + {%endfor%} + </select> + <span class="form-text text-muted">Select the population for your data from + the list below.</span> + </div> + + <button type="submit" class="btn btn-primary" />select population</button> +</form> +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html index 74f8f69..74f8f69 100644 --- a/uploader/templates/rqtl2/select-probeset-dataset.html +++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html index e3fd9cc..e3fd9cc 100644 --- a/uploader/templates/rqtl2/select-probeset-study-id.html +++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html index fe3080a..fe3080a 100644 --- a/uploader/templates/rqtl2/select-tissue.html +++ b/uploader/templates/populations/rqtl2/select-tissue.html diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html index 0adba2e..0adba2e 100644 --- a/uploader/templates/rqtl2/summary-info.html +++ b/uploader/templates/populations/rqtl2/summary-info.html diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html index 9d45c5f..9d45c5f 100644 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html index 8210ed0..8210ed0 100644 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index 1e2964e..b23caeb 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -15,7 +15,7 @@ {%endif%}> <a href="{{url_for('species.populations.view_population', species_id=species.SpeciesId, - population_id=population.InbredSetId)}}">view population</a> + population_id=population.InbredSetId)}}">view</a> </li> {%endblock%} @@ -62,29 +62,35 @@ <nav class="nav"> <ul> <li> - <a href="{{url_for('species.populations.genotypes.list_genotypes', + <a href="{{url_for('species.populations.samples.list_samples', species_id=species.SpeciesId, population_id=population.Id)}}" - title="Upload genotypes for {{species.FullName}}">Upload Genotypes</a> + title="Manage samples: Add new or delete existing."> + manage samples</a> </li> <li> - <a href="{{url_for('species.populations.samples.list_samples', + <a href="{{url_for('species.populations.genotypes.list_genotypes', species_id=species.SpeciesId, population_id=population.Id)}}" - title="Manage samples: Add new or delete existing."> - manage samples</a> + title="Manage genotypes for {{species.FullName}}">Manage Genotypes</a> </li> <li> - <a href="#" title="Upload expression data">upload expression data</a> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Manage phenotype data.">manage phenotype data</a> </li> <li> - <a href="#" title="Upload phenotype data">upload phenotype data</a> + <a href="#" title="Manage expression data" + class="not-implemented">manage expression data</a> </li> <li> - <a href="#" title="Upload individual data">upload individual data</a> + <a href="#" title="Manage individual data" + class="not-implemented">manage individual data</a> </li> <li> - <a href="#" title="Upload RNA-Seq data">upload RNA-Seq data</a> + <a href="#" title="Manage RNA-Seq data" + class="not-implemented">manage RNA-Seq data</a> </li> </ul> </nav> diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html deleted file mode 100644 index bb6d63d..0000000 --- a/uploader/templates/rqtl2/create-geno-dataset-success.html +++ /dev/null @@ -1,55 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Select Genotypes Dataset</h2> - -<div class="explainer"> - <p>You successfully created the genotype dataset with the following - information. - <dl> - <dt>ID</dt> - <dd>{{geno_dataset.id}}</dd> - - <dt>Name</dt> - <dd>{{geno_dataset.name}}</dd> - - <dt>Full Name</dt> - <dd>{{geno_dataset.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{geno_dataset.sname}}</dd> - - <dt>Created On</dt> - <dd>{{geno_dataset.today}}</dd> - - <dt>Public?</dt> - <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd> - </dl> - </p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" - value="{{geno_dataset.id}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html deleted file mode 100644 index 03b75c7..0000000 --- a/uploader/templates/rqtl2/create-probe-dataset-success.html +++ /dev/null @@ -1,59 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Create ProbeSet Dataset</h2> - -<div class="row"> - <p>You successfully created the ProbeSet dataset with the following - information. - <dl> - <dt>Averaging Method</dt> - <dd>{{avgmethod.Name}}</dd> - - <dt>ID</dt> - <dd>{{dataset.datasetid}}</dd> - - <dt>Name</dt> - <dd>{{dataset.name2}}</dd> - - <dt>Full Name</dt> - <dd>{{dataset.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{dataset.sname}}</dd> - - <dt>Created On</dt> - <dd>{{dataset.today}}</dd> - - <dt>DataScale</dt> - <dd>{{dataset.datascale}}</dd> - </dl> - </p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.Id}}" /> - <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html deleted file mode 100644 index e293f6f..0000000 --- a/uploader/templates/rqtl2/create-probe-study-success.html +++ /dev/null @@ -1,49 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Create ProbeSet Study</h2> - -<div class="row"> - <p>You successfully created the ProbeSet study with the following - information. - <dl> - <dt>ID</dt> - <dd>{{study.id}}</dd> - - <dt>Name</dt> - <dd>{{study.name}}</dd> - - <dt>Full Name</dt> - <dd>{{study.fname}}</dd> - - <dt>Short Name</dt> - <dd>{{study.sname}}</dd> - - <dt>Created On</dt> - <dd>{{study.today}}</dd> - </dl> - </p> - - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet study</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.studyid}}" /> - - <button type="submit" class="btn btn-primary">continue</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html deleted file mode 100644 index 8ce13bf..0000000 --- a/uploader/templates/rqtl2/index.html +++ /dev/null @@ -1,36 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Data Upload{%endblock%} - -{%block contents%} -<h1 class="heading">R/qtl2 data upload</h1> - -<h2>R/qtl2 Upload</h2> - -<form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}" - id="frm-rqtl2-upload"> - <legend class="heading">upload R/qtl2 bundle</legend> - {{flash_messages("error-rqtl2")}} - - <div class="form-group"> - <label for="select:species" class="form-label">Species</label> - <select id="select:species" - name="species_id" - required="required" - class="form-control"> - <option value="">Select species</option> - {%for spec in species%} - <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> - {%endfor%} - </select> - <small class="form-text text-muted"> - Data that you upload to the system should belong to a know species. - Here you can select the species that you wish to upload data for. - </small> - </div> - - <button type="submit" class="btn btn-primary" />submit</button> -</form> - -{%endblock%} diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html deleted file mode 100644 index 1db51e0..0000000 --- a/uploader/templates/rqtl2/select-geno-dataset.html +++ /dev/null @@ -1,144 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Upload R/qtl2 Bundle{%endblock%} - -{%block contents%} -<h2 class="heading">Select Genotypes Dataset</h2> - -<div class="row"> - <p>Your R/qtl2 files bundle contains a "geno" specification. You will - therefore need to select from one of the existing Genotype datasets or - create a new one.</p> - <p>This is the dataset where your data will be organised under.</p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.select_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-select-geno-dataset")}} - - <div class="form-group"> - <legend>Datasets</legend> - <label for="select:geno-datasets" class="form-label">Dataset</label> - <select id="select:geno-datasets" - name="geno-dataset-id" - required="required" - {%if datasets | length == 0%} - disabled="disabled" - {%endif%} - class="form-control" - aria-describedby="help-geno-dataset-select-dataset"> - <option value="">Select dataset</option> - {%for dset in datasets%} - <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> - {%endfor%} - </select> - <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> - Select from the existing genotype datasets for species - {{species.SpeciesName}} ({{species.FullName}}). - </span> - </div> - - <button type="submit" class="btn btn-primary">select dataset</button> - </form> -</div> - -<div class="row"> - <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> -</div> - -<div class="row"> - <form id="frm-upload-rqtl2-bundle" - action="{{url_for('expression-data.rqtl2.create_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">create a new genotype dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-create-geno-dataset")}} - - <div class="form-group"> - <label for="txt:dataset-name" class="form-label">Name</label> - <input type="text" - id="txt:dataset-name" - name="dataset-name" - maxlength="100" - required="required" - class="form-control" - aria-describedby="help-geno-dataset-name" /> - <span id="help-geno-dataset-name" class="form-text text-muted"> - Provide the new name for the genotype dataset, e.g. "BXDGeno" - </span> - </div> - - <div class="form-group"> - <label for="txt:dataset-fullname" class="form-label">Full Name</label> - <input type="text" - id="txt:dataset-fullname" - name="dataset-fullname" - required="required" - maxlength="100" - class="form-control" - aria-describedby="help-geno-dataset-fullname" /> - - <span id="help-geno-dataset-fullname" class="form-text text-muted"> - Provide a longer name that better describes the genotype dataset, e.g. - "BXD Genotypes" - </span> - </div> - - <div class="form-group"> - <label for="txt:dataset-shortname" class="form-label">Short Name</label> - <input type="text" - id="txt:dataset-shortname" - name="dataset-shortname" - maxlength="100" - class="form-control" - aria-describedby="help-geno-dataset-shortname" /> - - <span id="help-geno-dataset-shortname" class="form-text text-muted"> - Provide a short name for the genotype dataset. This is optional. If not - provided, we'll default to the same value as the "Name" above. - </span> - </div> - - <div class="form-group"> - <input type="checkbox" - id="chk:dataset-public" - name="dataset-public" - checked="checked" - class="form-check" - aria-describedby="help-geno-datasent-public" /> - <label for="chk:dataset-public" class="form-check-label">Public?</label> - - <span id="help-geno-dataset-public" class="form-text text-muted"> - Specify whether the dataset will be available publicly. Check to make the - dataset publicly available and uncheck to limit who can access the dataset. - </span> - </div> - - <button type="submit" class="btn btn-primary">create new dataset</button> - </form> -</div> - -{%endblock%} diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html deleted file mode 100644 index 7d27303..0000000 --- a/uploader/templates/rqtl2/select-population.html +++ /dev/null @@ -1,136 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Select Grouping/Population{%endblock%} - -{%block contents%} -<h1 class="heading">Select grouping/population</h1> - -<div class="explainer"> - <p>The data is organised in a hierarchical form, beginning with - <em>species</em> at the very top. Under <em>species</em> the data is - organised by <em>population</em>, sometimes referred to as <em>grouping</em>. - (In some really old documents/systems, you might see this referred to as - <em>InbredSet</em>.)</p> - <p>In this section, you get to define what population your data is to be - organised by.</p> -</div> - -<form method="POST" - action="{{url_for('expression-data.rqtl2.select_population', species_id=species.SpeciesId)}}"> - <legend class="heading">select grouping/population</legend> - {{flash_messages("error-select-population")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - - <div class="form-group"> - <label for="select:inbredset" class="form-label">population</label> - <select id="select:inbredset" - name="inbredset_id" - required="required" - class="form-control"> - <option value="">Select a grouping/population</option> - {%for pop in populations%} - <option value="{{pop.InbredSetId}}"> - {{pop.InbredSetName}} ({{pop.FullName}})</option> - {%endfor%} - </select> - <span class="form-text text-muted">If you are adding data to an already existing - population, simply pick the population from this drop-down selector. If - you cannot find your population from this list, try the form below to - create a new one..</span> - </div> - - <button type="submit" class="btn btn-primary" />select population</button> -</form> - -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> - -<form method="POST" - action="{{url_for('expression-data.rqtl2.create_population', species_id=species.SpeciesId)}}"> - <legend class="heading">create new grouping/population</legend> - {{flash_messages("error-create-population")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - - <div class="form-group"> - <legend class="heading">mandatory</legend> - - <div class="form-group"> - <label for="txt:inbredset-name" class="form-label">name</label> - <input id="txt:inbredset-name" - name="inbredset_name" - type="text" - required="required" - maxlength="30" - placeholder="Enter grouping/population name" - class="form-control" /> - <span class="form-text text-muted">This is a short name that identifies the - population. Useful for menus, and quick scanning.</span> - </div> - - <div class="form-group"> - <label for="txt:" class="form-label">full name</label> - <input id="txt:inbredset-fullname" - name="inbredset_fullname" - type="text" - required="required" - maxlength="100" - placeholder="Enter the grouping/population's full name" - class="form-control" /> - <span class="form-text text-muted">This can be the same as the name above, or can - be longer. Useful for documentation, and human communication.</span> - </div> - </div> - - <div class="form-group"> - <legend class="heading">optional</legend> - - <div class="form-group"> - <label for="num:public" class="form-label">public?</label> - <select id="num:public" - name="public" - class="form-control"> - <option value="0">0 - Only accessible to authorised users</option> - <option value="1">1 - Publicly accessible to all users</option> - <option value="2" selected> - 2 - Publicly accessible to all users</option> - </select> - <span class="form-text text-muted">This determines whether the - population/grouping will appear on the menus for users.</span> - </div> - - <div class="form-group"> - <label for="txt:inbredset-family" class="form-label">family</label> - <input id="txt:inbredset-family" - name="inbredset_family" - type="text" - placeholder="I am not sure what this is about." - class="form-control" /> - <span class="form-text text-muted">I do not currently know what this is about. - This is a failure on my part to figure out what this is and provide a - useful description. Please feel free to remind me.</span> - </div> - - <div class="form-group"> - <label for="txtarea:" class="form-label">Description</label> - <textarea id="txtarea:description" - name="description" - rows="5" - placeholder="Enter a description of this grouping/population" - class="form-control"></textarea> - <span class="form-text text-muted"> - A long-form description of what the population consists of. Useful for - humans.</span> - </div> - </div> - - <button type="submit" class="btn btn-primary" /> - create grouping/population</button> -</form> - -{%endblock%} - - -{%block javascript%} -{%endblock%} diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html index ee4a63e..ee98734 100644 --- a/uploader/templates/samples/index.html +++ b/uploader/templates/samples/index.html @@ -17,3 +17,7 @@ {{select_species_form(url_for("species.populations.samples.index"), species)}} </div> {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html index 13e5cec..185e784 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -73,7 +73,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Auxilliary Name</th> <th>Symbol</th> diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html index f437780..1cc7573 100644 --- a/uploader/templates/samples/select-population.html +++ b/uploader/templates/samples/select-population.html @@ -12,28 +12,15 @@ {{flash_all_messages()}} <div class="row"> - <p>You have selected "{{species.FullName}}" as the species that your data relates to.</p> - <p>Next, we need information regarding the population your data relates to. Do please select the population from the existing ones below</p> -</div> - -<div class="row"> {{select_population_form( - url_for("species.populations.samples.select_population", species_id=species.SpeciesId), - populations)}} -</div> - -<div class="row"> - <p> - If you cannot find the population your data relates to in the drop-down - above, you might want to - <a href="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}" - title="Create a new population for species '{{species.FullName}},"> - add a new population to GeneNetwork</a> - instead. + url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}} </div> {%endblock%} {%block sidebarcontents%} {{display_species_card(species)}} {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%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%} diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html index 04391db..f64f72b 100644 --- a/uploader/templates/species/base.html +++ b/uploader/templates/species/base.html @@ -6,7 +6,12 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if species is mapping%} + <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}"> + {{species.Name}}</a> + {%else%} <a href="{{url_for('species.list_species')}}">Species</a> + {%endif%} </li> {%block lvl2_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html index 0d0bedf..138dbaa 100644 --- a/uploader/templates/species/create-species.html +++ b/uploader/templates/species/create-species.html @@ -19,72 +19,88 @@ <div class="row"> <form id="frm-create-species" method="POST" - action="{{url_for('species.create_species')}}"> + action="{{url_for('species.create_species', return_to=return_to)}}" + class="form-horizontal"> <legend>Create Species</legend> {{flash_all_messages()}} + <input type="hidden" name="return_to" value="{{return_to}}"> + <div class="form-group"> - <label for="txt-taxonomy-id" class="form-label"> + <label for="txt-taxonomy-id" class="control-label col-sm-2"> Taxonomy ID</label> - <div class="input-group"> - <input id="txt-taxonomy-id" - name="species_taxonomy_id" - type="text" - class="form-control" /> - <span class="input-group-btn"> - <button id="btn-search-taxonid" class="btn btn-info">Search</button> - </span> + <div class="col-sm-10"> + <div class="input-group"> + <input id="txt-taxonomy-id" + name="species_taxonomy_id" + type="text" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-search-taxonid" class="btn btn-info">Search</button> + </span> + </div> + <small class="form-text text-small text-muted"> + Use + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/" + title="NCBI's Taxonomy Browser homepage" + target="_blank"> + NCBI's Taxonomy Browser homepage</a> to search for the species you + want. If the species exists on NCBI, they will have a Taxonomy ID. Copy + that Taxonomy ID to this field, and click "Search" to auto-fill the + details.<br /> + This field is optional.</small> </div> - <small class="form-text text-small text-muted">Provide the taxonomy ID for - your species that can be used to link to external sites like NCBI. Enter - the taxonomy ID and click "Search" to auto-fill the form with data. - <br /> - While it is recommended to provide a value for this field, doing so is - optional. - </small> </div> <div class="form-group"> - <label for="txt-species-name" class="form-label">Common Name</label> - <input id="txt-species-name" - name="common_name" - type="text" - class="form-control" - required="required" /> - <small class="form-text text-muted">Provide the common, possibly - non-scientific name for the species here, e.g. Human, Mouse, etc.</small> + <label for="txt-species-name" class="control-label col-sm-2">Common Name</label> + <div class="col-sm-10"> + <input id="txt-species-name" + name="common_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the day-to-day term used by + laymen, e.g. Mouse (instead of Mus musculus), round worm (instead of + Ascaris lumbricoides), etc.<br /> + For species without this, just enter the scientific name. + </small> + </div> </div> <div class="form-group"> - <label for="txt-species-scientific" class="form-label"> + <label for="txt-species-scientific" class="control-label col-sm-2"> Scientific Name</label> - <input id="txt-species-scientific" - name="scientific_name" - type="text" - class="form-control" - required="required" /> - <small class="form-text text-muted">Provide the scientific name for the - species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small> + <div class="col-sm-10"> + <input id="txt-species-scientific" + name="scientific_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the scientific name for the + species e.g. Homo sapiens, Mus musculus, etc.</small> + </div> </div> <div class="form-group"> - <label for="select-species-family" class="form-label">Family</label> - <select id="select-species-family" - name="species_family" - required="required" - class="form-control"> - <option value="">Please select a grouping</option> - {%for family in families%} - <option value="{{family}}">{{family}}</option> - {%endfor%} - </select> - <small class="form-text text-muted"> - This is a generic grouping for the species that determines under which - grouping the species appears in the GeneNetwork menus</small> + <label for="select-species-family" class="control-label col-sm-2">Family</label> + <div class="col-sm-10"> + <select id="select-species-family" + name="species_family" + required="required" + class="form-control"> + <option value="ungrouped">I do not know what to pick</option> + {%for family in families%} + <option value="{{family}}">{{family}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + This is a rough grouping of the species.</small> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="create new species" class="btn btn-primary" /> @@ -113,7 +129,7 @@ } msg = ( "Request to '${uri}' failed with message '${textStatus}'. " - + "Please try again later, or fill the details manually."); + + "Please try again later, or fill the details manually."); alert(msg); console.error(msg, data, textStatus); return false; diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html index 85c9d40..64084b0 100644 --- a/uploader/templates/species/list-species.html +++ b/uploader/templates/species/list-species.html @@ -29,7 +29,7 @@ <caption>Available Species</caption> <thead> <tr> - <th>#</td> + <th></td> <th title="A common, layman's name for the species.">Common Name</th> <th title="The scientific name for the species">Organism Name</th> <th title="An identifier for the species in the NCBI taxonomy database"> diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html index 857c0f0..166c7b9 100644 --- a/uploader/templates/species/macro-display-species-card.html +++ b/uploader/templates/species/macro-display-species-card.html @@ -3,13 +3,19 @@ <div class="card-body"> <h5 class="card-title">Species</h5> <div class="card-text"> - <dl> - <dt>Common Name</dt> - <dd>{{species.SpeciesName}}</dd> + <table class="table"> + <tbody> + <tr> + <td>Common Name</td> + <td>{{species.SpeciesName}}</td> + </tr> - <dt>Scientific Name</dt> - <dd>{{species.FullName}}</dd> - </dl> + <tr> + <td>Scientific Name</td> + <td>{{species.FullName}}</td> + </tr> + </tbody> + </table> </div> </div> </div> diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html index 6955134..3714ae4 100644 --- a/uploader/templates/species/macro-select-species.html +++ b/uploader/templates/species/macro-select-species.html @@ -1,38 +1,59 @@ +{%from "macro-step-indicator.html" import step_indicator%} + {%macro select_species_form(form_action, species)%} -{%if species | length > 0%} -<form method="GET" action="{{form_action}}"> - <legend>Select Species</legend> - - <div class="form-group"> - <label for="select-species" class="form-label">Species</label> - <select id="select-species" - name="species_id" - class="form-control" - required="required"> - <option value="">Select Species</option> - {%for group in species%} - {{group}} - <optgroup {%if group[0][1] is not none%} - label="{{group[0][1].capitalize()}}" - {%else%} - label="Undefined" - {%endif%}> - {%for aspecies in group[1]%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> - {%endfor%} - </optgroup> - {%endfor%} - </select> +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("1")}} What species do you want to work with?</h2> + + {%if species | length != 0%} + + <p class="form-text">Search for, and select the species from the table below + and click "Continue"</p> + + <div class="radio"> + <label for="rdo-cant-find-species" + style="font-weight: 1;"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + I could not find the species I want (create it). + </label> </div> - <div class="form-group"> - <input type="submit" value="Select" class="btn btn-primary" /> + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary" + value="continue" /> </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-species" class="table compact stripe" + data-species-list='{{species | tojson}}'> + <div class=""> + <thead> + <tr> + <th></th> + <th>Species Name</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + + <label class="control-label" for="rdo-cant-find-species"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + There are no species to select from. Create the first one.</label> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary col-sm-offset-1" + value="continue" /> + </div> + + {%endif%} + </form> -{%else%} -<p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-mark"></span> - We could not find species to select from! -</p> -{%endif%} {%endmacro%} diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html index b01864d..2d02f7e 100644 --- a/uploader/templates/species/view-species.html +++ b/uploader/templates/species/view-species.html @@ -45,6 +45,12 @@ title="Create/Edit populations for {{species.FullName}}"> Manage populations</a> </li> + <li> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Create/Edit sequencing platforms for {{species.FullName}}"> + Manage sequencing platforms</a> + </li> </ol> diff --git a/uploader/ui.py b/uploader/ui.py index 4115b02..1994056 100644 --- a/uploader/ui.py +++ b/uploader/ui.py @@ -8,6 +8,7 @@ def make_template_renderer(default): template, **{ **kwargs, + "activemenu": default, "activelink": kwargs.get("activelink", default) }) return render_template |