diff options
Diffstat (limited to 'uploader')
75 files changed, 3507 insertions, 919 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index cae531b..98e8141 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -3,19 +3,33 @@ import os import sys import logging from pathlib import Path +from typing import Optional from flask import Flask, request + +from cachelib import FileSystemCache + +from gn_libs import jobs as gnlibs_jobs + from flask_session import Session + 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 .publications import pubbp from .oauth2.views import oauth2 from .expression_data import exprdatabp from .errors import register_error_handlers +from .background_jobs import background_jobs_bp + +logging.basicConfig( + format=("%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s " + "(%(thread)d:%(threadName)s): %(message)s") +) def override_settings_with_envvars( app: Flask, ignore: tuple[str, ...]=tuple()) -> None: @@ -50,10 +64,26 @@ def setup_logging(app: Flask) -> Flask: "SERVER_SOFTWARE", "").split('/') return __log_gunicorn__(app) if bool(software) else __log_dev__(app) +def setup_modules_logging(app_logger, modules): + """Setup module-level loggers to the same log-level as the application.""" + loglevel = logging.getLevelName(app_logger.getEffectiveLevel()) + for module in modules: + _logger = logging.getLogger(module) + _logger.setLevel(loglevel) + + +def create_app(config: Optional[dict] = None): + """The application factory. + + config: dict + Useful to override settings in the settings files and environment + especially in environments such as testing.""" + if config is None: + config = {} -def create_app(): - """The application factory""" app = Flask(__name__) + + ### BEGIN: Application configuration app.config.from_pyfile( Path(__file__).parent.joinpath("default_settings.py")) if "UPLOADER_CONF" in os.environ: @@ -68,8 +98,19 @@ def create_app(): if secretsfile.exists(): # Silently ignore secrets if the file does not exist. app.config.from_pyfile(secretsfile) + app.config.update(config) # Override everything with passed in config + ### END: Application configuration + + app.config["SESSION_CACHELIB"] = FileSystemCache( + cache_dir=Path(app.config["SESSION_FILESYSTEM_CACHE_PATH"]).absolute(), + threshold=int(app.config["SESSION_FILESYSTEM_CACHE_THRESHOLD"]), + default_timeout=int(app.config["SESSION_FILESYSTEM_CACHE_TIMEOUT"])) setup_logging(app) + setup_modules_logging(app.logger, ( + "uploader.publications.models", + "uploader.publications.datatables", + "uploader.phenotypes.models")) # setup jinja2 symbols app.add_template_global(lambda : request.url, name="request_url") @@ -86,6 +127,9 @@ def create_app(): app.register_blueprint(files, url_prefix="/files") app.register_blueprint(oauth2, url_prefix="/oauth2") app.register_blueprint(speciesbp, url_prefix="/species") + app.register_blueprint(pubbp, url_prefix="/publications") + app.register_blueprint(background_jobs_bp, url_prefix="/background-jobs/") register_error_handlers(app) + gnlibs_jobs.init_app(app) return app diff --git a/uploader/authorisation.py b/uploader/authorisation.py index a283980..3cf3585 100644 --- a/uploader/authorisation.py +++ b/uploader/authorisation.py @@ -16,13 +16,12 @@ def require_login(function): @wraps(function) def __is_session_valid__(*args, **kwargs): """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 signed in.", "alert-danger big-alert") + def __alert_needs_sign_in__(_no_token): + flash("You need to be signed in.", "alert alert-danger big-alert") return redirect("/") return session.user_token().either( - __clear_session__, + __alert_needs_sign_in__, lambda token: function(*args, **kwargs)) return __is_session_valid__ @@ -49,7 +48,7 @@ def require_token(func: Callable) -> Callable: """ def __invalid_token__(_whatever): logging.debug("==========> Failure log: %s", _whatever) - raise Exception( + raise Exception(# pylint: disable=[broad-exception-raised] "You attempted to access a feature of the system that requires " "authorisation. Unfortunately, we could not verify you have the " "appropriate authorisation to perform the action you requested. " diff --git a/uploader/background_jobs.py b/uploader/background_jobs.py new file mode 100644 index 0000000..d33c498 --- /dev/null +++ b/uploader/background_jobs.py @@ -0,0 +1,118 @@ +"""Generic views and utilities to handle background jobs.""" +import uuid +import importlib +from typing import Callable +from functools import partial + +from flask import ( + url_for, + redirect, + Response, + Blueprint, + render_template, + current_app as app) + +from gn_libs import jobs +from gn_libs import sqlite3 +from gn_libs.jobs.jobs import JobNotFound + +from uploader.authorisation import require_login + +background_jobs_bp = Blueprint("background-jobs", __name__) +HandlerType = Callable[[dict], Response] + + +def __default_error_handler__(job: dict) -> Response: + return redirect(url_for("background-jobs.job_error", job_id=job["job_id"])) + +def register_handlers( + job_type: str, + success_handler: HandlerType, + # pylint: disable=[redefined-outer-name] + error_handler: HandlerType = __default_error_handler__ + # pylint: disable=[redefined-outer-name] +) -> str: + """Register success and error handlers for each job type.""" + if not bool(app.config.get("background-jobs")): + app.config["background-jobs"] = {} + + if not bool(app.config["background-jobs"].get(job_type)): + app.config["background-jobs"][job_type] = { + "success": success_handler, + "error": error_handler + } + + return job_type + + +def register_job_handlers(job: str): + """Related to register handlers above.""" + def __load_handler__(absolute_function_path): + _parts = absolute_function_path.split(".") + app.logger.debug("THE PARTS ARE: %s", _parts) + assert len(_parts) > 1, f"Invalid path: {absolute_function_path}" + module = importlib.import_module(f".{_parts[-2]}", + package=".".join(_parts[0:-2])) + return getattr(module, _parts[-1]) + + metadata = job["metadata"] + if metadata.get("success_handler"): + _success_handler = __load_handler__(metadata["success_handler"]) + try: + _error_handler = __load_handler__(metadata["error_handler"]) + except Exception as _exc:# pylint: disable=[broad-exception-caught] + _error_handler = __default_error_handler__ + register_handlers( + metadata["job-type"], _success_handler, _error_handler) + + +def handler(job: dict, handler_type: str) -> HandlerType: + """Fetch a handler for the job.""" + _job_type = job["metadata"]["job-type"] + _handler = app.config.get( + "background-jobs", {} + ).get( + _job_type, {} + ).get(handler_type) + if bool(_handler): + return _handler(job) + return render_template("background-jobs/default-success-page.html", job=job) + + +error_handler = partial(handler, handler_type="error") +success_handler = partial(handler, handler_type="success") + + +@background_jobs_bp.route("/status/<uuid:job_id>") +@require_login +def job_status(job_id: uuid.UUID): + """View the job status.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + try: + job = jobs.job(conn, job_id, fulldetails=True) + status = job["metadata"]["status"] + + register_job_handlers(job) + if status == "error": + return error_handler(job) + + if status == "completed": + return success_handler(job) + + return render_template("jobs/job-status.html", job=job) + except JobNotFound as _jnf: + return render_template( + "jobs/job-not-found.html", + job_id=job_id) + + +@background_jobs_bp.route("/error/<uuid:job_id>") +@require_login +def job_error(job_id: uuid.UUID): + """Handle job errors in a generic manner.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + try: + job = jobs.job(conn, job_id, fulldetails=True) + return render_template("jobs/job-error.html", job=job) + except JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) diff --git a/uploader/datautils.py b/uploader/datautils.py index 46a55c4..d132c42 100644 --- a/uploader/datautils.py +++ b/uploader/datautils.py @@ -1,5 +1,7 @@ """Generic data utilities: Rename module.""" import math +import json +import base64 from functools import reduce from typing import Union, Sequence @@ -36,3 +38,13 @@ def safe_int(val: Union[str, int, float]) -> int: return int(val) except ValueError: return 0 + + +def base64_encode_dict(dct: dict, **kwargs) -> bytes: + """Base64 encode a dictionary. Takes the same keywords as `json.dumps` function.""" + return base64.urlsafe_b64encode(json.dumps(dct, **kwargs).encode("utf-8")) + + +def base64_decode_to_dict(value: str, **kwargs) -> dict: + """Base64 encode a dictionary. Takes the same keywords as `json.loads` function.""" + return json.loads(base64.urlsafe_b64decode(value), **kwargs) diff --git a/uploader/db/datasets.py b/uploader/db/datasets.py index 767ec41..4b263f5 100644 --- a/uploader/db/datasets.py +++ b/uploader/db/datasets.py @@ -53,7 +53,7 @@ def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]: _study = cursor.fetchone() return dict(_study) if bool(_study) else None -def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments] +def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments] populationid: int, platformid: int, tissueid: int, @@ -87,7 +87,7 @@ def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-argume (studyid, studyid)) return {**studydata, "studyid": studyid} -def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments] +def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments, too-many-positional-arguments] studyid: int, averageid: int, datasetname: str, diff --git a/uploader/default_settings.py b/uploader/default_settings.py index 1136ff8..c5986ab 100644 --- a/uploader/default_settings.py +++ b/uploader/default_settings.py @@ -2,7 +2,6 @@ The default configuration file. The values here should be overridden in the actual configuration file used for the production and staging systems. """ -import hashlib LOG_LEVEL = "WARNING" SECRET_KEY = b"<Please! Please! Please! Change This!>" @@ -25,7 +24,7 @@ SESSION_FILESYSTEM_CACHE_PATH = "./flask_session" SESSION_FILESYSTEM_CACHE_THRESHOLD = 500 SESSION_FILESYSTEM_CACHE_TIMEOUT = 300 SESSION_FILESYSTEM_CACHE_MODE = 0o600 -SESSION_FILESYSTEM_CACHE_HASH_METHOD = hashlib.md5 +SESSION_FILESYSTEM_CACHE_HASH_METHOD = None # default: hashlib.md5 ## --- END: Settings for CacheLib session type --- ## JWKS_ROTATION_AGE_DAYS = 7 # Days (from creation) to keep a JWK in use. diff --git a/uploader/files/views.py b/uploader/files/views.py index ddf5350..29059c7 100644 --- a/uploader/files/views.py +++ b/uploader/files/views.py @@ -1,4 +1,6 @@ """Module for generic files endpoints.""" +import time +import random import traceback from pathlib import Path @@ -56,10 +58,13 @@ 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: + app.logger.error("Merging chunk: %s", chunkfile) with open(chunkfile, "rb") as _chunkdata: _target.write(_chunkdata.read()) - chunkfile.unlink(missing_ok=True) + chunkfile.unlink() # Don't use `missing_ok=True` — chunk MUST exist + # If chunk does't exist, it might indicate a race condition. Handle + # that instead. return targetfile @@ -92,15 +97,51 @@ def resumable_upload_post(): 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() + ### HACK: Break possible race condition ### + # Looks like sometimes, there are multiple threads/requests trying + # to merge one file, leading to race conditions and in some rare + # instances, actual data corruption. This hack is meant to break + # that race condition. + _delays = ( + 101, 103, 107, 109, 113, 127, 131, 137, 139, 149, 151, 157, 163, + 167, 173, 179, 181, 191, 193, 197, 199, 211, 223, 227, 229, 233, + 239, 241, 251, 257, 263, 269, 271, 277, 281, 283, 293) + _lockfile = Path(chunks_directory(_fileid), "merge.lock") + while True: + time.sleep(random.choice(_delays) / 1000) + if (chunks_directory(_fileid).exists() + and not (_lockfile.exists() and _targetfile.exists())): + # merge_files and clean up chunks + _lockfile.touch() + __merge_chunks__(_targetfile, chunkpaths) + _lockfile.unlink() + chunks_directory(_fileid).rmdir() + continue + + if (_targetfile.exists() + and not ( + chunks_directory(_fileid).exists() + and _lockfile.exists())): + # merge complete + break + + # There is still a thread that's merging this file + continue + ### END: HACK: Break possible race condition ### + + if _targetfile.exists(): + return jsonify({ + "uploaded-file": _targetfile.name, + "original-name": _uploadfilename, + "message": "File was uploaded successfully!", + "statuscode": 200 + }), 200 return jsonify({ "uploaded-file": _targetfile.name, "original-name": _uploadfilename, - "message": "File was uploaded successfully!", - "statuscode": 200 - }), 200 + "message": "Uploaded file is missing!", + "statuscode": 404 + }), 404 return jsonify({ "message": f"Chunk {int(_chunk)} uploaded successfully.", "statuscode": 201 diff --git a/uploader/jobs.py b/uploader/jobs.py index e86ee05..5968c03 100644 --- a/uploader/jobs.py +++ b/uploader/jobs.py @@ -41,7 +41,8 @@ def error_filename(jobid, error_dir): "Compute the path of the file where errors will be dumped." return f"{error_dir}/job_{jobid}.error" -def initialise_job(# pylint: disable=[too-many-arguments] +def initialise_job( + # pylint: disable=[too-many-arguments, too-many-positional-arguments] rconn: Redis, rprefix: str, jobid: str, command: list, job_type: str, ttl_seconds: int = 86400, extra_meta: Optional[dict] = None) -> dict: "Initialise a job 'object' and put in on redis" @@ -54,7 +55,8 @@ def initialise_job(# pylint: disable=[too-many-arguments] name=job_key(rprefix, jobid), time=timedelta(seconds=ttl_seconds)) return the_job -def build_file_verification_job(#pylint: disable=[too-many-arguments] +def build_file_verification_job( + #pylint: disable=[too-many-arguments, too-many-positional-arguments] redis_conn: Redis, dburi: str, redisuri: str, @@ -77,7 +79,8 @@ def build_file_verification_job(#pylint: disable=[too-many-arguments] "filename": os.path.basename(filepath), "percent": 0 }) -def data_insertion_job(# pylint: disable=[too-many-arguments] +def data_insertion_job( + # pylint: disable=[too-many-arguments, too-many-positional-arguments] redis_conn: Redis, filepath: str, filetype: str, totallines: int, speciesid: int, platformid: int, datasetid: int, databaseuri: str, redisuri: str, ttl_seconds: int) -> dict: diff --git a/uploader/monadic_requests.py b/uploader/monadic_requests.py index f1f5c77..eda42d0 100644 --- a/uploader/monadic_requests.py +++ b/uploader/monadic_requests.py @@ -59,6 +59,11 @@ def get(url, params=None, **kwargs) -> Either: :rtype: pymonad.either.Either """ + timeout = kwargs.get("timeout") + kwargs = {key: val for key,val in kwargs.items() if key != "timeout"} + if timeout is None: + timeout = (9.13, 20) + try: resp = requests.get(url, params=params, **kwargs) if resp.status_code in SUCCESS_CODES: @@ -76,6 +81,11 @@ def post(url, data=None, json=None, **kwargs) -> Either: :rtype: pymonad.either.Either """ + timeout = kwargs.get("timeout") + kwargs = {key: val for key,val in kwargs.items() if key != "timeout"} + if timeout is None: + timeout = (9.13, 20) + try: resp = requests.post(url, data=data, json=json, **kwargs) if resp.status_code in SUCCESS_CODES: @@ -95,10 +105,10 @@ def make_either_error_handler(msg): try: _data = error.json() except Exception as _exc: - raise Exception(error.content) from _exc - raise Exception(_data) + raise Exception(error.content) from _exc# pylint: disable=[broad-exception-raised] + raise Exception(_data)# pylint: disable=[broad-exception-raised] app.logger.debug("\n\n%s\n\n", msg) - raise Exception(error) + raise Exception(error)# pylint: disable=[broad-exception-raised] return __fail__ diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py index 1efa299..b94a044 100644 --- a/uploader/oauth2/client.py +++ b/uploader/oauth2/client.py @@ -1,6 +1,7 @@ """OAuth2 client utilities.""" import json import time +import uuid import random from datetime import datetime, timedelta from urllib.parse import urljoin, urlparse @@ -42,7 +43,8 @@ def __fetch_auth_server_jwks__() -> KeySet: return KeySet([ JsonWebKey.import_key(key) for key in requests.get( - urljoin(authserver_uri(), "auth/public-jwks") + urljoin(authserver_uri(), "auth/public-jwks"), + timeout=(9.13, 20) ).json()["jwks"]]) @@ -146,9 +148,24 @@ def oauth2_client(): __client__) +def fetch_user_details() -> Either: + """Retrieve user details from the auth server""" + suser = session.session_info()["user"] + if suser["email"] == "anon@ymous.user": + udets = oauth2_get("auth/user/").then( + lambda usrdets: session.set_user_details({ + "user_id": uuid.UUID(usrdets["user_id"]), + "name": usrdets["name"], + "email": usrdets["email"], + "token": session.user_token()})) + return udets + return Right(suser) + + def user_logged_in(): """Check whether the user has logged in.""" suser = session.session_info()["user"] + fetch_user_details() return suser["logged_in"] and suser["token"].is_right() diff --git a/uploader/oauth2/tokens.py b/uploader/oauth2/tokens.py new file mode 100644 index 0000000..eb650f6 --- /dev/null +++ b/uploader/oauth2/tokens.py @@ -0,0 +1,47 @@ +"""Utilities for dealing with tokens.""" +import uuid +from typing import Union +from urllib.parse import urljoin +from datetime import datetime, timedelta + +from authlib.jose import jwt +from flask import current_app as app + +from uploader import monadic_requests as mrequests + +from . import jwks +from .client import (SCOPE, authserver_uri, oauth2_clientid) + + +def request_token(token_uri: str, user_id: Union[uuid.UUID, str], **kwargs): + """Request token from the auth server.""" + issued = datetime.now() + jwtkey = jwks.newest_jwk_with_rotation( + jwks.jwks_directory(app, "UPLOADER_SECRETS"), + int(app.config["JWKS_ROTATION_AGE_DAYS"])) + _mins2expiry = kwargs.get("minutes_to_expiry", 5) + return mrequests.post( + token_uri, + json={ + "grant_type": "urn:ietf:params:oauth:grant-type:jwt-bearer", + "scope": kwargs.get("scope", SCOPE), + "assertion": jwt.encode( + header={ + "alg": "RS256", + "typ": "JWT", + "kid": jwtkey.as_dict()["kid"] + }, + payload={ + "iss": str(oauth2_clientid()), + "sub": str(user_id), + "aud": urljoin(authserver_uri(), "auth/token"), + "exp": (issued + timedelta(minutes=_mins2expiry)).timestamp(), + "nbf": int(issued.timestamp()), + "iat": int(issued.timestamp()), + "jti": str(uuid.uuid4()) + }, + key=jwtkey).decode("utf8"), + "client_id": oauth2_clientid(), + **kwargs.get("extra_params", {}) + } + ) diff --git a/uploader/oauth2/views.py b/uploader/oauth2/views.py index a7211cb..1ee4257 100644 --- a/uploader/oauth2/views.py +++ b/uploader/oauth2/views.py @@ -1,9 +1,6 @@ """Views for OAuth2 related functionality.""" -import uuid -from datetime import datetime, timedelta from urllib.parse import urljoin, urlparse, urlunparse -from authlib.jose import jwt from flask import ( flash, jsonify, @@ -18,28 +15,29 @@ from uploader import monadic_requests as mrequests from uploader.monadic_requests import make_error_handler from . import jwks +from .tokens import request_token from .client import ( - SCOPE, - oauth2_get, user_logged_in, authserver_uri, oauth2_clientid, + fetch_user_details, oauth2_clientsecret) oauth2 = Blueprint("oauth2", __name__) + @oauth2.route("/code") def authorisation_code(): """Receive authorisation code from auth server and use it to get token.""" - def __process_error__(resp_or_exception): - app.logger.debug("ERROR: (%s)", resp_or_exception) + def __process_error__(error_response): + app.logger.debug("ERROR: (%s)", error_response.content) flash("There was an error retrieving the authorisation token.", - "alert-danger") + "alert alert-danger") return redirect("/") def __fail_set_user_details__(_failure): app.logger.debug("Fetching user details fails: %s", _failure) - flash("Could not retrieve the user details", "alert-danger") + flash("Could not retrieve the user details", "alert alert-danger") return redirect("/") def __success_set_user_details__(_success): @@ -48,52 +46,24 @@ def authorisation_code(): def __success__(token): session.set_user_token(token) - return oauth2_get("auth/user/").then( - lambda usrdets: session.set_user_details({ - "user_id": uuid.UUID(usrdets["user_id"]), - "name": usrdets["name"], - "email": usrdets["email"], - "token": session.user_token(), - "logged_in": True})).either( + return fetch_user_details().either( __fail_set_user_details__, __success_set_user_details__) code = request.args.get("code", "").strip() if not bool(code): - flash("AuthorisationError: No code was provided.", "alert-danger") + flash("AuthorisationError: No code was provided.", "alert alert-danger") return redirect("/") baseurl = urlparse(request.base_url, scheme=request.scheme) - issued = datetime.now() - jwtkey = jwks.newest_jwk_with_rotation( - jwks.jwks_directory(app, "UPLOADER_SECRETS"), - int(app.config["JWKS_ROTATION_AGE_DAYS"])) - return mrequests.post( - urljoin(authserver_uri(), "auth/token"), - json={ - "grant_type": "urn:ietf:params:oauth:grant-type:jwt-bearer", + return request_token( + token_uri=urljoin(authserver_uri(), "auth/token"), + user_id=request.args["user_id"], + extra_params={ "code": code, - "scope": SCOPE, "redirect_uri": urljoin( urlunparse(baseurl), url_for("oauth2.authorisation_code")), - "assertion": jwt.encode( - header={ - "alg": "RS256", - "typ": "JWT", - "kid": jwtkey.as_dict()["kid"] - }, - payload={ - "iss": str(oauth2_clientid()), - "sub": request.args["user_id"], - "aud": urljoin(authserver_uri(),"auth/token"), - "exp": (issued + timedelta(minutes=5)).timestamp(), - "nbf": int(issued.timestamp()), - "iat": int(issued.timestamp()), - "jti": str(uuid.uuid4()) - }, - key=jwtkey).decode("utf8"), - "client_id": oauth2_clientid() }).either(__process_error__, __success__) @oauth2.route("/public-jwks") @@ -116,7 +86,7 @@ def logout(): _user = session_info["user"] _user_str = f"{_user['name']} ({_user['email']})" session.clear_session_info() - flash("Successfully signed out.", "alert-success") + flash("Successfully signed out.", "alert alert-success") return redirect("/") if user_logged_in(): @@ -134,5 +104,5 @@ def logout(): cleanup_thunk=lambda: __unset_session__( session.session_info())), lambda res: __unset_session__(session.session_info())) - flash("There is no user that is currently logged in.", "alert-info") + flash("There is no user that is currently logged in.", "alert alert-info") return redirect("/") diff --git a/uploader/phenotypes/misc.py b/uploader/phenotypes/misc.py new file mode 100644 index 0000000..cbe3b7f --- /dev/null +++ b/uploader/phenotypes/misc.py @@ -0,0 +1,26 @@ +"""Miscellaneous functions handling phenotypes and phenotypes data.""" +import logging + +logger = logging.getLogger(__name__) + + +def phenotypes_data_differences( + filedata: tuple[dict, ...], dbdata: tuple[dict, ...] +) -> tuple[dict, ...]: + """Compute differences between file data and db data""" + diff = tuple() + for filerow, dbrow in zip( + sorted(filedata, key=lambda item: (item["phenotype_id"], item["xref_id"])), + sorted(dbdata, key=lambda item: (item["PhenotypeId"], item["xref_id"]))): + for samplename, value in filerow["data"].items(): + if value != dbrow["data"].get(samplename, {}).get("value"): + diff = diff + ({ + "PhenotypeId": filerow["phenotype_id"], + "xref_id": filerow["xref_id"], + "DataId": dbrow["DataId"], + "StrainId": dbrow["data"].get(samplename, {}).get("StrainId"), + "StrainName": samplename, + "value": value + },) + + return diff diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index ce7720c..e40155f 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -1,14 +1,31 @@ """Database and utility functions for phenotypes.""" -from typing import Optional +import logging +import tempfile +from pathlib import Path from functools import reduce from datetime import datetime +from typing import Optional, Iterable import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor -from flask import current_app as app from gn_libs.mysqldb import debug_query +from functional_tools import take + +logger = logging.getLogger(__name__) + + +__PHENO_DATA_TABLES__ = { + "PublishData": { + "table": "PublishData", "valueCol": "value", "DataIdCol": "Id"}, + "PublishSE": { + "table": "PublishSE", "valueCol": "error", "DataIdCol": "DataId"}, + "NStrain": { + "table": "NStrain", "valueCol": "count", "DataIdCol": "DataId"} +} + + def datasets_by_population( conn: mdb.Connection, species_id: int, @@ -32,10 +49,10 @@ def dataset_by_id(conn: mdb.Connection, """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", + "SELECT Species.SpeciesId, PublishFreeze.* FROM Species " + "INNER JOIN InbredSet ON Species.Id=InbredSet.SpeciesId " + "INNER JOIN PublishFreeze ON InbredSet.Id=PublishFreeze.InbredSetId " + "WHERE Species.Id=%s AND InbredSet.Id=%s AND PublishFreeze.Id=%s", (species_id, population_id, dataset_id)) return dict(cursor.fetchone()) @@ -75,7 +92,8 @@ def dataset_phenotypes(conn: mdb.Connection, limit: Optional[int] = None) -> tuple[dict, ...]: """Fetch the actual phenotypes.""" _query = ( - "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode FROM Phenotype AS pheno " + "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, 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 " @@ -83,7 +101,7 @@ def dataset_phenotypes(conn: mdb.Connection, 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) + debug_query(cursor, logger) return tuple(dict(row) for row in cursor.fetchall()) @@ -94,7 +112,7 @@ def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids): cursor.execute("SELECT * FROM PublishSE WHERE (DataId, StrainId) IN " f"({paramstr})", flat) - debug_query(cursor, app.logger) + debug_query(cursor, logger) _se = { (row["DataId"], row["StrainId"]): { "DataId": row["DataId"], @@ -107,7 +125,7 @@ def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids): cursor.execute("SELECT * FROM NStrain WHERE (DataId, StrainId) IN " f"({paramstr})", flat) - debug_query(cursor, app.logger) + debug_query(cursor, logger) _n = { (row["DataId"], row["StrainId"]): { "DataId": row["DataId"], @@ -137,6 +155,7 @@ def __organise_by_phenotype__(pheno, row): "Pre_publication_abbreviation": row["Pre_publication_abbreviation"], "Post_publication_abbreviation": row["Post_publication_abbreviation"], "xref_id": row["pxr.Id"], + "DataId": row["DataId"], "data": { **(_pheno["data"] if bool(_pheno) else {}), (row["DataId"], row["StrainId"]): { @@ -200,7 +219,7 @@ def phenotype_by_id( ).values()) } if bool(_pheno) and len(_pheno.keys()) > 1: - raise Exception( + raise Exception(# pylint: disable=[broad-exception-raised] "We found more than one phenotype with the same identifier!") return None @@ -225,7 +244,7 @@ def phenotypes_data(conn: mdb.Connection, 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) + debug_query(cursor, logger) return tuple(dict(row) for row in cursor.fetchall()) @@ -252,7 +271,7 @@ def save_new_dataset(cursor: Cursor, "%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, " "%(users)s)", params) - debug_query(cursor, app.logger) + debug_query(cursor, logger) return {**params, "Id": cursor.lastrowid} @@ -262,8 +281,11 @@ def phenotypes_data_by_ids( ) -> tuple[dict, ...]: """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Phenotype AS pheno " + _query = ("SELECT " + "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " + "FROM Publication AS pub " + "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " + "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " "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 " @@ -277,6 +299,213 @@ def phenotypes_data_by_ids( for item in (row["population_id"], row["phenoid"], row["xref_id"]))) - debug_query(cursor, app.logger) + debug_query(cursor, logger) return tuple( reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values()) + + +def __pre_process_phenotype_data__(row): + _desc = row.get("description", "") + _pre_pub_desc = row.get("pre_publication_description", _desc) + _orig_desc = row.get("original_description", _desc) + _post_pub_desc = row.get("post_publication_description", _orig_desc) + _pre_pub_abbr = row.get("pre_publication_abbreviation", row["id"]) + _post_pub_abbr = row.get("post_publication_abbreviation", _pre_pub_abbr) + return { + "pre_publication_description": _pre_pub_desc, + "post_publication_description": _post_pub_desc, + "original_description": _orig_desc, + "units": row["units"], + "pre_publication_abbreviation": _pre_pub_abbr, + "post_publication_abbreviation": _post_pub_abbr + } + + +def create_new_phenotypes(# pylint: disable=[too-many-locals] + conn: mdb.Connection, + population_id: int, + publication_id: int, + phenotypes: Iterable[dict] +) -> tuple[dict, ...]: + """Add entirely new phenotypes to the database. WARNING: Not thread-safe.""" + _phenos = tuple() + with conn.cursor(cursorclass=DictCursor) as cursor: + def make_next_id(idcol, table): + cursor.execute(f"SELECT MAX({idcol}) AS last_id FROM {table}") + _last_id = int(cursor.fetchone()["last_id"]) + def __next_id__(): + _next_id = _last_id + 1 + while True: + yield _next_id + _next_id = _next_id + 1 + + return __next_id__ + + ### Bottleneck: Everything below makes this function not ### + ### thread-safe because we have to retrieve the last IDs from ### + ### the database and increment those to compute the next IDs. ### + ### This is an unfortunate result from the current schema that ### + ### has a cross-reference table that requires that a phenotype ### + ### be linked to an existing publication, and have data IDs to ### + ### link to that phenotype's data. ### + ### The fact that the IDs are sequential also compounds the ### + ### bottleneck. ### + ### + ### For extra safety, ensure the following tables are locked ### + ### for `WRITE`: ### + ### - PublishXRef ### + ### - Phenotype ### + ### - PublishXRef ### + __next_xref_id = make_next_id("Id", "PublishXRef")() + __next_pheno_id__ = make_next_id("Id", "Phenotype")() + __next_data_id__ = make_next_id("DataId", "PublishXRef")() + + def __build_params_and_prepubabbrevs__(acc, row): + processed = __pre_process_phenotype_data__(row) + return ( + acc[0] + ({ + **processed, + "population_id": population_id, + "publication_id": publication_id, + "phenotype_id": next(__next_pheno_id__), + "xref_id": next(__next_xref_id), + "data_id": next(__next_data_id__) + },), + acc[1] + (processed["pre_publication_abbreviation"],)) + while True: + batch = take(phenotypes, 1000) + if len(batch) == 0: + break + + params, abbrevs = reduce(__build_params_and_prepubabbrevs__, + batch, + (tuple(), tuple())) + # Check for uniqueness for all "Pre_publication_description" values + abbrevs_paramsstr = ", ".join(["%s"] * len(abbrevs)) + _query = ("SELECT PublishXRef.PhenotypeId, Phenotype.* " + "FROM PublishXRef " + "INNER JOIN Phenotype " + "ON PublishXRef.PhenotypeId=Phenotype.Id " + "WHERE PublishXRef.InbredSetId=%s " + "AND Phenotype.Pre_publication_abbreviation IN " + f"({abbrevs_paramsstr})") + cursor.execute(_query, + ((population_id,) + abbrevs)) + existing = tuple(row["Pre_publication_abbreviation"] + for row in cursor.fetchall()) + if len(existing) > 0: + # Narrow this exception, perhaps? + raise Exception(# pylint: disable=[broad-exception-raised] + "Found already existing phenotypes with the following " + "'Pre-publication abbreviations':\n\t" + "\n\t".join(f"* {item}" for item in existing)) + + cursor.executemany( + ( + "INSERT INTO " + "Phenotype(" + "Id, " + "Pre_publication_description, " + "Post_publication_description, " + "Original_description, " + "Units, " + "Pre_publication_abbreviation, " + "Post_publication_abbreviation, " + "Authorized_Users" + ")" + "VALUES (" + "%(phenotype_id)s, " + "%(pre_publication_description)s, " + "%(post_publication_description)s, " + "%(original_description)s, " + "%(units)s, " + "%(pre_publication_abbreviation)s, " + "%(post_publication_abbreviation)s, " + "'robwilliams'" + ")"), + params) + _comments = f"Created at {datetime.now().isoformat()}" + cursor.executemany( + ("INSERT INTO PublishXRef(" + "Id, " + "InbredSetId, " + "PhenotypeId, " + "PublicationId, " + "DataId, " + "comments" + ")" + "VALUES(" + "%(xref_id)s, " + "%(population_id)s, " + "%(phenotype_id)s, " + "%(publication_id)s, " + "%(data_id)s, " + f"'{_comments}'" + ")"), + params) + _phenos = _phenos + params + + return _phenos + + +def save_phenotypes_data( + conn: mdb.Connection, + table: str, + data: Iterable[dict] +) -> int: + """Save new phenotypes data into the database.""" + _table_details = __PHENO_DATA_TABLES__[table] + with conn.cursor(cursorclass=DictCursor) as cursor: + _count = 0 + while True: + batch = take(data, 100000) + if len(batch) == 0: + logger.warning("Got an empty batch. This needs investigation.") + break + + logger.debug("Saving batch of %s items.", len(batch)) + cursor.executemany( + (f"INSERT INTO {_table_details['table']}" + f"({_table_details['DataIdCol']}, StrainId, {_table_details['valueCol']}) " + "VALUES " + f"(%(data_id)s, %(sample_id)s, %(value)s) "), + tuple(batch)) + debug_query(cursor, logger) + _count = _count + len(batch) + + + logger.debug("Saved a total of %s data rows", _count) + return _count + + +def quick_save_phenotypes_data( + conn: mdb.Connection, + table: str, + dataitems: Iterable[dict], + tmpdir: Path +) -> int: + """Save data items to the database, but using """ + _table_details = __PHENO_DATA_TABLES__[table] + with (tempfile.NamedTemporaryFile( + prefix=f"{table}_data", mode="wt", dir=tmpdir) as tmpfile, + conn.cursor(cursorclass=DictCursor) as cursor): + _count = 0 + logger.debug("Write data rows to text file.") + for row in dataitems: + tmpfile.write( + f'{row["data_id"]}\t{row["sample_id"]}\t{row["value"]}\n') + _count = _count + 1 + tmpfile.flush() + + logger.debug("Load text file into database (table: %s)", + _table_details["table"]) + cursor.execute( + f"LOAD DATA LOCAL INFILE '{tmpfile.name}' " + f"INTO TABLE {_table_details['table']} " + "(" + f"{_table_details['DataIdCol']}, " + "StrainId, " + f"{_table_details['valueCol']}" + ")") + debug_query(cursor, logger) + return _count diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 407493c..7002ccd 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,46 +1,53 @@ -"""Views handling ('classical') phenotypes.""" +"""Views handling ('classical') phenotypes."""# pylint: disable=[too-many-lines] import sys -import csv import uuid import json -import datetime -import tempfile +import logging 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 urllib.parse import urljoin, urlparse, ParseResult, urlunparse, urlencode + +import datetime from redis import Redis from pymonad.either import Left from requests.models import Response from MySQLdb.cursors import DictCursor -from werkzeug.utils import secure_filename + +from gn_libs import sqlite3 +from gn_libs import jobs as gnlibs_jobs +from gn_libs.jobs.jobs import JobNotFound from gn_libs.mysqldb import database_connection + from flask import (flash, request, url_for, jsonify, redirect, Blueprint, - send_file, 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 import session from uploader.files import save_file#, fullpath from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post +from uploader.oauth2.tokens import request_token from uploader.authorisation import require_login +from uploader.oauth2 import client as oauth2client +from uploader.route_utils import build_next_argument from uploader.route_utils import generic_select_population from uploader.datautils import safe_int, enumerate_sequence from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler +from uploader.publications.models import fetch_publication_by_id from uploader.request_checks import with_species, with_population -from uploader.samples.models import samples_by_species_and_population from uploader.input_validation import (encode_errors, decode_errors, is_valid_representative_name) @@ -51,9 +58,9 @@ from .models import (dataset_by_id, save_new_dataset, dataset_phenotypes, datasets_by_population, - phenotypes_data_by_ids, phenotype_publication_data) +logger = logging.getLogger(__name__) phenotypesbp = Blueprint("phenotypes", __name__) render_template = make_template_renderer("phenotypes") @@ -227,11 +234,6 @@ def view_phenotype(# pylint: disable=[unused-argument] 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, @@ -240,19 +242,14 @@ def view_phenotype(# pylint: disable=[unused-argument] 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 - ), + publication=(phenotype_publication_data(conn, phenotype["Id"]) or {}), + privileges=privileges, + next=build_next_argument( + uri="species.populations.phenotypes.view_phenotype", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"], + xref_id=xref_id), activelink="view-phenotype") def __fail__(error): @@ -359,10 +356,17 @@ def process_phenotypes_individual_files(error_uri): 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")): + for rqtlkey, formkey, _type in ( + ("phenocovar", "phenotype-descriptions", "mandatory"), + ("pheno", "phenotype-data", "mandatory"), + ("phenose", "phenotype-se", "optional"), + ("phenonum", "phenotype-n", "optional")): + if _type == "optional" and not bool(form.get(formkey)): + continue # skip if an optional key does not exist. + + cdata[f"{rqtlkey}_transposed"] = ( + (form.get(f"{formkey}-transposed") or "off") == "on") + if form.get("resumable-upload", False): # Chunked upload of large files was used filedata = json.loads(form[formkey]) @@ -371,7 +375,7 @@ def process_phenotypes_individual_files(error_uri): arcname=filedata["original-name"]) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]] else: - # TODO: Check this path: fix any bugs. + # T0DO: Check this path: fix any bugs. _sentfile = request.files[formkey] if not bool(_sentfile): flash(f"Expected file ('{formkey}') was not provided.", @@ -385,6 +389,7 @@ def process_phenotypes_individual_files(error_uri): arcname=filepath.name) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name] + zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2)) return bundlepath @@ -409,10 +414,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p 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 - ): + with Redis.from_url(_redisuri, decode_responses=True) as rconn: if request.method == "GET": today = datetime.date.today() return render_template( @@ -447,24 +449,20 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p [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()], + logging.getLevelName( + app.logger.getEffectiveLevel() + ).lower(), "--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())})}), + "bundle": str(phenobundle.absolute()), + **({"publicationid": request.form["publication-id"]} + if request.form.get("publication-id") else {})})}), _redisuri, f"{app.config['UPLOAD_FOLDER']}/job_errors") @@ -537,7 +535,8 @@ def review_job_data( **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: + with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, + database_connection(app.config["SQL_URI"]) as conn): try: job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) except jobs.JobNotFound as _jnf: @@ -585,6 +584,7 @@ def review_job_data( filetype: __summarise__(filetype, meta) for filetype,meta in metadata.items() } + _job_metadata = json.loads(job["job-metadata"]) return render_template("phenotypes/review-job-data.html", species=species, population=population, @@ -592,9 +592,103 @@ def review_job_data( job_id=job_id, job=job, summary=summary, + publication=( + fetch_publication_by_id( + conn, int(_job_metadata["publicationid"])) + if _job_metadata.get("publicationid") + else None), activelink="add-phenotypes") +def load_phenotypes_success_handler(job): + """Handle loading new phenotypes into the database successfully.""" + return redirect(url_for( + "species.populations.phenotypes.load_data_success", + species_id=job["metadata"]["species_id"], + population_id=job["metadata"]["population_id"], + dataset_id=job["metadata"]["dataset_id"], + job_id=job["job_id"])) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/load-data-to-database", + methods=["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 load_data_to_database( + species: dict, + population: dict, + dataset: dict, + **kwargs +):# pylint: disable=[unused-argument] + """Load the data from the given QC job into the database.""" + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, + sqlite3.connection(_jobs_db) as conn): + # T0DO: Maybe break the connection between the jobs here, pass: + # - the bundle name (rebuild the full path here.) + # - publication details, where separate + # - details about the files: e.g. total lines, etc + qc_job = jobs.job(rconn, jobs.jobsnamespace(), request.form["data-qc-job-id"]) + _meta = json.loads(qc_job["job-metadata"]) + _load_job_id = uuid.uuid4() + _loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower() + command = [ + sys.executable, + "-u", + "-m", + "scripts.load_phenotypes_to_db", + app.config["SQL_URI"], + _jobs_db, + str(_load_job_id), + "--log-level", + _loglevel + ] + + def __handle_error__(resp): + return render_template("http-error.html", *resp.json()) + + def __handle_success__(load_job): + app.logger.debug("The phenotypes loading job: %s", load_job) + return redirect(url_for( + "background-jobs.job_status", job_id=load_job["job_id"])) + + + return request_token( + token_uri=urljoin(oauth2client.authserver_uri(), "auth/token"), + user_id=session.user_details()["user_id"] + ).then( + lambda token: gnlibs_jobs.initialise_job( + conn, + _load_job_id, + command, + "load-new-phenotypes-data", + extra_meta={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "bundle_file": _meta["bundle"], + "publication_id": _meta["publicationid"], + "authserver": oauth2client.authserver_uri(), + "token": token["access_token"], + "success_handler": ( + "uploader.phenotypes.views" + ".load_phenotypes_success_handler") + }) + ).then( + lambda job: gnlibs_jobs.launch_job( + job, + _jobs_db, + Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), + worker_manager="gn_libs.jobs.launcher", + loglevel=_loglevel) + ).either(__handle_error__, __handle_success__) + + def update_phenotype_metadata(conn, metadata: dict): """Update a phenotype's basic metadata values.""" with conn.cursor(cursorclass=DictCursor) as cursor: @@ -747,12 +841,7 @@ def edit_phenotype_data(# pylint: disable=[unused-argument] 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 - ) + "privileges": kwargs.get("privileges", tuple()) } return render_template( "phenotypes/edit-phenotype.html", @@ -852,82 +941,137 @@ def edit_phenotype_data(# pylint: disable=[unused-argument] xref_id=xref_id)) -def process_phenotype_data_for_download(pheno: dict) -> dict: - """Sanitise data for download.""" - return { - "UniqueIdentifier": f"phId:{pheno['Id']}::xrId:{pheno['xref_id']}", - **{ - key: val for key, val in pheno.items() - if key not in ("Id", "xref_id", "data", "Units") - }, - **{ - data_item["StrainName"]: data_item["value"] - for data_item in pheno.get("data", {}).values() - } - } +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/load-data-success/<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 load_data_success( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs +):# pylint: disable=[unused-argument] + """Display success page if loading data to database was successful.""" + with (database_connection(app.config["SQL_URI"]) as conn, + sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) + as jobsconn): + try: + gn2_uri = urlparse(app.config["GN2_SERVER_URL"]) + job = gnlibs_jobs.job(jobsconn, job_id, fulldetails=True) + app.logger.debug("THE JOB: %s", job) + _xref_ids = tuple( + str(item) for item + in json.loads(job["metadata"].get("xref_ids", "[]"))) + _publication = fetch_publication_by_id( + conn, int(job["metadata"].get("publication_id", "0"))) + _search_terms = (item for item in + (str(_publication["PubMed_ID"] or ""), + _publication["Authors"], + (_publication["Title"] or "")) + if item != "") + return render_template("phenotypes/load-phenotypes-success.html", + species=species, + population=population, + dataset=dataset, + job=job, + search_page_uri=urlunparse(ParseResult( + scheme=gn2_uri.scheme, + netloc=gn2_uri.netloc, + path="/search", + params="", + query=urlencode({ + "species": species["Name"], + "group": population["Name"], + "type": "Phenotypes", + "dataset": dataset["Name"], + "search_terms_or": ( + # Very long URLs will cause + # errors. + " ".join(_xref_ids) + if len(_xref_ids) <= 100 + else ""), + "search_terms_and": " ".join( + _search_terms).strip(), + "accession_id": "None", + "FormID": "searchResult" + }), + fragment=""))) + except JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" - "/<int:dataset_id>/download", + "/<int:dataset_id>/recompute-means", methods=["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 download_phenotype_data(# pylint: disable=[unused-argument] +def recompute_means(# pylint: disable=[unused-argument] species: dict, population: dict, dataset: dict, **kwargs ): - formdata = request.json - with database_connection(app.config["SQL_URI"]) as conn: - samples_list = [ - sample["Name"] for sample in samples_by_species_and_population( - conn, species["SpeciesId"], population["Id"])] - data = ( - process_phenotype_data_for_download(pheno) - for pheno in phenotypes_data_by_ids(conn, tuple({ + """Compute/Recompute the means for phenotypes in a particular population.""" + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + _job_id = uuid.uuid4() + _xref_ids = tuple(int(item.split("_")[-1]) + for item in request.form.getlist("selected-phenotypes")) + + _loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower() + command = [ + sys.executable, + "-u", + "-m", + "scripts.compute_phenotype_means", + app.config["SQL_URI"], + _jobs_db, + str(population["Id"]), + "--log-level", + _loglevel] + ( + ["--cross-ref-ids", ",".join(str(_id) for _id in _xref_ids)] + if len(_xref_ids) > 0 else + []) + logger.debug("%s.recompute_means: command (%s)", __name__, command) + + with sqlite3.connection(_jobs_db) as conn: + _job = gnlibs_jobs.launch_job( + gnlibs_jobs.initialise_job( + conn, + _job_id, + command, + "(re)compute-phenotype-means", + extra_meta={ + "species_id": species["SpeciesId"], "population_id": population["Id"], - "phenoid": row["phenotype_id"], - "xref_id": row["xref_id"] - } for row in formdata))) - - with (tempfile.TemporaryDirectory( - prefix=app.config["TEMPORARY_DIRECTORY"]) as tmpdir): - filename = Path(tmpdir).joinpath("tempfile.tsv") - with open(filename, mode="w") as outfile: - outfile.write( - "# **DO NOT** delete the 'UniqueIdentifier' field. It is used " - "by the system to identify and edit the correct row(s) in the " - "database.\n") - outfile.write( - "# The '…_description' fields are useful for you to figure out " - "what row you are working on. Changing any of this fields will " - "also update the database, so do be careful.\n") - outfile.write( - "# Leave a field empty to delete the value in the database.\n") - outfile.write( - "# Any line beginning with a '#' character is considered a " - "comment line. This line, and all the lines above it, are " - "all comment lines. Comment lines will be ignored.\n") - writer = csv.DictWriter(outfile, - fieldnames=[ - "UniqueIdentifier", - "Post_publication_description", - "Pre_publication_abbreviation", - "Pre_publication_description", - "Original_description", - "Post_publication_abbreviation" - ] + samples_list, - dialect="excel-tab") - writer.writeheader() - writer.writerows(data) - outfile.flush() - - return send_file( - filename, - mimetype="text/csv", - as_attachment=True, - download_name=secure_filename(f"{dataset['Name']}_data")) + "dataset_id": dataset["Id"], + "success_handler": ( + "uploader.phenotypes.views." + "recompute_phenotype_means_success_handler") + }), + _jobs_db, + Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), + worker_manager="gn_libs.jobs.launcher", + loglevel=_loglevel) + return redirect(url_for("background-jobs.job_status", + job_id=_job["job_id"])) + + +def recompute_phenotype_means_success_handler(job): + """Handle loading new phenotypes into the database successfully.""" + flash("Means computed successfully!", "alert alert-success") + return redirect(url_for( + "species.populations.phenotypes.view_dataset", + species_id=job["metadata"]["species_id"], + population_id=job["metadata"]["population_id"], + dataset_id=job["metadata"]["dataset_id"], + job_id=job["job_id"])) diff --git a/uploader/platforms/models.py b/uploader/platforms/models.py index a859371..0dd9368 100644 --- a/uploader/platforms/models.py +++ b/uploader/platforms/models.py @@ -56,7 +56,8 @@ def platform_by_species_and_id( return None -def save_new_platform(# pylint: disable=[too-many-arguments] +def save_new_platform( + # pylint: disable=[too-many-arguments, too-many-positional-arguments] cursor: Cursor, species_id: int, geo_platform: str, diff --git a/uploader/population/models.py b/uploader/population/models.py index d78a821..4d95065 100644 --- a/uploader/population/models.py +++ b/uploader/population/models.py @@ -26,13 +26,23 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: return tuple() +__GENERIC_POPULATION_FAMILIES__ = ( + "Reference Populations (replicate average, SE, N)", + "Crosses and Heterogeneous Stock (individuals)", + "Groups Without Genotypes") -def population_families(conn) -> tuple: +def population_families(conn, species_id: int) -> tuple[str]: """Fetch the families under which populations are grouped.""" with conn.cursor(cursorclass=DictCursor) as cursor: + paramstr = ", ".join(["%s"] * len(__GENERIC_POPULATION_FAMILIES__)) cursor.execute( - "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL") - return tuple(row["Family"] for row in cursor.fetchall()) + "SELECT DISTINCT(Family) FROM InbredSet " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL " + f"AND Family NOT IN ({paramstr})", + (species_id, *__GENERIC_POPULATION_FAMILIES__)) + return __GENERIC_POPULATION_FAMILIES__ + tuple( + row["Family"] for row in cursor.fetchall()) def population_genetic_types(conn) -> tuple: @@ -47,9 +57,11 @@ def population_genetic_types(conn) -> tuple: def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dict: """Save the population details to the db.""" cursor.execute("SELECT DISTINCT(Family), FamilyOrder FROM InbredSet " - "WHERE Family IS NOT NULL AND Family != '' " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL AND Family != '' " "AND FamilyOrder IS NOT NULL " - "ORDER BY FamilyOrder ASC") + "ORDER BY FamilyOrder ASC", + (population_details["SpeciesId"],)) _families = { row["Family"]: int(row["FamilyOrder"]) for row in cursor.fetchall() diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py index 044cdd4..97d4854 100644 --- a/uploader/population/rqtl2.py +++ b/uploader/population/rqtl2.py @@ -12,9 +12,9 @@ import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection +from markupsafe import escape from flask import ( flash, - escape, request, url_for, redirect, diff --git a/uploader/population/views.py b/uploader/population/views.py index 270dd5f..87a33d9 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -100,7 +100,7 @@ def create_population(species_id: int): return render_template( "populations/create-population.html", species=species, - families = population_families(conn), + families = population_families(conn, species["SpeciesId"]), genetic_types = population_genetic_types(conn), mapping_methods=( {"id": "0", "value": "No mapping support"}, @@ -153,7 +153,7 @@ def create_population(species_id: int): "FullName": population_fullname, "InbredSetCode": request.form.get("population_code") or None, "Description": request.form.get("population_description") or None, - "Family": request.form.get("population_family") or None, + "Family": request.form.get("population_family").strip() or None, "MappingMethodId": request.form.get("population_mapping_method_id"), "GeneticType": request.form.get("population_genetic_type") or None }) diff --git a/uploader/publications/__init__.py b/uploader/publications/__init__.py new file mode 100644 index 0000000..7efcabb --- /dev/null +++ b/uploader/publications/__init__.py @@ -0,0 +1,2 @@ +"""Package for handling publications.""" +from .views import pubbp diff --git a/uploader/publications/datatables.py b/uploader/publications/datatables.py new file mode 100644 index 0000000..e07fafd --- /dev/null +++ b/uploader/publications/datatables.py @@ -0,0 +1,52 @@ +"""Fetch data for datatables.""" +import logging +from typing import Optional + +from MySQLdb.cursors import DictCursor + +from gn_libs.mysqldb import Connection, debug_query + +logger = logging.getLogger(__name__) + +def fetch_publications( + conn: Connection, + search: Optional[str] = None, + offset: int = 0, + limit: int = -1 +) -> tuple[dict, int, int, int]: + """Fetch publications from the database.""" + _query = "SELECT * FROM Publication" + _count_query = "SELECT COUNT(*) FROM Publication" + _params = None + _where_clause = "" + _limit_clause = "" + if search is not None and bool(search): + _where_clause = ("WHERE PubMed_ID LIKE %s " + "OR Authors LIKE %s " + "OR Title LIKE %s") + _params = (f"%{search}%",) * 3 + + if limit > 0: + _limit_clause = f"LIMIT {limit} OFFSET {offset}" + + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT COUNT(*) FROM Publication") + _total_rows = int(cursor.fetchone()["COUNT(*)"]) + + cursor.execute(f"{_count_query} {_where_clause}", _params) + debug_query(cursor, logger) + _result = cursor.fetchone() + _total_filtered = int(_result["COUNT(*)"] if bool(_result) else 0) + + cursor.execute(f"{_query} {_where_clause} {_limit_clause}", _params) + debug_query(cursor, logger) + _current_filtered = tuple( + {**dict(row), "index": idx} + for idx, row + in enumerate(cursor.fetchall(), start=offset+1)) + + return ( + _current_filtered, + len(_current_filtered), + _total_filtered, + _total_rows) diff --git a/uploader/publications/misc.py b/uploader/publications/misc.py new file mode 100644 index 0000000..fca6f71 --- /dev/null +++ b/uploader/publications/misc.py @@ -0,0 +1,25 @@ +"""Miscellaneous functions dealing with publications.""" + + +def publications_differences( + filedata: tuple[dict, ...], + dbdata: tuple[dict, ...], + pubmedid2pubidmap: tuple[dict, ...] +) -> tuple[dict, ...]: + """Compute the differences between file data and db data""" + diff = tuple() + for filerow, dbrow in zip( + sorted(filedata, key=lambda item: ( + item["phenotype_id"], item["xref_id"])), + sorted(dbdata, key=lambda item: ( + item["PhenotypeId"], item["xref_id"]))): + if filerow["PubMed_ID"] == dbrow["PubMed_ID"]: + continue + + newpubmed = filerow["PubMed_ID"] + diff = diff + ({ + **dbrow, + "PubMed_ID": newpubmed, + "PublicationId": pubmedid2pubidmap.get(newpubmed)},) + + return diff diff --git a/uploader/publications/models.py b/uploader/publications/models.py new file mode 100644 index 0000000..dcfa02b --- /dev/null +++ b/uploader/publications/models.py @@ -0,0 +1,119 @@ +"""Module to handle persistence and retrieval of publication to/from MariaDB""" +import logging +from typing import Iterable + +from MySQLdb.cursors import DictCursor + +from gn_libs.mysqldb import Connection, debug_query + +logger = logging.getLogger(__name__) + + +def fetch_phenotype_publications( + conn: Connection, + ids: tuple[tuple[int, int], ...] +) -> tuple[dict, ...]: + """Fetch publication from database by ID.""" + paramstr = ",".join(["(%s, %s)"] * len(ids)) + query = ( + "SELECT " + "pxr.PhenotypeId, pxr.Id AS xref_id, pxr.PublicationId, pub.PubMed_ID " + "FROM PublishXRef AS pxr INNER JOIN Publication AS pub " + "ON pxr.PublicationId=pub.Id " + f"WHERE (pxr.PhenotypeId, pxr.Id) IN ({paramstr})") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(query, tuple(item for row in ids for item in row)) + return tuple(dict(row) for row in cursor.fetchall()) + + +def create_new_publications( + conn: Connection, + publications: tuple[dict, ...] +) -> tuple[dict, ...]: + """Create new publications in the database.""" + if len(publications) > 0: + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.executemany( + ("INSERT INTO " + "Publication( " + "PubMed_ID, Abstract, Authors, Title, Journal, Volume, Pages, " + "Month, Year" + ") " + "VALUES(" + "%(pubmed_id)s, %(abstract)s, %(authors)s, %(title)s, " + "%(journal)s, %(volume)s, %(pages)s, %(month)s, %(year)s" + ") " + "RETURNING *"), + publications) + return tuple({ + **row, "publication_id": row["Id"] + } for row in cursor.fetchall()) + + return tuple() + + +def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tuple[dict, ...]: + """Update details for multiple publications""" + if len(publications) > 0: + with conn.cursor(cursorclass=DictCursor) as cursor: + logger.debug("UPDATING PUBLICATIONS: %s", publications) + cursor.executemany( + ("UPDATE Publication SET " + "PubMed_ID=%(pubmed_id)s, Abstract=%(abstract)s, " + "Authors=%(authors)s, Title=%(title)s, Journal=%(journal)s, " + "Volume=%(volume)s, Pages=%(pages)s, Month=%(month)s, " + "Year=%(year)s " + "WHERE Id=%(publication_id)s"), + publications) + debug_query(cursor, logger) + return publications + return tuple() + return tuple() + + +def delete_publications(conn: Connection , publications: tuple[dict, ...]): + """Delete multiple publications""" + publications = tuple(pub for pub in publications if bool(pub)) + if len(publications) > 0: + _pub_ids = tuple(pub["Id"] for pub in publications) + _paramstr = ", ".join(["%s"] * len(_pub_ids)) + _phenos_query = ( + "SELECT PublicationId, COUNT(PhenotypeId) FROM PublishXRef " + f"WHERE PublicationId IN ({_paramstr}) GROUP BY PublicationId;") + + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_phenos_query, _pub_ids) + _linked_phenos = cursor.fetchall() + if len(_linked_phenos) > 0: + raise Exception(# pylint: disable=[broad-exception-raised] + "Cannot delete publications with linked phenotypes.") + + cursor.execute( + f"DELETE FROM Publication WHERE Id IN ({_paramstr})", _pub_ids) + + +def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict: + """Fetch a specific publication from the database.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM Publication WHERE Id=%s", + (publication_id,)) + _res = cursor.fetchone() + return dict(_res) if _res else {} + + +def fetch_publication_phenotypes( + conn: Connection, publication_id: int) -> Iterable[dict]: + """Fetch all phenotypes linked to this publication.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT pxr.Id AS xref_id, pxr.PublicationId, phe.* " + "FROM PublishXRef AS pxr INNER JOIN Phenotype AS phe " + "ON pxr.PhenotypeId=phe.Id " + "WHERE pxr.PublicationId=%s", + (publication_id,)) + while True: + row = cursor.fetchone() + if row: + yield row + else: + break diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py new file mode 100644 index 0000000..2531c4a --- /dev/null +++ b/uploader/publications/pubmed.py @@ -0,0 +1,102 @@ +"""Module to interact with NCBI's PubMed""" +import logging + +import requests +from lxml import etree + +logger = logging.getLogger(__name__) + + +def __pub_date__(pubdate: etree.Element): + pubyear = pubdate.find("Year") + pubmonth = pubdate.find("Month") + pubday = pubdate.find("Day") + return { + "year": pubyear.text if pubyear is not None else None, + "month": pubmonth.text if pubmonth is not None else None, + "day": pubday.text if pubday is not None else None + } + + +def __journal__(journal: etree.Element) -> dict: + volume = journal.find("JournalIssue/Volume") + issue = journal.find("JournalIssue/Issue") + return { + "volume": volume.text if volume is not None else None, + "issue": issue.text if issue is not None else None, + **__pub_date__(journal.find("JournalIssue/PubDate")), + "journal": journal.find("Title").text + } + +def __author__(author: etree.Element) -> str: + return f'{author.find("LastName").text} {author.find("Initials").text}' + + +def __pages__(pagination: etree.Element) -> str: + start = pagination.find("StartPage") + end = pagination.find("EndPage") + return (start.text + ( + f"-{end.text}" if end is not None else "" + )) if start is not None else "" + + +def __abstract__(article: etree.Element) -> str: + abstract = article.find("Abstract/AbstractText") + return abstract.text if abstract is not None else None + + +def __article__(pubmed_article: etree.Element) -> dict: + article = pubmed_article.find("MedlineCitation/Article") + return { + "pubmed_id": int(pubmed_article.find("MedlineCitation/PMID").text), + "title": article.find("ArticleTitle").text, + **__journal__(article.find("Journal")), + "abstract": __abstract__(article), + "pages": __pages__(article.find("Pagination")), + "authors": ", ".join(__author__(author) + for author in article.findall("AuthorList/Author")) + } + + +def __process_pubmed_publication_data__(text) -> tuple[dict, ...]: + """Process the data from PubMed into usable data.""" + doc = etree.XML(text) + articles = doc.xpath("//PubmedArticle") + logger.debug("Retrieved %s publications from NCBI", len(articles)) + return tuple(__article__(article) for article in articles) + +def fetch_publications(pubmed_ids: tuple[int, ...]) -> tuple[dict, ...]: + """Retrieve data on new publications from NCBI.""" + # See whether we can retrieve multiple publications in one go + # Parse data and save to DB + # Return PublicationId(s) for new publication(s). + if len(pubmed_ids) == 0: + logger.debug("There are no new PubMed IDs to fetch") + return tuple() + + logger.info("Fetching publications data for the following PubMed IDs: %s", + ", ".join((str(pid) for pid in pubmed_ids))) + + # Should we, perhaps, pass this in from a config variable? + uri = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" + try: + response = requests.get( + uri, + params={ + "db": "pubmed", + "retmode": "xml", + "id": ",".join(str(item) for item in pubmed_ids) + }, + timeout=(9.13, 20)) + + if response.status_code == 200: + return __process_pubmed_publication_data__(response.text) + + logger.error( + "Could not fetch the new publication from %s (status code: %s)", + uri, + response.status_code) + except requests.exceptions.ConnectionError: + logger.error("Could not find the domain %s", uri) + + return tuple() diff --git a/uploader/publications/views.py b/uploader/publications/views.py new file mode 100644 index 0000000..805d6f0 --- /dev/null +++ b/uploader/publications/views.py @@ -0,0 +1,185 @@ +"""Endpoints for publications""" +import json + +from gn_libs.mysqldb import database_connection +from flask import ( + flash, + request, + url_for, + redirect, + Blueprint, + render_template, + current_app as app) + +from uploader.authorisation import require_login +from uploader.route_utils import redirect_to_next + +from .models import ( + delete_publications, + update_publications, + fetch_publication_by_id, + create_new_publications, + fetch_publication_phenotypes) + +from .datatables import fetch_publications + +pubbp = Blueprint("publications", __name__) + + +@pubbp.route("/", methods=["GET"]) +@require_login +def index(): + """Index page for publications.""" + return render_template("publications/index.html") + + +@pubbp.route("/list", methods=["GET"]) +@require_login +def list_publications(): + """Fetch publications that fulfill a specific search, or all of them, if + there is no search term.""" + # request breakdown: + # https://datatables.net/manual/server-side + _page = int(request.args.get("draw")) + _length = int(request.args.get("length") or '-1') + _start = int(request.args.get("start") or '0') + _search = request.args["search[value]"] + with database_connection(app.config["SQL_URI"]) as conn: + _publications, _current_rows, _totalfiltered, _totalrows = fetch_publications( + conn, + _search, + offset=_start, + limit=_length) + + return json.dumps({ + "draw": _page, + "recordsTotal": _totalrows, + "recordsFiltered": _totalfiltered, + "publications": _publications, + "status": "success" + }) + + +@pubbp.route("/view/<int:publication_id>", methods=["GET"]) +@require_login +def view_publication(publication_id: int): + """View more details on a particular publication.""" + with database_connection(app.config["SQL_URI"]) as conn: + publication = fetch_publication_by_id(conn, publication_id) + + if not bool(publication): + flash("Requested publication was not found!", "alert-warning") + return redirect(url_for('publications.index')) + + return render_template( + "publications/view-publication.html", + publication=publication, + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id))) + + +@pubbp.route("/create", methods=["GET", "POST"]) +@require_login +def create_publication(): + """Create a new publication.""" + if request.method == "GET": + return render_template("publications/create-publication.html") + form = request.form + authors = form.get("publication-authors").encode("utf8") + if authors is None or authors == "": + flash("The publication's author(s) MUST be provided!", "alert alert-danger") + return redirect(url_for("publications.create", **request.args)) + + with database_connection(app.config["SQL_URI"]) as conn: + publications = create_new_publications(conn, ({ + "pubmed_id": form.get("pubmed-id") or None, + "abstract": form.get("publication-abstract").encode("utf8") or None, + "authors": authors, + "title": form.get("publication-title").encode("utf8") or None, + "journal": form.get("publication-journal").encode("utf8") or None, + "volume": form.get("publication-volume").encode("utf8") or None, + "pages": form.get("publication-pages").encode("utf8") or None, + "month": (form.get("publication-month") or "").encode("utf8").capitalize() or None, + "year": form.get("publication-year").encode("utf8") or None + },)) + flash("New publication created!", "alert alert-success") + return redirect(url_for( + request.args.get("return_to") or "publications.view_publication", + publication_id=publications[0]["publication_id"], + **request.args)) + + flash("Publication creation failed!", "alert alert-danger") + app.logger.debug("Failed to create the new publication.", exc_info=True) + return redirect(url_for("publications.create_publication")) + + +@pubbp.route("/edit/<int:publication_id>", methods=["GET", "POST"]) +@require_login +def edit_publication(publication_id: int): + """Edit a publication's details.""" + with database_connection(app.config["SQL_URI"]) as conn: + if request.method == "GET": + return render_template( + "publications/edit-publication.html", + publication=fetch_publication_by_id(conn, publication_id), + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id)), + publication_id=publication_id) + + form = request.form + _pub = update_publications(conn, ({ + "publication_id": publication_id, + "pubmed_id": form.get("pubmed-id") or None, + "abstract": form.get("publication-abstract").encode("utf8") or None, + "authors": form.get("publication-authors").encode("utf8"), + "title": form.get("publication-title").encode("utf8") or None, + "journal": form.get("publication-journal").encode("utf8") or None, + "volume": form.get("publication-volume").encode("utf8") or None, + "pages": form.get("publication-pages").encode("utf8") or None, + "month": (form.get("publication-month") or "").encode("utf8").capitalize() or None, + "year": form.get("publication-year").encode("utf8") or None + },)) + + if not _pub: + flash("There was an error updating the publication details.", + "alert-danger") + return redirect(url_for( + "publications.edit_publication", publication_id=publication_id)) + + flash("Successfully updated the publication details.", + "alert-success") + return redirect_to_next({ + "uri": "publications.view_publication", + "publication_id": publication_id + }) + + +@pubbp.route("/delete/<int:publication_id>", methods=["GET", "POST"]) +@require_login +def delete_publication(publication_id: int): + """Delete a particular publication.""" + with database_connection(app.config["SQL_URI"]) as conn: + publication = fetch_publication_by_id(conn, publication_id) + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id)) + + if not bool(publication): + flash("Requested publication was not found!", "alert-warning") + return redirect(url_for('publications.index')) + + if len(linked_phenotypes) > 0: + flash("Cannot delete publication with linked phenotypes!", + "alert-warning") + return redirect(url_for( + "publications.view_publication", publication_id=publication_id)) + + if request.method == "GET": + return render_template( + "publications/delete-publication.html", + publication=publication, + linked_phenotypes=linked_phenotypes, + publication_id=publication_id) + + delete_publications(conn, (publication,)) + flash("Deleted the publication successfully.", "alert-success") + return render_template("publications/delete-publication-success.html") diff --git a/uploader/route_utils.py b/uploader/route_utils.py index 18eadda..53247e6 100644 --- a/uploader/route_utils.py +++ b/uploader/route_utils.py @@ -1,12 +1,24 @@ """Generic routing utilities.""" -from flask import flash, url_for, redirect, render_template, current_app as app +import logging +from json.decoder import JSONDecodeError + +from flask import (flash, + url_for, + request, + redirect, + render_template, + current_app as app) from gn_libs.mysqldb import database_connection +from uploader.datautils import base64_encode_dict, base64_decode_to_dict from uploader.population.models import (populations_by_species, population_by_species_and_id) -def generic_select_population(# pylint: disable=[too-many-arguments] +logger = logging.getLogger(__name__) + +def generic_select_population( + # pylint: disable=[too-many-arguments, too-many-positional-arguments] species: dict, template: str, population_id: str, @@ -39,3 +51,40 @@ def generic_select_population(# pylint: disable=[too-many-arguments] return redirect(url_for(forward_to, species_id=species["SpeciesId"], population_id=population["Id"])) + + +def redirect_to_next(default: dict): + """Redirect to the next uri if specified, else redirect to default.""" + assert "uri" in default, "You must provide at least the 'uri' value." + try: + next_page = base64_decode_to_dict(request.args.get("next")) + _uri = next_page["uri"] + next_page.pop("uri") + return redirect(url_for(_uri, **next_page)) + except (TypeError, JSONDecodeError) as _err: + logger.debug("We could not decode the next value '%s'", + next_page, + exc_info=True) + + return redirect(url_for( + default["uri"], + **{key:value for key,value in default.items() if key != "uri"})) + + +def build_next_argument(uri: str, **kwargs) -> str: + """Build the `next` URI argument from provided details.""" + dumps_keywords = ( + "skipkeys", "ensure_ascii", "check_circular", "allow_nan", "cls", + "indent", "separators", "default", "sort_keys") + return base64_encode_dict( + { + "uri": uri, + **{ + key: val for key,val in kwargs.items() + if key not in dumps_keywords + } + }, + **{ + key: val for key,val in kwargs.items() + if key in dumps_keywords + }) diff --git a/uploader/samples/models.py b/uploader/samples/models.py index d7d5384..1e9293f 100644 --- a/uploader/samples/models.py +++ b/uploader/samples/models.py @@ -15,11 +15,11 @@ def samples_by_species_and_population( """Fetch the samples by their species and population.""" with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( - "SELECT iset.InbredSetId, s.* FROM InbredSet AS iset " - "INNER JOIN StrainXRef AS sxr ON iset.InbredSetId=sxr.InbredSetId " - "INNER JOIN Strain AS s ON sxr.StrainId=s.Id " - "WHERE s.SpeciesId=%(species_id)s " - "AND iset.InbredSetId=%(population_id)s", + "SELECT InbredSet.InbredSetId, Strain.* FROM InbredSet " + "INNER JOIN StrainXRef ON InbredSet.InbredSetId=StrainXRef.InbredSetId " + "INNER JOIN Strain ON StrainXRef.StrainId=Strain.Id " + "WHERE Strain.SpeciesId=%(species_id)s " + "AND InbredSet.InbredSetId=%(population_id)s", {"species_id": species_id, "population_id": population_id}) return tuple(cursor.fetchall()) @@ -34,8 +34,7 @@ def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs else ("Name", "Name2", "Symbol", "Alias")), delimiter=separator, quotechar=kwargs.get("quotechar", '"')) - for row in reader: - yield row + yield from reader def save_samples_data(conn: mdb.Connection, diff --git a/uploader/samples/views.py b/uploader/samples/views.py index 27e5d3c..4705a96 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -96,7 +96,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u activelink="list-samples") -def build_sample_upload_job(# pylint: disable=[too-many-arguments] +def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments] speciesid: int, populationid: int, samplesfile: Path, @@ -159,7 +159,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "alert-error") return samples_uploads_page - firstlineheading = (request.form.get("first_line_heading") == "on") + firstlineheading = request.form.get("first_line_heading") == "on" separator = request.form.get("separator", ",") if separator == "other": @@ -172,7 +172,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma redisuri = app.config["REDIS_URL"] with Redis.from_url(redisuri, decode_responses=True) as rconn: - #TODO: Add a QC step here — what do we check? + #T0DO: Add a QC step here — what do we check? # 1. Does any sample in the uploaded file exist within the database? # If yes, what is/are its/their species and population? # 2. If yes 1. above, provide error with notes on which species and @@ -221,7 +221,10 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): if status == "error": return redirect(url_for( - "species.populations.samples.upload_failure", job_id=job_id)) + "species.populations.samples.upload_failure", + species_id=species["SpeciesId"], + population_id=population["Id"], + job_id=job_id)) error_filename = Path(jobs.error_filename( job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) @@ -241,9 +244,14 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): species=species, population=population), 400 -@samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"]) + +@samplesbp.route("<int:species_id>/populations/<int:population_id>/" + "upload-samples/failure/<uuid:job_id>", + methods=["GET"]) @require_login -def upload_failure(job_id: uuid.UUID): +@with_population(species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] """Display the errors of the samples upload failure.""" job = with_redis_connection(lambda rconn: jobs.job( rconn, jobs.jobsnamespace(), job_id)) @@ -257,4 +265,7 @@ def upload_failure(job_id: uuid.UUID): if stat.st_size > 0: return render_template("worker_failure.html", job_id=job_id) - return render_template("samples/upload-failure.html", job=job) + return render_template("samples/upload-failure.html", + species=species, + population=population, + job=job) diff --git a/uploader/session.py b/uploader/session.py index b538187..5af5827 100644 --- a/uploader/session.py +++ b/uploader/session.py @@ -77,12 +77,15 @@ def set_user_token(token: str) -> SessionInfo: """Set the user's token.""" info = session_info() return save_session_info({ - **info, "user": {**info["user"], "token": Right(token)}})#type: ignore[misc] + **info, + "user": {**info["user"], "token": Right(token), "logged_in": True} + })#type: ignore[misc] def set_user_details(userdets: UserDetails) -> SessionInfo: """Set the user details information""" - return save_session_info({**session_info(), "user": userdets})#type: ignore[misc] + info = session_info() + return save_session_info({**info, "user": {**info["user"], **userdets}})#type: ignore[misc] def user_details() -> UserDetails: """Retrieve user details.""" diff --git a/uploader/species/models.py b/uploader/species/models.py index db53d48..acfa51e 100644 --- a/uploader/species/models.py +++ b/uploader/species/models.py @@ -92,7 +92,7 @@ def save_species(conn: mdb.Connection, } -def update_species(# pylint: disable=[too-many-arguments] +def update_species(# pylint: disable=[too-many-arguments, too-many-positional-arguments] conn: mdb.Connection, species_id: int, common_name: str, diff --git a/uploader/static/css/layout-large.css b/uploader/static/css/layout-large.css new file mode 100644 index 0000000..d1b3aa1 --- /dev/null +++ b/uploader/static/css/layout-large.css @@ -0,0 +1,66 @@ +* { + box-sizing: border-box; +} + +@media screen and (min-width: 20.1in) { + body { + display: grid; + grid-template-columns: 7fr 3fr; + grid-gap: 1em; + } + + #header { + /* 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; + } + + #header #header-text { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + + /* Content styling */ + padding-left: 1em; + } + + #header #header-nav { + /* Place it in the parent element */ + grid-column-start: 2; + grid-column-end: 3; + } + + #main { + /* 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; + grid-gap: 1.5em; + } + + #main #breadcrumbs { + grid-column-start: 1; + grid-column-end: 3; + padding: 0 3px; + } + + #main #main-content { + /*background: #FFFFFF;*/ + /*max-width: 80%;*/ + + grid-column-start: 1; + grid-column-end: 2; + } + + #main #sidebar-content { + grid-column-start: 2; + grid-column-end: 3; + } +} diff --git a/uploader/static/css/layout-medium.css b/uploader/static/css/layout-medium.css new file mode 100644 index 0000000..f504073 --- /dev/null +++ b/uploader/static/css/layout-medium.css @@ -0,0 +1,68 @@ +* { + box-sizing: border-box; +} + +@media screen and (width > 8in) and (max-width: 20in) { + body { + display: grid; + grid-template-columns: 65fr 35fr; + grid-gap: 1em; + } + + #header { + /* 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; + } + + #header #header-text { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + + /* Content styling */ + padding-left: 1em; + } + + #header #header-nav { + /* Place it in the parent element */ + grid-column-start: 2; + grid-column-end: 3; + } + + #main { + /* 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; + grid-gap: 5px; + } + + #main #breadcrumbs { + grid-column-start: 1; + grid-column-end: 3; + padding: 0 3px; + } + + #main #main-content { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + grid-gap: 5px; + + /* Define layout for the children elements */ + max-width: 70%; + } + + #main #sidebar-content { + grid-column-start: 2; + grid-column-end: 3; + } +} diff --git a/uploader/static/css/layout-small.css b/uploader/static/css/layout-small.css new file mode 100644 index 0000000..cd32a71 --- /dev/null +++ b/uploader/static/css/layout-small.css @@ -0,0 +1,66 @@ +* { + box-sizing: border-box; +} + +@media screen and (max-width: 8in) { + body { + display: grid; + grid-template-columns: 1fr; + grid-template-rows: 1fr 2fr 7fr; + grid-gap: 1em; + } + + #header { + /* 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: 1fr; + } + + #header #header-text { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + + /* Content styling */ + padding-left: 1em; + } + + #header #header-nav { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + } + + #main { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + display: grid; + + /* Define layout for the children elements */ + grid-template-rows: 1.5em 80% 20%; + grid-template-columns: 1fr; + } + + #main #breadcrumbs { + grid-row-start: 1; + grid-row-end: 2; + + } + + #main #main-content { + grid-row-start: 2; + grid-row-end: 3; + } + + #main #sidebar-content { + grid-row-start: 3; + grid-row-end: 4; + + background: #E5E5FF; + } +} diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css index 80c5a56..df50dec 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -5,7 +5,7 @@ body { margin: 0.7em; display: grid; - grid-template-columns: 1fr 9fr; + grid-template-columns: 2fr 8fr; grid-gap: 20px; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; @@ -100,15 +100,32 @@ body { padding-left: 0.5em; } -#main #all-content { - /* Place it in the parent element */ - grid-column-start: 1; - grid-column-end: 3; +@media screen and (max-width: 20in) { + #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; + /* Define layout for the children elements */ + max-width: 80%; + } + + #sidebar-content { + display: none; + } +} + +@media screen and (min-width: 20.1in) { + #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; + grid-gap: 1.5em; + } } #main #all-content .row { @@ -162,3 +179,9 @@ table.dataTable thead th, table.dataTable tfoot th{ table.dataTable tbody tr.selected td { background-color: #ffee99 !important; } + +.form-group { + margin-bottom: 2em; + padding-bottom: 0.2em; + border-bottom: solid gray 1px; +} diff --git a/uploader/static/css/theme.css b/uploader/static/css/theme.css new file mode 100644 index 0000000..09e5a52 --- /dev/null +++ b/uploader/static/css/theme.css @@ -0,0 +1,85 @@ +body { + margin: 0.7em; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-style: normal; + font-size: 20px; + background: black; +} + +#header { + background-color: #336699; + color: #FFFFFF; + border-radius: 3px; + min-height: 30px; +} + +#header #header-nav .nav li a { + /* Content styling */ + color: #FFFFFF; + background: #4477AA; + border: solid 5px #336699; + border-radius: 5px; + font-size: 0.7em; + text-align: center; + padding: 1px 7px; +} + +#main #breadcrumbs { + background: #eaeaea; + border-radius:3px; + text-align: center; +} + +#main #main-content { + background: #e5e5ff; + + border-radius: 5px; + padding: 0 5px; +} + +#main #sidebar-content { + background: red; + + border-radius: 5px; + padding: 0 5px; +} + +#main .row { + margin: 0 2px; +} + + +.heading { + border-bottom: solid #EEBB88; + text-transform: capitalize; +} + +.subheading { + padding: 1em 0 0.1em 0.5em; + border-bottom: solid #88BBEE; + text-transform: capitalize; +} + +input[type="search"] { + border-radius: 5px; +} + +.btn { + text-transform: Capitalize; +} + +table.dataTable thead th, table.dataTable tfoot th{ + border-right: 1px solid white; + color: white; + background-color: #369 !important; +} + +table.dataTable tbody tr.selected td { + background-color: #ffee99 !important; +} + +.form-group { + margin-bottom: 2em; + padding-bottom: 0.2em; + border-bottom: solid gray 1px; +} diff --git a/uploader/static/js/debug.js b/uploader/static/js/debug.js new file mode 100644 index 0000000..eb01209 --- /dev/null +++ b/uploader/static/js/debug.js @@ -0,0 +1,40 @@ +/** + * The entire purpose of this function is for use to debug values inline + * without changing the flow of the code too much. + * + * This **MUST** be a non-arrow function to allow access to the `arguments` + * object. + * + * This function expects at least one argument. + * + * If more than one argument is provided, then: + * a) the last argument is considered the value, and will be returned + * b) all other arguments will be converted to string and output + * + * If only one argument is provided, it is considered the value, and will be + * returned. + * + * Zero arguments is an error condition. + **/ +function __pk__(val) { + /* Handle zero arguments */ + if (arguments.length < 1) { + throw new Error("Invalid arguments: Expected at least one argument."); + } + + msg = "/********** DEBUG **********/"; + if (arguments.length > 1) { + msg = Array.from( + arguments + ).slice( + 0, + arguments.length - 1 + ).map((val) => { + return String(val); + }).join("; ") + } + + value = arguments[arguments.length - 1]; + console.debug("/********** " + msg + " **********/", value); + return value; +} diff --git a/uploader/static/js/files.js b/uploader/static/js/files.js index 9d6bca1..0bde6f7 100644 --- a/uploader/static/js/files.js +++ b/uploader/static/js/files.js @@ -84,8 +84,8 @@ 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"); + add_class(fileinput, "visually-hidden"); + remove_class(droparea, "visually-hidden"); // Define UI elements for browse and drag&drop resumable.assignDrop(droparea); diff --git a/uploader/static/js/misc.js b/uploader/static/js/misc.js deleted file mode 100644 index cf7b39e..0000000 --- a/uploader/static/js/misc.js +++ /dev/null @@ -1,6 +0,0 @@ -"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 index be1231f..89ededa 100644 --- a/uploader/static/js/populations.js +++ b/uploader/static/js/populations.js @@ -13,9 +13,24 @@ $(() => { } }, { + searchable: true, data: (apopulation) => { return `${apopulation.FullName} (${apopulation.InbredSetName})`; } } - ]); + ], + { + select: "single", + paging: true, + scrollY: 700, + deferRender: true, + scroller: true, + scrollCollapse: true, + layout: { + topStart: "info", + topEnd: "search", + bottomStart: "pageLength", + bottomEnd: false + } + }); }); diff --git a/uploader/static/js/pubmed.js b/uploader/static/js/pubmed.js new file mode 100644 index 0000000..f425f49 --- /dev/null +++ b/uploader/static/js/pubmed.js @@ -0,0 +1,113 @@ +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()] || "January") : "January", + "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) => { + console.debug(entry[1].toLowerCase()); + 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, "visually-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, "visually-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" + }); +}; diff --git a/uploader/static/js/species.js b/uploader/static/js/species.js index 9ea3017..d42e081 100644 --- a/uploader/static/js/species.js +++ b/uploader/static/js/species.js @@ -16,5 +16,19 @@ $(() => { return `${aspecies.FullName} (${aspecies.SpeciesName})`; } } - ]); + ], + { + select: "single", + paging: true, + scrollY: 700, + deferRender: true, + scroller: true, + scrollCollapse: true, + layout: { + topStart: "info", + topEnd: "search", + bottomStart: "pageLength", + bottomEnd: false + } + }); }); diff --git a/uploader/static/js/utils.js b/uploader/static/js/utils.js index 045dd47..1b31661 100644 --- a/uploader/static/js/utils.js +++ b/uploader/static/js/utils.js @@ -8,3 +8,30 @@ function trigger_change_event(element) { evt = new Event("change"); element.dispatchEvent(evt); } + + +var remove_class = (element, classvalue) => { + new_classes = (element.attr("class") || "").split(" ").map((val) => { + return val.trim(); + }).filter((val) => { + return ((val !== classvalue) && + (val !== "")) + }).join(" "); + + if(new_classes === "") { + element.removeAttr("class"); + } else { + element.attr("class", new_classes); + } +}; + + +var add_class = (element, classvalue) => { + remove_class(element, classvalue); + element.attr("class", (element.attr("class") || "") + " " + classvalue); +}; + +$(".not-implemented").click((event) => { + event.preventDefault(); + alert("This feature is not implemented yet. Please bear with us."); +}); diff --git a/uploader/templates/background-jobs/default-success-page.html b/uploader/templates/background-jobs/default-success-page.html new file mode 100644 index 0000000..5732456 --- /dev/null +++ b/uploader/templates/background-jobs/default-success-page.html @@ -0,0 +1,17 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs: Success{%endblock%} + +{%block pagetitle%}Background Jobs: Success{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Job <strong>{{job.job_id}}</strong>, + {%if job.get("metadata", {}).get("job-type")%} + of type '<em>{{job.metadata["job-type"]}}</em> + {%endif%}' completed successfully.</p> +</div> +{%endblock%} diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 09e6470..3c0d0d4 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -32,7 +32,7 @@ <a href="{{url_for('oauth2.logout')}}" title="Log out of the system"> <span class="glyphicon glyphicon-user"></span> - Sign Out</a> + {{user_email()}} Sign Out</a> {%else%} <a href="{{authserver_authorise_uri()}}" title="Log in to the system">Sign In</a> @@ -46,6 +46,9 @@ <ul class="nav flex-column"> <li {%if activemenu=="home"%}class="activemenu"{%endif%}> <a href="/" >Home</a></li> + <li {%if activemenu=="publications"%}class="activemenu"{%endif%}> + <a href="{{url_for('publications.index')}}" + title="View and manage publications.">Publications</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> @@ -151,7 +154,7 @@ <!-- local dependencies --> - <script type="text/javascript" src="/static/js/misc.js"></script> + <script type="text/javascript" src="/static/js/utils.js"></script> <script type="text/javascript" src="/static/js/datatables.js"></script> {%block javascript%}{%endblock%} </body> diff --git a/uploader/templates/base2.html b/uploader/templates/base2.html new file mode 100644 index 0000000..4c5d613 --- /dev/null +++ b/uploader/templates/base2.html @@ -0,0 +1,111 @@ +<!DOCTYPE html> +<html lang="en"> + + <head> + + <meta charset="UTF-8" /> + <meta application-name="GeneNetwork Quality-Control Application" /> + <meta name="viewport" content="width=device-width, initial-scale=1.0" /> + {%block extrameta%}{%endblock%} + + <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> + + <link rel="stylesheet" type="text/css" + href="{{url_for('base.bootstrap', + filename='css/bootstrap.min.css')}}" /> + <link rel="stylesheet" type="text/css" + href="{{url_for('base.datatables', + filename='css/dataTables.bootstrap5.min.css')}}" /> + <link rel="stylesheet" type="text/css" href="/static/css/styles2.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-large.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-medium.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-small.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/theme.css" /> + + {%block css%}{%endblock%} + + </head> + + <body> + <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> + {{user_email()}} Sign Out</a> + {%else%} + <a href="{{authserver_authorise_uri()}}" + title="Log in to the system">Sign In</a> + {%endif%} + </li> + </ul> + </nav> + </header> + + + <main id="main" class="main"> + <nav id="breadcrumbs" aria-label="breadcrumb"> + <ol class="breadcrumb"> + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Home</a></li> + {%block extra_breadcrumbs%} + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Page01</a></li> + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Page02</a></li> + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Page03</a></li> + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Page04</a></li> + {%endblock%} + </ol> + </nav> + + <div id="main-content"> + {%block contents%}{%endblock%} + </div> + + <div id="sidebar-content"> + {%block sidebarcontents%}{%endblock%} + </div> + </main> + + + + <script type="text/javascript" src="/static/js/debug.js"></script> + <!-- + Core dependencies + --> + <script src="{{url_for('base.jquery', + filename='jquery.min.js')}}"></script> + <script src="{{url_for('base.bootstrap', + filename='js/bootstrap.min.js')}}"></script> + + <!-- + DataTables dependencies + --> + <script type="text/javascript" + src="{{url_for('base.datatables', + filename='js/dataTables.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='scroller/js/dataTables.scroller.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='buttons/js/dataTables.buttons.min.js')}}"></script> + <script type="text/javascript" + src="{{url_for('base.datatables_extensions', + filename='select/js/dataTables.select.min.js')}}"></script> + + <!-- + local dependencies + --> + <script type="text/javascript" src="/static/js/utils.js"></script> + <script type="text/javascript" src="/static/js/datatables.js"></script> + {%block javascript%}{%endblock%} + </body> +</html> diff --git a/uploader/templates/flash_messages.html b/uploader/templates/flash_messages.html index b7af178..b42e64e 100644 --- a/uploader/templates/flash_messages.html +++ b/uploader/templates/flash_messages.html @@ -1,11 +1,11 @@ {%macro flash_all_messages()%} {%with messages = get_flashed_messages(with_categories=true)%} {%if messages:%} -<ul> +<div> {%for category, message in messages:%} - <li class="{{category}}">{{message}}</li> + <div class="alert {{category}}">{{message}}</div> {%endfor%} -</ul> +</div> {%endif%} {%endwith%} {%endmacro%} @@ -13,13 +13,13 @@ {%macro flash_messages(filter_class)%} {%with messages = get_flashed_messages(with_categories=true)%} {%if messages:%} -<ul> +<div> {%for category, message in messages:%} {%if filter_class in category%} - <li class="{{category}}">{{message}}</li> + <div class="alert {{category}}">{{message}}</div> {%endif%} {%endfor%} -</ul> +</div> {%endif%} {%endwith%} {%endmacro%} diff --git a/uploader/templates/index2.html b/uploader/templates/index2.html new file mode 100644 index 0000000..72fea2f --- /dev/null +++ b/uploader/templates/index2.html @@ -0,0 +1,48 @@ +{%extends "base2.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Home{%endblock%} + +{%block pagetitle%}Home{%endblock%} + +{%block extra_breadcrumbs%}{%endblock%} + +{%block contents%} + +<div class="row">{{flash_all_messages()}}</div> + +{%if user_logged_in()%} +<div class="row"> + <p>Select from:</p> + <ul> + <li>Species</li> + <li>Publications</li> + </ul> +</div> +{%else%} +<div class="row"> + <p> + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system" + class="btn btn-primary">Sign in</a> + to continue.</p> +</div> +{%endif%} + +{%endblock%} + + + +{%block sidebarcontents%} +<div class="row"> + <form id="frm-quick-navigation"> + <legend>Quick Navigation</legend> + <div class="form-group"> + <label for="fqn-species-id">Species</label> + <select name="species_id"> + <option value="">Select species</option> + </select> + </div> + </form> +</div> +{%endblock%} diff --git a/uploader/templates/jobs/job-error.html b/uploader/templates/jobs/job-error.html new file mode 100644 index 0000000..b3015fc --- /dev/null +++ b/uploader/templates/jobs/job-error.html @@ -0,0 +1,17 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs: Error{%endblock%} + +{%block pagetitle%}Background Jobs: Error{%endblock%} + +{%block contents%} + +<h1>Background Jobs: Error</h1> +<p>Job <strong>{{job["job_id"]}}</strong> failed!</p> +<p>The error details are in the "STDERR" section below.</p> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> +{%endblock%} diff --git a/uploader/templates/jobs/job-not-found.html b/uploader/templates/jobs/job-not-found.html new file mode 100644 index 0000000..a71e66f --- /dev/null +++ b/uploader/templates/jobs/job-not-found.html @@ -0,0 +1,11 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} +<p>Could not find job with ID: {{job_id}}</p> +{%endblock%} diff --git a/uploader/templates/jobs/job-status.html b/uploader/templates/jobs/job-status.html new file mode 100644 index 0000000..83c02fd --- /dev/null +++ b/uploader/templates/jobs/job-status.html @@ -0,0 +1,24 @@ +{%extends "base.html"%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5" /> +{%endblock%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} + +<p>Status: {{job["metadata"]["status"]}}</p> +<p>Job Type: {{job["metadata"]["job-type"]}}</p> + +<h2>STDOUT</h2> +<pre>{{job["stdout"]}}</pre> + +<h2>STDERR</h2> +<pre>{{job["stderr"]}}</pre> + +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html index 97b55f2..9909c20 100644 --- a/uploader/templates/phenotypes/add-phenotypes-base.html +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -42,110 +42,30 @@ {%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"> + <fieldset id="fldset-publication-info"> <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> + <input type="hidden" name="publication-id" id="txt-publication-id" /> + <span class="form-text text-muted"> + Select a publication for your data. <br /> + Can't find a publication you can use? Go ahead and + <a href="{{url_for( + 'publications.create_publication', + return_to='species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">create a new publication</a>.</span> + <table id="tbl-select-publication" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> </fieldset> <div class="form-group"> @@ -165,165 +85,80 @@ {%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; - } + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-select-publication", + [], + [ + {data: "index"}, + { + searchable: true, + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + searchable: true, + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + searchable: true, + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + serverSide: true, + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + select: "single", + paging: true, + scrollY: 700, + deferRender: true, + scroller: true, + scrollCollapse: true, + layout: { + topStart: "info", + topEnd: "search" + } + }); + publicationsDataTable.on("select", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + console.debug(datatable.row(element).data()); + $("#frm-add-phenotypes #txt-publication-id").val( + datatable.row(element).data().Id); + }); + }); + publicationsDataTable.on("deselect", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + $("#frm-add-phenotypes #txt-publication-id").val(null); + }); }); - }; - - 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> diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html index 7f8d8b0..67b56e3 100644 --- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -105,111 +105,213 @@ </div> </fieldset> -<fieldset id="fldset-data-files"> +<fieldset id="fldset-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>')}} + <fieldset id="fldset-descriptions-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-descriptions-transposed" + name="phenotype-descriptions-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-descriptions-transposed" + class="form-check-label"> + Description file transposed?</label> + </div> + + <div class="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>Drag and drop the CSV file that contains the descriptions of your + phenotypes here.</p> + + <p>The CSV file should be a matrix of + <strong>phenotypes × descriptions</strong> i.e. The first column + contains the phenotype names/identifiers whereas the first row is a list + of metadata fields like, "description", "units", etc.</p> + + <p>If the format is transposed (i.e. + <strong>descriptions × phenotypes</strong>) select the checkbox above. + </p> + + <p>Please see the + <a href="#docs-file-phenotype-description" + title="Documentation of the phenotype data file format."> + "Phenotypes Descriptions" documentation</a> section below for more + information on the expected format of the file provided here.</p>')}} + {{display_preview_table( + "tbl-preview-pheno-desc", "phenotype descriptions")}} + </div> + </fieldset> + + + <fieldset id="fldset-data-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-data-transposed" + name="phenotype-data-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-data-transposed" class="form-check-label"> + Data file transposed?</label> + </div> + + <div class="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>Drag and drop a CSV file that contains the phenotypes numerical data + here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + <p>Please see the + <a href="#docs-file-phenotype-data" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format for the file provided here.</p>')}} + {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}} + </div> + </fieldset> - <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>')}} + {%if population.Family in families_with_se_and_n%} + <fieldset id="fldset-se-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-se-transposed" + name="phenotype-se-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-se-transposed" class="form-check-label"> + Standard-Errors file transposed?</label> + </div> + <div class="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>Drag and drop a CSV file that contains the phenotypes standard-errors + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{display_preview_table("tbl-preview-pheno-se", "standard errors")}} + </div> + </fieldset> + + + <fieldset id="fldset-n-file"> + <div class="form-group"> + <div class="form-check"> + <input id="chk-phenotype-n-transposed" + name="phenotype-n-transposed" + type="checkbox" + class="form-check-input" + style="border: solid #8EABF0" /> + <label for="chk-phenotype-n-transposed" class="form-check-label"> + Counts file transposed?</label> + </div> + <div class="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>Drag and drop a CSV file that contains the samples\' phenotypes counts + data here. You can click the "Browse" button (below and to the right) to + select the file from your computer.</p> + + <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, + i.e. The first column contains the samples identifiers while the first + row is the list of phenotypes identifiers occurring in the phenotypes + descriptions file.</p> + + <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) + select the checkbox above.</p> + + <p>Please see the + <a href="#docs-file-phenotype-se" + title="Documentation of the phenotype data file format."> + "Phenotypes Data" documentation</a> section below for more information + on the expected format of the file provided here.</p>')}} + + {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} + </div> + </fieldset> </fieldset> {%endif%} {%endblock%} @@ -322,15 +424,15 @@ <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> + <p>The data is a matrix of <em>samples(or individuals) × phenotypes</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 /> + id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br /> + IND001,61.400002,49,62.5,55.099998,…<br /> + IND002,54.099998,50.099998,53.299999,55.099998,…<br /> + IND003,483,403,501,403,…<br /> + IND004,49.799999,45.5,62.900002,NA,…<br /> ⋮<br /></code> <p>where <code>IND001,IND002,IND003,IND004,…</code> are the @@ -346,12 +448,6 @@ {%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%} @@ -429,9 +525,9 @@ }); if(table.find("tbody tr.data-row").length > 0) { - add_class(table.find(".data-row-template"), "hidden"); + add_class(table.find(".data-row-template"), "visually-hidden"); } else { - remove_class(table.find(".data-row-template"), "hidden"); + remove_class(table.find(".data-row-template"), "visually-hidden"); } }; @@ -467,13 +563,24 @@ Object.entries(preview_tables_to_elements_map).forEach((mapentry) => { var preview_table = $(mapentry[0]); var file_input = $(mapentry[1]); - if(file_input.length === 1) { + if(file_input[0].files.length > 0) { readFirstNLines( file_input[0].files[0], 10, [makePreviewUpdater(preview_table)]); } }); + + if(typeof(resumables) !== "undefined") { + resumables.forEach((resumable) => { + if(resumable.files.length > 0) { + readFirstNLines( + resumable.files[0].file, + 10, + [makePreviewUpdater(resumable.preview_table)]); + } + }); + } }; [ @@ -506,7 +613,7 @@ var display_element = display_area .find(".file-display-template") .clone(); - remove_class(display_element, "hidden"); + remove_class(display_element, "visually-hidden"); remove_class(display_element, "file-display-template"); add_class(display_element, "file-display"); display_element.find(".filename").text(file.name @@ -526,7 +633,7 @@ return () => {/*Has no event!*/ var progress = (resumable.progress() * 100).toFixed(2); var pbar = progress_bar.find(".progress-bar"); - remove_class(progress_bar, "hidden"); + remove_class(progress_bar, "visually-hidden"); pbar.css("width", progress+"%"); pbar.attr("aria-valuenow", progress); pbar.text("Uploading: " + progress + "%"); @@ -536,9 +643,9 @@ 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"); + add_class(retry_button, "visually-hidden"); + remove_class(cancel_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); }); }; @@ -549,18 +656,18 @@ file.abort(); } }); - add_class(cancel_button, "hidden"); - remove_class(retry_button, "hidden"); - remove_class(browse_button, "hidden"); + add_class(cancel_button, "visually-hidden"); + remove_class(retry_button, "visually-hidden"); + remove_class(browse_button, "visually-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"); + remove_class(cancel_button, "visually-hidden"); + add_class(retry_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); }; }; @@ -574,6 +681,7 @@ })); }); formdata.append("resumable-upload", "true"); + formdata.append("publication-id", $("#txt-publication-id").val()); return formdata; } @@ -642,7 +750,7 @@ file_input.parent(), $("#" + resumable_element_id), submit_button, - ["csv", "tsv"]), + ["csv", "tsv", "txt"]), file_input.parent(), $("#" + resumable_element_id), $("#" + resumable_element_id + "-browse-button")), @@ -678,13 +786,20 @@ ["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]); + r = makeResumableObject(row[0], row[1], row[2], row[3]); + r.preview_table = $("#" + row[3]); + return r; }).filter((val) => { return Boolean(val); }); $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { event.preventDefault(); + console.debug(); + if ($("#txt-publication-id").val() == "") { + alert("You MUST provide a publication for the phenotypes."); + return false; + } // TODO: Check all the relevant files exist // TODO: Verify that files are not duplicated var filenames = []; diff --git a/uploader/templates/phenotypes/bulk-edit-upload.html b/uploader/templates/phenotypes/bulk-edit-upload.html new file mode 100644 index 0000000..d0f38f5 --- /dev/null +++ b/uploader/templates/phenotypes/bulk-edit-upload.html @@ -0,0 +1,62 @@ +{%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%} +<div class="row"> + <p>Upload the edited file you downloaded and edited.</p> +</div> + +<div class="row"> + <form id="frm-bulk-edit-upload" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_upload_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + enctype="multipart/form-data"> + + <div class="form-group row"> + <label for="file-upload-bulk-edit-upload" + class="form-label col-form-label col-sm-2"> + Edited File</label> + <div class="col-sm-10"> + <input id="file-upload-bulk-edit-upload" + name="file-upload-bulk-edit-upload" + class="form-control" + type="file" + accept="text/tab-separated-values" + required="required" /> + </div> + </div> + + <input type="submit" class="btn btn-primary" + value="upload to edit" /> + + </form> +</div> +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html index 8e45491..19a2b34 100644 --- a/uploader/templates/phenotypes/create-dataset.html +++ b/uploader/templates/phenotypes/create-dataset.html @@ -42,7 +42,7 @@ <input type="text" name="dataset-name" id="txt-dataset-name" - value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}" + value="{{original_formdata.get('dataset-name') or (population.Name + 'Publish')}}" {%if errors["dataset-name"] is defined%} class="form-control danger" {%else%} @@ -51,7 +51,7 @@ 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. + <p>Recommended: Use the population name 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> @@ -86,7 +86,7 @@ name="dataset-shortname" type="text" class="form-control" - value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" /> + value="{{original_formdata.get('dataset-shortname') or (population.Name + '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 diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html index 32c903f..115d6af 100644 --- a/uploader/templates/phenotypes/edit-phenotype.html +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -201,130 +201,6 @@ </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%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html index 12963c1..257f726 100644 --- a/uploader/templates/phenotypes/job-status.html +++ b/uploader/templates/phenotypes/job-status.html @@ -105,7 +105,7 @@ <td>{{error.filename}}</td> <td>{{error.rowtitle}}</td> <td>{{error.coltitle}}</td> - <td>{%if error.cellvalue | length > 25%} + <td>{%if error.cellvalue is not none and error.cellvalue | length > 25%} {{error.cellvalue[0:24]}}… {%else%} {{error.cellvalue}} diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html new file mode 100644 index 0000000..645be16 --- /dev/null +++ b/uploader/templates/phenotypes/load-phenotypes-success.html @@ -0,0 +1,42 @@ +{%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=="load-phenotypes-success"%} + 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%} +<div class="row"> + <p>You have successfully loaded + <!-- maybe indicate the number of phenotypes here? -->your + new phenotypes into the database.</p> + <!-- TODO: Maybe notify user that they have sole access. --> + <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. --> + <p>View your data + <a href="{{search_page_uri}}" + target="_blank">on GeneNetwork2</a>. + You might need to login to GeneNetwork2 to view specific traits.</p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html index f54c53e..5a4c422 100644 --- a/uploader/templates/phenotypes/macro-display-preview-table.html +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -1,7 +1,7 @@ {%macro display_preview_table(tableid, filetype)%} -<div class="card" style="max-width: 676px;"> +<div class="card"> <div class="card-body"> - <h5 class="card-title">Phenotypes '{{filetype | title}}' File Preview</h5> + <h5 class="card-title">{{filetype | title}}: File Preview</h5> <div class="card-text" style="overflow: scroll;"> <table id="{{tableid}}" class="table table-condensed table-responsive"> <thead> @@ -9,9 +9,7 @@ </tr> <tbody> <tr> - <td class="data-row-template text-info"> - Provide a phenotype '{{filetype | lower}}' file to preview. - </td> + <td class="data-row-template text-info"></td> </tr> </tbody> </table> diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html index b0bf1b5..ed14ea5 100644 --- a/uploader/templates/phenotypes/macro-display-resumable-elements.html +++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html @@ -1,6 +1,6 @@ {%macro display_resumable_elements(id, title, help)%} <div id="{{id}}" - class="resumable-elements hidden" + class="resumable-elements visually-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> @@ -9,7 +9,7 @@ <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 panel-info file-display-template visually-hidden"> <div class="panel-heading filename">The Filename Goes Here!</div> <div class="panel-body"> <ul> @@ -33,10 +33,10 @@ <a id="{{id}}-browse-button" class="resumable-browse-button btn btn-info" - href="#" + href="#{{id}}" style="margin-left: 80%;">Browse</a> - <div id="{{id}}-progress-bar" class="progress hidden"> + <div id="{{id}}-progress-bar" class="progress visually-hidden"> <div class="progress-bar" role="progress-bar" aria-valuenow="60" @@ -49,11 +49,11 @@ <div id="{{id}}-cancel-resume-buttons"> <a id="{{id}}-resume-button" - class="resumable-resume-button btn btn-info hidden" + class="resumable-resume-button btn btn-info visually-hidden" href="#">resume upload</a> <a id="{{id}}-cancel-button" - class="resumable-cancel-button btn btn-danger hidden" + class="resumable-cancel-button btn btn-danger visually-hidden" href="#">cancel upload</a> </div> </div> diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html index 7bc8c62..859df74 100644 --- a/uploader/templates/phenotypes/review-job-data.html +++ b/uploader/templates/phenotypes/review-job-data.html @@ -35,14 +35,28 @@ {%if job%} <div class="row"> <h3 class="heading">Data Review</h3> + <p class="text-info"><strong> + The data has <em>NOT</em> been added/saved yet. Review the details below + and click "Continue" to save the data.</strong></p> <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> + <ul> + {%if publication%} + <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes + are linked to the following publication: + <ul> + <li><strong>Publication Title:</strong> + {{publication.Title or "—"}}</li> + <li><strong>Author(s):</strong> + {{publication.Authors or "—"}}</li> + </ul> + </li> + {%endif%} {%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 @@ -53,11 +67,21 @@ {%endif%} to the database. </li> - </ul> {%endif%} {%endfor%} + </ul> - <a href="#" class="not-implemented btn btn-primary">continue</a> + <form id="frm-review-phenotype-data" + method="POST" + action="{{url_for('species.populations.phenotypes.load_data_to_database', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> + <input type="submit" + value="continue" + class="btn btn-primary" /> + </form> </div> {%else%} <div class="row"> diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index fa1044b..6a261fc 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -46,12 +46,32 @@ </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 class="col"> + <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> + </div> + + <div class="col"> + <form id="frm-recompute-phenotype-means" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.recompute_means', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}" + class="d-flex flex-row align-items-center flex-wrap" + style="display: inline;"> + <input type="submit" + title="Compute/Recompute the means for all phenotypes." + class="btn btn-info" + value="(rec/c)ompute means" + id="submit-frm-recompute-phenotype-means" /> + </form> + </div> </div> <div class="row"> @@ -133,74 +153,6 @@ { select: "multi+shift", layout: { - top2: { - buttons: [ - { - extend: "selectAll", - className: "btn btn-info", - titleAttr: "Click to select ALL records in the table." - }, - { - extend: "selectNone", - className: "btn btn-info", - titleAttr: "Click to deselect ANY selected record(s) in the table." - }, - { - text: "Bulk Edit (Download Data)", - action: (event, dt, node, config) => { - var phenoids = []; - var selected = dt.rows({selected: true, page: "all"}).data(); - for(var idx = 0; idx < selected.length; idx++) { - phenoids.push({ - phenotype_id: selected[idx].Id, - xref_id: selected[idx].xref_id - }); - } - if(phenoids.length == 0) { - alert("No record selected. Nothing to do!"); - return false; - } - $.ajax( - (`/species/${species_id}/populations/` + - `${population_id}/phenotypes/datasets/` + - `${dataset_id}/download`), - { - method: "POST", - data: JSON.stringify(phenoids), - xhrFields: { - responseType: "blob" - }, - success: (data, textStatus, jqXHR) => { - var link = document.createElement("a"); - uri = window.URL.createObjectURL(data); - link.href = uri; - link.download = `${dataset_name}_data.tsv`; - - document.body.appendChild(link); - link.click(); - window.URL.revokeObjectURL(uri); - link.remove(); - }, - error: (jQXHR, textStatus, errorThrown) => { - console.log("Experienced an error: ", textStatus); - console.log("The ERROR: ", errorThrown); - }, - contentType: "application/json" - }); - }, - className: "btn btn-info", - titleAttr: "Click to download data for editing." - }, - { - text: "Bulk Edit (Upload Data)", - action: (event, dt, node, config) => { - alert("Not implemented yet!") - }, - className: "btn btn-info", - titleAttr: "Click to upload edited data you got by clicking the `Bulk Edit (Download Data)` button." - } - ] - }, top1Start: { pageLength: { text: "Show _MENU_ of _TOTAL_" diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 21ac501..75e3c1e 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -24,8 +24,10 @@ {{flash_all_messages()}} <div class="row"> - <div class="panel panel-default"> - <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> + <div class="card"> + <div class="card-header"> + <h5 class="card-title">Basic Phenotype Details</h5> + </div> <table class="table"> <tbody> @@ -41,24 +43,46 @@ <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> +<div class="row" style="margin-top:5px;"> + <div class="card"> + <div class="card-header"> + <h5 class="card-title">Publication Details</h5> + </div> + + <div class="card-body"> + <table class="table"> + <tbody> + <tr> + {%for key in ("PubMed_ID", "Authors", "Title", "Journal"):%} + <tr> + <td><strong>{{key}}</strong></td> + <td>{{publication.get(key, "")}}</td> + </tr> + {%else%} + <tr> + <td colspan="2" class="text-muted"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + No publication data found. + </td> + </tr> + {%endfor%} + </tr> + </tbody> + </table> + <div style="text-align: right;"> + <a href="{{url_for('publications.edit_publication', publication_id=publication.Id, next=next)}}" + class="btn btn-info">edit</a> + <a href="#" class="btn btn-danger not-implemented">change</a> + </div> + </div> + </div> +</div> + {%if "group:resource:edit-resource" in privileges or "group:resource:delete-resource" in privileges%} <div class="row"> diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index c0c4f45..007b6bf 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -154,24 +154,35 @@ {%else%} class="form-group" {%endif%}> - <label for="select-population-family" class="form-label">Family</label> - <select id="select-population-family" - name="population_family" - class="form-control" - required="required"> - <option value="">Please select a family</option> + <label for="txt-population-family" class="form-label">Family</label> + <input type="text" + id="txt-population-family" + name="population_family" + class="form-control" + list="families-list" /> + <datalist id="families-list"> {%for family in families%} - <option value="{{family}}" - {%if error_values.population_family == family%} - selected="selected" - {%endif%}>{{family}}</option> + <option value="{{family}}">{{family}}</option> {%endfor%} - </select> + </datalist> <small class="form-text text-muted"> <p> - This is a rough grouping of the populations in GeneNetwork into lists - of common types of populations. - </p> + This is <strong>optional</strong> metadata. It is used to group + populations into "families" for presentation in the menus. + {%if families | length > 0%} + Examples of currently existing families are: + <ul> + {%for family in families[0:7]%} + <li>{{family}}</li> + {%endfor%} + <li>etc.</li> + </ul> + {%endif%} + + You can + {%if families|length>0%} select from existing families, or {%endif%} + create a new family by typing in the input box above. You can also + leave the family blank.</p> </small> </div> diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index f780e94..a092e34 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -54,7 +54,7 @@ <th></th> <th>Name</th> <th>Full Name</th> - <th>Description</th> + <th>Information</th> </tr> </thead> @@ -71,7 +71,10 @@ </a> </td> <td>{{population.FullName}}</td> - <td>{{population.Description}}</td> + <td><a href="https://info.genenetwork.org/species/source.php?SpeciesName={{species.Name}}&InbredSetName={{population.Name}}" + title="Link to detailed information on this population." + class="btn btn-info" + target="_blank">info</a></td> </tr> {%else%} <tr> diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index b23caeb..3b9661b 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -42,8 +42,10 @@ <dt>Family</dt> <dd>{{population.Family}}</dd> - <dt>Description</dt> - <dd><pre>{{population.Description or "-"}}</pre></dd> + <dt>Information</dt> + <dd><a href="https://info.genenetwork.org/species/source.php?SpeciesName={{species.Name}}&InbredSetName={{population.Name}}" + title="Link to detailed information on this population." + target="_blank">Population Information</a></dd> </dl> </div> diff --git a/uploader/templates/publications/base.html b/uploader/templates/publications/base.html new file mode 100644 index 0000000..db80bfa --- /dev/null +++ b/uploader/templates/publications/base.html @@ -0,0 +1,12 @@ +{%extends "base.html"%} + +{%block lvl1_breadcrumbs%} +<li {%if activelink=="publications"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('publications.index')}}">Publications</a> +</li> +{%block lvl2_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html new file mode 100644 index 0000000..3f828a9 --- /dev/null +++ b/uploader/templates/publications/create-publication.html @@ -0,0 +1,191 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-create-publication" + method="POST" + action="{{url_for('publications.create_publication', **request.args)}}" + class="form-horizontal"> + + <div class="row mb-3"> + <label for="txt-pubmed-id" class="col-sm-2 col-form-label"> + PubMed ID</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + id="txt-pubmed-id" + name="pubmed-id" + class="form-control"/> + <div class="input-group-text"> + <button class="btn btn-outline-primary" + id="btn-search-pubmed-id">search</button> + </div> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger visually-hidden"> + </span> + <span class="form-text text-muted">This is the publication's ID on + <a href="https://pubmed.ncbi.nlm.nih.gov/" + title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a> + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-title" class="col-sm-2 col-form-label"> + Title</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-title" + name="publication-title" + class="form-control" /> + <span class="form-text text-muted">Provide the publication's title here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-authors" class="col-sm-2 col-form-label"> + Authors</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-authors" + name="publication-authors" + required="required" + class="form-control" /> + <span class="form-text text-muted"> + A publication <strong>MUST</strong> have an author. You <em>must</em> + provide a value for the authors field. + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-journal" class="col-sm-2 col-form-label"> + Journal</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-journal" + name="publication-journal" + class="form-control" /> + <span class="form-text text-muted">Provide the name journal where the + publication was done, here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="select-publication-month" + class="col-sm-2 col-form-label"> + Month</label> + <div class="col-sm-4"> + <select class="form-control" + id="select-publication-month" + name="publication-month"> + <option value="">Select a month</option> + <option value="january">January</option> + <option value="february">February</option> + <option value="march">March</option> + <option value="april">April</option> + <option value="may">May</option> + <option value="june">June</option> + <option value="july">July</option> + <option value="august">August</option> + <option value="september">September</option> + <option value="october">October</option> + <option value="november">November</option> + <option value="december">December</option> + </select> + <span class="form-text text-muted">Month of publication</span> + </div> + + <label for="txt-publication-year" + class="col-sm-2 col-form-label"> + Year</label> + <div class="col-sm-4"> + <input type="number" + id="txt-publication-year" + name="publication-year" + class="form-control" + min="1960" /> + <span class="form-text text-muted">Year of publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-volume" + class="col-sm-2 col-form-label"> + Volume</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-volume" + name="publication-volume" + class="form-control"> + <span class="form-text text-muted">Journal volume</span> + </div> + + <label for="txt-publication-pages" + class="col-sm-2 col-form-label"> + Pages</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-pages" + name="publication-pages" + class="form-control" /> + <span class="form-text text-muted">Journal pages for the publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" + name="publication-abstract" + class="form-control" + rows="7"></textarea> + </div> + </div> + + <div class="row mb-3"> + <div class="col-sm-2"></div> + <div class="col-sm-8"> + <input type="submit" class="btn btn-primary" value="Add" /> + <input type="reset" class="btn btn-danger" /> + </div> + </div> + +</form> +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/pubmed.js"></script> +<script type="text/javascript"> + $(function() { + $("#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> +{%endblock%} diff --git a/uploader/templates/publications/delete-publication-success.html b/uploader/templates/publications/delete-publication-success.html new file mode 100644 index 0000000..53a44ec --- /dev/null +++ b/uploader/templates/publications/delete-publication-success.html @@ -0,0 +1,18 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() {}); +</script> +{%endblock%} diff --git a/uploader/templates/publications/delete-publication.html b/uploader/templates/publications/delete-publication.html new file mode 100644 index 0000000..0ac93ec --- /dev/null +++ b/uploader/templates/publications/delete-publication.html @@ -0,0 +1,88 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} +<div class="row"> + <p>You are about to delete the publication with the following details:</p> +</div> + +<div class="row"> + <table class="table"> + <tr> + <th>Linked Phenotypes</th> + <td>{{linked_phenotypes | count}}</td> + </tr> + <tr> + <th>PubMed</th> + <td> + {%if publication.PubMed_ID%} + <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/" + target="_blank">{{publication.PubMed_ID}}</a> + {%else%} + — + {%endif%} + </td> + </tr> + <tr> + <th>Title</th> + <td>{{publication.Title or "—"}}</td> + </tr> + <tr> + <th>Authors</th> + <td>{{publication.Authors or "—"}}</td> + </tr> + <tr> + <th>Journal</th> + <td>{{publication.Journal or "—"}}</td> + </tr> + <tr> + <th>Published</th> + <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td> + </tr> + <tr> + <th>Volume</th> + <td>{{publication.Volume or "—"}}</td> + </tr> + <tr> + <th>Pages</th> + <td>{{publication.Pages or "—"}}</td> + </tr> + <tr> + <th>Abstract</th> + <td> + {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%} + <p>{{line}}</p> + {%endfor%} + </td> + </tr> + </table> +</div> + +<div class="row"> + <p>If you are sure that is what you want, click the button below to delete the + publication</p> + <p class="form-text text-small"> + <small>You will not be able to recover the data if you click + delete below.</small></p> + + <form action="{{url_for('publications.delete_publication', publication_id=publication_id)}}" + method="POST"> + <div class="form-group"> + <input type="submit" value="delete" class="btn btn-danger" /> + </div> + </form> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() {}); +</script> +{%endblock%} diff --git a/uploader/templates/publications/edit-publication.html b/uploader/templates/publications/edit-publication.html new file mode 100644 index 0000000..540ecf1 --- /dev/null +++ b/uploader/templates/publications/edit-publication.html @@ -0,0 +1,194 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-create-publication" + method="POST" + action="{{url_for('publications.edit_publication', publication_id=publication_id, **request.args)}}" + class="form-horizontal"> + + <div class="row mb-3"> + <label for="txt-pubmed-id" class="col-sm-2 col-form-label"> + PubMed ID</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + id="txt-pubmed-id" + name="pubmed-id" + value="{{publication.PubMed_ID or ''}}" + class="form-control" /> + <div class="input-group-text"> + <button class="btn btn-outline-primary" + id="btn-search-pubmed-id">search</button> + </div> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger visually-hidden"> + </span> + <span class="form-text text-muted">This is the publication's ID on + <a href="https://pubmed.ncbi.nlm.nih.gov/" + title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a> + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-title" class="col-sm-2 col-form-label"> + Title</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-title" + name="publication-title" + value="{{publication.Title}}" + class="form-control" /> + <span class="form-text text-muted">Provide the publication's title here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-authors" class="col-sm-2 col-form-label"> + Authors</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-authors" + name="publication-authors" + value="{{publication.Authors}}" + required="required" + class="form-control" /> + <span class="form-text text-muted"> + A publication <strong>MUST</strong> have an author. You <em>must</em> + provide a value for the authors field. + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-journal" class="col-sm-2 col-form-label"> + Journal</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-journal" + name="publication-journal" + value="{{publication.Journal}}" + class="form-control" /> + <span class="form-text text-muted">Provide the name journal where the + publication was done, here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="select-publication-month" + class="col-sm-2 col-form-label"> + Month</label> + <div class="col-sm-4"> + <select class="form-control" + id="select-publication-month" + name="publication-month"> + <option value="">Select a month</option> + {%for month in ("january", "february", "march", "april", "may", "june", "july", "august", "september", "october", "november", "december"):%} + <option value="{{month}}" + {%if publication.Month | lower == month %} + selected="selected" + {%endif%}> + {{month | title}} + </option> + {%endfor%} + </select> + <span class="form-text text-muted">Month of publication</span> + </div> + + <label for="txt-publication-year" + class="col-sm-2 col-form-label"> + Year</label> + <div class="col-sm-4"> + <input type="number" + id="txt-publication-year" + name="publication-year" + value="{{publication.Year}}" + class="form-control" + min="1960" /> + <span class="form-text text-muted">Year of publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-volume" + class="col-sm-2 col-form-label"> + Volume</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-volume" + name="publication-volume" + value="{{publication.Volume}}" + class="form-control"> + <span class="form-text text-muted">Journal volume</span> + </div> + + <label for="txt-publication-pages" + class="col-sm-2 col-form-label"> + Pages</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-pages" + name="publication-pages" + value="{{publication.Pages}}" + class="form-control" /> + <span class="form-text text-muted">Journal pages for the publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" + name="publication-abstract" + class="form-control" + rows="7">{{publication.Abstract or ""}}</textarea> + </div> + </div> + + <div class="row mb-3"> + <div class="col-sm-2"></div> + <div class="col-sm-8"> + <input type="submit" class="btn btn-primary" value="Save" /> + <input type="reset" class="btn btn-danger" /> + </div> + </div> + +</form> +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/pubmed.js"></script> +<script type="text/javascript"> + $(function() { + $("#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> +{%endblock%} diff --git a/uploader/templates/publications/index.html b/uploader/templates/publications/index.html new file mode 100644 index 0000000..369812b --- /dev/null +++ b/uploader/templates/publications/index.html @@ -0,0 +1,100 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Publications{%endblock%} + +{%block pagetitle%}Publications{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row" style="padding-bottom: 1em;"> + <a href="{{url_for('publications.create_publication')}}" + class="btn btn-primary"> + add new publication</a> +</div> + +<div class="row"> + <table id="tbl-list-publications" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-list-publications", + [], + [ + {data: "index"}, + { + searchable: true, + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + searchable: true, + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + searchable: true, + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + serverSide: true, + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + scrollY: 700, + scroller: true, + scrollCollapse: true, + paging: true, + deferRender: true, + layout: { + topStart: "info", + topEnd: "search", + bottomStart: "pageLength", + bottomEnd: false + } + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/publications/view-publication.html b/uploader/templates/publications/view-publication.html new file mode 100644 index 0000000..0bd7bc5 --- /dev/null +++ b/uploader/templates/publications/view-publication.html @@ -0,0 +1,82 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <table class="table"> + <tr> + <th>Linked Phenotypes</th> + <td>{{linked_phenotypes | count}}</td> + </tr> + <tr> + <th>PubMed</th> + <td> + {%if publication.PubMed_ID%} + <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/" + target="_blank">{{publication.PubMed_ID}}</a> + {%else%} + — + {%endif%} + </td> + </tr> + <tr> + <th>Title</th> + <td>{{publication.Title or "—"}}</td> + </tr> + <tr> + <th>Authors</th> + <td>{{publication.Authors or "—"}}</td> + </tr> + <tr> + <th>Journal</th> + <td>{{publication.Journal or "—"}}</td> + </tr> + <tr> + <th>Published</th> + <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td> + </tr> + <tr> + <th>Volume</th> + <td>{{publication.Volume or "—"}}</td> + </tr> + <tr> + <th>Pages</th> + <td>{{publication.Pages or "—"}}</td> + </tr> + <tr> + <th>Abstract</th> + <td> + {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%} + <p>{{line}}</p> + {%endfor%} + </td> + </tr> + </table> +</div> + +<div class="row"> + <div> + <a href="{{url_for('publications.edit_publication', publication_id=publication.Id)}}" + title="Edit details for this publication." + class="btn btn-primary">Edit</a> + {%if linked_phenotypes | length == 0%} + <a href="{{url_for('publications.delete_publication', publication_id=publication.Id)}}" + class="btn btn-danger">delete</a> + {%endif%} + </div> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() {}); +</script> +{%endblock%} diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html index 185e784..aed27c3 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -29,6 +29,19 @@ </p> </div> +<div class="row"> + <p> + <a href="{{url_for('species.populations.samples.upload_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Add samples for population '{{population.FullName}}' from species + '{{species.FullName}}'." + class="btn btn-primary"> + add samples + </a> + </p> +</div> + {%if samples | length > 0%} <div class="row"> <p> @@ -96,32 +109,17 @@ <p> <a href="#" - title="Add samples for population '{{population.FullName}}' from species + title="Delete samples from population '{{population.FullName}}' from species '{{species.FullName}}'." - class="btn btn-danger"> + class="btn btn-danger not-implemented"> delete all samples </a> </p> </div> - {%else%} - <div class="row"> - <p> - There are no samples entered for this population. Do please go ahead and add - the samples for this population by clicking on the button below. - </p> - - <p> - <a href="{{url_for('species.populations.samples.upload_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Add samples for population '{{population.FullName}}' from species - '{{species.FullName}}'." - class="btn btn-primary"> - add samples - </a> - </p> + <p>There are no samples entered for this population. Click the "Add Samples" + button above, to add some new samples.</p> </div> {%endif%} diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html index 458ab55..2cf8053 100644 --- a/uploader/templates/samples/upload-failure.html +++ b/uploader/templates/samples/upload-failure.html @@ -15,7 +15,7 @@ <h3>Debugging Information</h3> <ul> - <li><strong>job id</strong>: {{job.job_id}}</li> + <li><strong>job id</strong>: {{job.jobid}}</li> <li><strong>status</strong>: {{job.status}}</li> <li><strong>job type</strong>: {{job["job-type"]}}</li> </ul> diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html index 25d3290..6422094 100644 --- a/uploader/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html @@ -66,7 +66,7 @@ <div class="form-group"> <label for="file-samples" class="form-label">select file</label> <input type="file" name="samples_file" id="file:samples" - accept="text/csv, text/tab-separated-values" + accept="text/csv, text/tab-separated-values, text/plain" class="form-control" /> </div> |