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-rw-r--r--scripts/qc_on_rqtl2_bundle2.py346
-rw-r--r--scripts/rqtl2/phenotypes_qc.py7
-rw-r--r--uploader/__init__.py2
-rw-r--r--uploader/authorisation.py2
-rw-r--r--uploader/base_routes.py17
-rw-r--r--uploader/default_settings.py13
-rw-r--r--uploader/files/__init__.py5
-rw-r--r--uploader/files/chunks.py32
-rw-r--r--uploader/files/functions.py (renamed from uploader/files.py)25
-rw-r--r--uploader/files/views.py116
-rw-r--r--uploader/genotypes/views.py45
-rw-r--r--uploader/monadic_requests.py10
-rw-r--r--uploader/oauth2/client.py3
-rw-r--r--uploader/oauth2/views.py2
-rw-r--r--uploader/phenotypes/models.py83
-rw-r--r--uploader/phenotypes/views.py535
-rw-r--r--uploader/platforms/views.py10
-rw-r--r--uploader/population/models.py2
-rw-r--r--uploader/population/rqtl2.py123
-rw-r--r--uploader/population/views.py26
-rw-r--r--uploader/route_utils.py41
-rw-r--r--uploader/samples/views.py76
-rw-r--r--uploader/species/models.py8
-rw-r--r--uploader/species/views.py15
-rw-r--r--uploader/static/css/styles.css200
-rw-r--r--uploader/static/js/datatables.js75
-rw-r--r--uploader/static/js/files.js118
-rw-r--r--uploader/static/js/populations.js21
-rw-r--r--uploader/static/js/species.js20
-rw-r--r--uploader/templates/base.html111
-rw-r--r--uploader/templates/genotypes/index.html4
-rw-r--r--uploader/templates/genotypes/select-population.html16
-rw-r--r--uploader/templates/index.html134
-rw-r--r--uploader/templates/login.html7
-rw-r--r--uploader/templates/macro-step-indicator.html15
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-base.html129
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-raw-files.html435
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html4
-rw-r--r--uploader/templates/phenotypes/create-dataset.html6
-rw-r--r--uploader/templates/phenotypes/edit-phenotype.html332
-rw-r--r--uploader/templates/phenotypes/index.html15
-rw-r--r--uploader/templates/phenotypes/job-status.html26
-rw-r--r--uploader/templates/phenotypes/list-datasets.html9
-rw-r--r--uploader/templates/phenotypes/macro-display-preview-table.html21
-rw-r--r--uploader/templates/phenotypes/macro-display-resumable-elements.html60
-rw-r--r--uploader/templates/phenotypes/review-job-data.html101
-rw-r--r--uploader/templates/phenotypes/select-population.html12
-rw-r--r--uploader/templates/phenotypes/view-dataset.html94
-rw-r--r--uploader/templates/phenotypes/view-phenotype.html83
-rw-r--r--uploader/templates/platforms/index.html4
-rw-r--r--uploader/templates/platforms/list-platforms.html2
-rw-r--r--uploader/templates/populations/create-population.html14
-rw-r--r--uploader/templates/populations/index.html4
-rw-r--r--uploader/templates/populations/list-populations.html2
-rw-r--r--uploader/templates/populations/macro-display-population-card.html5
-rw-r--r--uploader/templates/populations/macro-select-population.html72
-rw-r--r--uploader/templates/samples/index.html4
-rw-r--r--uploader/templates/samples/list-samples.html2
-rw-r--r--uploader/templates/samples/select-population.html23
-rw-r--r--uploader/templates/species/create-species.html112
-rw-r--r--uploader/templates/species/list-species.html2
-rw-r--r--uploader/templates/species/macro-select-species.html83
62 files changed, 2741 insertions, 1180 deletions
diff --git a/scripts/qc_on_rqtl2_bundle2.py b/scripts/qc_on_rqtl2_bundle2.py
deleted file mode 100644
index 7e5d253..0000000
--- a/scripts/qc_on_rqtl2_bundle2.py
+++ /dev/null
@@ -1,346 +0,0 @@
-"""Run Quality Control checks on R/qtl2 bundle."""
-import os
-import sys
-import json
-from time import sleep
-from pathlib import Path
-from zipfile import ZipFile
-from argparse import Namespace
-from datetime import timedelta
-import multiprocessing as mproc
-from functools import reduce, partial
-from logging import Logger, getLogger, StreamHandler
-from typing import Union, Sequence, Callable, Iterator
-
-import MySQLdb as mdb
-from redis import Redis
-
-from quality_control.errors import InvalidValue
-from quality_control.checks import decimal_points_error
-
-from uploader import jobs
-from uploader.db_utils import database_connection
-from uploader.check_connections import check_db, check_redis
-
-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 r_qtl import fileerrors as rqfe
-
-from scripts.process_rqtl2_bundle import parse_job
-from scripts.redis_logger import setup_redis_logger
-from scripts.cli_parser import init_cli_parser, add_global_data_arguments
-from scripts.rqtl2.bundleutils import build_line_joiner, build_line_splitter
-
-
-def check_for_missing_files(
- rconn: Redis, fqjobid: str, extractpath: Path, logger: Logger) -> bool:
- """Check that all files listed in the control file do actually exist."""
- logger.info("Checking for missing files.")
- missing = rqc.missing_files(extractpath)
- # add_to_errors(rconn, fqjobid, "errors-generic", tuple(
- # rqfe.MissingFile(
- # mfile[0], mfile[1], (
- # f"File '{mfile[1]}' is listed in the control file under "
- # f"the '{mfile[0]}' key, but it does not actually exist in "
- # "the bundle."))
- # for mfile in missing))
- if len(missing) > 0:
- logger.error(f"Missing files in the bundle!")
- return True
- return False
-
-
-def open_file(file_: Path) -> Iterator:
- """Open file and return one line at a time."""
- with open(file_, "r", encoding="utf8") as infile:
- for line in infile:
- yield line
-
-
-def check_markers(
- filename: str,
- row: tuple[str, ...],
- save_error: lambda val: val
-) -> tuple[rqfe.InvalidValue]:
- """Check that the markers are okay"""
- errors = tuple()
- counts = {}
- for marker in row:
- counts = {**counts, marker: counts.get(marker, 0) + 1}
- if marker is None or marker == "":
- errors = errors + (save_error(rqfe.InvalidValue(
- filename,
- "markers"
- "-",
- marker,
- "A marker MUST be a valid value.")),)
-
- return errors + tuple(
- save_error(rqfe.InvalidValue(
- filename,
- "markers",
- key,
- f"Marker '{key}' was repeated {value} times"))
- for key,value in counts.items() if value > 1)
-
-
-def check_geno_line(
- filename: str,
- headers: tuple[str, ...],
- row: tuple[Union[str, None]],
- cdata: dict,
- save_error: lambda val: val
-) -> tuple[rqfe.InvalidValue]:
- """Check that the geno line is correct."""
- errors = tuple()
- # Verify that line has same number of columns as headers
- if len(headers) != len(row):
- errors = errors + (save_error(rqfe.InvalidValue(
- filename,
- headers[0],
- row[0],
- row[0],
- "Every line MUST have the same number of columns.")),)
-
- # First column is the individuals/cases/samples
- if not bool(row[0]):
- errors = errors + (save_error(rqfe.InvalidValue(
- filename,
- headers[0],
- row[0],
- row[0],
- "The sample/case MUST be a valid value.")),)
-
- def __process_value__(val):
- if val in cdata["na.strings"]:
- return None
- if val in cdata["alleles"]:
- return cdata["genotypes"][val]
-
- genocode = cdata.get("genotypes", {})
- for coltitle, cellvalue in zip(headers[1:],row[1:]):
- if (
- bool(genocode) and
- cellvalue is not None and
- cellvalue not in genocode.keys()
- ):
- errors = errors + (save_error(rqfe.InvalidValue(
- filename, row[0], coltitle, cellvalue,
- f"Value '{cellvalue}' is invalid. Expected one of "
- f"'{', '.join(genocode.keys())}'.")),)
-
- return errors
-
-
-def push_file_error_to_redis(rconn: Redis, key: str, error: InvalidValue) -> InvalidValue:
- """Push the file error to redis a json string
-
- Parameters
- ----------
- rconn: Connection to redis
- key: The name of the list where we push the errors
- error: The file error to save
-
- Returns
- -------
- Returns the file error it saved
- """
- if bool(error):
- rconn.rpush(key, json.dumps(error._asdict()))
- return error
-
-
-def file_errors_and_details(
- redisargs: dict[str, str],
- file_: Path,
- filetype: str,
- cdata: dict,
- linesplitterfn: Callable,
- linejoinerfn: Callable,
- headercheckers: tuple[Callable, ...],
- bodycheckers: tuple[Callable, ...]
-) -> dict:
- """Compute errors, and other file metadata."""
- errors = tuple()
- if cdata[f"{filetype}_transposed"]:
- rqtl2.transpose_csv_with_rename(file_, linesplitterfn, linejoinerfn)
-
- with Redis.from_url(redisargs["redisuri"], decode_responses=True) as rconn:
- save_error_fn = partial(push_file_error_to_redis,
- rconn,
- error_list_name(filetype, file_.name))
- for lineno, line in enumerate(open_file(file_), start=1):
- row = linesplitterfn(line)
- if lineno == 1:
- headers = tuple(row)
- errors = errors + reduce(
- lambda errs, fnct: errs + fnct(
- file_.name, row[1:], save_error_fn),
- headercheckers,
- tuple())
- continue
-
- errors = errors + reduce(
- lambda errs, fnct: errs + fnct(
- file_.name, headers, row, cdata, save_error_fn),
- bodycheckers,
- tuple())
-
- filedetails = {
- "filename": file_.name,
- "filesize": os.stat(file_).st_size,
- "linecount": lineno
- }
- rconn.hset(redisargs["fqjobid"],
- f"file-details:{filetype}:{file_.name}",
- json.dumps(filedetails))
- return {**filedetails, "errors": errors}
-
-
-def error_list_name(filetype: str, filename: str):
- """Compute the name of the list where the errors will be pushed.
-
- Parameters
- ----------
- filetype: The type of file. One of `r_qtl.r_qtl2.FILE_TYPES`
- filename: The name of the file.
- """
- return f"errors:{filetype}:{filename}"
-
-
-def check_for_geno_errors(
- redisargs: dict[str, str],
- extractdir: Path,
- cdata: dict,
- linesplitterfn: Callable[[str], tuple[Union[str, None]]],
- linejoinerfn: Callable[[tuple[Union[str, None], ...]], str],
- logger: Logger
-) -> bool:
- """Check for errors in genotype files."""
- if "geno" in cdata or "founder_geno" in cdata:
- genofiles = tuple(
- extractdir.joinpath(fname) for fname in cdata.get("geno", []))
- fgenofiles = tuple(
- extractdir.joinpath(fname) for fname in cdata.get("founder_geno", []))
- allgenofiles = genofiles + fgenofiles
- with Redis.from_url(redisargs["redisuri"], decode_responses=True) as rconn:
- error_list_names = [
- error_list_name("geno", file_.name) for file_ in allgenofiles]
- for list_name in error_list_names:
- rconn.delete(list_name)
- rconn.hset(
- redisargs["fqjobid"],
- "geno-errors-lists",
- json.dumps(error_list_names))
- processes = [
- mproc.Process(target=file_errors_and_details,
- args=(
- redisargs,
- file_,
- ftype,
- cdata,
- linesplitterfn,
- linejoinerfn,
- (check_markers,),
- (check_geno_line,))
- )
- for ftype, file_ in (
- tuple(("geno", file_) for file_ in genofiles) +
- tuple(("founder_geno", file_) for file_ in fgenofiles))
- ]
- for process in processes:
- process.start()
- # Set expiry for any created error lists
- for key in error_list_names:
- rconn.expire(name=key,
- time=timedelta(seconds=redisargs["redisexpiry"]))
-
- # TOD0: Add the errors to redis
- if any(rconn.llen(errlst) > 0 for errlst in error_list_names):
- logger.error("At least one of the 'geno' files has (an) error(s).")
- return True
- logger.info("No error(s) found in any of the 'geno' files.")
-
- else:
- logger.info("No 'geno' files to check.")
-
- return False
-
-
-# def check_for_pheno_errors(...):
-# """Check for errors in phenotype files."""
-# pass
-
-
-# def check_for_phenose_errors(...):
-# """Check for errors in phenotype, standard-error files."""
-# pass
-
-
-# def check_for_phenocovar_errors(...):
-# """Check for errors in phenotype-covariates files."""
-# pass
-
-
-def run_qc(rconn: Redis, args: Namespace, fqjobid: str, logger: Logger) -> int:
- """Run quality control checks on R/qtl2 bundles."""
- thejob = parse_job(rconn, args.redisprefix, args.jobid)
- print(f"THE JOB =================> {thejob}")
- jobmeta = thejob["job-metadata"]
- inpath = Path(jobmeta["rqtl2-bundle-file"])
- extractdir = inpath.parent.joinpath(f"{inpath.name}__extraction_dir")
- with ZipFile(inpath, "r") as zfile:
- rqtl2.extract(zfile, extractdir)
-
- ### BEGIN: The quality control checks ###
- cdata = rqtl2.control_data(extractdir)
- splitter = build_line_splitter(cdata)
- joiner = build_line_joiner(cdata)
-
- redisargs = {
- "fqjobid": fqjobid,
- "redisuri": args.redisuri,
- "redisexpiry": args.redisexpiry
- }
- check_for_missing_files(rconn, fqjobid, extractdir, logger)
- # check_for_pheno_errors(...)
- check_for_geno_errors(redisargs, extractdir, cdata, splitter, joiner, logger)
- # check_for_phenose_errors(...)
- # check_for_phenocovar_errors(...)
- ### END: The quality control checks ###
-
- def __fetch_errors__(rkey: str) -> tuple:
- return tuple(json.loads(rconn.hget(fqjobid, rkey) or "[]"))
-
- return (1 if any((
- bool(__fetch_errors__(key))
- for key in
- ("errors-geno", "errors-pheno", "errors-phenos", "errors-phenocovar")))
- else 0)
-
-
-if __name__ == "__main__":
- def main():
- """Enter R/qtl2 bundle QC runner."""
- args = add_global_data_arguments(init_cli_parser(
- "qc-on-rqtl2-bundle", "Run QC on R/qtl2 bundle.")).parse_args()
- check_redis(args.redisuri)
- check_db(args.databaseuri)
-
- logger = getLogger("qc-on-rqtl2-bundle")
- logger.addHandler(StreamHandler(stream=sys.stderr))
- logger.setLevel("DEBUG")
-
- fqjobid = jobs.job_key(args.redisprefix, args.jobid)
- with Redis.from_url(args.redisuri, decode_responses=True) as rconn:
- logger.addHandler(setup_redis_logger(
- rconn, fqjobid, f"{fqjobid}:log-messages",
- args.redisexpiry))
-
- exitcode = run_qc(rconn, args, fqjobid, logger)
- rconn.hset(
- jobs.job_key(args.redisprefix, args.jobid), "exitcode", exitcode)
- return exitcode
-
- sys.exit(main())
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index ba28ed0..76ecb8d 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -290,10 +290,15 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments]
push_error, rconn, file_fqkey(fqkey, "errors", filepath))
_csvfile = rqtl2.read_csv_file(filepath, separator, comment_char)
_headings: tuple[str, ...] = tuple(
+ # select lowercase for comparison purposes
heading.lower() for heading in next(_csvfile))
_errors: tuple[InvalidValue, ...] = tuple()
- _absent = tuple(pheno for pheno in _headings[1:] if pheno not in phenonames)
+ _absent = tuple(pheno for pheno in _headings[1:] if pheno
+ not in tuple(
+ # lower to have consistent case with headings for
+ # comparison
+ phe.lower() for phe in phenonames))
if len(_absent) > 0:
_errors = _errors + (save_error(InvalidValue(
filepath.name,
diff --git a/uploader/__init__.py b/uploader/__init__.py
index 9fdb383..cae531b 100644
--- a/uploader/__init__.py
+++ b/uploader/__init__.py
@@ -11,6 +11,7 @@ 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 .oauth2.views import oauth2
from .expression_data import exprdatabp
@@ -82,6 +83,7 @@ def create_app():
# setup blueprints
app.register_blueprint(base, url_prefix="/")
+ app.register_blueprint(files, url_prefix="/files")
app.register_blueprint(oauth2, url_prefix="/oauth2")
app.register_blueprint(speciesbp, url_prefix="/species")
diff --git a/uploader/authorisation.py b/uploader/authorisation.py
index ee8fe97..a283980 100644
--- a/uploader/authorisation.py
+++ b/uploader/authorisation.py
@@ -18,7 +18,7 @@ def require_login(function):
"""Check that the user is logged in and their token is valid."""
def __clear_session__(_no_token):
session.clear_session_info()
- flash("You need to be logged in.", "alert-danger")
+ flash("You need to be signed in.", "alert-danger big-alert")
return redirect("/")
return session.user_token().either(
diff --git a/uploader/base_routes.py b/uploader/base_routes.py
index 742a254..74a3b90 100644
--- a/uploader/base_routes.py
+++ b/uploader/base_routes.py
@@ -35,8 +35,8 @@ def appenv():
@base.route("/bootstrap/<path:filename>")
def bootstrap(filename):
"""Fetch bootstrap files."""
- return send_from_directory(
- appenv(), f"share/genenetwork2/javascript/bootstrap/{filename}")
+ return send_from_directory(appenv(), f"share/web/bootstrap/{filename}")
+
@base.route("/jquery/<path:filename>")
@@ -46,6 +46,19 @@ def jquery(filename):
appenv(), f"share/genenetwork2/javascript/jquery/{filename}")
+@base.route("/datatables/<path:filename>")
+def datatables(filename):
+ """Fetch DataTables files."""
+ return send_from_directory(
+ appenv(), f"share/genenetwork2/javascript/DataTables/{filename}")
+
+@base.route("/datatables-extensions/<path:filename>")
+def datatables_extensions(filename):
+ """Fetch DataTables files."""
+ return send_from_directory(
+ appenv(), f"share/genenetwork2/javascript/DataTablesExtensions/{filename}")
+
+
@base.route("/node-modules/<path:filename>")
def node_modules(filename):
"""Fetch node-js modules."""
diff --git a/uploader/default_settings.py b/uploader/default_settings.py
index 1acb247..f07f89e 100644
--- a/uploader/default_settings.py
+++ b/uploader/default_settings.py
@@ -2,6 +2,8 @@
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!>"
UPLOAD_FOLDER = "/tmp/qc_app_files"
@@ -12,9 +14,18 @@ SQL_URI = ""
GN2_SERVER_URL = "https://genenetwork.org/"
-SESSION_TYPE = "redis"
SESSION_PERMANENT = True
SESSION_USE_SIGNER = True
+SESSION_TYPE = "cachelib"
+## --- Settings for CacheLib session type --- ##
+## --- These are on flask-session config variables --- ##
+## --- https://cachelib.readthedocs.io/en/stable/file/ --- ##
+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
+## --- END: Settings for CacheLib session type --- ##
JWKS_ROTATION_AGE_DAYS = 7 # Days (from creation) to keep a JWK in use.
JWKS_DELETION_AGE_DAYS = 14 # Days (from creation) to keep a JWK around before deleting it.
diff --git a/uploader/files/__init__.py b/uploader/files/__init__.py
new file mode 100644
index 0000000..53c3176
--- /dev/null
+++ b/uploader/files/__init__.py
@@ -0,0 +1,5 @@
+"""General files and chunks utilities."""
+from .chunks import chunked_binary_read
+from .functions import (fullpath,
+ save_file,
+ sha256_digest_over_file)
diff --git a/uploader/files/chunks.py b/uploader/files/chunks.py
new file mode 100644
index 0000000..c4360b5
--- /dev/null
+++ b/uploader/files/chunks.py
@@ -0,0 +1,32 @@
+"""Functions dealing with chunking of files."""
+from pathlib import Path
+from typing import Iterator
+
+from flask import current_app as app
+from werkzeug.utils import secure_filename
+
+
+def chunked_binary_read(filepath: Path, chunksize: int = 2048) -> Iterator:
+ """Read a file in binary mode in chunks."""
+ with open(filepath, "rb") as inputfile:
+ while True:
+ data = inputfile.read(chunksize)
+ if data != b"":
+ yield data
+ continue
+ break
+
+def chunk_name(uploadfilename: str, chunkno: int) -> str:
+ """Generate chunk name from original filename and chunk number"""
+ if uploadfilename == "":
+ raise ValueError("Name cannot be empty!")
+ if chunkno < 1:
+ raise ValueError("Chunk number must be greater than zero")
+ return f"{secure_filename(uploadfilename)}_part_{chunkno:05d}"
+
+
+def chunks_directory(uniqueidentifier: str) -> Path:
+ """Compute the directory where chunks are temporarily stored."""
+ if uniqueidentifier == "":
+ raise ValueError("Unique identifier cannot be empty!")
+ return Path(app.config["UPLOAD_FOLDER"], f"tempdir_{uniqueidentifier}")
diff --git a/uploader/files.py b/uploader/files/functions.py
index d37a53e..7b9f06b 100644
--- a/uploader/files.py
+++ b/uploader/files/functions.py
@@ -1,7 +1,6 @@
"""Utilities to deal with uploaded files."""
import hashlib
from pathlib import Path
-from typing import Iterator
from datetime import datetime
from flask import current_app
@@ -9,12 +8,17 @@ from flask import current_app
from werkzeug.utils import secure_filename
from werkzeug.datastructures import FileStorage
-def save_file(fileobj: FileStorage, upload_dir: Path) -> Path:
+from .chunks import chunked_binary_read
+
+def save_file(fileobj: FileStorage, upload_dir: Path, hashed: bool = True) -> Path:
"""Save the uploaded file and return the path."""
assert bool(fileobj), "Invalid file object!"
- hashed_name = hashlib.sha512(
- f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8")
- ).hexdigest()
+ hashed_name = (
+ hashlib.sha512(
+ f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8")
+ ).hexdigest()
+ if hashed else
+ fileobj.filename)
filename = Path(secure_filename(hashed_name)) # type: ignore[arg-type]
if not upload_dir.exists():
upload_dir.mkdir()
@@ -29,17 +33,6 @@ def fullpath(filename: str):
return Path(current_app.config["UPLOAD_FOLDER"], filename).absolute()
-def chunked_binary_read(filepath: Path, chunksize: int = 2048) -> Iterator:
- """Read a file in binary mode in chunks."""
- with open(filepath, "rb") as inputfile:
- while True:
- data = inputfile.read(chunksize)
- if data != b"":
- yield data
- continue
- break
-
-
def sha256_digest_over_file(filepath: Path) -> str:
"""Compute the sha256 digest over a file's contents."""
filehash = hashlib.sha256()
diff --git a/uploader/files/views.py b/uploader/files/views.py
new file mode 100644
index 0000000..ddf5350
--- /dev/null
+++ b/uploader/files/views.py
@@ -0,0 +1,116 @@
+"""Module for generic files endpoints."""
+import traceback
+from pathlib import Path
+
+from flask import request, jsonify, Blueprint, current_app as app
+
+from .chunks import chunk_name, chunks_directory
+
+files = Blueprint("files", __name__)
+
+def target_file(fileid: str) -> Path:
+ """Compute the full path for the target file."""
+ return Path(app.config["UPLOAD_FOLDER"], fileid)
+
+
+@files.route("/upload/resumable", methods=["GET"])
+def resumable_upload_get():
+ """Used for checking whether **ALL** chunks have been uploaded."""
+ fileid = request.args.get("resumableIdentifier", type=str) or ""
+ filename = request.args.get("resumableFilename", type=str) or ""
+ chunk = request.args.get("resumableChunkNumber", type=int) or 0
+ if not(fileid or filename or chunk):
+ return jsonify({
+ "message": "At least one required query parameter is missing.",
+ "error": "BadRequest",
+ "statuscode": 400
+ }), 400
+
+ # If the complete target file exists, return 200 for all chunks.
+ _targetfile = target_file(fileid)
+ if _targetfile.exists():
+ return jsonify({
+ "uploaded-file": _targetfile.name,
+ "original-name": filename,
+ "chunk": chunk,
+ "message": "The complete file already exists.",
+ "statuscode": 200
+ }), 200
+
+ if Path(chunks_directory(fileid),
+ chunk_name(filename, chunk)).exists():
+ return jsonify({
+ "chunk": chunk,
+ "message": f"Chunk {chunk} exists.",
+ "statuscode": 200
+ }), 200
+
+ return jsonify({
+ "message": f"Chunk {chunk} was not found.",
+ "error": "NotFound",
+ "statuscode": 404
+ }), 404
+
+
+def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path:
+ """Merge the chunks into a single file."""
+ with open(targetfile, "ab") as _target:
+ for chunkfile in chunkpaths:
+ with open(chunkfile, "rb") as _chunkdata:
+ _target.write(_chunkdata.read())
+
+ chunkfile.unlink(missing_ok=True)
+ return targetfile
+
+
+@files.route("/upload/resumable", methods=["POST"])
+def resumable_upload_post():
+ """Do the actual chunks upload here."""
+ _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0
+ _chunk = request.form.get("resumableChunkNumber", default=1, type=int)
+ _uploadfilename = request.form.get(
+ "resumableFilename", default="", type=str) or ""
+ _fileid = request.form.get(
+ "resumableIdentifier", default="", type=str) or ""
+ _targetfile = target_file(_fileid)
+
+ if _targetfile.exists():
+ return jsonify({
+ "uploaded-file": _targetfile.name,
+ "original-name": _uploadfilename,
+ "message": "File was uploaded successfully!",
+ "statuscode": 200
+ }), 200
+
+ try:
+ chunks_directory(_fileid).mkdir(exist_ok=True, parents=True)
+ request.files["file"].save(Path(chunks_directory(_fileid),
+ chunk_name(_uploadfilename, _chunk)))
+
+ # Check whether upload is complete
+ chunkpaths = tuple(
+ Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk))
+ for _achunk in range(1, _totalchunks+1))
+ if all(_file.exists() for _file in chunkpaths):
+ # merge_files and clean up chunks
+ __merge_chunks__(_targetfile, chunkpaths)
+ chunks_directory(_fileid).rmdir()
+ return jsonify({
+ "uploaded-file": _targetfile.name,
+ "original-name": _uploadfilename,
+ "message": "File was uploaded successfully!",
+ "statuscode": 200
+ }), 200
+ return jsonify({
+ "message": f"Chunk {int(_chunk)} uploaded successfully.",
+ "statuscode": 201
+ }), 201
+ except Exception as exc:# pylint: disable=[broad-except]
+ msg = "Error processing uploaded file chunks."
+ app.logger.error(msg, exc_info=True, stack_info=True)
+ return jsonify({
+ "message": msg,
+ "error": type(exc).__name__,
+ "error-description": " ".join(str(arg) for arg in exc.args),
+ "error-trace": traceback.format_exception(exc)
+ }), 500
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0433420..54c2444 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -12,12 +12,12 @@ from flask import (flash,
from uploader.ui import make_template_renderer
from uploader.oauth2.client import oauth2_post
from uploader.authorisation import require_login
+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.request_checks import with_species, with_population
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import (populations_by_species,
- population_by_species_and_id)
+from uploader.population.models import population_by_species_and_id
from .models import (genotype_markers,
genotype_dataset,
@@ -35,8 +35,15 @@ def index():
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template("genotypes/index.html",
- species=order_by_family(all_species(conn)),
+ species=all_species(conn),
activelink="genotypes")
+
+ species_id = request.args.get("species_id")
+ if species_id == "CREATE-SPECIES":
+ return redirect(url_for(
+ "species.create_species",
+ return_to="species.populations.genotypes.select_population"))
+
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
@@ -50,28 +57,16 @@ def index():
methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.genotypes.index")
-def select_population(species: dict, species_id: int):
+def select_population(species: dict, species_id: int):# pylint: disable=[unused-argument]
"""Select the population under which the genotypes go."""
- with database_connection(app.config["SQL_URI"]) as conn:
- if not bool(request.args.get("population_id")):
- return render_template("genotypes/select-population.html",
- species=species,
- populations=order_by_family(
- populations_by_species(conn, species_id),
- order_key="FamilyOrder"),
- activelink="genotypes")
-
- population = population_by_species_and_id(
- conn, species_id, request.args.get("population_id"))
- if not bool(population):
- flash("Invalid population selected!", "alert-danger")
- return redirect(url_for(
- "species.populations.genotypes.select_population",
- species_id=species_id))
-
- return redirect(url_for("species.populations.genotypes.list_genotypes",
- species_id=species_id,
- population_id=population["Id"]))
+ return generic_select_population(
+ species,
+ "genotypes/select-population.html",
+ request.args.get("population_id") or "",
+ "species.populations.genotypes.select_population",
+ "species.populations.genotypes.list_genotypes",
+ "genotypes",
+ "Invalid population selected!")
@genotypesbp.route(
diff --git a/uploader/monadic_requests.py b/uploader/monadic_requests.py
index c492df5..f1f5c77 100644
--- a/uploader/monadic_requests.py
+++ b/uploader/monadic_requests.py
@@ -5,12 +5,12 @@ from typing import Union, Optional, Callable
import requests
from requests.models import Response
from pymonad.either import Left, Right, Either
+from markupsafe import escape as markupsafe_escape
from flask import (flash,
request,
redirect,
render_template,
- current_app as app,
- escape as flask_escape)
+ current_app as app)
# HTML Status codes indicating a successful request.
SUCCESS_CODES = (200, 201, 202, 203, 204, 205, 206, 207, 208, 226)
@@ -39,9 +39,9 @@ def make_error_handler(
trace=traceback.format_exception(resp_or_exc))
if isinstance(resp_or_exc, Response):
flash("The authorisation server responded with "
- f"({flask_escape(resp_or_exc.status_code)}, "
- f"{flask_escape(resp_or_exc.reason)}) for the request to "
- f"'{flask_escape(resp_or_exc.request.url)}'",
+ f"({markupsafe_escape(resp_or_exc.status_code)}, "
+ f"{markupsafe_escape(resp_or_exc.reason)}) for the request to "
+ f"'{markupsafe_escape(resp_or_exc.request.url)}'",
"alert-danger")
return redirect_to
diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py
index e7128de..1efa299 100644
--- a/uploader/oauth2/client.py
+++ b/uploader/oauth2/client.py
@@ -112,7 +112,8 @@ def oauth2_client():
try:
jwt = JsonWebToken(["RS256"]).decode(
token["access_token"], key=jwk)
- return datetime.now().timestamp() > jwt["exp"]
+ if bool(jwt.get("exp")):
+ return datetime.now().timestamp() > jwt["exp"]
except BadSignatureError as _bse:
pass
diff --git a/uploader/oauth2/views.py b/uploader/oauth2/views.py
index 61037f3..a7211cb 100644
--- a/uploader/oauth2/views.py
+++ b/uploader/oauth2/views.py
@@ -116,7 +116,7 @@ def logout():
_user = session_info["user"]
_user_str = f"{_user['name']} ({_user['email']})"
session.clear_session_info()
- flash("Successfully logged out.", "alert-success")
+ flash("Successfully signed out.", "alert-success")
return redirect("/")
if user_logged_in():
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 73b1cce..e1ec0c9 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -54,6 +54,20 @@ def phenotypes_count(conn: mdb.Connection,
return int(cursor.fetchone()["total_phenos"])
+def phenotype_publication_data(conn, phenotype_id) -> Optional[dict]:
+ """Retrieve the publication data for a phenotype if it exists."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT DISTINCT pxr.PhenotypeId, pub.* FROM PublishXRef AS pxr "
+ "INNER JOIN Publication as pub ON pxr.PublicationId=pub.Id "
+ "WHERE pxr.PhenotypeId=%s",
+ (phenotype_id,))
+ res = cursor.fetchone()
+ if res is None:
+ return res
+ return dict(res)
+
+
def dataset_phenotypes(conn: mdb.Connection,
population_id: int,
dataset_id: int,
@@ -61,7 +75,7 @@ def dataset_phenotypes(conn: mdb.Connection,
limit: Optional[int] = None) -> tuple[dict, ...]:
"""Fetch the actual phenotypes."""
_query = (
- "SELECT pheno.*, pxr.Id, ist.InbredSetCode FROM Phenotype AS pheno "
+ "SELECT pheno.*, pxr.Id AS xref_id, ist.InbredSetCode FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
@@ -73,31 +87,41 @@ def dataset_phenotypes(conn: mdb.Connection,
return tuple(dict(row) for row in cursor.fetchall())
-def __phenotype_se__(cursor: Cursor,
- species_id: int,
- population_id: int,
- dataset_id: int,
- xref_id: str) -> dict:
+def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids):
"""Fetch standard-error values (if they exist) for a phenotype."""
- _sequery = (
- "SELECT pxr.Id AS xref_id, pxr.DataId, str.Id AS StrainId, pse.error, nst.count "
- "FROM Phenotype AS pheno "
- "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
- "INNER JOIN PublishSE AS pse ON pxr.DataId=pse.DataId "
- "INNER JOIN NStrain AS nst ON pse.DataId=nst.DataId "
- "INNER JOIN Strain AS str ON nst.StrainId=str.Id "
- "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
- "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
- "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
- "WHERE (str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)")
- cursor.execute(_sequery,
- (species_id, population_id, dataset_id, xref_id))
- return {(row["DataId"], row["StrainId"]): {
- "xref_id": row["xref_id"],
- "DataId": row["DataId"],
- "error": row["error"],
- "count": row["count"]
- } for row in cursor.fetchall()}
+ paramstr = ", ".join(["(%s, %s)"] * len(dataids_and_strainids))
+ flat = tuple(item for sublist in dataids_and_strainids for item in sublist)
+ cursor.execute("SELECT * FROM PublishSE WHERE (DataId, StrainId) IN "
+ f"({paramstr})",
+ flat)
+ debug_query(cursor, app.logger)
+ _se = {
+ (row["DataId"], row["StrainId"]): {
+ "DataId": row["DataId"],
+ "StrainId": row["StrainId"],
+ "error": row["error"]
+ }
+ for row in cursor.fetchall()
+ }
+
+ cursor.execute("SELECT * FROM NStrain WHERE (DataId, StrainId) IN "
+ f"({paramstr})",
+ flat)
+ debug_query(cursor, app.logger)
+ _n = {
+ (row["DataId"], row["StrainId"]): {
+ "DataId": row["DataId"],
+ "StrainId": row["StrainId"],
+ "count": row["count"]
+ }
+ for row in cursor.fetchall()
+ }
+
+ keys = set(tuple(_se.keys()) + tuple(_n.keys()))
+ return {
+ key: {"xref_id": xref_id, **_se.get(key,{}), **_n.get(key,{})}
+ for key in keys
+ }
def __organise_by_phenotype__(pheno, row):
"""Organise disparate data rows into phenotype 'objects'."""
@@ -117,6 +141,7 @@ def __organise_by_phenotype__(pheno, row):
**(_pheno["data"] if bool(_pheno) else {}),
(row["DataId"], row["StrainId"]): {
"DataId": row["DataId"],
+ "StrainId": row["StrainId"],
"mean": row["mean"],
"Locus": row["Locus"],
"LRS": row["LRS"],
@@ -170,11 +195,9 @@ def phenotype_by_id(
**_pheno,
"data": tuple(__merge_pheno_data_and_se__(
_pheno["data"],
- __phenotype_se__(cursor,
- species_id,
- population_id,
- dataset_id,
- xref_id)).values())
+ __phenotype_se__(
+ cursor, xref_id, tuple(_pheno["data"].keys()))
+ ).values())
}
if bool(_pheno) and len(_pheno.keys()) > 1:
raise Exception(
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index c4aa67a..dc2df8f 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -3,17 +3,21 @@ import sys
import uuid
import json
import datetime
+from typing import Any
from pathlib import Path
-from functools import wraps
+from zipfile import ZipFile
+from functools import wraps, reduce
from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING
from redis import Redis
+from pymonad.either import Left
from requests.models import Response
from MySQLdb.cursors import DictCursor
from gn_libs.mysqldb import database_connection
from flask import (flash,
request,
url_for,
+ jsonify,
redirect,
Blueprint,
current_app as app)
@@ -27,12 +31,11 @@ from uploader.files import save_file#, fullpath
from uploader.ui import make_template_renderer
from uploader.oauth2.client import oauth2_post
from uploader.authorisation import require_login
+from uploader.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.request_checks import with_species, with_population
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import (populations_by_species,
- population_by_species_and_id)
from uploader.input_validation import (encode_errors,
decode_errors,
is_valid_representative_name)
@@ -42,11 +45,15 @@ from .models import (dataset_by_id,
phenotypes_count,
save_new_dataset,
dataset_phenotypes,
- datasets_by_population)
+ datasets_by_population,
+ phenotype_publication_data)
phenotypesbp = Blueprint("phenotypes", __name__)
render_template = make_template_renderer("phenotypes")
+_FAMILIES_WITH_SE_AND_N_ = (
+ "Reference Populations (replicate average, SE, N)",)
+
@phenotypesbp.route("/phenotypes", methods=["GET"])
@require_login
def index():
@@ -54,10 +61,16 @@ def index():
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template("phenotypes/index.html",
- species=order_by_family(all_species(conn)),
+ species=all_species(conn),
activelink="phenotypes")
- species = species_by_id(conn, request.args.get("species_id"))
+ species_id = request.args.get("species_id")
+ if species_id == "CREATE-SPECIES":
+ return redirect(url_for(
+ "species.create_species",
+ return_to="species.populations.phenotypes.select_population"))
+
+ species = species_by_id(conn, species_id)
if not bool(species):
flash("No such species!", "alert-danger")
return redirect(url_for("species.populations.phenotypes.index"))
@@ -71,27 +84,14 @@ def index():
@with_species(redirect_uri="species.populations.phenotypes.index")
def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""Select the population for your phenotypes."""
- with database_connection(app.config["SQL_URI"]) as conn:
- if not bool(request.args.get("population_id")):
- return render_template("phenotypes/select-population.html",
- species=species,
- populations=order_by_family(
- populations_by_species(
- conn, species["SpeciesId"]),
- order_key="FamilyOrder"),
- activelink="phenotypes")
-
- population = population_by_species_and_id(
- conn, species["SpeciesId"], int(request.args["population_id"]))
- if not bool(population):
- flash("No such population found!", "alert-danger")
- return redirect(url_for(
- "species.populations.phenotypes.select_population",
- species_id=species["SpeciesId"]))
-
- return redirect(url_for("species.populations.phenotypes.list_datasets",
- species_id=species["SpeciesId"],
- population_id=population["Id"]))
+ return generic_select_population(
+ species,
+ "phenotypes/select-population.html",
+ request.args.get("population_id") or "",
+ "species.populations.phenotypes.select_population",
+ "species.populations.phenotypes.list_datasets",
+ "phenotypes",
+ "No such population found!")
@@ -189,12 +189,10 @@ def view_dataset(# pylint: disable=[unused-argument]
phenotype_count=phenotypes_count(
conn, population["Id"], dataset["Id"]),
phenotypes=enumerate_sequence(
- dataset_phenotypes(conn,
- population["Id"],
- dataset["Id"],
- offset=start_at,
- limit=count),
- start=start_at+1),
+ dataset_phenotypes(
+ conn,
+ population["Id"],
+ dataset["Id"])),
start_from=start_at,
count=count,
activelink="view-dataset")
@@ -218,16 +216,31 @@ def view_phenotype(# pylint: disable=[unused-argument]
):
"""View an individual phenotype from the dataset."""
def __render__(privileges):
+ phenotype = phenotype_by_id(conn,
+ species["SpeciesId"],
+ population["Id"],
+ dataset["Id"],
+ xref_id)
+ def __non_empty__(value) -> bool:
+ if isinstance(value, str):
+ return value.strip() != ""
+ return bool(value)
+
return render_template(
"phenotypes/view-phenotype.html",
species=species,
population=population,
dataset=dataset,
- phenotype=phenotype_by_id(conn,
- species["SpeciesId"],
- population["Id"],
- dataset["Id"],
- xref_id),
+ 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",
@@ -307,6 +320,70 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
population_id=population["Id"]))
+def process_phenotypes_rqtl2_bundle(error_uri):
+ """Process phenotypes from the uploaded R/qtl2 bundle."""
+ _redisuri = app.config["REDIS_URL"]
+ _sqluri = app.config["SQL_URI"]
+ try:
+ ## Handle huge files here...
+ phenobundle = save_file(request.files["phenotypes-bundle"],
+ Path(app.config["UPLOAD_FOLDER"]))
+ rqc.validate_bundle(phenobundle)
+ return phenobundle
+ except AssertionError as _aerr:
+ app.logger.debug("File upload error!", exc_info=True)
+ flash("Expected a zipped bundle of files with phenotypes' "
+ "information.",
+ "alert-danger")
+ return error_uri
+ except rqe.RQTLError as rqtlerr:
+ app.logger.debug("Bundle validation error!", exc_info=True)
+ flash("R/qtl2 Error: " + " ".join(rqtlerr.args), "alert-danger")
+ return error_uri
+
+
+def process_phenotypes_individual_files(error_uri):
+ """Process the uploaded individual files."""
+ form = request.form
+ cdata = {
+ "sep": form["file-separator"],
+ "comment.char": form["file-comment-character"],
+ "na.strings": form["file-na"].split(" "),
+ }
+ bundlepath = Path(app.config["UPLOAD_FOLDER"],
+ f"{str(uuid.uuid4()).replace('-', '')}.zip")
+ with ZipFile(bundlepath,mode="w") as zfile:
+ for rqtlkey, formkey in (("phenocovar", "phenotype-descriptions"),
+ ("pheno", "phenotype-data"),
+ ("phenose", "phenotype-se"),
+ ("phenonum", "phenotype-n")):
+ if form.get("resumable-upload", False):
+ # Chunked upload of large files was used
+ filedata = json.loads(form[formkey])
+ zfile.write(
+ Path(app.config["UPLOAD_FOLDER"], filedata["uploaded-file"]),
+ arcname=filedata["original-name"])
+ cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]]
+ else:
+ # TODO: Check this path: fix any bugs.
+ _sentfile = request.files[formkey]
+ if not bool(_sentfile):
+ flash(f"Expected file ('{formkey}') was not provided.",
+ "alert-danger")
+ return error_uri
+
+ filepath = save_file(
+ _sentfile, Path(app.config["UPLOAD_FOLDER"]), hashed=False)
+ zfile.write(
+ Path(app.config["UPLOAD_FOLDER"], filepath),
+ arcname=filepath.name)
+ cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name]
+
+ zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2))
+
+ return bundlepath
+
+
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
"/<int:dataset_id>/add-phenotypes",
@@ -318,6 +395,7 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
redirect_uri="species.populations.phenotypes.list_datasets")
def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# pylint: disable=[unused-argument, too-many-locals]
"""Add one or more phenotypes to the dataset."""
+ use_bundle = request.args.get("use_bundle", "").lower() == "true"
add_phenos_uri = redirect(url_for(
"species.populations.phenotypes.add_phenotypes",
species_id=species["SpeciesId"],
@@ -333,8 +411,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
today = datetime.date.today()
return render_template(
("phenotypes/add-phenotypes-with-rqtl2-bundle.html"
- if request.args.get("use_bundle", "").lower() == "true"
- else "phenotypes/add-phenotypes-raw-files.html"),
+ if use_bundle else "phenotypes/add-phenotypes-raw-files.html"),
species=species,
population=population,
dataset=dataset,
@@ -345,25 +422,13 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
"December"),
current_month=today.strftime("%B"),
current_year=int(today.strftime("%Y")),
- families_with_se_and_n=(
- "Reference Populations (replicate average, SE, N)",),
+ families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_,
+ use_bundle=use_bundle,
activelink="add-phenotypes")
- try:
- ## Handle huge files here...
- phenobundle = save_file(request.files["phenotypes-bundle"],
- Path(app.config["UPLOAD_FOLDER"]))
- rqc.validate_bundle(phenobundle)
- except AssertionError as _aerr:
- app.logger.debug("File upload error!", exc_info=True)
- flash("Expected a zipped bundle of files with phenotypes' "
- "information.",
- "alert-danger")
- return add_phenos_uri
- except rqe.RQTLError as rqtlerr:
- app.logger.debug("Bundle validation error!", exc_info=True)
- flash("R/qtl2 Error: " + " ".join(rqtlerr.args), "alert-danger")
- return add_phenos_uri
+ phenobundle = (process_phenotypes_rqtl2_bundle(add_phenos_uri)
+ if use_bundle else
+ process_phenotypes_individual_files(add_phenos_uri))
_jobid = uuid.uuid4()
_namespace = jobs.jobsnamespace()
@@ -377,7 +442,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
_redisuri, _namespace, str(_jobid), str(species["SpeciesId"]),
str(population["Id"]),
# str(dataset["Id"]),
- str(phenobundle),
+ str(phenobundle),
"--loglevel",
{
INFO: "INFO",
@@ -398,12 +463,20 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
f"{app.config['UPLOAD_FOLDER']}/job_errors")
app.logger.debug("JOB DETAILS: %s", _job)
-
- return redirect(url_for("species.populations.phenotypes.job_status",
- species_id=species["SpeciesId"],
- population_id=population["Id"],
- dataset_id=dataset["Id"],
- job_id=str(_job["jobid"])))
+ jobstatusuri = url_for("species.populations.phenotypes.job_status",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ dataset_id=dataset["Id"],
+ job_id=str(_job["jobid"]))
+ return ((jsonify({
+ "redirect-to": jobstatusuri,
+ "statuscode": 200,
+ "message": ("Follow the 'redirect-to' URI to see the state "
+ "of the quality-control job started for your "
+ "uploaded files.")
+ }), 200)
+ if request.form.get("resumable-upload", False) else
+ redirect(jobstatusuri))
@phenotypesbp.route(
@@ -439,3 +512,335 @@ def job_status(
metadata=jobs.job_files_metadata(
rconn, jobs.jobsnamespace(), job['jobid']),
activelink="add-phenotypes")
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+ "/<int:dataset_id>/job/<uuid:job_id>/review",
+ methods=["GET"])
+@require_login
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
+def review_job_data(
+ species: dict,
+ population: dict,
+ dataset: dict,
+ job_id: uuid.UUID,
+ **kwargs
+):# pylint: disable=[unused-argument]
+ """Review data one more time before entering it into the database."""
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ try:
+ job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id))
+ except jobs.JobNotFound as _jnf:
+ job = None
+
+ def __metadata_by_type__(by_type, item):
+ filetype = item[1]["filetype"]
+ return {
+ **by_type,
+ filetype: (by_type.get(filetype, tuple())
+ + ({"filename": item[0], **item[1]},))
+ }
+ metadata: dict[str, Any] = reduce(
+ __metadata_by_type__,
+ (jobs.job_files_metadata(
+ rconn, jobs.jobsnamespace(), job['jobid'])
+ if job else {}).items(),
+ {})
+
+ def __desc__(filetype):
+ match filetype:
+ case "phenocovar":
+ desc = "phenotypes"
+ case "pheno":
+ desc = "phenotypes data"
+ case "phenose":
+ desc = "phenotypes standard-errors"
+ case "phenonum":
+ desc = "phenotypes samples"
+ case _:
+ desc = f"unknown file type '{filetype}'."
+
+ return desc
+
+ def __summarise__(filetype, files):
+ return {
+ "filetype": filetype,
+ "number-of-files": len(files),
+ "total-data-rows": sum(
+ int(afile["linecount"]) - 1 for afile in files),
+ "description": __desc__(filetype)
+ }
+
+ summary = {
+ filetype: __summarise__(filetype, meta)
+ for filetype,meta in metadata.items()
+ }
+ return render_template("phenotypes/review-job-data.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ job_id=job_id,
+ job=job,
+ summary=summary,
+ activelink="add-phenotypes")
+
+
+def update_phenotype_metadata(conn, metadata: dict):
+ """Update a phenotype's basic metadata values."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM Phenotype WHERE Id=%(phenotype-id)s",
+ metadata)
+ res = {
+ **{
+ _key: _val for _key,_val in {
+ key.lower().replace("_", "-"): value
+ for key, value in (cursor.fetchone() or {}).items()
+ }.items()
+ if _key in metadata.keys()
+ },
+ "phenotype-id": metadata.get("phenotype-id")
+ }
+ if res == metadata:
+ return False
+
+ cursor.execute(
+ "UPDATE Phenotype SET "
+ "Pre_publication_description=%(pre-publication-description)s, "
+ "Post_publication_description=%(post-publication-description)s, "
+ "Original_description=%(original-description)s, "
+ "Units=%(units)s, "
+ "Pre_publication_abbreviation=%(pre-publication-abbreviation)s, "
+ "Post_publication_abbreviation=%(post-publication-abbreviation)s "
+ "WHERE Id=%(phenotype-id)s",
+ metadata)
+ return cursor.rowcount
+
+
+def update_phenotype_values(conn, values):
+ """Update a phenotype's data values."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "UPDATE PublishData SET value=%(new)s "
+ "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in values if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM PublishData "
+ "WHERE Id=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in values if item["new"] is None))
+ return len(values)
+ return 0
+
+
+def update_phenotype_se(conn, serrs):
+ """Update a phenotype's standard-error values."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "INSERT INTO PublishSE(DataId, StrainId, error) "
+ "VALUES(%(data_id)s, %(strain_id)s, %(new)s) "
+ "ON DUPLICATE KEY UPDATE error=VALUES(error)",
+ tuple(item for item in serrs if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM PublishSE "
+ "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in serrs if item["new"] is None))
+ return len(serrs)
+ return 0
+
+
+def update_phenotype_n(conn, counts):
+ """Update a phenotype's strain counts."""
+ with conn.cursor() as cursor:
+ cursor.executemany(
+ "INSERT INTO NStrain(DataId, StrainId, count) "
+ "VALUES(%(data_id)s, %(strain_id)s, %(new)s) "
+ "ON DUPLICATE KEY UPDATE count=VALUES(count)",
+ tuple(item for item in counts if item["new"] is not None))
+ cursor.executemany(
+ "DELETE FROM NStrain "
+ "WHERE DataId=%(data_id)s AND StrainId=%(strain_id)s",
+ tuple(item for item in counts if item["new"] is None))
+ return len(counts)
+
+ return 0
+
+
+def update_phenotype_data(conn, data: dict):
+ """Update the numeric data for a phenotype."""
+ def __organise_by_dataid_and_strainid__(acc, current):
+ _key, dataid, strainid = current[0].split("::")
+ _keysrc, _keytype = _key.split("-")
+ newkey = f"{dataid}::{strainid}"
+ newitem = acc.get(newkey, {})
+ newitem[_keysrc] = newitem.get(_keysrc, {})
+ newitem[_keysrc][_keytype] = current[1]
+ return {**acc, newkey: newitem}
+
+ def __separate_items__(acc, row):
+ key, val = row
+ return ({
+ **acc[0],
+ key: {
+ **val["value"],
+ "changed?": (not val["value"]["new"] == val["value"]["original"])
+ }
+ }, {
+ **acc[1],
+ key: {
+ **val["se"],
+ "changed?": (not val["se"]["new"] == val["se"]["original"])
+ }
+ },{
+ **acc[2],
+ key: {
+ **val["n"],
+ "changed?": (not val["n"]["new"] == val["n"]["original"])
+ }
+ })
+
+ values, serrs, counts = tuple(
+ tuple({
+ "data_id": row[0].split("::")[0],
+ "strain_id": row[0].split("::")[1],
+ "new": row[1]["new"]
+ } for row in item)
+ for item in (
+ filter(lambda val: val[1]["changed?"], item.items())# type: ignore[arg-type]
+ for item in reduce(# type: ignore[var-annotated]
+ __separate_items__,
+ reduce(__organise_by_dataid_and_strainid__,
+ data.items(),
+ {}).items(),
+ ({}, {}, {}))))
+
+ return (update_phenotype_values(conn, values),
+ update_phenotype_se(conn, serrs),
+ update_phenotype_n(conn, counts))
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+ "/<int:dataset_id>/phenotype/<int:xref_id>/edit",
+ methods=["GET", "POST"])
+@require_login
+@with_dataset(
+ species_redirect_uri="species.populations.phenotypes.index",
+ population_redirect_uri="species.populations.phenotypes.select_population",
+ redirect_uri="species.populations.phenotypes.list_datasets")
+def edit_phenotype_data(# pylint: disable=[unused-argument]
+ species: dict,
+ population: dict,
+ dataset: dict,
+ xref_id: int,
+ **kwargs
+):
+ """Edit the data for a particular phenotype."""
+ def __render__(**kwargs):
+ processed_kwargs = {
+ **kwargs,
+ "privileges": (kwargs.get("privileges", tuple())
+ ### For demo! Do not commit this part
+ + ("group:resource:edit-resource",
+ "group:resource:delete-resource",)
+ ### END: For demo! Do not commit this part
+ )
+ }
+ return render_template(
+ "phenotypes/edit-phenotype.html",
+ species=species,
+ population=population,
+ dataset=dataset,
+ xref_id=xref_id,
+ families_with_se_and_n=_FAMILIES_WITH_SE_AND_N_,
+ **processed_kwargs,
+ activelink="edit-phenotype")
+
+ with database_connection(app.config["SQL_URI"]) as conn:
+ if request.method == "GET":
+ def __fetch_phenotype__(privileges):
+ phenotype = phenotype_by_id(conn,
+ species["SpeciesId"],
+ population["Id"],
+ dataset["Id"],
+ xref_id)
+ if phenotype is None:
+ msg = ("Could not find the phenotype with cross-reference ID"
+ f" '{xref_id}' from dataset '{dataset['FullName']}' "
+ f" from the '{population['FullName']}' population of "
+ f" species '{species['FullName']}'.")
+ return Left({"privileges": privileges, "phenotype-error": msg})
+ return {"privileges": privileges, "phenotype": phenotype}
+
+ def __fetch_publication_data__(**kwargs):
+ pheno = kwargs["phenotype"]
+ return {
+ **kwargs,
+ "publication_data": phenotype_publication_data(
+ conn, pheno["Id"])
+ }
+
+ def __fail__(failure_object):
+ # process the object
+ return __render__(failure_object=failure_object)
+
+ return oauth2_post(
+ "/auth/resource/phenotypes/individual/linked-resource",
+ json={
+ "species_id": species["SpeciesId"],
+ "population_id": population["Id"],
+ "dataset_id": dataset["Id"],
+ "xref_id": xref_id
+ }
+ ).then(
+ lambda resource: tuple(
+ privilege["privilege_id"] for role in resource["roles"]
+ for privilege in role["privileges"])
+ ).then(
+ __fetch_phenotype__
+ ).then(
+ lambda args: __fetch_publication_data__(**args)
+ ).either(__fail__, lambda args: __render__(**args))
+
+ ## POST
+ _change = False
+ match request.form.get("submit", "invalid-action"):
+ case "update basic metadata":
+ _change = update_phenotype_metadata(conn, {
+ key: value.strip() if bool(value.strip()) else None
+ for key, value in request.form.items()
+ if key not in ("submit",)
+ })
+ msg = "Basic metadata was updated successfully."
+ case "update data":
+ _update = update_phenotype_data(conn, {
+ key: value.strip() if bool(value.strip()) else None
+ for key, value in request.form.items()
+ if key not in ("submit",)
+ })
+ msg = (f"{_update[0]} value rows, {_update[1]} standard-error "
+ f"rows and {_update[2]} 'N' rows were updated.")
+ _change = any(item != 0 for item in _update)
+ case "update publication":
+ flash("NOT IMPLEMENTED: Would update publication data.", "alert-success")
+ case _:
+ flash("Invalid phenotype editing action.", "alert-danger")
+
+ if _change:
+ flash(msg, "alert-success")
+ return redirect(url_for(
+ "species.populations.phenotypes.view_phenotype",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ dataset_id=dataset["Id"],
+ xref_id=xref_id))
+
+ flash("No change was made by the user.", "alert-info")
+ return redirect(url_for(
+ "species.populations.phenotypes.edit_phenotype_data",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ dataset_id=dataset["Id"],
+ xref_id=xref_id))
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index c20ab44..d12a9ef 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -12,7 +12,7 @@ from flask import (
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.species.models import all_species, species_by_id
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
+from uploader.datautils import safe_int, enumerate_sequence
from .models import (save_new_platform,
platforms_by_species,
@@ -29,9 +29,15 @@ def index():
if not bool(request.args.get("species_id")):
return render_template(
"platforms/index.html",
- species=order_by_family(all_species(conn)),
+ species=all_species(conn),
activelink="platforms")
+ species_id = request.args.get("species_id")
+ if species_id == "CREATE-SPECIES":
+ return redirect(url_for(
+ "species.create_species",
+ return_to="species.platforms.list_platforms"))
+
species = species_by_id(conn, request.args["species_id"])
if not bool(species):
flash("No species selected.", "alert-danger")
diff --git a/uploader/population/models.py b/uploader/population/models.py
index 6dcd85e..d78a821 100644
--- a/uploader/population/models.py
+++ b/uploader/population/models.py
@@ -61,7 +61,7 @@ def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dic
**population_details,
"FamilyOrder": _families.get(
population_details["Family"],
- max(_families.values())+1)
+ max((0,) + tuple(_families.values()))+1)
}
cursor.execute(
"INSERT INTO InbredSet("
diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py
index 436eca0..044cdd4 100644
--- a/uploader/population/rqtl2.py
+++ b/uploader/population/rqtl2.py
@@ -11,13 +11,11 @@ from typing import Union, Callable, Optional
import MySQLdb as mdb
from redis import Redis
from MySQLdb.cursors import DictCursor
-from werkzeug.utils import secure_filename
from gn_libs.mysqldb import database_connection
from flask import (
flash,
escape,
request,
- jsonify,
url_for,
redirect,
Response,
@@ -191,127 +189,6 @@ def trigger_rqtl2_bundle_qc(
return jobid
-def chunk_name(uploadfilename: str, chunkno: int) -> str:
- """Generate chunk name from original filename and chunk number"""
- if uploadfilename == "":
- raise ValueError("Name cannot be empty!")
- if chunkno < 1:
- raise ValueError("Chunk number must be greater than zero")
- return f"{secure_filename(uploadfilename)}_part_{chunkno:05d}"
-
-
-def chunks_directory(uniqueidentifier: str) -> Path:
- """Compute the directory where chunks are temporarily stored."""
- if uniqueidentifier == "":
- raise ValueError("Unique identifier cannot be empty!")
- return Path(app.config["UPLOAD_FOLDER"], f"tempdir_{uniqueidentifier}")
-
-
-@rqtl2.route(("<int:species_id>/populations/<int:population_id>/rqtl2/"
- "/rqtl2-bundle-chunked"),
- methods=["GET"])
-@require_login
-def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"]
- species_id: int,
- population_id: int
-):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that provides a way
- for testing whether all the chunks have been uploaded and to assist with
- resuming a failed expression-data.
- """
- fileid = request.args.get("resumableIdentifier", type=str) or ""
- filename = request.args.get("resumableFilename", type=str) or ""
- chunk = request.args.get("resumableChunkNumber", type=int) or 0
- if not(fileid or filename or chunk):
- return jsonify({
- "message": "At least one required query parameter is missing.",
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- if Path(chunks_directory(fileid),
- chunk_name(filename, chunk)).exists():
- return "OK"
-
- return jsonify({
- "message": f"Chunk {chunk} was not found.",
- "error": "NotFound",
- "statuscode": 404
- }), 404
-
-
-def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path:
- """Merge the chunks into a single file."""
- with open(targetfile, "ab") as _target:
- for chunkfile in chunkpaths:
- with open(chunkfile, "rb") as _chunkdata:
- _target.write(_chunkdata.read())
-
- chunkfile.unlink()
- return targetfile
-
-
-@rqtl2.route(("<int:species_id>/population/<int:population_id>/rqtl2/upload/"
- "/rqtl2-bundle-chunked"),
- methods=["POST"])
-@require_login
-def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that allows large
- files to be uploaded in chunks.
-
- This should hopefully speed up uploads, and if done right, even enable
- resumable uploads
- """
- _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0
- _chunk = request.form.get("resumableChunkNumber", default=1, type=int)
- _uploadfilename = request.form.get(
- "resumableFilename", default="", type=str) or ""
- _fileid = request.form.get(
- "resumableIdentifier", default="", type=str) or ""
- _targetfile = Path(app.config["UPLOAD_FOLDER"], _fileid)
-
- if _targetfile.exists():
- return jsonify({
- "message": (
- "A file with a similar unique identifier has previously been "
- "uploaded and possibly is/has being/been processed."),
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- try:
- # save chunk data
- chunks_directory(_fileid).mkdir(exist_ok=True, parents=True)
- request.files["file"].save(Path(chunks_directory(_fileid),
- chunk_name(_uploadfilename, _chunk)))
-
- # Check whether upload is complete
- chunkpaths = tuple(
- Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk))
- for _achunk in range(1, _totalchunks+1))
- if all(_file.exists() for _file in chunkpaths):
- # merge_files and clean up chunks
- __merge_chunks__(_targetfile, chunkpaths)
- chunks_directory(_fileid).rmdir()
- jobid = trigger_rqtl2_bundle_qc(
- species_id, population_id, _targetfile, _uploadfilename)
- return url_for(
- "expression-data.rqtl2.rqtl2_bundle_qc_status", jobid=jobid)
- except Exception as exc:# pylint: disable=[broad-except]
- msg = "Error processing uploaded file chunks."
- app.logger.error(msg, exc_info=True, stack_info=True)
- return jsonify({
- "message": msg,
- "error": type(exc).__name__,
- "error-description": " ".join(str(arg) for arg in exc.args),
- "error-trace": traceback.format_exception(exc)
- }), 500
-
- return "OK"
-
-
@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>",
methods=["GET", "POST"])
@require_login
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 4f985f5..270dd5f 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -2,6 +2,7 @@
import json
import base64
+from markupsafe import escape
from MySQLdb.cursors import DictCursor
from gn_libs.mysqldb import database_connection
from flask import (flash,
@@ -19,11 +20,9 @@ from uploader.genotypes.views import genotypesbp
from uploader.datautils import enumerate_sequence
from uploader.phenotypes.views import phenotypesbp
from uploader.expression_data.views import exprdatabp
+from uploader.species.models import all_species, species_by_id
from uploader.monadic_requests import make_either_error_handler
from uploader.input_validation import is_valid_representative_name
-from uploader.species.models import (all_species,
- species_by_id,
- order_species_by_family)
from .models import (save_population,
population_families,
@@ -48,7 +47,15 @@ def index():
if not bool(request.args.get("species_id")):
return render_template(
"populations/index.html",
- species=order_species_by_family(all_species(conn)))
+ species=all_species(conn),
+ activelink="populations")
+
+ species_id = request.args.get("species_id")
+ if species_id == "CREATE-SPECIES":
+ return redirect(url_for(
+ "species.create_species",
+ return_to="species.populations.list_species_populations"))
+
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash("Invalid species identifier provided!", "alert-danger")
@@ -101,6 +108,7 @@ def create_population(species_id: int):
{"id": "2", "value": "GEMMA"},
{"id": "3", "value": "R/qtl"},
{"id": "4", "value": "GEMMA, PLINK"}),
+ return_to=(request.args.get("return_to") or ""),
activelink="create-population",
**error_values)
@@ -151,7 +159,15 @@ def create_population(species_id: int):
})
def __flash_success__(_success):
- flash("Successfully created resource.", "alert-success")
+ flash("Successfully created population "
+ f"{escape(new_population['FullName'])}.",
+ "alert-success")
+ return_to = request.form.get("return_to") or ""
+ if return_to:
+ return redirect(url_for(
+ return_to,
+ species_id=species["SpeciesId"],
+ population_id=new_population["InbredSetId"]))
return redirect(url_for(
"species.populations.view_population",
species_id=species["SpeciesId"],
diff --git a/uploader/route_utils.py b/uploader/route_utils.py
new file mode 100644
index 0000000..18eadda
--- /dev/null
+++ b/uploader/route_utils.py
@@ -0,0 +1,41 @@
+"""Generic routing utilities."""
+from flask import flash, url_for, redirect, render_template, current_app as app
+
+from gn_libs.mysqldb import database_connection
+
+from uploader.population.models import (populations_by_species,
+ population_by_species_and_id)
+
+def generic_select_population(# pylint: disable=[too-many-arguments]
+ species: dict,
+ template: str,
+ population_id: str,
+ back_to: str,
+ forward_to: str,
+ activelink: str,
+ error_message: str = "No such population found!"
+):
+ """Handles common flow for 'select population' step."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ if not bool(population_id):
+ return render_template(
+ template,
+ species=species,
+ populations=populations_by_species(conn, species["SpeciesId"]),
+ activelink=activelink)
+
+ if population_id == "CREATE-POPULATION":
+ return redirect(url_for(
+ "species.populations.create_population",
+ species_id=species["SpeciesId"],
+ return_to=forward_to))
+
+ population = population_by_species_and_id(
+ conn, species["SpeciesId"], int(population_id))
+ if not bool(population):
+ flash(error_message, "alert-danger")
+ return redirect(url_for(back_to, species_id=species["SpeciesId"]))
+
+ return redirect(url_for(forward_to,
+ species_id=species["SpeciesId"],
+ population_id=population["Id"]))
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index ed79101..27e5d3c 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -16,16 +16,15 @@ from uploader import jobs
from uploader.files import save_file
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
-from uploader.request_checks import with_population
from uploader.input_validation import is_integer_input
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import population_by_id, populations_by_species
+from uploader.population.models import population_by_id
+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.request_checks import with_species, with_population
from uploader.db_utils import (with_db_connection,
database_connection,
with_redis_connection)
-from uploader.species.models import (all_species,
- species_by_id,
- order_species_by_family)
from .models import samples_by_species_and_population
@@ -40,8 +39,15 @@ def index():
if not bool(request.args.get("species_id")):
return render_template(
"samples/index.html",
- species=order_species_by_family(all_species(conn)),
+ species=all_species(conn),
activelink="samples")
+
+ species_id = request.args.get("species_id")
+ if species_id == "CREATE-SPECIES":
+ return redirect(url_for(
+ "species.create_species",
+ return_to="species.populations.samples.select_population"))
+
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash("No such species!", "alert-danger")
@@ -52,57 +58,31 @@ def index():
@samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"])
@require_login
-def select_population(species_id: int):
+@with_species(redirect_uri="species.populations.samples.index")
+def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""Select the population to use for the samples."""
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- if not bool(species):
- flash("Invalid species!", "alert-danger")
- return redirect(url_for("species.populations.samples.index"))
-
- if not bool(request.args.get("population_id")):
- return render_template("samples/select-population.html",
- species=species,
- populations=order_by_family(
- populations_by_species(
- conn,
- species_id),
- order_key="FamilyOrder"),
- activelink="samples")
-
- population = population_by_id(conn, request.args.get("population_id"))
- if not bool(population):
- flash("Population not found!", "alert-danger")
- return redirect(url_for(
- "species.populations.samples.select_population",
- species_id=species_id))
-
- return redirect(url_for("species.populations.samples.list_samples",
- species_id=species_id,
- population_id=population["Id"]))
+ return generic_select_population(
+ species,
+ "samples/select-population.html",
+ request.args.get("population_id") or "",
+ "species.populations.samples.select_population",
+ "species.populations.samples.list_samples",
+ "samples",
+ "Population not found!")
@samplesbp.route("<int:species_id>/populations/<int:population_id>/samples")
@require_login
-def list_samples(species_id: int, population_id: int):
+@with_population(
+ species_redirect_uri="species.populations.samples.index",
+ redirect_uri="species.populations.samples.select_population")
+def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""
List the samples in a particular population and give the ability to upload
new ones.
"""
with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- if not bool(species):
- flash("Invalid species!", "alert-danger")
- return redirect(url_for("species.populations.samples.index"))
-
- population = population_by_id(conn, population_id)
- if not bool(population):
- flash("Population not found!", "alert-danger")
- return redirect(url_for(
- "species.populations.samples.select_population",
- species_id=species_id))
-
all_samples = enumerate_sequence(samples_by_species_and_population(
- conn, species_id, population_id))
+ conn, species["SpeciesId"], population["Id"]))
total_samples = len(all_samples)
offset = max(safe_int(request.args.get("from") or 0), 0)
count = int(request.args.get("count") or 20)
diff --git a/uploader/species/models.py b/uploader/species/models.py
index 51f941c..db53d48 100644
--- a/uploader/species/models.py
+++ b/uploader/species/models.py
@@ -58,7 +58,8 @@ def save_species(conn: mdb.Connection,
common_name: The species' common name.
scientific_name; The species' scientific name.
"""
- genus, species_name = scientific_name.split(" ")
+ genus, *species_parts = scientific_name.split(" ")
+ species_name: str = " ".join(species_parts)
families = species_families(conn)
with conn.cursor() as cursor:
cursor.execute("SELECT MAX(OrderId) FROM Species")
@@ -68,7 +69,7 @@ def save_species(conn: mdb.Connection,
"menu_name": f"{common_name} ({genus[0]}. {species_name.lower()})",
"scientific_name": scientific_name,
"family": family,
- "family_order": families[family],
+ "family_order": families.get(family, 999999),
"taxon_id": taxon_id,
"species_order": cursor.fetchone()[0] + 5
}
@@ -116,7 +117,8 @@ def update_species(# pylint: disable=[too-many-arguments]
species_order: The ordering of this species in relation to others
"""
with conn.cursor(cursorclass=DictCursor) as cursor:
- genus, species_name = scientific_name.split(" ")
+ genus, *species_parts = scientific_name.split(" ")
+ species_name = " ".join(species_parts)
species = {
"species_id": species_id,
"common_name": common_name,
diff --git a/uploader/species/views.py b/uploader/species/views.py
index fee5c75..cea2f68 100644
--- a/uploader/species/views.py
+++ b/uploader/species/views.py
@@ -1,4 +1,5 @@
"""Endpoints handling species."""
+from markupsafe import escape
from pymonad.either import Left, Right, Either
from gn_libs.mysqldb import database_connection
from flask import (flash,
@@ -62,6 +63,8 @@ def create_species():
if request.method == "GET":
return render_template("species/create-species.html",
families=species_families(conn),
+ return_to=(
+ request.args.get("return_to") or ""),
activelink="create-species")
error = False
@@ -79,7 +82,7 @@ def create_species():
error = True
parts = tuple(name.strip() for name in scientific_name.split(" "))
- if len(parts) != 2 or not all(bool(name) for name in parts):
+ if (len(parts) != 2 and len(parts) != 3) or not all(bool(name) for name in parts):
flash("The scientific name you provided is invalid.", "alert-danger")
error = True
@@ -113,7 +116,15 @@ def create_species():
species = save_species(
conn, common_name, scientific_name, family, taxon_id)
- flash("Species saved successfully!", "alert-success")
+ flash(
+ f"You have successfully added species "
+ f"'{escape(species['scientific_name'])} "
+ f"({escape(species['common_name'])})'.",
+ "alert-success")
+
+ return_to = request.form.get("return_to").strip()
+ if return_to:
+ return redirect(url_for(return_to, species_id=species["species_id"]))
return redirect(url_for("species.view_species", species_id=species["species_id"]))
diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css
index f482c1b..8366c67 100644
--- a/uploader/static/css/styles.css
+++ b/uploader/static/css/styles.css
@@ -1,161 +1,173 @@
+* {
+ box-sizing: border-box;
+}
+
body {
margin: 0.7em;
- box-sizing: border-box;
display: grid;
- grid-template-columns: 1fr 6fr;
- grid-template-rows: 5em 100%;
+ grid-template-columns: 1fr 9fr;
grid-gap: 20px;
- font-family: Georgia, Garamond, serif;
+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
font-style: normal;
+ font-size: 20px;
}
#header {
- grid-column: 1/3;
- width: 100%;
- /* background: cyan; */
- padding-top: 0.5em;
- border-radius: 0.5em;
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 3;
+
+ /* Define layout for the children elements */
+ display: grid;
+ grid-template-columns: 8fr 2fr;
+ /* Content styling */
background-color: #336699;
- border-color: #080808;
color: #FFFFFF;
- background-image: none;
+ border-radius: 3px;
+ min-height: 30px;
}
-#header .header {
- font-size: 2em;
- display: inline-block;
- text-align: start;
-}
+#header #header-text {
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 2;
-#header .header-nav {
- display: inline-block;
- color: #FFFFFF;
+ /* Content styling */
+ padding-left: 1em;
}
-#header .header-nav li {
- border-width: 1px;
- border-color: #FFFFFF;
- vertical-align: middle;
- margin: 0.2em;
- border-style: solid;
- border-width: 2px;
- border-radius: 0.5em;
- text-align: center;
+#header #header-nav {
+ /* Place it in the parent element */
+ grid-column-start: 2;
+ grid-column-end: 3;
}
-#header .header-nav a {
+#header #header-nav .nav li a {
+ /* Content styling */
color: #FFFFFF;
- text-decoration: none;
+ background: #4477AA;
+ border: solid 5px #336699;
+ border-radius: 5px;
+ font-size: 0.7em;
+ text-align: center;
+ padding: 1px 7px;
}
#nav-sidebar {
- grid-column: 1/2;
- /* background: #e5e5ff; */
- padding-top: 0.5em;
- border-radius: 0.5em;
- font-size: 1.2em;
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 2;
}
-#main {
- grid-column: 2/3;
- width: 100%;
- /* background: gray; */
+#nav-sidebar .nav li a:hover {
border-radius: 0.5em;
}
-.pagetitle {
- padding-top: 0.5em;
- /* background: pink; */
+#nav-sidebar .nav .activemenu {
+ border-style: solid;
border-radius: 0.5em;
- /* background-color: #6699CC; */
- /* background-color: #77AADD; */
- background-color: #88BBEE;
+ border-color: #AAAAAA;
+ background-color: #EFEFEF;
}
-.pagetitle h1 {
- text-align: start;
- text-transform: capitalize;
- padding-left: 0.25em;
-}
+#main {
+ /* Place it in the parent element */
+ grid-column-start: 2;
+ grid-column-end: 3;
-.pagetitle .breadcrumb {
- background: none;
+ /* Define layout for the children elements */
+ display: grid;
+ grid-template-columns: 1fr;
+ grid-template-rows: 4em 100%;
+ grid-gap: 1em;
}
-.pagetitle .breadcrumb .active a {
- color: #333333;
-}
+#main #pagetitle {
+ /* Place it in the parent element */
+ grid-column-start: 1;
+ grid-column-end: 3;
-.pagetitle .breadcrumb a {
- color: #666666;
+ /* Content-styling */
+ border-radius: 3px;
+ background-color: #88BBEE;
}
-.main-content {
- font-size: 1.275em;
+#main #pagetitle .title {
+ font-size: 1.4em;
+ text-transform: capitalize;
+ padding-left: 0.5em;
}
-.breadcrumb {
- text-transform: capitalize;
+#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;
}
-dd {
- margin-left: 3em;
- font-size: 0.88em;
- padding-bottom: 1em;
+#main #all-content .row {
+ margin: 0 2px;
}
-input[type="submit"], .btn {
- text-transform: capitalize;
+#main #all-content #main-content {
+ background: #FFFFFF;
+ max-width: 950px;
}
-.card {
- margin-top: 0.3em;
- border-width: 1px;
- border-style: solid;
- border-radius: 0.3em;
- border-color: #AAAAAA;
- padding: 0.5em;
+#pagetitle .breadcrumb {
+ background: none;
+ text-transform: capitalize;
+ font-size: 0.75em;
}
-.activemenu {
- border-style: solid;
- border-radius: 0.5em;
- border-color: #AAAAAA;
- background-color: #EFEFEF;
+#pagetitle .breadcrumb .active a {
+ color: #333333;
}
-.danger {
- color: #A94442;
- border-color: #DCA7A7;
- background-color: #F2DEDE;
+#pagetitle .breadcrumb a {
+ color: #666666;
}
.heading {
border-bottom: solid #EEBB88;
+ text-transform: capitalize;
}
.subheading {
padding: 1em 0 0.1em 0.5em;
border-bottom: solid #88BBEE;
+ text-transform: capitalize;
}
-form {
- margin-top: 0.3em;
- background: #E5E5FF;
- padding: 0.5em;
- border-radius:0.5em;
+input[type="search"] {
+ border-radius: 5px;
}
-form .form-control {
- background-color: #EAEAFF;
+.btn {
+ text-transform: Capitalize;
}
-.sidebar-content .card .card-title {
- font-size: 1.5em;
+table.dataTable thead th, table.dataTable tfoot th{
+ border-right: 1px solid white;
+ color: white;
+ background-color: #369;
}
-.sidebar-content .card-text table tbody td:nth-child(1) {
- font-weight: bolder;
+table.dataTable tbody tr.selected td {
+ background-color: #ffee99 !important;
+}
+
+
+.dt-scroll-body > table > thead {
+ /***
+Fixes bug with DataTables Scroller extension which leads to 2 table headers
+being displayed.
+ **/
+ display: none;
}
diff --git a/uploader/static/js/datatables.js b/uploader/static/js/datatables.js
new file mode 100644
index 0000000..a72245c
--- /dev/null
+++ b/uploader/static/js/datatables.js
@@ -0,0 +1,75 @@
+/** Handlers for events in datatables **/
+
+var addTableLength = (menuList, lengthToAdd, dataLength) => {
+ if(dataLength >= lengthToAdd) {
+ newList = structuredClone(menuList);//menuList.slice(0, menuList.length); // shallow copy
+ newList.push(lengthToAdd);
+ return newList;
+ }
+ return menuList;
+};
+
+var defaultLengthMenu = (data) => {
+ menuList = []
+ var lengths = [10, 25, 50, 100, 1000, data.length];
+ lengths.forEach((len) => {
+ menuList = addTableLength(menuList, len, data.length);
+ });
+ return menuList;
+};
+
+var buildDataTable = (tableId, data = [], columns = [], userSettings = {}) => {
+ var defaultSettings = {
+ responsive: true,
+ layout: {
+ topStart: null,
+ topEnd: null,
+ bottomStart: null,
+ bottomEnd: null,
+ },
+ select: true,
+ /* == Scroller settings == */
+ scroller: true,
+ paging: true, // MUST be true for scroller to work
+ scrollY: "750px",
+ deferRender: true,
+ /* == END: Scroller settings == */
+ lengthMenu: defaultLengthMenu(data),
+ language: {
+ processing: "Processing… Please wait.",
+ loadingRecords: "Loading table data… Please wait.",
+ lengthMenu: "",
+ info: ""
+ },
+ data: data,
+ columns: columns,
+ drawCallback: (settings) => {
+ $(this[0]).find("tbody tr").each((idx, row) => {
+ var arow = $(row);
+ var checkboxOrRadio = arow.find(".chk-row-select");
+ if (checkboxOrRadio) {
+ if (arow.hasClass("selected")) {
+ checkboxOrRadio.prop("checked", true);
+ } else {
+ checkboxOrRadio.prop("checked", false);
+ }
+ }
+ });
+ }
+ }
+ var theDataTable = $(tableId).DataTable({
+ ...defaultSettings,
+ ...userSettings
+ });
+ theDataTable.on("select", (event, datatable, type, cell, originalEvent) => {
+ datatable.rows({selected: true}).nodes().each((node, index) => {
+ $(node).find(".chk-row-select").prop("checked", true)
+ });
+ });
+ theDataTable.on("deselect", (event, datatable, type, cell, originalEvent) => {
+ datatable.rows({selected: false}).nodes().each((node, index) => {
+ $(node).find(".chk-row-select").prop("checked", false)
+ });
+ });
+ return theDataTable;
+};
diff --git a/uploader/static/js/files.js b/uploader/static/js/files.js
new file mode 100644
index 0000000..9d6bca1
--- /dev/null
+++ b/uploader/static/js/files.js
@@ -0,0 +1,118 @@
+var readFirstNLines = (thefile, count, process_content_fns) => {
+ var reader = new FileReader();
+ if(typeof thefile !== "undefined" && thefile !== null) {
+ reader.addEventListener("load", (event) => {
+ var content = event
+ .target
+ .result
+ .split("\n")
+ .slice(0, count)
+ .map((line) => {return line.trim("\r");});
+ process_content_fns.forEach((fn) => {fn(content);});
+ });
+ reader.readAsText(thefile);
+ }
+};
+var read_first_n_lines = readFirstNLines;
+
+
+var readBinaryFile = (file) => {
+ return new Promise((resolve, reject) => {
+ var _reader = new FileReader();
+ _reader.onload = (event) => {resolve(_reader.result);};
+ _reader.readAsArrayBuffer(file);
+ });
+};
+
+
+var Uint8ArrayToHex = (arr) => {
+ var toHex = (val) => {
+ _hex = val.toString(16);
+ if(_hex.length < 2) {
+ return "0" + val;
+ }
+ return _hex;
+ };
+ _hexstr = ""
+ arr.forEach((val) => {_hexstr += toHex(val)});
+ return _hexstr
+};
+
+
+var computeFileChecksum = (file) => {
+ return readBinaryFile(file)
+ .then((content) => {
+ return window.crypto.subtle.digest(
+ "SHA-256", new Uint8Array(content));
+ }).then((digest) => {
+ return Uint8ArrayToHex(new Uint8Array(digest))
+ });
+};
+
+
+var defaultResumableHandler = (event) => {
+ throw new Error("Please provide a valid event handler!");
+};
+
+var addHandler = (resumable, handlername, handler) => {
+ if(resumable.support) {
+ resumable.on(handlername, (handler || defaultResumableHandler));
+ }
+ return resumable;
+};
+
+
+var makeResumableHandler = (handlername) => {
+ return (resumable, handler) => {
+ return addHandler(resumable, handlername, handler);
+ };
+};
+
+
+var fileSuccessHandler = makeResumableHandler("fileSuccess");
+var fileProgressHandler = makeResumableHandler("fileProgress");
+var fileAddedHandler = makeResumableHandler("fileAdded");
+var filesAddedHandler = makeResumableHandler("filesAdded");
+var filesRetryHandler = makeResumableHandler("filesRetry");
+var filesErrorHandler = makeResumableHandler("filesError");
+var uploadStartHandler = makeResumableHandler("uploadStart");
+var completeHandler = makeResumableHandler("complete");
+var progressHandler = makeResumableHandler("progress");
+var errorHandler = makeResumableHandler("error");
+
+
+var markResumableDragAndDropElement = (resumable, fileinput, droparea, browsebutton) => {
+ if(resumable.support) {
+ //Hide file input element and display drag&drop UI
+ add_class(fileinput, "hidden");
+ remove_class(droparea, "hidden");
+
+ // Define UI elements for browse and drag&drop
+ resumable.assignDrop(droparea);
+ resumable.assignBrowse(browsebutton);
+ }
+
+ return resumable;
+};
+
+
+var makeResumableElement = (targeturi, fileinput, droparea, uploadbutton, filetype) => {
+ var resumable = Resumable({
+ target: targeturi,
+ fileType: filetype,
+ maxFiles: 1,
+ forceChunkSize: true,
+ generateUniqueIdentifier: (file, event) => {
+ return computeFileChecksum(file).then((checksum) => {
+ var _relativePath = (file.webkitRelativePath
+ || file.relativePath
+ || file.fileName
+ || file.name);
+ return checksum + "-" + _relativePath.replace(
+ /[^a-zA-Z0-9_-]/img, "");
+ });
+ }
+ });
+
+ return resumable;
+};
diff --git a/uploader/static/js/populations.js b/uploader/static/js/populations.js
new file mode 100644
index 0000000..be1231f
--- /dev/null
+++ b/uploader/static/js/populations.js
@@ -0,0 +1,21 @@
+$(() => {
+ var populationsDataTable = buildDataTable(
+ "#tbl-select-population",
+ JSON.parse(
+ $("#tbl-select-population").attr("data-populations-list")),
+ [
+ {
+ data: (apopulation) => {
+ return `<input type="radio" name="population_id"`
+ + `id="rdo_population_id_${apopulation.InbredSetId}" `
+ + `value="${apopulation.InbredSetId}" `
+ + `class="chk-row-select">`;
+ }
+ },
+ {
+ data: (apopulation) => {
+ return `${apopulation.FullName} (${apopulation.InbredSetName})`;
+ }
+ }
+ ]);
+});
diff --git a/uploader/static/js/species.js b/uploader/static/js/species.js
new file mode 100644
index 0000000..9ea3017
--- /dev/null
+++ b/uploader/static/js/species.js
@@ -0,0 +1,20 @@
+$(() => {
+ var speciesDataTable = buildDataTable(
+ "#tbl-select-species",
+ JSON.parse(
+ $("#tbl-select-species").attr("data-species-list")),
+ [
+ {
+ data: (aspecies) => {
+ return `<input type="radio" name="species_id"`
+ + `id="rdo_species_id_${aspecies.SpeciesId}" `
+ + `value="${aspecies.SpeciesId}" class="chk-row-select">`;
+ }
+ },
+ {
+ data: (aspecies) => {
+ return `${aspecies.FullName} (${aspecies.SpeciesName})`;
+ }
+ }
+ ]);
+});
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 3a8ef16..873b9e8 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
{%block extrameta%}{%endblock%}
- <title>GN Uploader: {%block title%}{%endblock%}</title>
+ <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title>
<link rel="stylesheet" type="text/css"
href="{{url_for('base.bootstrap',
@@ -23,25 +23,26 @@
</head>
<body>
- <header id="header" class="container-fluid">
- <div class="row">
- <span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span>
- <nav class="header-nav col-lg-3">
- <ul class="nav justify-content-end">
- <li>
- {%if user_logged_in()%}
- <a href="{{url_for('oauth2.logout')}}"
- title="Log out of the system">{{user_email()}} &mdash; Log Out</a>
- {%else%}
- <a href="{{authserver_authorise_uri()}}"
- title="Log in to the system">Log In</a>
- {%endif%}
- </li>
- </ul>
- </nav>
+ <header id="header">
+ <span id="header-text">GeneNetwork</span>
+ <nav id="header-nav">
+ <ul class="nav justify-content-end">
+ <li>
+ {%if user_logged_in()%}
+ <a href="{{url_for('oauth2.logout')}}"
+ title="Log out of the system">
+ <span class="glyphicon glyphicon-user"></span>
+ Sign Out</a>
+ {%else%}
+ <a href="{{authserver_authorise_uri()}}"
+ title="Log in to the system">Sign In</a>
+ {%endif%}
+ </li>
+ </ul>
+ </nav>
</header>
- <aside id="nav-sidebar" class="container-fluid">
+ <aside id="nav-sidebar">
<ul class="nav flex-column">
<li {%if activemenu=="home"%}class="activemenu"{%endif%}>
<a href="/" >Home</a></li>
@@ -70,6 +71,7 @@
<li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.phenotypes.index')}}"
title="Upload phenotype data.">Phenotype Data</a></li>
+ <!--
<li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.populations.expression-data.index')}}"
title="Upload expression data."
@@ -87,47 +89,70 @@
class="not-implemented"
title="View and manage the backgroud jobs you have running">
Background Jobs</a></li>
+ -->
</ul>
</aside>
- <main id="main" class="main container-fluid">
+ <main id="main" class="main">
- <div class="pagetitle row">
- <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
- <nav>
- <ol class="breadcrumb">
- <li {%if activelink is not defined or activelink=="home"%}
- class="breadcrumb-item active"
- {%else%}
- class="breadcrumb-item"
- {%endif%}>
- <a href="{{url_for('base.index')}}">Home</a>
- </li>
- {%block lvl1_breadcrumbs%}{%endblock%}
- </ol>
- </nav>
+ <div id="pagetitle" class="pagetitle">
+ <span class="title">Data Upload and Quality Control: {%block pagetitle%}{%endblock%}</span>
+ <!--
+ <nav>
+ <ol class="breadcrumb">
+ <li {%if activelink is not defined or activelink=="home"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('base.index')}}">Home</a>
+ </li>
+ {%block lvl1_breadcrumbs%}{%endblock%}
+ </ol>
+ </nav>
+ -->
</div>
- <div class="row">
- <div class="container-fluid">
- <div class="col-md-8 main-content">
- {%block contents%}{%endblock%}
- </div>
- <div class="sidebar-content col-md-4">
- {%block sidebarcontents%}{%endblock%}
- </div>
+ <div id="all-content">
+ <div id="main-content">
+ {%block contents%}{%endblock%}
+ </div>
+ <div id="sidebar-content">
+ {%block sidebarcontents%}{%endblock%}
</div>
</div>
</main>
+ <!--
+ 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/misc.js"></script>
+ <script type="text/javascript" src="/static/js/datatables.js"></script>
{%block javascript%}{%endblock%}
-
</body>
-
</html>
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
index e749f5a..b50ebc5 100644
--- a/uploader/templates/genotypes/index.html
+++ b/uploader/templates/genotypes/index.html
@@ -26,3 +26,7 @@
species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html
index 7c81943..acdd063 100644
--- a/uploader/templates/genotypes/select-population.html
+++ b/uploader/templates/genotypes/select-population.html
@@ -12,20 +12,14 @@
{{flash_all_messages()}}
<div class="row">
- <p>
- You have indicated that you intend to upload the genotypes for species
- '{{species.FullName}}'. We now just require the population for your
- experiment/study, and you should be good to go.
- </p>
-</div>
-
-<div class="row">
- {{select_population_form(url_for("species.populations.genotypes.select_population",
- species_id=species.SpeciesId),
- populations)}}
+ {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/index.html b/uploader/templates/index.html
index d6f57eb..aa1414e 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -10,90 +10,98 @@
<div class="row">
{{flash_all_messages()}}
<div class="explainer">
- <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p>
+ <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control
+ System</strong>.</p>
+ <p>This tool helps you prepare and upload research data to GeneNetwork for
+ analysis.</p>
- <p>The sections below provide an overview of what features the menu items on
- the left provide to you. Please peruse the information to get a good
- big-picture understanding of what the system provides you and how to get
- the most out of it.</p>
+ <h2 class="heading">Getting Started</h2>
+ <p>The sections below explain the features of the system. Review this guide
+ to learn how to use the system.</p>
{%block extrapageinfo%}{%endblock%}
- <h2>Species</h2>
-
- <p>The GeneNetwork service provides datasets and tools for doing genetic
- studies &mdash; from
- <a href="{{gn2server_intro}}"
- target="_blank"
- title="GeneNetwork introduction — opens in a new tab.">
- its introduction</a>:
-
- <blockquote class="blockquote">
- <p>GeneNetwork is a group of linked data sets and tools used to study
- complex networks of genes, molecules, and higher order gene function
- and phenotypes. &hellip;</p>
- </blockquote>
- </p>
-
- <p>With this in mind, it follows that the data in the system is centered
- aroud a variety of species. The <strong>species section</strong> will
- list the currently available species in the system, and give you the
- ability to add new ones, if the one you want to work on does not currently
- exist on GeneNetwork</p>
-
- <h2>Populations</h2>
-
- <p>Your studies will probably focus on a particular subset of the entire
- species you are interested in &ndash; your population.</p>
- <p>Populations are a way to organise the species data so as to link data to
- specific know populations for a particular species, e.g. The BXD
- population of mice (Mus musculus)</p>
- <p>In older GeneNetwork documentation, you might run into the term
- <em>InbredSet</em>. Should you run into it, it is a term that we've
- deprecated that essentially just means the population.</p>
-
- <h2>Samples</h2>
-
- <p>These are the samples or individuals (sometimes cases) that were involved
- in the experiment, and from whom the data was derived.</p>
-
- <h2>Genotype Data</h2>
-
- <p>This section will allow you to view and upload the genetic markers for
- your species, and the genotype encodings used for your particular
- population.</p>
- <p>While, technically, genetic markers relate to the species in general, and
- not to a particular population, the data (allele information) itself
- relates to the particular population it was generated from &ndash;
- specifically, to the actual individuals used in the experiment.</p>
- <p>This is the reason why the genotype data information comes under the
- population, and will check for the prior existence of the related
- samples/individuals before attempting an upload of your data.</p>
-
- <h2>Expression Data</h2>
+ <h3 class="subheading">Species</h3>
- <p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- <strong>TODO</strong>: Document this &hellip;</p>
+ <p>GeneNetwork supports genetic studies across multiple species (e.g. mice
+ [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) .
+ Here you can:</p>
+ <ul>
+ <li>View all species that are currently supported</li>
+ <li>Add new species not yet in the system</li>
+ </ul>
+
+ <h3 class="subheading">Populations</h3>
+
+ <p>A "population" refers to a specific subgroup within a species that you’re
+ studying (e.g., BXD mice). Here you can:</p>
+ <ul>
+ <li>View the populations that exist for a selected species</li>
+ <li>Add new populations of study for a selected species</li>
+ </ul>
+
+ <h3 class="subheading">Samples</h3>
+
+ <p>Manage individual specimens or cases used in your experiments. These
+ include:</p>
+
+ <ul>
+ <li>Experimental subjects</li>
+ <li>Data sources (e.g., tissue samples, clinical cases)</li>
+ <li>Strain means (instead of entering multiple BXD1 individuals, for
+ example, the mean would be entered for a single BXD1 strain)</li>
+ </ul>
+
+
+ <h3 class="subheading">Genotype Data</h3>
+
+ <p>Upload and review genetic markers and allele encodings for your
+ population. Key details:</p>
+
+ <ul>
+ <li>Markers are species-level (e.g., mouse SNP databases).</li>
+ <li>Allele data is population-specific (tied to your experimental
+ samples).</li>
+ </ul>
+
+ <p><strong>Requirement</strong>: Samples must already have been registered
+ in the system before uploading genotype data.</p>
+
+ <h3 class="subheading">Phenotype Data</h3>
+
+ <p>Phenotypes are the visible traits or features of a living thing. For
+ example, phenotypes include:</p>
+
+ <ul>
+ <li>Weight</li>
+ <li>Height</li>
+ <li>Color (such as the color of fur or eyes)</li>
+ </ul>
+
+ <p>This part of the system will allow you to upload and manage the values
+ for different phenotypes from various samples in your studies.</p>
+
+ <!--
- <h2>Phenotype Data</h2>
+ <h3 class="subheading">Expression Data</h3>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this &hellip;</p>
- <h2>Individual Data</h2>
+ <h3 class="subheading">Individual Data</h3>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this &hellip;</p>
- <h2>RNA-Seq Data</h2>
+ <h3 class="subheading">RNA-Seq Data</h3>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this &hellip;</p>
</div>
+ -->
</div>
{%endblock%}
diff --git a/uploader/templates/login.html b/uploader/templates/login.html
index 1f71416..e76c644 100644
--- a/uploader/templates/login.html
+++ b/uploader/templates/login.html
@@ -5,7 +5,8 @@
{%block pagetitle%}log in{%endblock%}
{%block extrapageinfo%}
-<p class="text-dark text-primary">
- You <strong>do need to be logged in</strong> to upload data onto this system.
- Please do that by clicking the "Log In" button at the top of the page.</p>
+<p class="text-dark">
+ You <strong>need to
+ <a href="{{authserver_authorise_uri()}}"
+ title="Sign in to the system">sign in</a></strong> to use this system.</p>
{%endblock%}
diff --git a/uploader/templates/macro-step-indicator.html b/uploader/templates/macro-step-indicator.html
new file mode 100644
index 0000000..ac0be77
--- /dev/null
+++ b/uploader/templates/macro-step-indicator.html
@@ -0,0 +1,15 @@
+{%macro step_indicator(step, width=100)%}
+<svg width="{{width}}" height="{{width}}" xmlns="http://www.w3.org/2000/svg">
+ <circle cx="{{0.5*width}}"
+ cy="{{0.5*width}}"
+ r="{{0.5*width}}"
+ fill="#E5E5FF" />
+ <text x="{{0.5*width}}"
+ y="{{0.6*width}}"
+ font-size="{{0.2*width}}"
+ text-anchor="middle"
+ fill="#555555">
+ Step {{step}}
+ </text>
+</svg>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html
index b3a53b0..97b55f2 100644
--- a/uploader/templates/phenotypes/add-phenotypes-base.html
+++ b/uploader/templates/phenotypes/add-phenotypes-base.html
@@ -30,7 +30,9 @@
action="{{url_for('species.populations.phenotypes.add_phenotypes',
species_id=species.SpeciesId,
population_id=population.Id,
- dataset_id=dataset.Id)}}">
+ dataset_id=dataset.Id,
+ use_bundle=use_bundle)}}"
+ data-resumable-target="{{url_for('files.resumable_upload_post')}}">
<legend>Add New Phenotypes</legend>
<div class="form-text help-block">
@@ -57,6 +59,9 @@
<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.
@@ -114,7 +119,7 @@
</div>
<div class="form-group">
- <label for="txt-publication-month" class="form-label">
+ <label for="select-publication-month" class="form-label">
Publication Month</label>
<select id="select-publication-month" name="publication-month"
class="form-control">
@@ -157,10 +162,6 @@
{%endblock%}
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
-
{%block javascript%}
<script type="text/javascript">
@@ -219,13 +220,12 @@
"journal": details[pubmed_id].fulljournalname,
"volume": details[pubmed_id].volume,
"pages": details[pubmed_id].pages,
- "month": months[_date[1].toLowerCase()],
+ "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan",
"year": _date[0],
};
};
var update_publication_details = (details) => {
- console.log("Updating with the following details:", details);
Object.entries(details).forEach((entry) => {;
switch(entry[0]) {
case "authors":
@@ -244,41 +244,7 @@
});
};
- var freds_variable = undefined;
- $("#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;
- }
-
- var flag_pub_details = false;
- var flag_pub_abstract = false;
- var enable_button = () => {
- search_button.disabled = !(flag_pub_details && flag_pub_abstract);
- };
- search_button.disabled = true;
- // Fetch publication details
- $.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
- update_publication_details(extract_details(
- pubmed_id, data.result));
- },
- "error": (jqXHR, textStatus, errorThrown) => {},
- "complete": () => {
- flag_pub_details = true;
- enable_button();
- },
- "dataType": "json"
- });
- // Fetch the abstract
+ var fetch_publication_abstract = (pubmed_id, pub_details) => {
$.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
{
"method": "GET",
@@ -289,25 +255,74 @@
"retmode": "xml"
},
"success": (data, textStatus, jqXHR) => {
- // process and update the abstract...
- freds_variable = data;
- console.log("ABSTRACT DETAILS:", data);
update_publication_details({
- "abstract": Array.from(data
- .getElementsByTagName(
- "Abstract")[0]
- .children)
- .map((elt) => {return elt.textContent.trim();})
- .join("\r\n")
- });
+ ...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) => {
- flag_pub_abstract = true;
- enable_button();
- },
+ "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 ef0895d..7f8d8b0 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -2,6 +2,8 @@
{%from "flash_messages.html" import flash_all_messages%}
{%from "macro-table-pagination.html" import table_pagination%}
{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
+{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%}
+{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%}
{%block title%}Phenotypes{%endblock%}
@@ -106,13 +108,14 @@
<fieldset id="fldset-data-files">
<legend>Data File(s)</legend>
- <div class="form-group">
+ <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,
@@ -121,44 +124,92 @@
the documentation for the expected format of the file</a>.</span>
</div>
- <div class="form-group">
+ {{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-phenotype-data"
+ <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">
+ <div class="form-group non-resumable-elements">
<label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
<input id="finput-phenotype-se"
name="phenotype-se"
class="form-control"
type="file"
+ data-preview-table="tbl-preview-pheno-se"
required="required" />
<span class="form-text text-muted">
Provide a file that contains only the standard errors for the phenotypes,
computed from the data above.</span>
</div>
+ {{display_resumable_elements(
+ "resumable-phenotype-se",
+ "standard errors",
+ '<p>You can drop a CSV file that contains the computed standard-errors data
+ here, or you can click the "Browse" button (below and to the right) to
+ select it from your computer.</p>
+ <p>The CSV file must conform to some standards, as documented in the
+ <a href="#docs-file-phenotype-se"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Data" documentation</a> section below.</p>')}}
- <div class="form-group">
+
+ <div class="form-group non-resumable-elements">
<label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
<input id="finput-phenotype-n"
name="phenotype-n"
class="form-control"
type="file"
+ data-preview-table="tbl-preview-pheno-n"
required="required" />
<span class="form-text text-muted">
Provide a file that contains only the number of samples/individuals used in
the computation of the standard errors above.</span>
</div>
+ {{display_resumable_elements(
+ "resumable-phenotype-n",
+ "number of samples/individuals",
+ '<p>You can drop a CSV file that contains the number of samples/individuals
+ used in computation of the standard-errors here, or you can click the
+ "Browse" button (below and to the right) to select it from your computer.
+ </p>
+ <p>The CSV file must conform to some standards, as documented in the
+ <a href="#docs-file-phenotype-n"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Data" documentation</a> section below.</p>')}}
</fieldset>
{%endif%}
{%endblock%}
@@ -268,9 +319,9 @@
comma as a way to separate the "general category and ontology terms".</p>
<h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3>
- <span id="docs-phenotype-data"></span>
- <span id="docs-phenotype-se"></span>
- <span id="docs-phenotype-n"></span>
+ <span id="docs-file-phenotype-data"></span>
+ <span id="docs-file-phenotype-se"></span>
+ <span id="docs-file-phenotype-n"></span>
<p>The data is a matrix of <em>phenotypes × individuals</em>, e.g.</p>
<code>
# num-cases: 2549
@@ -294,20 +345,388 @@
{%endblock%}
+{%block sidebarcontents%}
+{{display_preview_table("tbl-preview-pheno-desc", "descriptions")}}
+{{display_preview_table("tbl-preview-pheno-data", "data")}}
+{%if population.Family in families_with_se_and_n%}
+{{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
+{{display_preview_table("tbl-preview-pheno-n", "number of samples")}}
+{%endif%}
+{{display_pheno_dataset_card(species, population, dataset)}}
+{%endblock%}
+
{%block more_javascript%}
+<script src="{{url_for('base.node_modules',
+ filename='resumablejs/resumable.js')}}"></script>
+<script type="text/javascript" src="/static/js/files.js"></script>
+
<script type="text/javascript">
$("#btn-reset-file-separator").on("click", (event) => {
event.preventDefault();
$("#txt-file-separator").val("\t");
+ $("#txt-file-separator").trigger("change");
});
$("#btn-reset-file-comment-character").on("click", (event) => {
event.preventDefault();
$("#txt-file-comment-character").val("#");
+ $("#txt-file-comment-character").trigger("change");
});
$("#btn-reset-file-na").on("click", (event) => {
event.preventDefault();
$("#txt-file-na").val("- NA N/A");
+ $("#txt-file-na").trigger("change");
+ });
+
+ var update_preview = (table, filedata, formdata, numrows) => {
+ table.find("thead tr").remove()
+ table.find(".data-row").remove();
+ var linenum = 0;
+ var tableheader = table.find("thead");
+ var tablebody = table.find("tbody");
+ var numheadings = 0;
+ var navalues = formdata
+ .na_strings
+ .split(" ")
+ .map((v) => {return v.trim();})
+ .filter((v) => {return Boolean(v);});
+ filedata.forEach((line) => {
+ if(line.startsWith(formdata.comment_char) || linenum >= numrows) {
+ return false;
+ }
+ var row = $("<tr></tr>");
+ line.split(formdata.separator)
+ .map((field) => {
+ var value = field.trim();
+ if(navalues.includes(value)) {
+ return "⋘NUL⋙";
+ }
+ return value;
+ })
+ .filter((field) => {
+ return (field !== "" && field != undefined && field != null);
+ })
+ .forEach((field) => {
+ if(linenum == 0) {
+ numheadings += 1;
+ var tablefield = $("<th></th>");
+ tablefield.text(field);
+ row.append(tablefield);
+ } else {
+ add_class(row, "data-row");
+ var tablefield = $("<td></td>");
+ tablefield.text(field);
+ row.append(tablefield);
+ }
+ });
+
+ if(linenum == 0) {
+ tableheader.append(row);
+ } else {
+ tablebody.append(row);
+ }
+ linenum += 1;
+ });
+
+ if(table.find("tbody tr.data-row").length > 0) {
+ add_class(table.find(".data-row-template"), "hidden");
+ } else {
+ remove_class(table.find(".data-row-template"), "hidden");
+ }
+ };
+
+ var makePreviewUpdater = (preview_table) => {
+ return (data) => {
+ update_preview(
+ preview_table,
+ data,
+ filesMetadata(),
+ PREVIEW_ROWS);
+ };
+ };
+
+ var preview_tables_to_elements_map = {
+ "#tbl-preview-pheno-desc": "#finput-phenotype-descriptions",
+ "#tbl-preview-pheno-data": "#finput-phenotype-data",
+ "#tbl-preview-pheno-se": "#finput-phenotype-se",
+ "#tbl-preview-pheno-n": "#finput-phenotype-n"
+ };
+
+ var filesMetadata = () => {
+ return {
+ "separator": $("#txt-file-separator").val(),
+ "comment_char": $(
+ "#txt-file-comment-character").val(),
+ "na_strings": $("#txt-file-na").val()
+ }
+ };
+
+ var PREVIEW_ROWS = 5;
+
+ var handler_update_previews = (event) => {
+ Object.entries(preview_tables_to_elements_map).forEach((mapentry) => {
+ var preview_table = $(mapentry[0]);
+ var file_input = $(mapentry[1]);
+ if(file_input.length === 1) {
+ readFirstNLines(
+ file_input[0].files[0],
+ 10,
+ [makePreviewUpdater(preview_table)]);
+ }
+ });
+ };
+
+ [
+ "#txt-file-separator",
+ "#txt-file-comment-character",
+ "#txt-file-na"
+ ].forEach((elementid) => {
+ $(elementid).on("change", handler_update_previews);
+ });
+
+ [
+ "#finput-phenotype-descriptions",
+ "#finput-phenotype-data",
+ "#finput-phenotype-se",
+ "#finput-phenotype-n"
+ ].forEach((elementid) => {
+ $(elementid).on("change", (event) => {
+ readFirstNLines(
+ event.target.files[0],
+ 10,
+ [makePreviewUpdater(
+ $("#" + event.target.getAttribute("data-preview-table")))]);
+ });
+ });
+
+
+ var resumableDisplayFiles = (display_area, files) => {
+ files.forEach((file) => {
+ display_area.find(".file-display").remove();
+ var display_element = display_area
+ .find(".file-display-template")
+ .clone();
+ remove_class(display_element, "hidden");
+ remove_class(display_element, "file-display-template");
+ add_class(display_element, "file-display");
+ display_element.find(".filename").text(file.name
+ || file.fileName
+ || file.relativePath
+ || file.webkitRelativePath);
+ display_element.find(".filesize").text(
+ (file.size / (1024*1024)).toFixed(2) + "MB");
+ display_element.find(".fileuniqueid").text(file.uniqueIdentifier);
+ display_element.find(".filemimetype").text(file.file.type);
+ display_area.append(display_element);
+ });
+ };
+
+
+ var indicateProgress = (resumable, progress_bar) => {
+ return () => {/*Has no event!*/
+ var progress = (resumable.progress() * 100).toFixed(2);
+ var pbar = progress_bar.find(".progress-bar");
+ remove_class(progress_bar, "hidden");
+ pbar.css("width", progress+"%");
+ pbar.attr("aria-valuenow", progress);
+ pbar.text("Uploading: " + progress + "%");
+ };
+ };
+
+ var retryUpload = (retry_button, cancel_button) => {
+ retry_button.on("click", (event) => {
+ resumable.files.forEach((file) => {file.retry();});
+ add_class(retry_button, "hidden");
+ remove_class(cancel_button, "hidden");
+ add_class(browse_button, "hidden");
+ });
+ };
+
+ var cancelUpload = (cancel_button, retry_button) => {
+ cancel_button.on("click", (event) => {
+ resumable.files.forEach((file) => {
+ if(file.isUploading()) {
+ file.abort();
+ }
+ });
+ add_class(cancel_button, "hidden");
+ remove_class(retry_button, "hidden");
+ remove_class(browse_button, "hidden");
+ });
+ };
+
+
+ var startUpload = (browse_button, retry_button, cancel_button) => {
+ return (event) => {
+ remove_class(cancel_button, "hidden");
+ add_class(retry_button, "hidden");
+ add_class(browse_button, "hidden");
+ };
+ };
+
+ var processForm = (form) => {
+ var formdata = new FormData(form);
+ uploaded_files.forEach((msg) => {
+ formdata.delete(msg["file-input-name"]);
+ formdata.append(msg["file-input-name"], JSON.stringify({
+ "uploaded-file": msg["uploaded-file"],
+ "original-name": msg["original-name"]
+ }));
+ });
+ formdata.append("resumable-upload", "true");
+ return formdata;
+ }
+
+ var uploaded_files = new Set();
+ var submitForm = (new_file) => {
+ uploaded_files.add(new_file);
+ if(uploaded_files.size === resumables.length) {
+ var form = $("#frm-add-phenotypes");
+ if(form.length !== 1) {
+ // TODO: Handle error somehow?
+ alert("Could not find form!!!");
+ return false;
+ }
+
+ $.ajax({
+ "url": form.attr("action"),
+ "type": "POST",
+ "data": processForm(form[0]),
+ "processData": false,
+ "contentType": false,
+ "success": (data, textstatus, jqxhr) => {
+ // TODO: Redirect to endpoint that should come as part of the
+ // success/error message.
+ console.log("SUCCESS DATA: ", data);
+ console.log("SUCCESS STATUS: ", textstatus);
+ console.log("SUCCESS jqXHR: ", jqxhr);
+ window.location.assign(window.location.origin + data["redirect-to"]);
+ },
+ });
+ return false;
+ }
+ return false;
+ };
+
+ var uploadSuccess = (file_input_name) => {
+ return (file, message) => {
+ submitForm({...JSON.parse(message), "file-input-name": file_input_name});
+ };
+ };
+
+
+ var uploadError = () => {
+ return (message, file) => {
+ $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled");
+ console.log("THE FILE:", file);
+ console.log("THE ERROR MESSAGE:", message);
+ };
+ };
+
+
+
+ var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id) => {
+ var the_form = $("#" + form_id);
+ var file_input = $("#" + file_input_id);
+ var submit_button = the_form.find("input[type=submit]");
+ if(file_input.length != 1) {
+ return false;
+ }
+ var r = errorHandler(
+ fileSuccessHandler(
+ uploadStartHandler(
+ filesAddedHandler(
+ markResumableDragAndDropElement(
+ makeResumableElement(
+ the_form.attr("data-resumable-target"),
+ file_input.parent(),
+ $("#" + resumable_element_id),
+ submit_button,
+ ["csv", "tsv"]),
+ file_input.parent(),
+ $("#" + resumable_element_id),
+ $("#" + resumable_element_id + "-browse-button")),
+ (files) => {
+ // TODO: Also trigger preview!
+ resumableDisplayFiles(
+ $("#" + resumable_element_id + "-selected-files"), files);
+ files.forEach((file) => {
+ readFirstNLines(
+ file.file,
+ 10,
+ [makePreviewUpdater(
+ $("#" + preview_table_id))])
+ });
+ }),
+ startUpload($("#" + resumable_element_id + "-browse-button"),
+ $("#" + resumable_element_id + "-retry-button"),
+ $("#" + resumable_element_id + "-cancel-button"))),
+ uploadSuccess(file_input.attr("name"))),
+ uploadError());
+
+ /** Setup progress indicator **/
+ progressHandler(
+ r,
+ indicateProgress(r, $("#" + resumable_element_id + "-progress-bar")));
+
+ return r;
+ };
+
+ var resumables = [
+ ["frm-add-phenotypes", "finput-phenotype-descriptions", "resumable-phenotype-descriptions", "tbl-preview-pheno-desc"],
+ ["frm-add-phenotypes", "finput-phenotype-data", "resumable-phenotype-data", "tbl-preview-pheno-data"],
+ ["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"],
+ ["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"],
+ ].map((row) => {
+ return makeResumableObject(row[0], row[1], row[2], row[3]);
+ }).filter((val) => {
+ return Boolean(val);
+ });
+
+ $("#frm-add-phenotypes input[type=submit]").on("click", (event) => {
+ event.preventDefault();
+ // TODO: Check all the relevant files exist
+ // TODO: Verify that files are not duplicated
+ var filenames = [];
+ var nondupfiles = [];
+ resumables.forEach((r) => {
+ var fname = r.files[0].file.name;
+ filenames.push(fname);
+ if(!nondupfiles.includes(fname)) {
+ nondupfiles.push(fname);
+ }
+ });
+
+ // Check that all files were provided
+ if(resumables.length !== filenames.length) {
+ window.alert("You MUST provide all the files requested.");
+ event.target.removeAttribute("disabled");
+ return false;
+ }
+
+ // Check that there are no duplicate files
+ var duplicates = Object.entries(filenames.reduce(
+ (acc, curr, idx, arr) => {
+ acc[curr] = (acc[curr] || 0) + 1;
+ return acc;
+ },
+ {})).filter((entry) => {return entry[1] !== 1;});
+ if(duplicates.length > 0) {
+ var msg = "The file(s):\r\n";
+ msg = msg + duplicates.reduce(
+ (msgstr, afile) => {
+ return msgstr + " • " + afile[0] + "\r\n";
+ },
+ "");
+ msg = msg + "is(are) duplicated. Please fix and try again.";
+ window.alert(msg);
+ event.target.removeAttribute("disabled");
+ return false;
+ }
+ // TODO: Check all fields
+ // Start the uploads.
+ event.target.setAttribute("disabled", "disabled");
+ resumables.forEach((r) => {r.upload();});
});
</script>
{%endblock%}
diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
index 8f67baa..898fc0c 100644
--- a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
+++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
@@ -201,3 +201,7 @@
<em>phenotypes × individuals</em>.</p>
</div>
{%endblock%}
+
+{%block sidebarcontents%}
+{{display_pheno_dataset_card(species, population, dataset)}}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html
index 93de92f..8e45491 100644
--- a/uploader/templates/phenotypes/create-dataset.html
+++ b/uploader/templates/phenotypes/create-dataset.html
@@ -74,8 +74,10 @@
{%endif%}
required="required" />
<small class="form-text text-muted">
- <p>A longer, descriptive name for the dataset &mdash; useful for humans.
- </p></small>
+ <p>A longer, descriptive name for the dataset. The name is meant for use
+ by humans, and therefore, it should be clear what the dataset contains
+ from the name.</p>
+ </small>
</div>
<div class="form-group">
diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html
new file mode 100644
index 0000000..32c903f
--- /dev/null
+++ b/uploader/templates/phenotypes/edit-phenotype.html
@@ -0,0 +1,332 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="edit-phenotype"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">View Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <h2 class="heading">edit phenotype data</h2>
+ <p>The forms provided in this page help you update the data for the
+ phenotypes, and the publication information for the phenotype,
+ respectively.</p>
+</div>
+
+<div class="row">
+ <h3 class="subheading">Basic metadata</h3>
+ <form name="frm-phenotype-basic-metadata"
+ class="form-horizontal"
+ method="POST"
+ action="{{url_for(
+ 'species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">
+ <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" />
+ <div class="form-group">
+ <label for="txt-pre-publication-description"
+ class="control-label col-sm-2">Pre-Publication Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-pre-publication-description"
+ name="pre-publication-description"
+ class="form-control"
+ value="{{phenotype['Pre_publication_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-pre-publication-abbreviation"
+ class="control-label col-sm-2">Pre-Publication Abbreviation</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-pre-publication-abbreviation"
+ name="pre-publication-abbreviation"
+ class="form-control"
+ value="{{phenotype['Pre_publication_abbreviation'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-post-publication-description"
+ class="control-label col-sm-2">Post-Publication Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-post-publication-description"
+ name="post-publication-description"
+ class="form-control"
+ value="{{phenotype['Post_publication_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-post-publication-abbreviation"
+ class="control-label col-sm-2">Post-Publication Abbreviation</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-post-publication-abbreviation"
+ name="post-publication-abbreviation"
+ class="form-control"
+ value="{{phenotype['Post_publication_abbreviation'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-original-description"
+ class="control-label col-sm-2">Original Description</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-original-description"
+ name="original-description"
+ class="form-control"
+ value="{{phenotype['Original_description'] or ''}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-units"
+ class="control-label col-sm-2">units</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-units"
+ name="units"
+ class="form-control"
+ required="required"
+ value="{{phenotype['Units']}}" />
+ </div>
+ </div>
+
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary"
+ value="update basic metadata">
+ </div>
+ </div>
+ </form>
+</div>
+
+
+<div class="row">
+ <h3 class="subheading">phenotype data</h3>
+ <form id="frm-edit-phenotype-data"
+ class="form-horizontal"
+ method="POST"
+ action="{{url_for(
+ 'species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}">
+ <div style="max-height: 23.37em;overflow-y: scroll;">
+ <table class="table table-striped table-responsive table-form-table">
+ <thead style="position: sticky; top: 0;">
+ <tr>
+ <th>#</th>
+ <th>Sample</th>
+ <th>Value</th>
+ {%if population.Family in families_with_se_and_n%}
+ <th>Standard-Error</th>
+ <th>Number of Samples</th>
+ {%endif%}
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for item in phenotype.data%}
+ <tr>
+ <td>{{loop.index}}</td>
+ <td>{{item.StrainName}}</td>
+ <td>
+ <input type="text"
+ name="value-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.value}}"
+ class="form-control" />
+ <input type="hidden"
+ name="value-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.value}}" /></td>
+ {%if population.Family in families_with_se_and_n%}
+ <td>
+ <input type="text"
+ name="se-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.error or ''}}"
+ data-original-value="{{item.error or ''}}"
+ class="form-control" />
+ <input type="hidden"
+ name="se-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.error or ''}}" /></td>
+ <td>
+ <input type="text"
+ name="n-new::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.count or ''}}"
+ data-original-value="{{item.count or "-"}}"
+ class="form-control" />
+ <input type="hidden"
+ name="n-original::{{item.DataId}}::{{item.StrainId}}"
+ value="{{item.count or ''}}" /></td>
+ {%endif%}
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+ </div>
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary"
+ value="update data" />
+ </div>
+ </div>
+ </form>
+</div>
+
+
+<div class="row">
+ <h3 class="subheading">publication information</h3>
+ <p>Use the form below to update the publication information for this
+ phenotype.</p>
+ <form id="frm-edit-phenotype-pub-data"
+ class="form-horizontal"
+ method="POST"
+ action="#">
+ <div class="form-group">
+ <label for="txt-pubmed-id" class="control-label col-sm-2">Pubmed ID</label>
+ <div class="col-sm-10">
+ <input id="txt-pubmed-id" name="pubmed-id" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter your publication's PubMed ID.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-authors" class="control-label col-sm-2">Authors</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-authors" name="publication-authors"
+ type="text" class="form-control" />
+ <span class="form-text text-muted">
+ Enter the authors.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-title" class="control-label col-sm-2">
+ Publication Title</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-title" name="publication-title" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter your publication's title.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-abstract" class="control-label col-sm-2">
+ Publication Abstract</label>
+ <div class="col-sm-10">
+ <textarea id="txt-publication-abstract" name="publication-abstract"
+ class="form-control" rows="10"></textarea>
+ <span class="form-text text-muted">
+ Enter the abstract for your publication.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-journal" class="control-label col-sm-2">Journal</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-journal" name="journal" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the name of the journal where your work was published.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-volume" class="control-label col-sm-2">Volume</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-volume" name="publication-volume" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the volume in the following format &hellip;</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-pages" class="control-label col-sm-2">Pages</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-pages" name="publication-pages" type="text"
+ class="form-control" />
+ <span class="form-text text-muted">
+ Enter the journal volume where your work was published.</span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="select-publication-month" class="control-label col-sm-2">
+ Publication Month</label>
+ <div class="col-sm-10">
+ <select id="select-publication-month" name="publication-month"
+ class="form-control">
+ {%for month in monthnames%}
+ <option value="{{month | lower}}"
+ {%if current_month | lower == month | lower%}
+ selected="selected"
+ {%endif%}>{{month | capitalize}}</option>
+ {%endfor%}
+ </select>
+ <span class="form-text text-muted">
+ Select the month when the work was published.
+ <span class="text-danger">
+ This cannot be before, say 1600 and cannot be in the future!</span></span>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-publication-year" class="control-label col-sm-2">Publication Year</label>
+ <div class="col-sm-10">
+ <input id="txt-publication-year" name="publication-year" type="text"
+ class="form-control" value="{{current_year}}" />
+ <span class="form-text text-muted">
+ Enter the year your work was published.
+ <span class="text-danger">
+ This cannot be before, say 1600 and cannot be in the future!</span>
+ </span>
+ </div>
+ </div>
+ <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
+ <input type="submit"
+ name="submit"
+ class="btn btn-primary not-implemented"
+ value="update publication" />
+ </div>
+ </div>
+ </form>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html
index 0c691e6..689c28e 100644
--- a/uploader/templates/phenotypes/index.html
+++ b/uploader/templates/phenotypes/index.html
@@ -11,16 +11,11 @@
{{flash_all_messages()}}
<div class="row">
- <p>This section deals with phenotypes that
- <span class="text-warning">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- … what are the characteristics of these phenotypes? …</span></p>
- <p>Select the species to begin the process of viewing/uploading data about
- your phenotypes</p>
+ {{select_species_form(url_for("species.populations.phenotypes.index"), species)}}
</div>
+{%endblock%}
-<div class="row">
- {{select_species_form(url_for("species.populations.phenotypes.index"),
- species)}}
-</div>
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
{%endblock%}
diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html
index 5f13876..12963c1 100644
--- a/uploader/templates/phenotypes/job-status.html
+++ b/uploader/templates/phenotypes/job-status.html
@@ -31,10 +31,10 @@
{%if job%}
<h4 class="subheading">Progress</h4>
-<div class="row">
+<div class="row" style="overflow:scroll;">
<p><strong>Process Status:</strong> {{job.status}}</p>
{%if metadata%}
- <table class="table">
+ <table class="table table-responsive">
<thead>
<tr>
<th>File</th>
@@ -56,32 +56,39 @@
</tbody>
</table>
{%endif%}
+</div>
+
+<div class="row">
{%if job.status in ("completed:success", "success")%}
<p>
{%if errors | length == 0%}
- <a href="#"
- class="not-implemented btn btn-primary"
+ <a href="{{url_for('species.populations.phenotypes.review_job_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ job_id=job_id)}}"
+ class="btn btn-primary"
title="Continue to process data">Continue</a>
{%else%}
<span class="text-muted"
- disabled="disabled"
- style="border: solid 2px;border-radius: 5px;padding: 0.3em;">
+ disabled="disabled"
+ style="border: solid 2px;border-radius: 5px;padding: 0.3em;">
Cannot continue due to errors. Please fix the errors first.
- </a>
+ </span>
{%endif%}
</p>
{%endif%}
</div>
<h4 class="subheading">Errors</h4>
-<div class="row" style="max-height: 20em; overflow: auto;">
+<div class="row" style="max-height: 20em; overflow: scroll;">
{%if errors | length == 0 %}
<p class="text-info">
<span class="glyphicon glyphicon-info-sign"></span>
No errors found so far
</p>
{%else%}
- <table class="table">
+ <table class="table table-responsive">
<thead style="position: sticky; top: 0; background: white;">
<tr>
<th>File</th>
@@ -89,6 +96,7 @@
<th>Column</th>
<th>Value</th>
<th>Message</th>
+ </tr>
</thead>
<tbody style="font-size: 0.9em;">
diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html
index 2eaf43a..2cf2c7f 100644
--- a/uploader/templates/phenotypes/list-datasets.html
+++ b/uploader/templates/phenotypes/list-datasets.html
@@ -48,9 +48,12 @@
</tbody>
</table>
{%else%}
- <p class="text-warning">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- There is no dataset for this population!</p>
+ <p>Phenotypes need to go into a dataset. We do not currently have a dataset
+ for species <strong>'{{species["FullName"]}} ({{species["Name"]}})'</strong>
+ phenotypes.</p>
+
+ <p>Do, please, create a new dataset by clicking on the "Create Dataset" button
+ below and following the prompts/instructions.</p>
<p><a href="{{url_for('species.populations.phenotypes.create_dataset',
species_id=species.SpeciesId,
population_id=population.Id)}}"
diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html
new file mode 100644
index 0000000..f54c53e
--- /dev/null
+++ b/uploader/templates/phenotypes/macro-display-preview-table.html
@@ -0,0 +1,21 @@
+{%macro display_preview_table(tableid, filetype)%}
+<div class="card" style="max-width: 676px;">
+ <div class="card-body">
+ <h5 class="card-title">Phenotypes '{{filetype | title}}' File Preview</h5>
+ <div class="card-text" style="overflow: scroll;">
+ <table id="{{tableid}}" class="table table-condensed table-responsive">
+ <thead>
+ <tr>
+ </tr>
+ <tbody>
+ <tr>
+ <td class="data-row-template text-info">
+ Provide a phenotype '{{filetype | lower}}' file to preview.
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html
new file mode 100644
index 0000000..b0bf1b5
--- /dev/null
+++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html
@@ -0,0 +1,60 @@
+{%macro display_resumable_elements(id, title, help)%}
+<div id="{{id}}"
+ class="resumable-elements hidden"
+ style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;">
+ <strong style="line-height: 1.2em;">{{title | title}}</strong>
+
+ <span class="form-text text-muted">{{help | safe}}</span>
+
+ <div id="{{id}}-selected-files"
+ class="resumable-selected-files"
+ style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;">
+ <div class="panel panel-info file-display-template hidden">
+ <div class="panel-heading filename">The Filename Goes Here!</div>
+ <div class="panel-body">
+ <ul>
+ <li>
+ <strong>Name</strong>:
+ <span class="filename">the file's name</span></li>
+
+ <li><strong>Size</strong>: <span class="filesize">0 MB</span></li>
+
+ <li>
+ <strong>Unique Identifier</strong>:
+ <span class="fileuniqueid">brrr</span></li>
+
+ <li>
+ <strong>Mime</strong>:
+ <span class="filemimetype">text/csv</span></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+
+ <a id="{{id}}-browse-button"
+ class="resumable-browse-button btn btn-info"
+ href="#"
+ style="margin-left: 80%;">Browse</a>
+
+ <div id="{{id}}-progress-bar" class="progress hidden">
+ <div class="progress-bar"
+ role="progress-bar"
+ aria-valuenow="60"
+ aria-valuemin="0"
+ aria-valuemax="100"
+ style="width: 0%;">
+ Uploading: 60%
+ </div>
+ </div>
+
+ <div id="{{id}}-cancel-resume-buttons">
+ <a id="{{id}}-resume-button"
+ class="resumable-resume-button btn btn-info hidden"
+ href="#">resume upload</a>
+
+ <a id="{{id}}-cancel-button"
+ class="resumable-cancel-button btn btn-danger hidden"
+ href="#">cancel upload</a>
+ </div>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html
new file mode 100644
index 0000000..7bc8c62
--- /dev/null
+++ b/uploader/templates/phenotypes/review-job-data.html
@@ -0,0 +1,101 @@
+{%extends "phenotypes/base.html"%}
+{%from "cli-output.html" import cli_output%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-table-pagination.html" import table_pagination%}
+{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
+
+{%block extrameta%}
+{%if not job%}
+<meta http-equiv="refresh"
+ content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}" />
+{%endif%}
+{%endblock%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="add-phenotypes"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">View Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+
+{%if job%}
+<div class="row">
+ <h3 class="heading">Data Review</h3>
+ <p>The &#x201C;<strong>{{dataset.FullName}}</strong>&#x201D; dataset from the
+ &#x201C;<strong>{{population.FullName}}</strong>&#x201D; population of the
+ species &#x201C;<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>&#x201D;
+ will be updated as follows:</p>
+
+ {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%}
+ {%if summary.get(ftype, False)%}
+ <ul>
+ <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed
+ adding {%if ftype == "phenocovar"%}(possibly){%endif%}
+ {{summary[ftype]["total-data-rows"]}} new
+ {%if ftype == "phenocovar"%}
+ phenotypes
+ {%else%}
+ {{summary[ftype]["description"]}} rows
+ {%endif%}
+ to the database.
+ </li>
+ </ul>
+ {%endif%}
+ {%endfor%}
+
+ <a href="#" class="not-implemented btn btn-primary">continue</a>
+</div>
+{%else%}
+<div class="row">
+ <h4 class="subheading">Invalid Job</h3>
+ <p class="text-danger">
+ Could not find a job with the ID: <strong>{{job_id}}.</p>
+ <p>You will be redirected in
+ <span id="countdown-element" class="text-info">20</span> second(s)</p>
+ <p class="text-muted">
+ <small>
+ If you are not redirected, please
+ <a href="{{url_for(
+ 'species.populations.phenotypes.view_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">click here</a> to continue
+ </small>
+ </p>
+</div>
+{%endif%}
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_pheno_dataset_card(species, population, dataset)}}
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(document).ready(function() {
+ var countdown = 20;
+ var countdown_element = $("#countdown-element");
+ if(countdown_element.length === 1) {
+ intv = window.setInterval(function() {
+ countdown = countdown - 1;
+ countdown_element.html(countdown);
+ }, 1000);
+ }
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/select-population.html b/uploader/templates/phenotypes/select-population.html
index eafd4a7..48c19b1 100644
--- a/uploader/templates/phenotypes/select-population.html
+++ b/uploader/templates/phenotypes/select-population.html
@@ -11,18 +11,16 @@
{%block contents%}
{{flash_all_messages()}}
-<div class="row">
- <p>Select the population for your phenotypes to view and manage the phenotype
- datasets that relate to it.</p>
-</div>
<div class="row">
- {{select_population_form(url_for("species.populations.phenotypes.select_population",
- species_id=species.SpeciesId),
- populations)}}
+ {{select_population_form(url_for("species.populations.phenotypes.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 66de5d8..6b35f6a 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -57,36 +57,26 @@
<div class="row">
<h2>Phenotype Data</h2>
- <p>This dataset has a total of {{phenotype_count}} phenotypes.</p>
+ <p>Click on any of the phenotypes in the table below to view and edit that
+ phenotype's data.</p>
+ <p>Use the search to filter through all the phenotypes and find specific
+ phenotypes of interest.</p>
+</div>
- {{table_pagination(start_from, count, phenotype_count, url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id), "phenotypes")}}
- <table class="table">
+<div class="row">
+
+ <table id="tbl-phenotypes-list" class="table compact stripe cell-border">
<thead>
<tr>
- <th>#</th>
+ <th></th>
+ <th>Index</th>
<th>Record</th>
<th>Description</th>
</tr>
</thead>
- <tbody>
- {%for pheno in phenotypes%}
- <tr>
- <td>{{pheno.sequence_number}}</td>
- <td><a href="{{url_for('species.populations.phenotypes.view_phenotype',
- species_id=species.SpeciesId,
- population_id=population.Id,
- dataset_id=dataset.Id,
- xref_id=pheno['pxr.Id'])}}"
- title="View phenotype details">
- {{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</a></td>
- <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td>
- </tr>
- {%else%}
- <tr><td colspan="5"></td></tr>
- {%endfor%}
- </tbody>
+ <tbody></tbody>
</table>
</div>
{%endblock%}
@@ -94,3 +84,65 @@
{%block sidebarcontents%}
{{display_population_card(species, population)}}
{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {
+ var data = {{phenotypes | tojson}};
+ var dtPhenotypesList = buildDataTable(
+ "#tbl-phenotypes-list",
+ data,
+ [
+ {
+ data: function(pheno) {
+ return `<input type="checkbox" name="selected-phenotypes" `
+ + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `value="${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `class="chk-row-select" />`
+ }
+ },
+ {data: "sequence_number"},
+ {
+ data: function(pheno, type, set, meta) {
+ var spcs_id = {{species.SpeciesId}};
+ var pop_id = {{population.Id}};
+ var dtst_id = {{dataset.Id}};
+ return `<a href="/species/${spcs_id}` +
+ `/populations/${pop_id}` +
+ `/phenotypes/datasets/${dtst_id}` +
+ `/phenotype/${pheno.xref_id}` +
+ `" target="_blank">` +
+ `${pheno.InbredSetCode}_${pheno.xref_id}` +
+ `</a>`;
+ }
+ },
+ {
+ data: function(pheno) {
+ return (pheno.Post_publication_description ||
+ pheno.Original_description ||
+ pheno.Pre_publication_description);
+ }
+ }
+ ],
+ {
+ select: "multi+shift",
+ scrollY: "1000px",
+ layout: {
+ top1: "search",
+ topStart: {
+ buttons: [
+ {extend: "selectAll", className: "btn btn-info"},
+ {extend: "selectNone", className: "btn btn-info"}
+ ]
+ },
+ topEnd: "info",
+ bottomEnd: null
+ },
+ rowId: function(pheno) {
+ return `${pheno.InbredSetCode}_${pheno.xref_id}`;
+ }
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html
index 99bb8e5..21ac501 100644
--- a/uploader/templates/phenotypes/view-phenotype.html
+++ b/uploader/templates/phenotypes/view-phenotype.html
@@ -16,7 +16,7 @@
species_id=species.SpeciesId,
population_id=population.Id,
dataset_id=dataset.Id,
- xref_id=xref_id)}}">View Datasets</a>
+ xref_id=xref_id)}}">View Phenotype</a>
</li>
{%endblock%}
@@ -34,51 +34,58 @@
<td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}}
</tr>
<tr>
- <td><strong>Cross-Reference ID</strong></td>
- <td>{{phenotype.xref_id}}</td>
- </tr>
- <tr>
- <td><strong>Collation</strong></td>
+ <td><strong>Database</strong></td>
<td>{{dataset.FullName}}</td>
</tr>
<tr>
<td><strong>Units</strong></td>
<td>{{phenotype.Units}}</td>
</tr>
+ {%for key,value in publish_data.items()%}
+ <tr>
+ <td><strong>{{key}}</strong></td>
+ <td>{{value}}</td>
+ </tr>
+ {%else%}
+ <tr>
+ <td colspan="2" class="text-muted">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ No publication data found.
+ </td>
+ </tr>
+ {%endfor%}
</tbody>
</table>
+ </div>
+</div>
- <form action="#edit-delete-phenotype"
- method="POST"
- id="frm-delete-phenotype">
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id" value="{{population.Id}}" />
- <input type="hidden" name="dataset_id" value="{{dataset.Id}}" />
- <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" />
-
- <div class="btn-group btn-group-justified">
- <div class="btn-group">
- {%if "group:resource:edit-resource" in privileges%}
- <input type="submit"
- title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values."
- class="btn btn-primary not-implemented"
- value="edit" />
- {%endif%}
- </div>
- <div class="btn-group"></div>
- <div class="btn-group">
- {%if "group:resource:delete-resource" in privileges%}
- <input type="submit"
- title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype."
- class="btn btn-danger not-implemented"
- value="delete" />
- {%endif%}
- </div>
- </div>
- </form>
+{%if "group:resource:edit-resource" in privileges
+or "group:resource:delete-resource" in privileges%}
+<div class="row">
+ <div class="btn-group btn-group-justified">
+ <div class="btn-group">
+ {%if "group:resource:edit-resource" in privileges%}
+ <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id,
+ xref_id=xref_id)}}"
+ title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values."
+ class="btn btn-primary">Edit</a>
+ {%endif%}
+ </div>
+ <div class="btn-group"></div>
+ <div class="btn-group">
+ {%if "group:resource:delete-resource" in privileges%}
+ <a href="#"
+ title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype."
+ class="btn btn-danger not-implemented"
+ disabled="disabled">delete</a>
+ {%endif%}
+ </div>
</div>
</div>
+{%endif%}
<div class="row">
<div class="panel panel-default">
@@ -90,9 +97,10 @@
<th>#</th>
<th>Sample</th>
<th>Value</th>
- <th>Symbol</th>
+ {%if has_se%}
<th>SE</th>
<th>N</th>
+ {%endif%}
</tr>
</thead>
@@ -102,9 +110,10 @@
<td>{{loop.index}}</td>
<td>{{item.StrainName}}</td>
<td>{{item.value}}</td>
- <td>{{item.Symbol or "-"}}</td>
+ {%if has_se%}
<td>{{item.error or "-"}}</td>
<td>{{item.count or "-"}}</td>
+ {%endif%}
</tr>
{%endfor%}
</tbody>
diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html
index 35b6464..555b444 100644
--- a/uploader/templates/platforms/index.html
+++ b/uploader/templates/platforms/index.html
@@ -19,3 +19,7 @@
{{select_species_form(url_for("species.platforms.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html
index 718dd1d..a6bcfdc 100644
--- a/uploader/templates/platforms/list-platforms.html
+++ b/uploader/templates/platforms/list-platforms.html
@@ -58,7 +58,7 @@
<table class="table">
<thead>
<tr>
- <th>#</th>
+ <th></th>
<th>Platform Name</th>
<th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}"
title="Gene Expression Omnibus: Platforms section"
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html
index b05ce37..c0c4f45 100644
--- a/uploader/templates/populations/create-population.html
+++ b/uploader/templates/populations/create-population.html
@@ -37,12 +37,15 @@
<div class="row">
<form method="POST"
action="{{url_for('species.populations.create_population',
- species_id=species.SpeciesId)}}">
+ species_id=species.SpeciesId,
+ return_to=return_to)}}">
<legend>Create Population</legend>
{{flash_all_messages()}}
+ <input type="hidden" name="return_to" value="{{return_to}}">
+
<div {%if errors.population_fullname%}
class="form-group has-error"
{%else%}
@@ -107,9 +110,12 @@
value="{{error_values.population_code or ''}}"
class="form-control" />
<small class="form-text text-muted">
- <p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- What is this field is for? Confirm with Arthur and the rest.
+ <p class="form-text text-muted">
+ This is a 3-character code for your population, that is prepended to
+ the phenotype identifiers. e.g. For the "BXD Family" population, the
+ code is "BXD" and therefore, the phenotype identifiers for the
+ population look like the following examples: <em>BXD_10148</em>,
+ <em>BXD_10180</em>, <em>BXD_10197</em>, etc.
</p>
</small>
</div>
diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html
index 4354e02..d2bee77 100644
--- a/uploader/templates/populations/index.html
+++ b/uploader/templates/populations/index.html
@@ -22,3 +22,7 @@
{{select_species_form(url_for("species.populations.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html
index 7c7145f..f780e94 100644
--- a/uploader/templates/populations/list-populations.html
+++ b/uploader/templates/populations/list-populations.html
@@ -51,7 +51,7 @@
<caption>Populations for {{species.FullName}}</caption>
<thead>
<tr>
- <th>#</th>
+ <th></th>
<th>Name</th>
<th>Full Name</th>
<th>Description</th>
diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html
index 79f7925..16b477f 100644
--- a/uploader/templates/populations/macro-display-population-card.html
+++ b/uploader/templates/populations/macro-display-population-card.html
@@ -33,11 +33,6 @@
<td>Family</td>
<td>{{population.Family}}</td>
</tr>
-
- <tr>
- <td>Description</td>
- <td>{{(population.Description or "")[0:500]}}&hellip;</td>
- </tr>
</tbody>
</table>
</div>
diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html
index af4fd3a..14b0510 100644
--- a/uploader/templates/populations/macro-select-population.html
+++ b/uploader/templates/populations/macro-select-population.html
@@ -1,30 +1,52 @@
-{%macro select_population_form(form_action, populations)%}
-<form method="GET" action="{{form_action}}">
- <legend>Select Population</legend>
-
- <div class="form-group">
- <label for="select-population" class="form-label">Select Population</label>
- <select id="select-population"
- name="population_id"
- class="form-control"
- required="required">
- <option value="">Select Population</option>
- {%for family in populations%}
- <optgroup {%if family[0][1] is not none%}
- label="{{family[0][1]}}"
- {%else%}
- label="Undefined"
- {%endif%}>
- {%for population in family[1]%}
- <option value="{{population.Id}}">{{population.FullName}}</option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
+{%from "macro-step-indicator.html" import step_indicator%}
+
+{%macro select_population_form(form_action, species, populations)%}
+<form method="GET" action="{{form_action}}" class="form-horizontal">
+
+ <h2>{{step_indicator("2")}} What population do you want to work with?</h2>
+
+ {%if populations | length != 0%}
+
+ <p class="form-text">Search for, and select the population from the table
+ below and click "Continue"</p>
+
+ <div class="radio">
+ <label class="control-label" for="rdo-cant-find-population">
+ <input type="radio" id="rdo-cant-find-population"
+ name="population_id" value="CREATE-POPULATION" />
+ I cannot find the population I want &mdash; create it!
+ </label>
+ </div>
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit" value="continue" class="btn btn-primary" />
+ </div>
+
+ <div style="margin-top:3em;">
+ <table id="tbl-select-population" class="table compact stripe"
+ data-populations-list='{{populations | tojson}}'>
+ <thead>
+ <tr>
+ <th></th>
+ <th>Population</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
</div>
- <div class="form-group">
- <input type="submit" value="Select" class="btn btn-primary" />
+ {%else%}
+ <p class="form-text">
+ There are no populations currently defined for {{species['FullName']}}
+ ({{species['SpeciesName']}}).<br />
+ Click "Continue" to create the first!</p>
+ <input type="hidden" name="population_id" value="CREATE-POPULATION" />
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit" value="continue" class="btn btn-primary" />
</div>
+ {%endif%}
+
</form>
{%endmacro%}
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
index ee4a63e..ee98734 100644
--- a/uploader/templates/samples/index.html
+++ b/uploader/templates/samples/index.html
@@ -17,3 +17,7 @@
{{select_species_form(url_for("species.populations.samples.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html
index 13e5cec..185e784 100644
--- a/uploader/templates/samples/list-samples.html
+++ b/uploader/templates/samples/list-samples.html
@@ -73,7 +73,7 @@
<table class="table">
<thead>
<tr>
- <th>#</th>
+ <th></th>
<th>Name</th>
<th>Auxilliary Name</th>
<th>Symbol</th>
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
index f437780..1cc7573 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -12,28 +12,15 @@
{{flash_all_messages()}}
<div class="row">
- <p>You have selected "{{species.FullName}}" as the species that your data relates to.</p>
- <p>Next, we need information regarding the population your data relates to. Do please select the population from the existing ones below</p>
-</div>
-
-<div class="row">
{{select_population_form(
- url_for("species.populations.samples.select_population", species_id=species.SpeciesId),
- populations)}}
-</div>
-
-<div class="row">
- <p>
- If you cannot find the population your data relates to in the drop-down
- above, you might want to
- <a href="{{url_for('species.populations.create_population',
- species_id=species.SpeciesId)}}"
- title="Create a new population for species '{{species.FullName}},">
- add a new population to GeneNetwork</a>
- instead.
+ url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html
index 0d0bedf..138dbaa 100644
--- a/uploader/templates/species/create-species.html
+++ b/uploader/templates/species/create-species.html
@@ -19,72 +19,88 @@
<div class="row">
<form id="frm-create-species"
method="POST"
- action="{{url_for('species.create_species')}}">
+ action="{{url_for('species.create_species', return_to=return_to)}}"
+ class="form-horizontal">
<legend>Create Species</legend>
{{flash_all_messages()}}
+ <input type="hidden" name="return_to" value="{{return_to}}">
+
<div class="form-group">
- <label for="txt-taxonomy-id" class="form-label">
+ <label for="txt-taxonomy-id" class="control-label col-sm-2">
Taxonomy ID</label>
- <div class="input-group">
- <input id="txt-taxonomy-id"
- name="species_taxonomy_id"
- type="text"
- class="form-control" />
- <span class="input-group-btn">
- <button id="btn-search-taxonid" class="btn btn-info">Search</button>
- </span>
+ <div class="col-sm-10">
+ <div class="input-group">
+ <input id="txt-taxonomy-id"
+ name="species_taxonomy_id"
+ type="text"
+ class="form-control" />
+ <span class="input-group-btn">
+ <button id="btn-search-taxonid" class="btn btn-info">Search</button>
+ </span>
+ </div>
+ <small class="form-text text-small text-muted">
+ Use
+ <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/"
+ title="NCBI's Taxonomy Browser homepage"
+ target="_blank">
+ NCBI's Taxonomy Browser homepage</a> to search for the species you
+ want. If the species exists on NCBI, they will have a Taxonomy ID. Copy
+ that Taxonomy ID to this field, and click "Search" to auto-fill the
+ details.<br />
+ This field is optional.</small>
</div>
- <small class="form-text text-small text-muted">Provide the taxonomy ID for
- your species that can be used to link to external sites like NCBI. Enter
- the taxonomy ID and click "Search" to auto-fill the form with data.
- <br />
- While it is recommended to provide a value for this field, doing so is
- optional.
- </small>
</div>
<div class="form-group">
- <label for="txt-species-name" class="form-label">Common Name</label>
- <input id="txt-species-name"
- name="common_name"
- type="text"
- class="form-control"
- required="required" />
- <small class="form-text text-muted">Provide the common, possibly
- non-scientific name for the species here, e.g. Human, Mouse, etc.</small>
+ <label for="txt-species-name" class="control-label col-sm-2">Common Name</label>
+ <div class="col-sm-10">
+ <input id="txt-species-name"
+ name="common_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">This is the day-to-day term used by
+ laymen, e.g. Mouse (instead of Mus musculus), round worm (instead of
+ Ascaris lumbricoides), etc.<br />
+ For species without this, just enter the scientific name.
+ </small>
+ </div>
</div>
<div class="form-group">
- <label for="txt-species-scientific" class="form-label">
+ <label for="txt-species-scientific" class="control-label col-sm-2">
Scientific Name</label>
- <input id="txt-species-scientific"
- name="scientific_name"
- type="text"
- class="form-control"
- required="required" />
- <small class="form-text text-muted">Provide the scientific name for the
- species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small>
+ <div class="col-sm-10">
+ <input id="txt-species-scientific"
+ name="scientific_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">This is the scientific name for the
+ species e.g. Homo sapiens, Mus musculus, etc.</small>
+ </div>
</div>
<div class="form-group">
- <label for="select-species-family" class="form-label">Family</label>
- <select id="select-species-family"
- name="species_family"
- required="required"
- class="form-control">
- <option value="">Please select a grouping</option>
- {%for family in families%}
- <option value="{{family}}">{{family}}</option>
- {%endfor%}
- </select>
- <small class="form-text text-muted">
- This is a generic grouping for the species that determines under which
- grouping the species appears in the GeneNetwork menus</small>
+ <label for="select-species-family" class="control-label col-sm-2">Family</label>
+ <div class="col-sm-10">
+ <select id="select-species-family"
+ name="species_family"
+ required="required"
+ class="form-control">
+ <option value="ungrouped">I do not know what to pick</option>
+ {%for family in families%}
+ <option value="{{family}}">{{family}}</option>
+ {%endfor%}
+ </select>
+ <small class="form-text text-muted">
+ This is a rough grouping of the species.</small>
+ </div>
</div>
- <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
<input type="submit"
value="create new species"
class="btn btn-primary" />
@@ -113,7 +129,7 @@
}
msg = (
"Request to '${uri}' failed with message '${textStatus}'. "
- + "Please try again later, or fill the details manually.");
+ + "Please try again later, or fill the details manually.");
alert(msg);
console.error(msg, data, textStatus);
return false;
diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html
index 85c9d40..64084b0 100644
--- a/uploader/templates/species/list-species.html
+++ b/uploader/templates/species/list-species.html
@@ -29,7 +29,7 @@
<caption>Available Species</caption>
<thead>
<tr>
- <th>#</td>
+ <th></td>
<th title="A common, layman's name for the species.">Common Name</th>
<th title="The scientific name for the species">Organism Name</th>
<th title="An identifier for the species in the NCBI taxonomy database">
diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html
index dd086c0..3714ae4 100644
--- a/uploader/templates/species/macro-select-species.html
+++ b/uploader/templates/species/macro-select-species.html
@@ -1,36 +1,59 @@
+{%from "macro-step-indicator.html" import step_indicator%}
+
{%macro select_species_form(form_action, species)%}
-{%if species | length > 0%}
-<form method="GET" action="{{form_action}}">
- <div class="form-group">
- <label for="select-species" class="form-label">Species</label>
- <select id="select-species"
- name="species_id"
- class="form-control"
- required="required">
- <option value="">Select Species</option>
- {%for group in species%}
- {{group}}
- <optgroup {%if group[0][1] is not none%}
- label="{{group[0][1].capitalize()}}"
- {%else%}
- label="Undefined"
- {%endif%}>
- {%for aspecies in group[1]%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
+<form method="GET" action="{{form_action}}" class="form-horizontal">
+
+ <h2>{{step_indicator("1")}} What species do you want to work with?</h2>
+
+ {%if species | length != 0%}
+
+ <p class="form-text">Search for, and select the species from the table below
+ and click "Continue"</p>
+
+ <div class="radio">
+ <label for="rdo-cant-find-species"
+ style="font-weight: 1;">
+ <input id="rdo-cant-find-species" type="radio" name="species_id"
+ value="CREATE-SPECIES" />
+ I could not find the species I want (create it).
+ </label>
</div>
- <div class="form-group">
- <input type="submit" value="Select" class="btn btn-primary" />
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit"
+ class="btn btn-primary"
+ value="continue" />
</div>
+
+ <div style="margin-top:3em;">
+ <table id="tbl-select-species" class="table compact stripe"
+ data-species-list='{{species | tojson}}'>
+ <div class="">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Species Name</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
+ </div>
+
+ {%else%}
+
+ <label class="control-label" for="rdo-cant-find-species">
+ <input id="rdo-cant-find-species" type="radio" name="species_id"
+ value="CREATE-SPECIES" />
+ There are no species to select from. Create the first one.</label>
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit"
+ class="btn btn-primary col-sm-offset-1"
+ value="continue" />
+ </div>
+
+ {%endif%}
+
</form>
-{%else%}
-<p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-mark"></span>
- We could not find species to select from!
-</p>
-{%endif%}
{%endmacro%}