diff options
138 files changed, 3946 insertions, 3919 deletions
diff --git a/.dev/run-checks.sh b/.dev/run-checks.sh new file mode 100644 index 0000000..66ac681 --- /dev/null +++ b/.dev/run-checks.sh @@ -0,0 +1,2 @@ +pylint setup.py tests quality_control uploader r_qtl scripts && \ + mypy --show-error-codes . diff --git a/.guix-channel b/.guix-channel index 54206b2..f1a8fa6 100644 --- a/.guix-channel +++ b/.guix-channel @@ -35,11 +35,12 @@ (channel (name guix-bioinformatics) (url "https://git.genenetwork.org/guix-bioinformatics") - (commit "903465c85c9b2ae28480b236c3364da873ca8f51")) + (commit "9b0955f14ec725990abb1f6af3b9f171e4943f77")) (channel (name guix-past) (url "https://codeberg.org/guix-science/guix-past") (branch "master") + (commit "473c942b509ab3ead35159d27dfbf2031a36cd4d") (introduction (channel-introduction (version 0) @@ -50,6 +51,7 @@ (name guix-rust-past-crates) (url "https://codeberg.org/guix/guix-rust-past-crates.git") (branch "trunk") + (commit "b8b7ffbd1cec9f56f93fae4da3a74163bbc9c570") (introduction (channel-introduction (version 0) @@ -2,6 +2,10 @@ #+TITLE: GeneNetwork Quality Control Application #+OPTIONS: ^:{} +[[https://ci.genenetwork.org/jobs/gn-uploader][https://ci.genenetwork.org/badge/gn-uploader.svg]] +[[https://ci.genenetwork.org/jobs/gn-uploader-all-tests][https://ci.genenetwork.org/badge/gn-uploader-all-tests.svg]] + + ** Project Goals The project seeks to handle the checking of data files for correct syntax and @@ -219,7 +223,7 @@ To check for correct type usage in the application, run: Run unit tests with: #+BEGIN_SRC shell $ export UPLOADER_CONF=</path/to/configuration/file.py> - $ pytest -m unit_test + $ pytest -m unit_test -n auto #+END_SRC To run ALL tests (not just unit tests): @@ -1,5 +1,8 @@ [mypy] +[mypy-lxml.*] +ignore_missing_imports = True + [mypy-flask.*] ignore_missing_imports = True diff --git a/qc_app/default_settings.py b/qc_app/default_settings.py index 7a9da0f..7bb0bf8 100644 --- a/qc_app/default_settings.py +++ b/qc_app/default_settings.py @@ -7,7 +7,7 @@ import os LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING") SECRET_KEY = b"<Please! Please! Please! Change This!>" -UPLOAD_FOLDER = "/tmp/qc_app_files" +UPLOADS_DIRECTORY = "/tmp/qc_app_files" REDIS_URL = "redis://" JOBS_TTL_SECONDS = 1209600 # 14 days GNQC_REDIS_PREFIX="GNQC" diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2/__init__.py index 0ef487f..ce1dbf8 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2/__init__.py @@ -584,16 +584,16 @@ def read_csv_file_headers( comment_char: str = "#" ) -> tuple[str, ...]: """Read the 'true' headers of a CSV file.""" - headers = tuple() + headers: tuple[str, ...] = tuple() for line in read_text_file(filepath): if line.startswith(comment_char): continue - line = tuple(field.strip() for field in line.split(separator)) + row = tuple(field.strip() for field in line.split(separator)) if not transposed: - return line + return row - headers = headers + (line[0],) + headers = headers + (row[0],) continue return headers diff --git a/r_qtl/r_qtl2/types.py b/r_qtl/r_qtl2/types.py new file mode 100644 index 0000000..13b8db4 --- /dev/null +++ b/r_qtl/r_qtl2/types.py @@ -0,0 +1,164 @@ +"""The types used by our R/qtl2 system.""" +from enum import Enum +from pathlib import Path +from dataclasses import field, dataclass +from typing import (Union, + Literal, + Optional, + Sequence, + TypeAlias, + Annotated) + + +_ALLELE_COUNTS_BY_CROSSTYPE = { + "bc": 2, "f2": 2, "riself": 2, "risib": 2, "dh": 2, "haploid": 2, "ail": 2, + "ail3": 3, + "riself4": 4, "risib4": 4, + "dh6": 6, + "hs": 8, "do": 8, "riself8": 8, "risib8": 8, + "dof1": 9, # 8 DO founders + 1 base inbred line + "riself16": 16, + "magic19": 19 +} + + + +PathLike = Union[Path, str] + +AlleleLabel: TypeAlias = str + +GenoCodeAlleleValue = Union[ + Literal[-1, 0, 1], + Literal[1, 2, 3],# T0D0: reconcile this to genocodes of 0, 1, 2 instead + Annotated[float, "Value must be between 0.0 and 2.0"] +] + +GenoCode = dict[AlleleLabel, GenoCodeAlleleValue] + +# Sex information +SexKey = Union[str, int]# codes used in the covariate file +@dataclass(frozen=True) +class ControlDataSex: + """Sex information in the control file.""" + covar: Optional[str] = None + file: Optional[PathLike] = None + female: Optional[SexKey] = None + male: Optional[SexKey] = None + + +# Cross information +CrossType = Literal[ + # T0D0: Look at https://kbroman.org/qtl2/assets/vignettes/input_files.html#Backcross to implement appropriate QC dependent on the crosstype. + "bc",# Backcross + "f2",# F2 intercross + "riself",# RIL by self -- RIL: Recombinant Inbred Lines + "risib",# RIL by sib + "dh",# Double haploid + "haploid",# Haploid + "ail",# AIL -- Advanced Inbred Lines + "hs",# Heterogeneous stock + "do",# Diversity outbreds + "riself4",# Multi-parent recombinant inbred lines + "riself8",# Multi-parent recombinant inbred lines + "riself16",# Multi-parent recombinant inbred lines + "risib4",# Multi-parent recombinant inbred lines + "risib8",# Multi-parent recombinant inbred lines + "magic19",# 19-way MAGIC lines + "dh6",# 6-way doubled haploids + "dof1",# DOF1 + "ail3",# 3-way advanced intercross lines + "genail",# General advanced intercross lines + "genril",# General recombinant inbred lines +] + +class CrossDirection(Enum): + FORWARD = 0 + REVERSE = 1 + + +@dataclass(frozen=True) +class ShortCrossInfo: + """Cross information in the control file.""" + # "covar": indicates the name of the column in the covariate data + covar: Optional[str] = None + file: Optional[PathLike] = None + forward_crosses: Sequence[str] = field(default_factory=tuple) + reverse_crosses: Sequence[str] = field(default_factory=tuple) + + def __post_init__(self): + """Validate the cross info.""" + # A valid short config MUST have either a `covar` or a `file` source + # but not both. + if not (self.covar and self.file): + raise ValueError("ShortCrossInfo requires either a 'covar' or a " + "'file' parameter.") + if self.covar and self.file: + raise ValueError("ShortCrossInfo cannot define both 'covar' and " + "'file' simultaneously.") + + +LongCrossInfo: TypeAlias = PathLike +CrossInfo = Union[LongCrossInfo, ShortCrossInfo] + + +def expected_allele_count_for_crosstype( + alleles: Sequence[str], + crosstype: CrossType, + expected_counts: dict[CrossType, int] +) -> bool: + """Check that the number of alleles matches what crosstype expects.""" + def __validate__(expected, alleles): + if expected is not None and len(alleles) != expected: + raise ValueError( + f"Cross type '{crosstype}' expects exactly {expected} allele " + f"labels. Received {len(alleles)}: {alleles}") + + if crosstype.startswith(("genail", "genril")): + # genail and genril are dynamic (e.g., genail8) + # Extract the trailing digits to determine expected founder count + num_part = "".join(filter(str.isdigit, crosstype)) + if num_part: + return __validate__(int(num_part), alleles) + + return __validate__(expected_counts.get(crosstype), alleles) + + + +@dataclass(frozen=True) +class ControlData: + """Class for the R/qtl2 control data.""" + # File names: Force listings, rather than singular strings + geno: Sequence[PathLike] = field(default_factory=tuple) + founder_geno: Sequence[PathLike] = field(default_factory=tuple) + pheno: Sequence[PathLike] = field(default_factory=tuple) + covar: Sequence[PathLike] = field(default_factory=tuple) + phenocovar: Sequence[PathLike] = field(default_factory=tuple) + gmap: Sequence[PathLike] = field(default_factory=tuple) + pmap: Sequence[PathLike] = field(default_factory=tuple) + + # X Chromosome + x_chr: Optional[str] = None + + # Allele labels + alleles: Sequence[str] = field(default_factory=tuple) + + # Genotype codes + genotypes: GenoCode = field(default_factory=dict) + + # sex + sex: Optional[ControlDataSex] = None + + # Cross info + crosstype: Optional[CrossType] = None + cross_info: Optional[CrossInfo] = None + + + # CSV fields + na_strings: Sequence[str] = ("-", "NA", "N/A") + sep: str = "," + comment_char: Optional[str] = "#" + + def __post_init__(self): + if self.alleles and self.crosstype: + expected_allele_count_for_crosstype( + self.alleles, self.crosstype, _ALLELE_COUNTS_BY_CROSSTYPE) diff --git a/scripts/cli/options.py b/scripts/cli/options.py index 67f35dc..58d3df4 100644 --- a/scripts/cli/options.py +++ b/scripts/cli/options.py @@ -13,7 +13,7 @@ def add_logging(parser: ArgumentParser) -> ArgumentParser: type=str, default="INFO", choices=loglevels, - help=(f"Controls the severity of events to log. Valid values are: " + + help=("Controls the severity of events to log. Valid values are: " + ", ".join(f"'{level}'" for level in loglevels))) return parser @@ -44,3 +44,13 @@ def add_population_id(parser: ArgumentParser) -> ArgumentParser: type=int, help="The ID for the population to operate on.") return parser + + +def add_dataset_id(parser: ArgumentParser) -> ArgumentParser: + """Add dataset-id as a mandatory argument.""" + parser = add_population_id(parser) + parser.add_argument("dataset_id", + metavar="DATASET-ID", + type=int, + help="The ID for the dataset to operate on.") + return parser diff --git a/scripts/compute_phenotype_means.py b/scripts/compute_phenotype_means.py index ef2fabc..6d39ace 100644 --- a/scripts/compute_phenotype_means.py +++ b/scripts/compute_phenotype_means.py @@ -51,7 +51,7 @@ def run(args) -> int: T = TypeVar("T") -def comma_separated_list(val: str, itemstype: T = str) -> tuple[T, ...]: +def comma_separated_list(val: str, itemstype: type = str) -> tuple[T, ...]: """Convert val into a list of items of type 'itemstype'.""" return tuple(itemstype(item.strip()) for item in val.split(",")) diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py index fc029f9..96ae8e2 100644 --- a/scripts/insert_samples.py +++ b/scripts/insert_samples.py @@ -6,10 +6,10 @@ import argparse import traceback import MySQLdb as mdb -from redis import Redis + from gn_libs.mysqldb import database_connection -from uploader.check_connections import check_db, check_redis +from uploader.check_connections import check_db from uploader.species.models import species_by_id from uploader.population.models import population_by_id from uploader.samples.models import ( @@ -35,7 +35,6 @@ class SeparatorAction(argparse.Action): setattr(namespace, self.dest, (chr(9) if values == "\\t" else values)) def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments, too-many-positional-arguments] - rconn: Redis,# pylint: disable=[unused-argument] speciesid: int, populationid: int, samplesfile: pathlib.Path, @@ -119,11 +118,6 @@ if __name__ == "__main__": help=("The character used to delimit (surround?) the value in " "each column.")) - # == Script-specific extras == - parser.add_argument("--redisuri", - help="URL to initialise connection to redis", - default="redis:///") - args = parser.parse_args() return args @@ -132,17 +126,13 @@ if __name__ == "__main__": status_code = 1 # Exit with an Exception args = cli_args() check_db(args.databaseuri) - check_redis(args.redisuri) if not args.samplesfile.exists(): logging.error("File not found: '%s'.", args.samplesfile) return 2 - with (Redis.from_url(args.redisuri, decode_responses=True) as rconn, - database_connection(args.databaseuri) as dbconn): - + with database_connection(args.databaseuri) as dbconn: try: status_code = insert_samples(dbconn, - rconn, args.speciesid, args.populationid, args.samplesfile, diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index e449b82..31eb715 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -5,10 +5,10 @@ import json import time import logging import argparse -import datetime -from typing import Any from pathlib import Path from zipfile import ZipFile +from datetime import datetime +from typing import Any, Iterable from urllib.parse import urljoin from functools import reduce, partial @@ -55,7 +55,7 @@ def save_phenotypes( if control_data["phenocovar_transposed"]: logger.info("Undoing transposition of the files rows and columns.") - phenofiles = ( + phenofiles = tuple( rqtl2.transpose_csv_with_rename( _file, build_line_splitter(control_data), @@ -86,7 +86,7 @@ def __row_to_dataitems__( dataidmap: dict, pheno_name2id: dict[str, int], samples: dict -) -> tuple[dict, ...]: +) -> Iterable[dict]: samplename = sample_row["id"] return ({ @@ -134,7 +134,7 @@ def save_numeric_data(# pylint: disable=[too-many-positional-arguments,too-many- conn: mysqldb.Connection, dataidmap: dict, pheno_name2id: dict[str, int], - samples: tuple[dict, ...], + samples: dict, control_data: dict, filesdir: Path, filetype: str, @@ -198,13 +198,16 @@ save_phenotypes_n = partial(save_numeric_data, def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments,too-many-arguments] - authserver, - token, + auth_details, + resource_details, species, population, dataset, xrefdata): """Grant the user access to their data.""" + logger.info("Updating authorisation for the data.") + logger.debug("Resource details for the authorisation: %s", resource_details) + authserver, token = auth_details _tries = 0 _delay = 1 headers = { @@ -215,14 +218,14 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments return urljoin(authserver, endpoint) def __fetch_user_details__(): - logger.debug("… Fetching user details") + logger.info("… Fetching user details") return mrequests.get( authserveruri("/auth/user/"), headers=headers ) def __link_data__(user): - logger.debug("… linking uploaded data to user's group") + logger.info("… linking uploaded data to user's group") return mrequests.post( authserveruri("/auth/data/link/phenotype"), headers=headers, @@ -245,7 +248,7 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments }).then(lambda ld_results: (user, ld_results)) def __fetch_phenotype_category_details__(user, linkeddata): - logger.debug("… fetching phenotype category details") + logger.info("… fetching phenotype category details") return mrequests.get( authserveruri("/auth/resource/categories"), headers=headers @@ -258,20 +261,18 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments ) def __create_resource__(user, linkeddata, category): - logger.debug("… creating authorisation resource object") - now = datetime.datetime.now().isoformat() + logger.info("… creating authorisation resource object") return mrequests.post( authserveruri("/auth/resource/create"), headers=headers, json={ + **resource_details, "resource_category": category["resource_category_id"], - "resource_name": (f"{user['email']}—{dataset['Name']}—{now}—" - f"{len(xrefdata)} phenotypes"), "public": "off" }).then(lambda cr_results: (user, linkeddata, cr_results)) def __attach_data_to_resource__(user, linkeddata, resource): - logger.debug("… attaching data to authorisation resource object") + logger.info("… attaching data to authorisation resource object") return mrequests.post( authserveruri("/auth/resource/data/link"), headers=headers, @@ -288,8 +289,8 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments # This is hacky. If the auth already exists, something went wrong # somewhere. # This needs investigation to recover correctly. - logger.info( - "The authorisation for the data was already set up.") + logger.error( + "Error: The authorisation for the data was already set up.") return 0 logger.error("ERROR: Updating the authorisation for the data failed.") logger.debug( @@ -311,7 +312,9 @@ def update_auth(# pylint: disable=[too-many-locals,too-many-positional-arguments ).either(__handle_error__, __handle_success__) -def load_data(conn: mysqldb.Connection, job: dict) -> int:#pylint: disable=[too-many-locals] +def load_data(# pylint: disable=[too-many-locals] + conn: mysqldb.Connection, job: dict +) -> tuple[dict, dict, dict, tuple[int, ...]]: """Load the data attached in the given job.""" _job_metadata = job["metadata"] # Steps @@ -365,9 +368,8 @@ def load_data(conn: mysqldb.Connection, job: dict) -> int:#pylint: disable=[too- "publication_id": row["publication_id"], "data_id": row["data_id"] },))) - dataidmap, pheno_name2id, _xrefs = reduce(__build_phenos_maps__, - _phenos, - ({},{}, tuple())) + dataidmap, pheno_name2id, _xrefs = reduce(# type: ignore[var-annotated] + __build_phenos_maps__, _phenos, ({},{}, tuple())) # 3. a. Fetch the strain names and IDS: create name->ID map samples = { row["Name"]: row @@ -460,6 +462,25 @@ if __name__ == "__main__": logging.getLogger("uploader.phenotypes.models").setLevel(log_level) + def __parse_resource_details__(meta) -> dict: + """Parse out details regarding the wrapper resource from the metadata.""" + _key_mappings_ = { + # allow both 'data_*' and 'data*' for the metadata. + "data_description": "description", + "datadescription": "description" + } + return { + "resource_name": meta.get( + "dataname", + meta.get("data_name", + "Unnamed phenotypes - " + datetime.now().isoformat())), + "resource_metadata": { + rkey: meta[mkey] + for mkey, rkey in _key_mappings_.items() if mkey in meta + } + } + + def main(): """Entry-point for this script.""" args = parse_args() @@ -515,8 +536,10 @@ if __name__ == "__main__": # Update authorisations (break this down) — maybe loop until it works? logger.info("Updating authorisation.") _job_metadata = job["metadata"] - return update_auth(_job_metadata["authserver"], - _job_metadata["token"], + + return update_auth((_job_metadata["authserver"], + _job_metadata["token"]), + __parse_resource_details__(_job_metadata), *db_results) diff --git a/scripts/phenotypes/__init__.py b/scripts/phenotypes/__init__.py new file mode 100644 index 0000000..73ad839 --- /dev/null +++ b/scripts/phenotypes/__init__.py @@ -0,0 +1 @@ +"Scripts for dealing with phenotypes." diff --git a/scripts/phenotypes/delete_phenotypes.py b/scripts/phenotypes/delete_phenotypes.py new file mode 100644 index 0000000..461f3ec --- /dev/null +++ b/scripts/phenotypes/delete_phenotypes.py @@ -0,0 +1,173 @@ +"""Delete phenotypes.""" +import sys +import logging +from pathlib import Path +from typing import Optional +from urllib.parse import urljoin +from argparse import Namespace, ArgumentParser + +import requests +from MySQLdb.cursors import DictCursor, BaseCursor + +from gn_libs.mysqldb import database_connection + +from uploader.phenotypes.models import delete_phenotypes +from scripts.cli.logging import setup_logging +from scripts.cli.options import (add_logging, + add_mariadb_uri, + add_population_id) + +logger = logging.getLogger(__name__) + +def read_xref_ids_file(filepath: Optional[Path]) -> tuple[int, ...]: + """Read the phenotypes' cross-reference IDS from file.""" + if filepath is None: + return tuple() + + logger.debug("Using file '%s' to retrieve XREF IDs for deletion.", + filepath.name) + _ids: tuple[int, ...] = tuple() + with filepath.open(mode="r") as infile: + for line in infile.readlines(): + try: + _ids += (int(line.strip()),) + except TypeError: + pass + + return _ids + + +def fetch_all_xref_ids( + cursor: BaseCursor, population_id: int) -> tuple[int, ...]: + """Fetch all cross-reference IDs.""" + cursor.execute("SELECT Id FROM PublishXRef WHERE InbredSetId=%s", + (population_id,)) + return tuple(int(row["Id"]) for row in cursor.fetchall()) + + +def update_auth( + auth_details: tuple[str, str], + species_id: int, + population_id: int, + dataset_id: int, + xref_ids: tuple[int, ...] = tuple() +): + """Update the authorisation server: remove items to delete.""" + authserver, token = auth_details + resp = requests.post( + urljoin(authserver, + (f"/auth/data/phenotypes/{species_id}/{population_id}" + f"/{dataset_id}/delete")), + timeout=(9.13, 20), + headers={ + "Authorization": f"Bearer {token}", + "Content-Type": "application/json" + }, + json={"xref_ids": xref_ids}) + resp.raise_for_status() + + +def delete_the_phenotypes( + cursor: BaseCursor, + population_id: int, + xref_ids: tuple[int, ...] = tuple()) -> int: + """Process and delete the phenotypes.""" + delete_phenotypes(cursor, population_id, xref_ids) + + return 0 + +if __name__ == "__main__": + def parse_args() -> Namespace: + """Parse CLI arguments.""" + parser = add_logging( + add_population_id( + add_mariadb_uri( + ArgumentParser( + prog="delete-phenotypes", + description=( + "Script to delete phenotypes from the database."))))) + parser.add_argument( + "dataset_id", + metavar="DATASET-ID", + type=int, + help="The dataset identifier for phenotypes to delete.") + parser.add_argument( + "auth_server_uri", + metavar="AUTH-SERVER-URI", + type=str, + help="URI to the authorisation server.") + parser.add_argument( + "auth_token", + metavar="AUTH-TOKEN", + type=str, + help=("Token to use to update the authorisation system with the " + "deletions done.")) + parser.add_argument( + "--xref_ids_file", + metavar="XREF-IDS-FILE", + type=Path, + help=("Path to a file with phenotypes cross-reference IDs to " + "delete.")) + parser.add_argument( + "--delete-all", + action="store_true", + help=("If no 'XREF-IDS-FILE' is provided, this flag determines " + "whether or not all the phenotypes for the given population " + "will be deleted.")) + return parser.parse_args() + + + def main(): + """The `delete-phenotypes` script's entry point.""" + args = parse_args() + setup_logging(logger, args.log_level.upper(), tuple()) + with (database_connection(args.db_uri) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + xref_ids = read_xref_ids_file(args.xref_ids_file) + try: + assert not (len(xref_ids) > 0 and args.delete_all) + xref_ids = (fetch_all_xref_ids(cursor, args.population_id) + if args.delete_all else xref_ids) + logger.debug("Will delete %s phenotypes and related data", + len(xref_ids)) + if len(xref_ids) == 0: + print("No cross-reference IDs were provided. Aborting.") + return 0 + + print("Updating authorisations: ", end="") + update_auth((args.auth_server_uri, args.auth_token), + args.species_id, + args.population_id, + args.dataset_id, + xref_ids) + print("OK.") + print("Deleting the data: ", end="") + delete_phenotypes(cursor, args.population_id, xref_ids=xref_ids) + print("OK.") + if args.xref_ids_file is not None: + print("Deleting temporary file: ", end="") + args.xref_ids_file.unlink() + print("OK.") + + return 0 + except AssertionError: + logger.error( + "'DELETE-ALL' and 'XREF-IDS' are mutually exclusive. " + "If you specify the list of XREF-IDS (in a file) to delete " + "and also specify to 'DELETE-ALL' phenotypes in the " + "population, we have no way of knowing what it is you want.") + return 1 + except requests.exceptions.HTTPError as _exc: + resp = _exc.response + resp_data = resp.json() + logger.debug("%s: %s", + resp_data["error"], + resp_data["error_description"], + exc_info=True) + return 1 + except Exception as _exc:# pylint: disable=[broad-exception-caught] + logger.debug("Failed while attempting to delete phenotypes.", + exc_info=True) + return 1 + + sys.exit(main()) diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index 0207938..4e6ef00 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -40,7 +40,7 @@ def add_to_errors(rconn: Redis, """Add `errors` to a given list of errors""" errs = tuple(dict(item) for item in set( [dict2tuple(old) for old in - json.loads(rconn.hget(fqjobid, key) or "[]")] + + json.loads(rconn.hget(fqjobid, key) or "[]")] +# type: ignore[arg-type] [dict2tuple({"type": type(error).__name__, **error._asdict()}) for error in errors])) rconn.hset(fqjobid, key, json.dumps(errs)) @@ -83,7 +83,8 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals count = 0 checked = 0 cdata = rqtl2.control_data(zfile) - rconn.hset(fqjobid, f"{filetype}-filesize", compute_filesize(zfile, filetype)) + rconn.hset( + fqjobid, f"{filetype}-filesize", str(compute_filesize(zfile, filetype))) def __update_processed__(value): nonlocal checked checked = checked + len(value) @@ -104,7 +105,7 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals yield error __update_processed__(value) - rconn.hset(fqjobid, f"{filetype}-linecount", count) + rconn.hset(fqjobid, f"{filetype}-linecount", count)# type: ignore[arg-type] except rqe.MissingFileException: fname = cdata.get(filetype) yield rqfe.MissingFile(filetype, fname, ( @@ -295,7 +296,7 @@ def run_qc(rconn: Redis, return 1 def __fetch_errors__(rkey: str) -> tuple: - return tuple(json.loads(rconn.hget(fqjobid, rkey) or "[]")) + return tuple(json.loads(rconn.hget(fqjobid, rkey) or "[]")) # type: ignore[arg-type] return (1 if any(( bool(__fetch_errors__(key)) diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 8762655..5e6abb0 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -20,7 +20,7 @@ from scripts.rqtl2.entry import build_main from scripts.rqtl2.cli_parser import add_common_arguments from scripts.cli_parser import init_cli_parser, add_global_data_arguments -__MODULE__ = "scripts.rqtl2.install_genotypes" +logger = getLogger(__name__) def insert_markers( dbconn: mdb.Connection, @@ -191,7 +191,7 @@ def install_genotypes(#pylint: disable=[too-many-locals] dbconn: mdb.Connection, fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, - logger: Logger = getLogger(__name__) + logger: Logger = logger # pylint: disable=[redefined-outer-name] ) -> int: """Load any existing genotypes into the database.""" (speciesid, populationid, datasetid, rqtl2bundle) = ( @@ -257,5 +257,5 @@ if __name__ == "__main__": return parser.parse_args() - main = build_main(cli_args(), install_genotypes, __MODULE__) + main = build_main(cli_args(), install_genotypes, logger) sys.exit(main()) diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index 9059cd6..11ac8a4 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -19,7 +19,7 @@ from r_qtl import r_qtl2_qc as rqc from functional_tools import take -__MODULE__ = "scripts.rqtl2.install_phenos" +logger = getLogger(__name__) def insert_probesets(dbconn: mdb.Connection, platformid: int, @@ -101,7 +101,8 @@ def install_pheno_files(#pylint: disable=[too-many-locals] dbconn: mdb.Connection, fullyqualifiedjobid: str,#pylint: disable=[unused-argument] args: argparse.Namespace, - logger: Logger = getLogger()) -> int: + logger: Logger = logger # pylint: disable=[redefined-outer-name] +) -> int: """Load data in `pheno` files and other related files into the database.""" (speciesid, platformid, datasetid, rqtl2bundle) = ( args.speciesid, args.platformid, args.datasetid, args.rqtl2bundle) @@ -159,5 +160,5 @@ if __name__ == "__main__": return parser.parse_args() - main = build_main(cli_args(), install_pheno_files, __MODULE__) + main = build_main(cli_args(), install_pheno_files, logger) sys.exit(main()) diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 9f11f57..084c876 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -198,7 +198,7 @@ def qc_phenocovar_file( "-", "-", (f"File {filepath.name} is missing the {heading} heading " - "in the header line."))),) + "in the header row/line."))),) def collect_errors(errors_and_linecount, line): _errs, _lc = errors_and_linecount @@ -312,8 +312,9 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments, too-ma "header row", "-", ", ".join(_absent), - ("The following phenotype names do not exist in any of the " - f"provided phenocovar files: ({', '.join(_absent)})"))),) + ("The following trait names/identifiers do not exist in any of " + "the provided descriptions/covariates files: " + f"({', '.join(_absent)})"))),) def collect_errors(errors_and_linecount, line): _errs, _lc = errors_and_linecount @@ -376,7 +377,8 @@ def run_qc(# pylint: disable=[too-many-locals] rconn: Redis, dbconn: mdb.Connection, fullyqualifiedjobid: str, - args: Namespace + args: Namespace, + logger: Logger = logger # pylint: disable=[redefined-outer-name] ) -> int: """Run quality control checks on the bundle.""" print("Beginning the quality assurance checks.") diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py index ab58203..a461d9a 100644 --- a/scripts/run_qtlreaper.py +++ b/scripts/run_qtlreaper.py @@ -1,14 +1,15 @@ """Script to run rust-qtlreaper and update database with results.""" +import os import sys import csv import time import secrets import logging -import traceback import subprocess +import multiprocessing from pathlib import Path -from typing import Union from functools import reduce +from typing import Union, Iterator from argparse import Namespace, ArgumentParser from gn_libs import mysqldb @@ -57,7 +58,7 @@ def reconcile_samples( def generate_qtlreaper_traits_file( outdir: Path, samples: tuple[str, ...], - traits_data: dict[str, Union[int, float]], + traits_data: tuple[dict[str, Union[int, float]], ...], filename_prefix: str = "" ) -> Path: """Generate a file for use with qtlreaper that contains the traits' data.""" @@ -66,7 +67,7 @@ def generate_qtlreaper_traits_file( _dialect.quoting=0 _traitsfile = outdir.joinpath( - f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv") + f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined] with _traitsfile.open(mode="w", encoding="utf-8") as outptr: writer = csv.DictWriter( outptr, fieldnames=("Trait",) + samples, dialect=_dialect) @@ -80,14 +81,13 @@ def generate_qtlreaper_traits_file( return _traitsfile -def parse_tsv_file(results_file: Path) -> list[dict]: +def parse_tsv_file(results_file: Path) -> Iterator[dict]: """Parse the rust-qtlreaper output into usable python objects.""" with results_file.open("r", encoding="utf-8") as readptr: _dialect = csv.unix_dialect() _dialect.delimiter = "\t" reader = csv.DictReader(readptr, dialect=_dialect) - for row in reader: - yield row + yield from reader def __qtls_by_trait__(qtls, current): @@ -98,7 +98,8 @@ def __qtls_by_trait__(qtls, current): } -def save_qtl_values_to_db(conn, qtls: dict): +def save_qtl_values_to_db(conn, qtls: tuple[dict, ...]): + """Save computed QTLs to the database.""" with conn.cursor() as cursor: cursor.executemany( "UPDATE PublishXRef SET " @@ -107,7 +108,7 @@ def save_qtl_values_to_db(conn, qtls: dict): qtls) -def dispatch(args: Namespace) -> int: +def dispatch(args: Namespace) -> int:# pylint: disable=[too-many-locals] """Dispatch the actual logic.""" exitcode = 1 with mysqldb.database_connection(args.db_uri) as conn: @@ -132,11 +133,11 @@ def dispatch(args: Namespace) -> int: ", ".join(_samples_not_in_genofile)) # Fetch traits data: provided list, or all traits in db - _traitsdata = phenotypes_vector_data( + _traitsdata = tuple(phenotypes_vector_data( conn, args.species_id, args.population_id, - xref_ids=tuple(args.xref_ids)).values() + xref_ids=tuple(args.xref_ids)).values()) logger.debug("Successfully got traits data. Generating the QTLReaper's traits file…") _traitsfile = generate_qtlreaper_traits_file( args.working_dir, @@ -146,37 +147,63 @@ def dispatch(args: Namespace) -> int: logger.debug("QTLReaper's Traits file: %s", _traitsfile) _qtlreaper_main_output = args.working_dir.joinpath( - f"main-output-{secrets.token_urlsafe(15)}.tsv") + f"main-output-{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined] + _qtlreaper_permu_output = args.working_dir.joinpath( + f"permu-output-{secrets.token_urlsafe(15)}.tsv") logger.debug("Main output filename: %s", _qtlreaper_main_output) with subprocess.Popen( ("qtlreaper", "--n_permutations", "1000", "--geno", _genofile, "--traits", _traitsfile, - "--main_output", _qtlreaper_main_output)) as _qtlreaper: + "--main_output", _qtlreaper_main_output, + "--permu_output", _qtlreaper_permu_output, + "--threads", str(int(1+(multiprocessing.cpu_count()/2)))), + env=({**os.environ, "RUST_BACKTRACE": "full"} + if logger.getEffectiveLevel() == logging.DEBUG + else dict(os.environ))) as _qtlreaper: while _qtlreaper.poll() is None: logger.debug("QTLReaper process running…") time.sleep(1) - results = tuple(max(qtls, key=lambda qtl: qtl["LRS"]) - for qtls in - reduce(__qtls_by_trait__, - parse_tsv_file(_qtlreaper_main_output), - {}).values()) - save_qtl_values_to_db(conn, results) + results = ( + tuple(#type: ignore[var-annotated] + max(qtls, key=lambda qtl: qtl["LRS"]) + for qtls in + reduce(__qtls_by_trait__, + parse_tsv_file(_qtlreaper_main_output), + {}).values()) + if _qtlreaper_main_output.exists() + else tuple()) logger.debug("Cleaning up temporary files.") - _traitsfile.unlink() - _qtlreaper_main_output.unlink() + + # short-circuits to delete file if exists + if _traitsfile.exists(): + _traitsfile.unlink() + logger.info("Deleted generated traits' file for QTLReaper.") + + if _qtlreaper_main_output.exists(): + _qtlreaper_main_output.unlink() + logger.info("Deleted QTLReaper's main output file.") + + if _qtlreaper_permu_output.exists(): + _qtlreaper_permu_output.unlink() + logger.info("Deleted QTLReaper's permutations file.") + + if _qtlreaper.returncode != 0: + return _qtlreaper.returncode + + save_qtl_values_to_db(conn, results) logger.info("Successfully computed p values for %s traits.", len(_traitsdata)) - exitcode = 0 + return 0 except FileNotFoundError as fnf: - logger.error(", ".join(fnf.args), exc_info=False) + logger.error(", ".join(str(arg) for arg in fnf.args), exc_info=False) except AssertionError as aserr: logger.error(", ".join(aserr.args), exc_info=False) - except Exception as _exc: + except Exception as _exc:# pylint: disable=[broad-exception-caught] logger.debug("Type of exception: %s", type(_exc)) logger.error("General exception!", exc_info=True) - finally: - return exitcode + + return exitcode if __name__ == "__main__": @@ -205,7 +232,7 @@ if __name__ == "__main__": "in the population.")) args = parser.parse_args() setup_logging(logger, args.log_level) - + return dispatch(args) sys.exit(main()) diff --git a/tests/conftest.py b/tests/conftest.py index a716c52..2009aab 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -183,7 +183,7 @@ def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, jobs_prefix, def uploads_dir(client): # pylint: disable=[redefined-outer-name] """Returns the configured, uploads directory, creating it if it does not exist.""" - the_dir = client.application.config["UPLOAD_FOLDER"] + the_dir = client.application.config["UPLOADS_DIRECTORY"] if not os.path.exists(the_dir): os.mkdir(the_dir) diff --git a/tests/test_instance_dir/config.py b/tests/test_instance_dir/config.py index 2ee569b..f04b3df 100644 --- a/tests/test_instance_dir/config.py +++ b/tests/test_instance_dir/config.py @@ -6,6 +6,6 @@ import os LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING") SECRET_KEY = b"<Please! Please! Please! Change This!>" -UPLOAD_FOLDER = "/tmp/qc_app_files" +UPLOADS_DIRECTORY = "/tmp/qc_app_files" REDIS_URL = "redis://" JOBS_TTL_SECONDS = 600 # 10 minutes diff --git a/tests/uploader/test_parse.py b/tests/uploader/test_parse.py index 20c75b7..56e1b41 100644 --- a/tests/uploader/test_parse.py +++ b/tests/uploader/test_parse.py @@ -50,7 +50,7 @@ def test_parse_with_existing_uploaded_file( assert the_job["command"] == " ".join([ sys.executable, "-m", "scripts.validate_file", db_url, redis_url, jobs_prefix, job_id, "--redisexpiry", str(redis_ttl), str(speciesid), - filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}"]) + filetype, f"{client.application.config['UPLOADS_DIRECTORY']}/{filename}"]) @pytest.mark.parametrize( "filename,uri,error_msgs", diff --git a/uploader/__init__.py b/uploader/__init__.py index 7425b38..afaa78d 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -11,7 +11,7 @@ from cachelib import FileSystemCache from gn_libs import jobs as gnlibs_jobs -from flask_session import Session +from flask_session import Session# type: ignore[attr-defined] from uploader.oauth2.client import user_logged_in, authserver_authorise_uri @@ -73,6 +73,28 @@ def setup_modules_logging(app_logger, modules): _logger.setLevel(loglevel) +def __setup_scratch_directory__(app: Flask) -> Flask: + app.config["SCRATCH_DIRECTORY"] = Path( + app.config["SCRATCH_DIRECTORY"]).absolute() + return app + +def __setup_upload_directory__(app: Flask) -> Flask: + if app.config.get("UPLOADS_DIRECTORY", "").strip() == "": + app.config["UPLOADS_DIRECTORY"] = app.config[ + "SCRATCH_DIRECTORY"].joinpath("uploads") + else: + app.config["UPLOADS_DIRECTORY"] = Path( + app.config["UPLOADS_DIRECTORY"].strip()).absolute() + + return app + + +def update_unspecified_defaults(app: Flask) -> Flask: + """Setup the defaults for necessary configurations that do not have values + specified for them.""" + return __setup_upload_directory__(__setup_scratch_directory__(app)) + + def create_app(config: Optional[dict] = None): """The application factory. @@ -100,20 +122,17 @@ def create_app(config: Optional[dict] = None): # Silently ignore secrets if the file does not exist. app.config.from_pyfile(secretsfile) app.config.update(config) # Override everything with passed in config + update_unspecified_defaults(app) ### END: Application configuration app.config["SESSION_CACHELIB"] = FileSystemCache( - cache_dir=Path(app.config["SESSION_FILESYSTEM_CACHE_PATH"]).absolute(), + cache_dir=str(Path(app.config["SESSION_FILESYSTEM_CACHE_PATH"]).absolute()), threshold=int(app.config["SESSION_FILESYSTEM_CACHE_THRESHOLD"]), default_timeout=int(app.config["SESSION_FILESYSTEM_CACHE_TIMEOUT"])) setup_logging(app) - setup_modules_logging(app.logger, ( - "uploader.base_routes", - "uploader.flask_extensions", - "uploader.publications.models", - "uploader.publications.datatables", - "uploader.phenotypes.models")) + setup_modules_logging( + app.logger, tuple(app.config.get("LOGGABLE_MODULES", []))) # setup jinja2 symbols app.add_template_global(user_logged_in) diff --git a/uploader/background_jobs.py b/uploader/background_jobs.py index fc59ec7..a71dd44 100644 --- a/uploader/background_jobs.py +++ b/uploader/background_jobs.py @@ -1,39 +1,51 @@ """Generic views and utilities to handle background jobs.""" import uuid +import datetime import importlib from typing import Callable from functools import partial +from werkzeug.wrappers.response import Response from flask import ( + flash, request, redirect, - Response, Blueprint, - render_template, current_app as app) from gn_libs import jobs from gn_libs import sqlite3 from gn_libs.jobs.jobs import JobNotFound - -from uploader.sui import sui_template - -from uploader.flask_extensions import url_for +from uploader import session from uploader.authorisation import require_login +from uploader.flask_extensions import url_for, render_template background_jobs_bp = Blueprint("background-jobs", __name__) HandlerType = Callable[[dict], Response] -def __default_error_handler__(job: dict) -> Response: - return redirect(url_for("background-jobs.job_error", job_id=job["job_id"])) +def make_datetime_formatter(dtformat: str = "%A, %d %B %Y at %H:%M %Z") -> Callable[[str], str]: + """Make a datetime formatter with the provided `dtformat`""" + def __formatter__(val: str) -> str: + dt = datetime.datetime.fromisoformat(val) + return dt.strftime(dtformat.strip()) + + return __formatter__ + +__default_datetime_formatter__ = make_datetime_formatter() + + +def __default_handler__(_job): + return render_template("background-jobs/job-summary.html", + job=_job, + display_datetime=__default_datetime_formatter__) def register_handlers( job_type: str, success_handler: HandlerType, # pylint: disable=[redefined-outer-name] - error_handler: HandlerType = __default_error_handler__ + error_handler: HandlerType = __default_handler__ # pylint: disable=[redefined-outer-name] ) -> str: """Register success and error handlers for each job type.""" @@ -49,7 +61,7 @@ def register_handlers( return job_type -def register_job_handlers(job: str): +def register_job_handlers(job: dict): """Related to register handlers above.""" def __load_handler__(absolute_function_path): _parts = absolute_function_path.split(".") @@ -65,7 +77,7 @@ def register_job_handlers(job: str): try: _error_handler = __load_handler__(metadata["error_handler"]) except Exception as _exc:# pylint: disable=[broad-exception-caught] - _error_handler = __default_error_handler__ + _error_handler = __default_handler__ register_handlers( metadata["job-type"], _success_handler, _error_handler) @@ -80,8 +92,8 @@ def handler(job: dict, handler_type: str) -> HandlerType: ).get(handler_type) if bool(_handler): return _handler(job) - return render_template(sui_template("background-jobs/default-success-page.html"), - job=job) + + return __default_handler__(job) error_handler = partial(handler, handler_type="error") @@ -98,17 +110,17 @@ def job_status(job_id: uuid.UUID): status = job["metadata"]["status"] register_job_handlers(job) - if status == "error": + if status in ("error", "stopped"): return error_handler(job) if status == "completed": return success_handler(job) - return render_template(sui_template("jobs/job-status.html"), job=job) + return render_template("background-jobs/job-status.html", + job=job, + display_datetime=__default_datetime_formatter__) except JobNotFound as _jnf: - return render_template( - sui_template("jobs/job-not-found.html"), - job_id=job_id) + return render_template("jobs/job-not-found.html", job_id=job_id) @background_jobs_bp.route("/error/<uuid:job_id>") @@ -118,7 +130,96 @@ def job_error(job_id: uuid.UUID): with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: try: job = jobs.job(conn, job_id, fulldetails=True) - return render_template(sui_template("jobs/job-error.html"), job=job) + return render_template("jobs/job-error.html", job=job) + except JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@background_jobs_bp.route("/list") +@require_login +def list_jobs(): + """List background jobs.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + return render_template( + "background-jobs/list-jobs.html", + jobs=jobs.jobs_by_external_id( + conn, session.user_details()["user_id"]), + display_datetime=__default_datetime_formatter__) + + +@background_jobs_bp.route("/summary/<uuid:job_id>") +@require_login +def job_summary(job_id: uuid.UUID): + """Provide a summary for completed jobs.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + try: + job = jobs.job(conn, job_id, fulldetails=True) + status = job["metadata"]["status"] + + if status in ("completed", "error", "stopped"): + return render_template("background-jobs/job-summary.html", + job=job, + display_datetime=__default_datetime_formatter__) + return redirect(url_for( + "background-jobs.job_status", job_id=job["job_id"])) + except JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@background_jobs_bp.route("/delete/<uuid:job_id>", methods=["GET", "POST"]) +@require_login +def delete_single(job_id: uuid.UUID): + """Delete a single job.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + try: + job = jobs.job(conn, job_id, fulldetails=True) + status = job["metadata"]["status"] + if status not in ("completed", "error", "stopped"): + flash("We cannot delete a running job.", "alert alert-danger") + return redirect(url_for( + "background-jobs.job_summary", job_id=job_id)) + + if request.method == "GET": + return render_template("background-jobs/delete-job.html", + job=job, + display_datetime=__default_datetime_formatter__) + + if request.form["btn-confirm-delete"] == "delete": + jobs.delete_job(conn, job_id) + flash("Job was deleted successfully.", "alert alert-success") + return redirect(url_for("background-jobs.list_jobs")) + flash("Delete cancelled.", "alert alert-info") + return redirect(url_for( + "background-jobs.job_summary", job_id=job_id)) + except JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@background_jobs_bp.route("/stop/<uuid:job_id>", methods=["GET", "POST"]) +@require_login +def stop_job(job_id: uuid.UUID): + """Stop a running job.""" + with sqlite3.connection(app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]) as conn: + try: + job = jobs.job(conn, job_id, fulldetails=True) + status = job["metadata"]["status"] + if status != "running": + flash("Cannot stop a job that is not running.", "alert alert-danger") + return redirect(url_for( + "background-jobs.job_summary", job_id=job_id)) + + if request.method == "GET": + return render_template("background-jobs/stop-job.html", + job=job, + display_datetime=__default_datetime_formatter__) + + if request.form["btn-confirm-stop"] == "stop": + jobs.kill_job(conn, job_id) + flash("Job was stopped successfully.", "alert alert-success") + return redirect(url_for( + "background-jobs.job_summary", job_id=job_id)) + flash("Stop cancelled.", "alert alert-info") + return redirect(url_for( + "background-jobs.job_summary", job_id=job_id)) except JobNotFound as _jnf: - return render_template(sui_template("jobs/job-not-found.html"), - job_id=job_id) + return render_template("jobs/job-not-found.html", job_id=job_id) diff --git a/uploader/base_routes.py b/uploader/base_routes.py index cc2a270..72a8402 100644 --- a/uploader/base_routes.py +++ b/uploader/base_routes.py @@ -11,12 +11,8 @@ from flask import (flash, current_app as app, send_from_directory) - -from uploader.sui import sui_template - from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer -from uploader.oauth2.client import user_logged_in from uploader.species.models import all_species, species_by_id base = Blueprint("base", __name__) @@ -36,19 +32,15 @@ def favicon(): def index(): """Load the landing page""" streamlined_ui = request.args.get("streamlined_ui") - if not bool(streamlined_ui):# TODO: Remove this section - return render_template( - "index.html" if user_logged_in() else "login.html", - gn2server_intro=urljoin(app.config["GN2_SERVER_URL"], "/intro")) - with database_connection(app.config["SQL_URI"]) as conn: print("We found a species ID. Processing...") if not bool(request.args.get("species_id")): return render_template( - sui_template("index.html"), + "index.html", gn2server_intro=urljoin(app.config["GN2_SERVER_URL"], "/intro"), species=all_species(conn), - streamlined_ui=streamlined_ui) + view_under_construction=request.args.get( + "view_under_construction", False)) species = species_by_id(conn, request.args.get("species_id")) if not bool(species): diff --git a/uploader/configutils.py b/uploader/configutils.py new file mode 100644 index 0000000..c5db50b --- /dev/null +++ b/uploader/configutils.py @@ -0,0 +1,13 @@ +"""Functions to fetch settings.""" +from pathlib import Path + +def fetch_setting(app, setting): + """Fetch a specified configuration `setting` from the `app` object.""" + return app.config[setting] + +def uploads_dir(app) -> Path: + """Fetch the uploads directory""" + _dir = Path(fetch_setting(app, "UPLOADS_DIRECTORY")).absolute() + assert _dir.exists() and _dir.is_dir(), ( + f"'{_dir}' needs to be an existing directory.") + return _dir diff --git a/uploader/default_settings.py b/uploader/default_settings.py index bb3a967..04e1c0a 100644 --- a/uploader/default_settings.py +++ b/uploader/default_settings.py @@ -5,8 +5,14 @@ actual configuration file used for the production and staging systems. LOG_LEVEL = "WARNING" SECRET_KEY = b"<Please! Please! Please! Change This!>" -UPLOAD_FOLDER = "/tmp/qc_app_files" -TEMPORARY_DIRECTORY = "/tmp/gn-uploader-tmpdir" + +# Scratch directory and uploads: +# *** The scratch directory *** +# We avoid `/tmp` entirely for the scratch directory to avoid shared global +# mutable state with other users/applications/processes. +SCRATCH_DIRECTORY = "~/tmp/gn-uploader-scratchdir" +UPLOADS_DIRECTORY = ""# If not set, will be under scratch directory. + REDIS_URL = "redis://" JOBS_TTL_SECONDS = 1209600 # 14 days GNQC_REDIS_PREFIX="gn-uploader" @@ -32,4 +38,7 @@ JWKS_DELETION_AGE_DAYS = 14 # Days (from creation) to keep a JWK around before d ## --- Feature flags --- -FEATURE_FLAGS_HTTP = [] +FEATURE_FLAGS_HTTP: list[str] = [] + +## --- Modules for which to log output --- +LOGGABLE_MODULES: list[str] = [] diff --git a/uploader/errors.py b/uploader/errors.py index 3e7c893..2ac48b8 100644 --- a/uploader/errors.py +++ b/uploader/errors.py @@ -3,7 +3,8 @@ import traceback from werkzeug.exceptions import HTTPException import MySQLdb as mdb -from flask import Flask, request, render_template, current_app as app +from flask import Flask, request, current_app as app +from uploader.flask_extensions import render_template def handle_general_exception(exc: Exception): """Handle generic exceptions.""" diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py index 6d8ce80..7040698 100644 --- a/uploader/expression_data/dbinsert.py +++ b/uploader/expression_data/dbinsert.py @@ -94,7 +94,7 @@ def select_platform(): job = jobs.job(rconn, jobs.jobsnamespace(), job_id) if job: filename = job["filename"] - filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" + filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}" if os.path.exists(filepath): default_species = 1 gchips = genechips() @@ -367,7 +367,7 @@ def insert_data(): assert form.get("datasetid"), "dataset" filename = form["filename"] - filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" + filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}" redisurl = app.config["REDIS_URL"] if os.path.exists(filepath): with Redis.from_url(redisurl, decode_responses=True) as rconn: @@ -377,7 +377,7 @@ def insert_data(): form["species"], form["genechipid"], form["datasetid"], app.config["SQL_URI"], redisurl, app.config["JOBS_TTL_SECONDS"]), - redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors") + redisurl, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"])) return render_error(f"File '{filename}' no longer exists.") diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py index 0b318b7..0e9b072 100644 --- a/uploader/expression_data/views.py +++ b/uploader/expression_data/views.py @@ -162,7 +162,7 @@ def upload_file(species_id: int, population_id: int): species=species, population=population) - upload_dir = app.config["UPLOAD_FOLDER"] + upload_dir = app.config["UPLOADS_DIRECTORY"] request_errors = errors(request) if request_errors: for error in request_errors: @@ -225,7 +225,7 @@ def parse_file(species_id: int, population_id: int): _errors = True if filename: - filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename) + filepath = os.path.join(app.config["UPLOADS_DIRECTORY"], filename) if not os.path.exists(filepath): flash("Selected file does not exist (any longer)", "alert-danger") _errors = True @@ -241,7 +241,7 @@ def parse_file(species_id: int, population_id: int): species_id, filepath, filetype,# type: ignore[arg-type] app.config["JOBS_TTL_SECONDS"]), redisurl, - f"{app.config['UPLOAD_FOLDER']}/job_errors") + f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return redirect(url_for("species.populations.expression-data.parse_status", species_id=species_id, @@ -263,7 +263,7 @@ def parse_status(species_id: int, population_id: int, job_id: str): return render_template("no_such_job.html", job_id=job_id), 400 error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") + job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") if os.path.exists(error_filename): stat = os.stat(error_filename) if stat.st_size > 0: @@ -345,7 +345,7 @@ def fail(species_id: int, population_id: int, job_id: str): if job: error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") + job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") if os.path.exists(error_filename): stat = os.stat(error_filename) if stat.st_size > 0: diff --git a/uploader/files/chunks.py b/uploader/files/chunks.py index c4360b5..f63f32f 100644 --- a/uploader/files/chunks.py +++ b/uploader/files/chunks.py @@ -5,6 +5,8 @@ from typing import Iterator from flask import current_app as app from werkzeug.utils import secure_filename +from uploader.configutils import uploads_dir + def chunked_binary_read(filepath: Path, chunksize: int = 2048) -> Iterator: """Read a file in binary mode in chunks.""" @@ -29,4 +31,4 @@ 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}") + return Path(uploads_dir(app), f"tempdir_{uniqueidentifier}") diff --git a/uploader/files/functions.py b/uploader/files/functions.py index 7b9f06b..68f4e16 100644 --- a/uploader/files/functions.py +++ b/uploader/files/functions.py @@ -8,6 +8,8 @@ from flask import current_app from werkzeug.utils import secure_filename from werkzeug.datastructures import FileStorage +from uploader.configutils import uploads_dir + from .chunks import chunked_binary_read def save_file(fileobj: FileStorage, upload_dir: Path, hashed: bool = True) -> Path: @@ -30,7 +32,7 @@ def save_file(fileobj: FileStorage, upload_dir: Path, hashed: bool = True) -> Pa def fullpath(filename: str): """Get a file's full path. This makes use of `flask.current_app`.""" - return Path(current_app.config["UPLOAD_FOLDER"], filename).absolute() + return Path(uploads_dir(current_app), filename).absolute() def sha256_digest_over_file(filepath: Path) -> str: diff --git a/uploader/files/views.py b/uploader/files/views.py index 29059c7..ea0e827 100644 --- a/uploader/files/views.py +++ b/uploader/files/views.py @@ -6,13 +6,15 @@ from pathlib import Path from flask import request, jsonify, Blueprint, current_app as app +from uploader.configutils import uploads_dir + 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) + return Path(uploads_dir(app), fileid) @files.route("/upload/resumable", methods=["GET"]) diff --git a/uploader/flask_extensions.py b/uploader/flask_extensions.py index 30fbad7..0fc774a 100644 --- a/uploader/flask_extensions.py +++ b/uploader/flask_extensions.py @@ -2,19 +2,17 @@ import logging from typing import Any, Optional -from flask import (request, current_app as app, url_for as flask_url_for) +from flask import ( + request, + current_app as app, + url_for as flask_url_for, + render_template as flask_render_template) logger = logging.getLogger(__name__) -def url_for( - endpoint: str, - _anchor: Optional[str] = None, - _method: Optional[str] = None, - _scheme: Optional[str] = None, - _external: Optional[bool] = None, - **values: Any) -> str: - """Extension to flask's `url_for` function.""" +def fetch_flags(): + """Fetch get arguments that are defined as feature flags.""" flags = {} for flag in app.config["FEATURE_FLAGS_HTTP"]: flag_value = (request.args.get(flag) or request.form.get(flag) or "").strip() @@ -22,12 +20,33 @@ def url_for( flags[flag] = flag_value continue continue + logger.debug("HTTP FEATURE FLAGS: %s", flags) + return flags - logger.debug("HTTP FEATURE FLAGS: %s, other variables: %s", flags, values) + +def url_for( + endpoint: str, + _anchor: Optional[str] = None, + _method: Optional[str] = None, + _scheme: Optional[str] = None, + _external: Optional[bool] = None, + **values: Any) -> str: + """Extension to flask's `url_for` function.""" + logger.debug("other variables: %s", values) return flask_url_for(endpoint=endpoint, _anchor=_anchor, _method=_method, _scheme=_scheme, _external=_external, **values, - **flags) + **fetch_flags()) + + +def render_template(template_name_or_list, **context: Any) -> str: + """Extend flask's `render_template` function""" + return flask_render_template( + template_name_or_list, + **{ + **context, + **fetch_flags() # override any flag values + }) diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 4c3e634..41270da 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -1,13 +1,17 @@ """Functions for handling genotypes.""" +import logging from typing import Optional +from functools import reduce from datetime import datetime import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor -from flask import current_app as app from gn_libs.mysqldb import debug_query +logger = logging.getLogger(__name__) + + def genocode_by_population( conn: mdb.Connection, population_id: int) -> tuple[dict, ...]: """Get the allele/genotype codes.""" @@ -29,18 +33,102 @@ def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int: def genotype_markers( conn: mdb.Connection, species_id: int, + population_id: int, + offset: int = 0, + limit: int = -1# no limit if negative, zero returns empty list. +) -> tuple[tuple[dict, ...], int]: + """Retrieve markers from the database. + + Return: A tuple of: + - Listing of the markers, + - The total number of markers found in the system. + """ + _query_template = ( + "SELECT %%COLS%% " + "FROM Species AS spc " + "INNER JOIN InbredSet AS iset " + "ON spc.Id = iset.SpeciesId " + "INNER JOIN GenoFreeze AS gfr " + "ON iset.Id = gfr.InbredSetId " + "INNER JOIN GenoXRef AS gxr " + "ON gfr.Id = gxr.GenoFreezeId " + "INNER JOIN Geno AS gno " + "ON gxr.GenoId = gno.Id " + "WHERE spc.Id=%s " + "AND iset.Id=%s " + "%%LIMIT%%") + + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + _query_template.replace("%%LIMIT%%", "").replace( + "%%COLS%%", "COUNT(gno.Id) AS total_records"), + (species_id, population_id)) + _total_records = cursor.fetchone()["total_records"] + cursor.execute( + _query_template.replace("%%COLS%%", "gno.*, gxr.cM").replace( + "%%LIMIT%%", + (f"LIMIT {int(limit)} OFFSET {int(offset)}" + if bool(limit) and limit >= 0 + else "")), + (species_id, population_id)) + debug_query(cursor, logger) + _records = tuple(dict(row) for row in cursor.fetchall()) + return _records, _total_records + + +def genotype_records( + conn: mdb.Connection, + species_id: int, + population_id: int, offset: int = 0, - limit: Optional[int] = None -) -> tuple[dict, ...]: - """Retrieve markers from the database.""" - _query = "SELECT * FROM Geno WHERE SpeciesId=%s" - if bool(limit) and limit > 0:# type: ignore[operator] - _query = _query + f" LIMIT {limit} OFFSET {offset}" + limit: int = -1# no limit if negative, zero returns empty list. +) -> tuple[tuple[dict, ...], int]: + """Retrieve the actual genotype records from the database. + + Returns: A tuple of: + - the listing of the genotype data, + - the total number of genotype records for this population. + """ + def __organise_geno_records__(acc, row): + _current_row = acc.get(row["GenoId"], { + "GenoId": row["GenoId"], + "data": {} + }) + _current_row["data"][row["StrainName"]] = row["value"] + return { + **acc, + _current_row["GenoId"]: _current_row + } + + _query_template = ( + "SELECT gxr.GenoId, gxr.DataId, gdt.value, strn.Name AS StrainName " + "FROM GenoXRef AS gxr " + "INNER JOIN GenoData AS gdt ON gxr.DataId = gdt.Id " + "INNER JOIN Strain AS strn ON gdt.StrainId = strn.Id " + "WHERE gxr.GenoId IN (%%PARAMS_STR%%)") with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, (species_id,)) - debug_query(cursor, app.logger) - return tuple(dict(row) for row in cursor.fetchall()) + _markers, _num_records = genotype_markers( + conn, species_id, population_id, offset, limit) + if len(_markers) == 0: + return (tuple(), 0) + + _genoids = tuple(_marker["Id"] for _marker in _markers) + cursor.execute( + _query_template.replace( + "%%PARAMS_STR%%", ",".join(["%s"] * len(_genoids))), + _genoids) + debug_query(cursor, logger) + _records: dict[str, dict] = reduce( + __organise_geno_records__, cursor.fetchall(), {}) + return ( + tuple({ + **_marker, + "data": _records.get( + _marker["Id"], {} + ).get("data", {}) + } for _marker in _markers), + _num_records) def genotype_dataset( @@ -65,7 +153,7 @@ def genotype_dataset( with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute(_query, _params) - debug_query(cursor, app.logger) + debug_query(cursor, logger) result = cursor.fetchone() if bool(result): return dict(result) diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index d991614..454fee7 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,10 +1,18 @@ """Views for the genotypes.""" +import logging +from uuid import uuid4 + from MySQLdb.cursors import DictCursor +from pymonad.either import Left, Right, Either +from gn_libs.requests import request_json from gn_libs.mysqldb import database_connection +from werkzeug.exceptions import UnsupportedMediaType from flask import (flash, request, + jsonify, redirect, Blueprint, + make_response, render_template, current_app as app) @@ -12,114 +20,105 @@ from uploader.flask_extensions import url_for 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.species.models import species_by_id from uploader.monadic_requests import make_either_error_handler -from uploader.request_checks import with_species, with_population from uploader.population.models import population_by_species_and_id +from uploader.request_checks import with_dataset, with_population + from .models import (genotype_markers, + genotype_records, genotype_dataset, save_new_dataset, - genotype_markers_count, genocode_by_population) +logger = logging.getLogger(__name__) genotypesbp = Blueprint("genotypes", __name__) render_template = make_template_renderer("genotypes") -@genotypesbp.route("populations/genotypes", methods=["GET"]) + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes", + methods=["GET", "POST"]) @require_login -def index(): - """Direct entry-point for genotypes.""" +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") +def index(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Entry-point to the genotypes management section.""" with database_connection(app.config["SQL_URI"]) as conn: - if not bool(request.args.get("species_id")): - return render_template("genotypes/index.html", - species=all_species(conn), - activelink="genotypes") + form = request_json() + offset = int(form.get("start", "0")) + number_of_records = int(form.get("length", "10")) + _markers, _total_markers, = genotype_markers( + conn, species["SpeciesId"], population["Id"]) + _genotype_records, _count = genotype_records( + conn, + species["SpeciesId"], + population["Id"], + offset, + number_of_records) + _genotype_records = tuple( + {**_record, "index": _idx} + for _idx, _record + in enumerate(_genotype_records, start=offset+1)) - 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")) + ## Order these correctly + _samples = (tuple() if len(_genotype_records) == 0 + else tuple(_genotype_records[0]["data"].keys())) - species = species_by_id(conn, request.args.get("species_id")) - if not bool(species): - flash(f"Could not find species with ID '{request.args.get('species_id')}'!", - "alert-danger") - return redirect(url_for("species.populations.genotypes.index")) - return redirect(url_for("species.populations.genotypes.select_population", - species_id=species["SpeciesId"])) + if "application/json" in request.headers["Accept"]: + return make_response( + jsonify({ + "genotype_records": _genotype_records, + "total_genotype_records": _count, + "fetched_genotype_records": len(_genotype_records), + "samples_order": _samples, + "draw": int(request.args.get("draw", "0")) + }), 200) + if "text/html" in request.headers["Accept"]: + return render_template( + "genotypes/index.html", + species=species, + population=population, + genocode=genocode_by_population(conn, population["Id"]), + dataset=genotype_dataset( + conn, species["SpeciesId"], population["Id"]), + genotype_records=_genotype_records, + samples=_samples, + activelink="list-genotypes") -@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population", - methods=["GET"]) -@require_login -@with_species(redirect_uri="species.populations.genotypes.index") -def select_population(species: dict, species_id: int):# pylint: disable=[unused-argument] - """Select the population under which the genotypes go.""" - 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!") + raise UnsupportedMediaType("This endpoint can only server HTML or JSON") @genotypesbp.route( - "/<int:species_id>/populations/<int:population_id>/genotypes", + "/<int:species_id>/populations/<int:population_id>/genotypes/<int:dataset_id>/list-markers", methods=["GET"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") -def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] - """List genotype details for species and population.""" +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.index") +def list_markers(species: dict, population: dict, **_kwargs): + """List the markers that exist for this species.""" + args = request.args + offset = int(args.get("start") or 0) with database_connection(app.config["SQL_URI"]) as conn: - return render_template("genotypes/list-genotypes.html", - species=species, - population=population, - genocode=genocode_by_population( - conn, population["Id"]), - total_markers=genotype_markers_count( - conn, species["SpeciesId"]), - dataset=genotype_dataset(conn, - species["SpeciesId"], - population["Id"]), - activelink="list-genotypes") - + markers, total_records = genotype_markers( + conn, + species["SpeciesId"], + population["Id"], + offset=offset, + limit=int(args.get("length") or 0)) + return jsonify({ + **({"draw": int(args.get("draw", "0"))} + if bool(args.get("draw")) + else {}), + "recordsTotal": total_records, + "recordsFiltered": len(markers), + "markers": tuple({**marker, "index": idx} + for idx, marker in + enumerate(markers, start=offset+1)) + }) -@genotypesbp.route( - "/<int:species_id>/populations/<int:population_id>/genotypes/list-markers", - methods=["GET"]) -@require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") -def list_markers( - species: dict, - population: dict, - **kwargs -):# pylint: disable=[unused-argument] - """List a species' genetic markers.""" - with database_connection(app.config["SQL_URI"]) as conn: - start_from = max(safe_int(request.args.get("start_from") or 0), 0) - count = safe_int(request.args.get("count") or 20) - return render_template("genotypes/list-markers.html", - species=species, - population=population, - total_markers=genotype_markers_count( - conn, species["SpeciesId"]), - start_from=start_from, - count=count, - markers=enumerate_sequence( - genotype_markers(conn, - species["SpeciesId"], - offset=start_from, - limit=count), - start=start_from+1), - activelink="list-markers") @genotypesbp.route( "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" @@ -132,14 +131,14 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): species = species_by_id(conn, species_id) if not bool(species): flash("Invalid species provided!", "alert-danger") - return redirect(url_for("species.populations.genotypes.index")) + return redirect(url_for("species.list_species")) population = population_by_species_and_id( conn, species_id, population_id) if not bool(population): flash("Invalid population selected!", "alert-danger") return redirect(url_for( - "species.populations.genotypes.select_population", + "species.populations.list_species_populations", species_id=species_id)) dataset = genotype_dataset(conn, species_id, population_id, dataset_id) @@ -162,25 +161,32 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): "create", methods=["GET", "POST"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """Create a genotype dataset.""" + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-dataset") + with (database_connection(app.config["SQL_URI"]) as conn, conn.cursor(cursorclass=DictCursor) as cursor): - if request.method == "GET": - return render_template("genotypes/create-dataset.html", - species=species, - population=population, - activelink="create-dataset") - - form = request.form - new_dataset = save_new_dataset( - cursor, - population["Id"], - form["geno-dataset-name"], - form["geno-dataset-fullname"], - form["geno-dataset-shortname"]) + + def __save_dataset__() -> Either: + form = request.form + try: + return Right(save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"])) + except Exception:# pylint: disable=[broad-exception-caught] + msg = "Error adding new Genotype dataset to database." + logger.error(msg, exc_info=True) + return Left(Exception(msg)) def __success__(_success): flash("Successfully created genotype dataset.", "alert-success") @@ -189,19 +195,72 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= species_id=species["SpeciesId"], population_id=population["Id"])) - return oauth2_post( - "auth/resource/genotypes/create", - json={ - **dict(request.form), - "species_id": species["SpeciesId"], - "population_id": population["Id"], - "dataset_id": new_dataset["Id"], - "dataset_name": form["geno-dataset-name"], - "dataset_fullname": form["geno-dataset-fullname"], - "dataset_shortname": form["geno-dataset-shortname"], - "public": "on" - } + return __save_dataset__().then( + lambda new_dataset: oauth2_post( + "auth/resource/genotypes/create", + json={ + **dict(request.form), + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": new_dataset["Id"], + "dataset_name": new_dataset["Name"], + "dataset_fullname": new_dataset["FullName"], + "dataset_shortname": new_dataset["ShortName"], + "public": "on" + } + ) ).either( make_either_error_handler( "There was an error creating the genotype dataset."), __success__) + + +def genotype_csv_to_r_qtl2(uploadsdir: Path, csvfile, csv_meta: dict) -> Path: + """Convert given CSV genotype file into the R/qtl2 format.""" + bundlepath = Path(uploadsdir, f"{uuid.uuid4()}.zip".replace("-", "")) + raise NotImplementedError("This is not implemented yet.") + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "<int:dataset_id>/add-records", + methods=["GET", "POST"]) +@require_login +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") +@with_dataset(species_redirect_uri="species.list_species", + population_redirect_uri="species.populations.list_species_populations", + redirect_uri="species.populations.genotypes.index", + dataset_by_id=genotype_dataset) +def add_genotype_records(species: dict, population: dict, dataset: dict, **kwargs): + """Add new Genotype records to the dataset.""" + if request.method == "GET": + return render_template("genotypes/add-genotypes-records-csv.html", + species=species, + population=population, + dataset=dataset, + activelink="add-genotypes-records") + + # request.method is POST from here + # T0D0: Handle direct uploads (i.e. Not via javascript) + form = dict(request.form) # Request comes in as multipart/formdata + + bundlepath = genotype_csv_to_r_qtl2( + # T0D0: Actually, rather than generating the R/qtl2 bundle here, first + # off, do basic check through the data to collect the alleles and other + # necessary information. Also do basic QC. + Path(uploads_dir(app)), + form["uploaded-file"], + csv_meta: { + "sep": form.get("file-separator", ","), + "comment.char": form.get("file-comment-char", "#"), + "na.strings": form.get("file-na", "- NA N/A").split(" ") + }) + + if "application/json" in request.headers.get("Accept"): + return make_response( + jsonify({ + "message": ("Upload successful. Follow the 'redirect-to' URI " + "to continue") + }), + 200) diff --git a/uploader/jobs.py b/uploader/jobs.py index 5968c03..b2de54b 100644 --- a/uploader/jobs.py +++ b/uploader/jobs.py @@ -147,8 +147,8 @@ def job_errors( return take( ( json.loads(error) - for key in rconn.keys(f"{prefix}:{str(job_id)}:*:errors:*") - for error in rconn.lrange(key, 0, -1)), + for key in rconn.keys(f"{prefix}:{str(job_id)}:*:errors:*")# type: ignore[union-attr] + for error in rconn.lrange(key, 0, -1)),# type: ignore[union-attr] count) @@ -160,8 +160,8 @@ def job_files_metadata( """Get the metadata for specific job file.""" return { key.split(":")[-1]: { - **rconn.hgetall(key), + **rconn.hgetall(key),# type: ignore[dict-item] "filetype": key.split(":")[-3] } - for key in rconn.keys(f"{prefix}:{str(job_id)}:*:metadata*") + for key in rconn.keys(f"{prefix}:{str(job_id)}:*:metadata*")# type: ignore[union-attr] } diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py index b94a044..e37816d 100644 --- a/uploader/oauth2/client.py +++ b/uploader/oauth2/client.py @@ -4,7 +4,7 @@ import time import uuid import random from datetime import datetime, timedelta -from urllib.parse import urljoin, urlparse +from urllib.parse import urljoin, urlparse, urlencode import requests from flask import request, current_app as app @@ -18,6 +18,7 @@ from authlib.integrations.requests_client import OAuth2Session from uploader import session import uploader.monadic_requests as mrequests +from uploader.flask_extensions import fetch_flags SCOPE = ("profile group role resource register-client user masquerade " "introspect migrate-data") @@ -157,7 +158,10 @@ def fetch_user_details() -> Either: "user_id": uuid.UUID(usrdets["user_id"]), "name": usrdets["name"], "email": usrdets["email"], - "token": session.user_token()})) + "token": session.user_token(), + "logged_in": session.user_token().either( + lambda _e: False, lambda _t: True) + })) return udets return Right(suser) @@ -173,11 +177,13 @@ def authserver_authorise_uri(): """Build up the authorisation URI.""" req_baseurl = urlparse(request.base_url, scheme=request.scheme) host_uri = f"{req_baseurl.scheme}://{req_baseurl.netloc}/" - return urljoin( - authserver_uri(), - "auth/authorise?response_type=code" - f"&client_id={oauth2_clientid()}" - f"&redirect_uri={urljoin(host_uri, 'oauth2/code')}") + args = { + "response_type": "code", + "client_id": oauth2_clientid(), + "redirect_uri": ( + f"{urljoin(host_uri, 'oauth2/code')}?{urlencode(fetch_flags())}") + } + return f"{urljoin(authserver_uri(), 'auth/authorise')}?{urlencode(args)}" def __no_token__(_err) -> Left: diff --git a/uploader/phenotypes/misc.py b/uploader/phenotypes/misc.py index cbe3b7f..1924c07 100644 --- a/uploader/phenotypes/misc.py +++ b/uploader/phenotypes/misc.py @@ -8,7 +8,7 @@ def phenotypes_data_differences( filedata: tuple[dict, ...], dbdata: tuple[dict, ...] ) -> tuple[dict, ...]: """Compute differences between file data and db data""" - diff = tuple() + diff: tuple[dict, ...] = tuple() for filerow, dbrow in zip( sorted(filedata, key=lambda item: (item["phenotype_id"], item["xref_id"])), sorted(dbdata, key=lambda item: (item["PhenotypeId"], item["xref_id"]))): diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index af06376..3d656d2 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -1,4 +1,6 @@ """Database and utility functions for phenotypes.""" +import time +import random import logging import tempfile from pathlib import Path @@ -6,8 +8,8 @@ from functools import reduce from datetime import datetime from typing import Union, Optional, Iterable -import MySQLdb as mdb -from MySQLdb.cursors import Cursor, DictCursor +from MySQLdb.connections import Connection +from MySQLdb.cursors import Cursor, DictCursor, BaseCursor from gn_libs.mysqldb import debug_query @@ -27,7 +29,7 @@ __PHENO_DATA_TABLES__ = { def datasets_by_population( - conn: mdb.Connection, + conn: Connection, species_id: int, population_id: int ) -> tuple[dict, ...]: @@ -42,7 +44,7 @@ def datasets_by_population( return tuple(dict(row) for row in cursor.fetchall()) -def dataset_by_id(conn: mdb.Connection, +def dataset_by_id(conn: Connection, species_id: int, population_id: int, dataset_id: int) -> dict: @@ -57,7 +59,7 @@ def dataset_by_id(conn: mdb.Connection, return dict(cursor.fetchone()) -def phenotypes_count(conn: mdb.Connection, +def phenotypes_count(conn: Connection, population_id: int, dataset_id: int) -> int: """Count the number of phenotypes in the dataset.""" @@ -85,27 +87,46 @@ def phenotype_publication_data(conn, phenotype_id) -> Optional[dict]: return dict(res) -def dataset_phenotypes(conn: mdb.Connection, - population_id: int, - dataset_id: int, - offset: int = 0, - limit: Optional[int] = None) -> tuple[dict, ...]: +def dataset_phenotypes(# pylint: disable=[too-many-arguments, too-many-positional-arguments] + conn: Connection, + population_id: int, + dataset_id: int, + offset: int = 0, + limit: Optional[int] = None, + xref_ids: tuple[int, ...] = tuple() +) -> tuple[dict, ...]: """Fetch the actual phenotypes.""" - _query = ( - "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode " + _narrow_by_ids = ( + f" AND pxr.Id IN ({', '.join(['%s'] * len(xref_ids))})" + if len(xref_ids) > 0 else "") + _narrow_by_limit = ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "") + _pub_query = ( + "SELECT pub.* " + "FROM PublishXRef AS pxr " + "INNER JOIN Publication AS pub ON pxr.PublicationId=pub.Id " + "WHERE pxr.InbredSetId=%s") + _narrow_by_ids + _pheno_query = (( + "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, pxr.PublicationId, " + "ist.InbredSetCode " "FROM Phenotype AS pheno " "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId " "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id " - "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + ( - f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "") + "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + + _narrow_by_ids + + _narrow_by_limit) with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, (population_id, dataset_id)) + cursor.execute(_pub_query, (population_id,) + xref_ids) debug_query(cursor, logger) - return tuple(dict(row) for row in cursor.fetchall()) + _pubs = {row["Id"]: dict(row) for row in cursor.fetchall()} + cursor.execute(_pheno_query, (population_id, dataset_id) + xref_ids) + debug_query(cursor, logger) + return tuple({**dict(row), "publication": _pubs[row["PublicationId"]]} + for row in cursor.fetchall()) -def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids): +def __phenotype_se__(cursor: BaseCursor, xref_id, dataids_and_strainids): """Fetch standard-error values (if they exist) for a phenotype.""" paramstr = ", ".join(["(%s, %s)"] * len(dataids_and_strainids)) flat = tuple(item for sublist in dataids_and_strainids for item in sublist) @@ -187,7 +208,7 @@ def __merge_pheno_data_and_se__(data, sedata) -> dict: def phenotype_by_id( - conn: mdb.Connection, + conn: Connection, species_id: int, population_id: int, dataset_id: int, @@ -225,7 +246,7 @@ def phenotype_by_id( return None -def phenotypes_data(conn: mdb.Connection, +def phenotypes_data(conn: Connection, population_id: int, dataset_id: int, offset: int = 0, @@ -248,16 +269,16 @@ def phenotypes_data(conn: mdb.Connection, return tuple(dict(row) for row in cursor.fetchall()) -def phenotypes_vector_data( - conn: mdb.Connection, +def phenotypes_vector_data(# pylint: disable=[too-many-arguments, too-many-positional-arguments] + conn: Connection, species_id: int, population_id: int, xref_ids: tuple[int, ...] = tuple(), offset: int = 0, limit: Optional[int] = None -) -> dict[tuple[int, int, int]: dict[str, Union[int,float]]]: +) -> dict[tuple[int, int, int], dict[str, Union[int,float]]]: """Retrieve the vector data values for traits in the database.""" - _params = (species_id, population_id) + _params: tuple[int, ...] = (species_id, population_id) _query = ("SELECT " "Species.Id AS SpeciesId, iset.Id AS InbredSetId, " "pxr.Id AS xref_id, pdata.*, Strain.Id AS StrainId, " @@ -301,7 +322,7 @@ def phenotypes_vector_data( return reduce(__organise__, cursor.fetchall(), {}) -def save_new_dataset(cursor: Cursor, +def save_new_dataset(cursor: BaseCursor, population_id: int, dataset_name: str, dataset_fullname: str, @@ -328,35 +349,6 @@ def save_new_dataset(cursor: Cursor, return {**params, "Id": cursor.lastrowid} -def phenotypes_data_by_ids( - conn: mdb.Connection, - inbred_pheno_xref: dict[str, int] -) -> tuple[dict, ...]: - """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" - _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT " - "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Publication AS pub " - "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " - "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " - "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " - "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " - "INNER JOIN Strain AS str ON pd.StrainId=str.Id " - "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 " - f"WHERE (pxr.InbredSetId, pheno.Id, pxr.Id) IN ({_paramstr}) " - "ORDER BY pheno.Id") - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, tuple(item for row in inbred_pheno_xref - for item in (row["population_id"], - row["phenoid"], - row["xref_id"]))) - debug_query(cursor, logger) - return tuple( - reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values()) - - def __pre_process_phenotype_data__(row): _desc = row.get("description", "") _pre_pub_desc = row.get("pre_publication_description", _desc) @@ -375,13 +367,13 @@ def __pre_process_phenotype_data__(row): def create_new_phenotypes(# pylint: disable=[too-many-locals] - conn: mdb.Connection, + conn: Connection, population_id: int, publication_id: int, phenotypes: Iterable[dict] ) -> tuple[dict, ...]: """Add entirely new phenotypes to the database. WARNING: Not thread-safe.""" - _phenos = tuple() + _phenos: tuple[dict, ...] = tuple() with conn.cursor(cursorclass=DictCursor) as cursor: def make_next_id(idcol, table): cursor.execute(f"SELECT MAX({idcol}) AS last_id FROM {table}") @@ -430,9 +422,10 @@ def create_new_phenotypes(# pylint: disable=[too-many-locals] if len(batch) == 0: break - params, abbrevs = reduce(__build_params_and_prepubabbrevs__, - batch, - (tuple(), tuple())) + params, abbrevs = reduce(#type: ignore[var-annotated] + __build_params_and_prepubabbrevs__, + batch, + (tuple(), tuple())) # Check for uniqueness for all "Pre_publication_description" values abbrevs_paramsstr = ", ".join(["%s"] * len(abbrevs)) _query = ("SELECT PublishXRef.PhenotypeId, Phenotype.* " @@ -502,7 +495,7 @@ def create_new_phenotypes(# pylint: disable=[too-many-locals] def save_phenotypes_data( - conn: mdb.Connection, + conn: Connection, table: str, data: Iterable[dict] ) -> int: @@ -532,7 +525,7 @@ def save_phenotypes_data( def quick_save_phenotypes_data( - conn: mdb.Connection, + conn: Connection, table: str, dataitems: Iterable[dict], tmpdir: Path @@ -562,3 +555,134 @@ def quick_save_phenotypes_data( ")") debug_query(cursor, logger) return _count + + +def __sleep_random__(): + """Sleep a random amount of time chosen from 0.05s to 1s in increments of 0.05""" + time.sleep(random.choice(tuple(i / 20.0 for i in range(1, 21)))) + + +def delete_phenotypes_data( + cursor: BaseCursor, + data_ids: tuple[int, ...] +) -> tuple[int, int, int]: + """Delete numeric data for phenotypes with the given data IDs.""" + if len(data_ids) == 0: + return (0, 0, 0) + + # Loop to handle big deletes i.e. ≥ 10000 rows + _dcount, _secount, _ncount = (0, 0, 0)# Count total rows deleted + while True: + _paramstr = ", ".join(["%s"] * len(data_ids)) + cursor.execute( + "DELETE FROM PublishData " + f"WHERE Id IN ({_paramstr}) " + "ORDER BY Id ASC, StrainId ASC "# Make deletions deterministic + "LIMIT 1000", + data_ids) + _dcount_curr = cursor.rowcount + _dcount += _dcount_curr + + cursor.execute( + "DELETE FROM PublishSE " + f"WHERE DataId IN ({_paramstr}) " + "ORDER BY DataId ASC, StrainId ASC "# Make deletions deterministic + "LIMIT 1000", + data_ids) + _secount_curr = cursor.rowcount + _secount += _secount_curr + + cursor.execute( + "DELETE FROM NStrain " + f"WHERE DataId IN ({_paramstr}) " + "ORDER BY DataId ASC, StrainId ASC "# Make deletions deterministic + "LIMIT 1000", + data_ids) + _ncount_curr = cursor.rowcount + _ncount += _ncount_curr + __sleep_random__() + + if all((_dcount_curr == 0, _secount_curr == 0, _ncount_curr == 0)): + # end loop if there are no more rows to delete. + break + + return (_dcount, _secount, _ncount) + + +def __linked_ids__( + cursor: BaseCursor, + population_id: int, + xref_ids: tuple[int, ...] +) -> tuple[tuple[int, int, int], ...]: + """Retrieve `DataId` values from `PublishXRef` table.""" + _paramstr = ", ".join(["%s"] * len(xref_ids)) + cursor.execute("SELECT PhenotypeId, PublicationId, DataId " + "FROM PublishXRef " + f"WHERE InbredSetId=%s AND Id IN ({_paramstr})", + (population_id,) + xref_ids) + return tuple( + (int(row["PhenotypeId"]), int(row["PublicationId"]), int(row["DataId"])) + for row in cursor.fetchall()) + + +def delete_phenotypes( + conn_or_cursor: Union[Connection, Cursor], + population_id: int, + xref_ids: tuple[int, ...] +) -> tuple[int, int, int, int]: + """Delete phenotypes and all their data.""" + def __delete_phenos__(cursor: BaseCursor, pheno_ids: tuple[int, ...]) -> int: + """Delete data from the `Phenotype` table.""" + _paramstr = ", ".join(["%s"] * len(pheno_ids)) + + _pcount = 0 + while True: + cursor.execute( + "DELETE FROM Phenotype " + f"WHERE Id IN ({_paramstr}) " + "ORDER BY Id " + "LIMIT 1000", + pheno_ids) + _pcount_curr = cursor.rowcount + _pcount += _pcount_curr + __sleep_random__() + if _pcount_curr == 0: + break + + return cursor.rowcount + + def __delete_xrefs__(cursor: BaseCursor) -> int: + _paramstr = ", ".join(["%s"] * len(xref_ids)) + + _xcount = 0 + while True: + cursor.execute( + "DELETE FROM PublishXRef " + f"WHERE InbredSetId=%s AND Id IN ({_paramstr}) " + "ORDER BY Id " + "LIMIT 10000", + (population_id,) + xref_ids) + _xcount_curr = cursor.rowcount + _xcount += _xcount_curr + __sleep_random__() + if _xcount_curr == 0: + break + + return _xcount + + def __with_cursor__(cursor): + _phenoids, _pubids, _dataids = reduce( + lambda acc, curr: (acc[0] + (curr[0],), + acc[1] + (curr[1],), + acc[2] + (curr[2],)), + __linked_ids__(cursor, population_id, xref_ids), + (tuple(), tuple(), tuple())) + __delete_phenos__(cursor, _phenoids) + return (__delete_xrefs__(cursor),) + delete_phenotypes_data( + cursor, _dataids) + + if isinstance(conn_or_cursor, BaseCursor): + return __with_cursor__(conn_or_cursor) + + with conn_or_cursor.cursor(cursorclass=DictCursor) as cursor: + return __with_cursor__(cursor) diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 5b32fc0..85d6357 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,4 +1,6 @@ """Views handling ('classical') phenotypes."""# pylint: disable=[too-many-lines] +import io +import csv import sys import uuid import json @@ -6,7 +8,7 @@ import logging from typing import Any from pathlib import Path from zipfile import ZipFile -from functools import wraps, reduce +from functools import reduce from urllib.parse import urljoin, urlparse, ParseResult, urlunparse, urlencode import datetime @@ -21,22 +23,22 @@ from gn_libs import jobs as gnlibs_jobs from gn_libs.jobs.jobs import JobNotFound from gn_libs.mysqldb import database_connection +from werkzeug.datastructures import Headers from flask import (flash, request, jsonify, redirect, Blueprint, - current_app as app) + current_app as app, + Response as FlaskResponse) from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe - -from uploader.sui import sui_template - from uploader import jobs from uploader import session from uploader.files import save_file +from uploader.configutils import uploads_dir from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post @@ -49,7 +51,7 @@ from uploader.datautils import safe_int, enumerate_sequence from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.publications.models import fetch_publication_by_id -from uploader.request_checks import with_species, with_population +from uploader.request_checks import with_species, with_dataset, with_population from uploader.input_validation import (encode_errors, decode_errors, is_valid_representative_name) @@ -134,45 +136,6 @@ def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[ activelink="list-datasets") -def with_dataset( - species_redirect_uri: str, - population_redirect_uri: str, - redirect_uri: str -): - """Ensure the dataset actually exists.""" - def __decorator__(func): - @wraps(func) - @with_population(species_redirect_uri, population_redirect_uri) - def __with_dataset__(**kwargs): - try: - _spcid = int(kwargs["species_id"]) - _popid = int(kwargs["population_id"]) - _dsetid = int(kwargs.get("dataset_id")) - select_dataset_uri = redirect(url_for( - redirect_uri, species_id=_spcid, population_id=_popid)) - if not bool(_dsetid): - flash("You need to select a valid 'dataset_id' value.", - "alert-danger") - return select_dataset_uri - with database_connection(app.config["SQL_URI"]) as conn: - dataset = dataset_by_id(conn, _spcid, _popid, _dsetid) - if not bool(dataset): - flash("You must select a valid dataset.", - "alert-danger") - return select_dataset_uri - except ValueError as _verr: - app.logger.debug( - "Exception converting 'dataset_id' to integer: %s", - kwargs.get("dataset_id"), - exc_info=True) - flash("Expected 'dataset_id' value to be an integer." - "alert-danger") - return select_dataset_uri - return func(dataset=dataset, **kwargs) - return __with_dataset__ - return __decorator__ - - @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/view", @@ -181,16 +144,11 @@ def with_dataset( @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def view_dataset(# pylint: disable=[unused-argument] species: dict, population: dict, dataset: dict, **kwargs): """View a specific dataset""" - if bool(request.args.get("streamlined_ui")): - # Redirect back to the "View Population" page for the time being. - return redirect(url_for("species.populations.view_population", - species_id=species["SpeciesId"], - population_id=population["Id"])) - with database_connection(app.config["SQL_URI"]) as conn: dataset = dataset_by_id( conn, species["SpeciesId"], population["Id"], dataset["Id"]) @@ -227,7 +185,8 @@ def view_dataset(# pylint: disable=[unused-argument] @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def view_phenotype(# pylint: disable=[unused-argument] species: dict, population: dict, @@ -321,6 +280,11 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= dataset_shortname = ( form["dataset-shortname"] or form["dataset-name"]).strip() _pheno_dataset = save_new_dataset( + # It's not necessary to update the authorisation server to register + # new phenotype resource here, since each phenotype trait can, in + # theory, have its own access control allowing/disallowing access to + # it. In practice, however, we tend to gather multiple traits into a + # single resource for access control. cursor, population["Id"], form["dataset-name"].strip(), @@ -338,7 +302,7 @@ def process_phenotypes_rqtl2_bundle(error_uri): try: ## Handle huge files here... phenobundle = save_file(request.files["phenotypes-bundle"], - Path(app.config["UPLOAD_FOLDER"])) + uploads_dir(app)) rqc.validate_bundle(phenobundle) return phenobundle except AssertionError as _aerr: @@ -361,7 +325,7 @@ def process_phenotypes_individual_files(error_uri): "comment.char": form["file-comment-character"], "na.strings": form["file-na"].split(" "), } - bundlepath = Path(app.config["UPLOAD_FOLDER"], + bundlepath = Path(uploads_dir(app), f"{str(uuid.uuid4()).replace('-', '')}.zip") with ZipFile(bundlepath,mode="w") as zfile: for rqtlkey, formkey, _type in ( @@ -379,7 +343,7 @@ def process_phenotypes_individual_files(error_uri): # Chunked upload of large files was used filedata = json.loads(form[formkey]) zfile.write( - Path(app.config["UPLOAD_FOLDER"], filedata["uploaded-file"]), + Path(uploads_dir(app), filedata["uploaded-file"]), arcname=filedata["original-name"]) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]] else: @@ -391,9 +355,9 @@ def process_phenotypes_individual_files(error_uri): return error_uri filepath = save_file( - _sentfile, Path(app.config["UPLOAD_FOLDER"]), hashed=False) + _sentfile, uploads_dir(app), hashed=False) zfile.write( - Path(app.config["UPLOAD_FOLDER"], filepath), + Path(uploads_dir(app), filepath), arcname=filepath.name) cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name] @@ -411,7 +375,8 @@ def process_phenotypes_individual_files(error_uri): @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) 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" @@ -426,9 +391,9 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p if request.method == "GET": today = datetime.date.today() return render_template( - sui_template("phenotypes/add-phenotypes-with-rqtl2-bundle.html" - if use_bundle - else f"phenotypes/add-phenotypes-raw-files.html"), + ("phenotypes/add-phenotypes-with-rqtl2-bundle.html" + if use_bundle + else "phenotypes/add-phenotypes-raw-files.html"), species=species, population=population, dataset=dataset, @@ -473,7 +438,7 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p **({"publicationid": request.form["publication-id"]} if request.form.get("publication-id") else {})})}), _redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") + f"{uploads_dir(app)}/job_errors") app.logger.debug("JOB DETAILS: %s", _job) jobstatusuri = url_for("species.populations.phenotypes.job_status", @@ -500,7 +465,8 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def job_status( species: dict, population: dict, @@ -515,7 +481,7 @@ def job_status( except jobs.JobNotFound as _jnf: job = None - return render_template(sui_template("phenotypes/job-status.html"), + return render_template("phenotypes/job-status.html", species=species, population=population, dataset=dataset, @@ -530,13 +496,74 @@ def job_status( @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/job/<uuid:job_id>/download-errors", + 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", + dataset_by_id=dataset_by_id) +def download_errors( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs):# pylint: disable=[unused-argument] + """Download the list of errors as a CSV file.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + _prefix_ = jobs.jobsnamespace() + _jobid_ = job['jobid'] + def __generate_chunks__(): + _errors_ = ( + json.loads(error) + for key in rconn.keys( + f"{_prefix_}:{str(_jobid_)}:*:errors:*") + for error in rconn.lrange(key, 0, -1)) + _chunk_no_ = 0 + _all_errors_printed_ = False + while not _all_errors_printed_: + _chunk_ = [] + try: + for _ in range(0, 1000): + _chunk_.append(next(_errors_)) + except StopIteration: + _all_errors_printed_ = True + if len(_chunk_) <= 0: + raise + + _out_ = io.StringIO() + _writer_ = csv.DictWriter(_out_, fieldnames=tuple(_chunk_[0].keys())) + if _chunk_no_ == 0: + _writer_.writeheader() + _writer_.writerows(_chunk_) + _chunk_no_ += 1 + yield _out_.getvalue() + if _all_errors_printed_: + return + + headers = Headers() + headers.set("Content-Disposition", + "attachment", + filename=f"{job['job-type']}_{job['jobid']}.csv") + return FlaskResponse( + __generate_chunks__(), mimetype="text/csv", headers=headers) + except jobs.JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/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") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def review_job_data( species: dict, population: dict, @@ -595,7 +622,7 @@ def review_job_data( for filetype,meta in metadata.items() } _job_metadata = json.loads(job["job-metadata"]) - return render_template(sui_template("phenotypes/review-job-data.html"), + return render_template("phenotypes/review-job-data.html", species=species, population=population, dataset=dataset, @@ -607,6 +634,8 @@ def review_job_data( conn, int(_job_metadata["publicationid"])) if _job_metadata.get("publicationid") else None), + user=session.user_details(), + timestamp=datetime.datetime.now().isoformat(), activelink="add-phenotypes") @@ -620,6 +649,12 @@ def load_phenotypes_success_handler(job): job_id=job["job_id"])) +def proceed_to_job_status(job): + """A generic 'job success' handler for asynchronous phenotype jobs.""" + app.logger.debug("The new job: %s", job) + return redirect(url_for("background-jobs.job_status", job_id=job["job_id"])) + + @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/load-data-to-database", @@ -628,7 +663,8 @@ def load_phenotypes_success_handler(job): @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def load_data_to_database( species: dict, population: dict, @@ -662,11 +698,6 @@ def load_data_to_database( def __handle_error__(resp): return render_template("http-error.html", *resp.json()) - def __handle_success__(load_job): - app.logger.debug("The phenotypes loading job: %s", load_job) - return redirect(url_for( - "background-jobs.job_status", job_id=load_job["job_id"])) - return request_token( token_uri=urljoin(oauth2client.authserver_uri(), "auth/token"), @@ -685,18 +716,25 @@ def load_data_to_database( "publication_id": _meta["publicationid"], "authserver": oauth2client.authserver_uri(), "token": token["access_token"], + "dataname": request.form["data_name"].strip(), "success_handler": ( "uploader.phenotypes.views" - ".load_phenotypes_success_handler") - }) + ".load_phenotypes_success_handler"), + **{ + key: request.form[key] + for key in ("data_description",) + if key in request.form.keys() + } + }, + external_id=session.logged_in_user_id()) ).then( lambda job: gnlibs_jobs.launch_job( job, _jobs_db, - Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), + Path(f"{uploads_dir(app)}/job_errors"), worker_manager="gn_libs.jobs.launcher", loglevel=_loglevel) - ).either(__handle_error__, __handle_success__) + ).either(__handle_error__, proceed_to_job_status) def update_phenotype_metadata(conn, metadata: dict): @@ -811,7 +849,7 @@ def update_phenotype_data(conn, data: dict): } }) - values, serrs, counts = tuple( + values, serrs, counts = tuple(# type: ignore[var-annotated] tuple({ "data_id": row[0].split("::")[0], "strain_id": row[0].split("::")[1], @@ -839,7 +877,8 @@ def update_phenotype_data(conn, data: dict): @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def edit_phenotype_data(# pylint: disable=[unused-argument] species: dict, population: dict, @@ -959,7 +998,8 @@ def edit_phenotype_data(# pylint: disable=[unused-argument] @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def load_data_success( species: dict, population: dict, @@ -986,7 +1026,7 @@ def load_data_success( (_publication["Title"] or "")) if item != "") return render_template( - sui_template("phenotypes/load-phenotypes-success.html"), + "phenotypes/load-phenotypes-success.html", species=species, population=population, dataset=dataset, @@ -1025,7 +1065,8 @@ def load_data_success( @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def recompute_means(# pylint: disable=[unused-argument] species: dict, population: dict, @@ -1068,9 +1109,10 @@ def recompute_means(# pylint: disable=[unused-argument] "success_handler": ( "uploader.phenotypes.views." "recompute_phenotype_means_success_handler") - }), + }, + external_id=session.logged_in_user_id()), _jobs_db, - Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), + Path(f"{uploads_dir(app)}/job_errors"), worker_manager="gn_libs.jobs.launcher", loglevel=_loglevel) return redirect(url_for("background-jobs.job_status", @@ -1078,6 +1120,7 @@ def recompute_means(# pylint: disable=[unused-argument] def return_to_dataset_view_handler(job, msg: str): + """Handler for background jobs: Returns to `View Dataset` page.""" flash(msg, "alert alert-success") return redirect(url_for( "species.populations.phenotypes.view_dataset", @@ -1099,7 +1142,8 @@ def recompute_phenotype_means_success_handler(job): @with_dataset( species_redirect_uri="species.populations.phenotypes.index", population_redirect_uri="species.populations.phenotypes.select_population", - redirect_uri="species.populations.phenotypes.list_datasets") + redirect_uri="species.populations.phenotypes.list_datasets", + dataset_by_id=dataset_by_id) def rerun_qtlreaper(# pylint: disable=[unused-argument] species: dict, population: dict, @@ -1111,7 +1155,7 @@ def rerun_qtlreaper(# pylint: disable=[unused-argument] _job_id = uuid.uuid4() _loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower() - _workingdir = Path(app.config["TEMPORARY_DIRECTORY"]).joinpath("qtlreaper") + _workingdir = Path(app.config["SCRATCH_DIRECTORY"]).joinpath("qtlreaper") _workingdir.mkdir(exist_ok=True) command = [ sys.executable, @@ -1146,9 +1190,10 @@ def rerun_qtlreaper(# pylint: disable=[unused-argument] "success_handler": ( "uploader.phenotypes.views." "rerun_qtlreaper_success_handler") - }), + }, + external_id=session.logged_in_user_id()), _jobs_db, - Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"), + Path(f"{uploads_dir(app)}/job_errors"), worker_manager="gn_libs.jobs.launcher", loglevel=_loglevel) return redirect(url_for("background-jobs.job_status", @@ -1160,3 +1205,120 @@ def rerun_qtlreaper(# pylint: disable=[unused-argument] def rerun_qtlreaper_success_handler(job): """Handle success (re)running QTLReaper script.""" return return_to_dataset_view_handler(job, "QTLReaper ran successfully!") + + +def delete_phenotypes_success_handler(job): + """Handle success running the 'delete-phenotypes' script.""" + return return_to_dataset_view_handler( + job, "Phenotypes deleted successfully.") + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/delete", + 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", + dataset_by_id=dataset_by_id) +def delete_phenotypes(# pylint: disable=[unused-argument, too-many-locals] + species: dict, + population: dict, + dataset: dict, + **kwargs +): + """Delete the specified phenotype data.""" + _dataset_page = redirect(url_for( + "species.populations.phenotypes.view_dataset", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"])) + + def __handle_error__(resp): + flash( + "Error retrieving authorisation token. Phenotype deletion " + "failed. Please try again later.", + "alert alert-danger") + return _dataset_page + + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + with (database_connection(app.config["SQL_URI"]) as conn, + sqlite3.connection(_jobs_db) as jobsconn): + form = request.form + xref_ids = tuple(int(item) for item in set(form.getlist("xref_ids"))) + + match form.get("action"): + case "cancel": + return redirect(url_for( + "species.populations.phenotypes.view_dataset", + species_id=species["SpeciesId"], + population_id=population["Id"], + dataset_id=dataset["Id"])) + case "delete": + _loglevel = logging.getLevelName( + app.logger.getEffectiveLevel()).lower() + if form.get("confirm_delete_all_phenotypes", "") == "on": + _cmd = ["--delete-all"] + else: + # setup phenotypes xref_ids file + _xref_ids_file = Path( + app.config["SCRATCH_DIRECTORY"], + f"delete-phenotypes-{uuid.uuid4()}.txt") + with _xref_ids_file.open(mode="w", encoding="utf8") as ptr: + ptr.write("\n".join(str(_id) for _id in xref_ids)) + + _cmd = ["--xref_ids_file", str(_xref_ids_file)] + + _job_id = uuid.uuid4() + return request_token( + token_uri=urljoin( + oauth2client.authserver_uri(), "auth/token"), + user_id=session.user_details()["user_id"] + ).then( + lambda token: gnlibs_jobs.initialise_job( + jobsconn, + _job_id, + [ + sys.executable, + "-u", + "-m", + "scripts.phenotypes.delete_phenotypes", + "--log-level", _loglevel, + app.config["SQL_URI"], + str(species["SpeciesId"]), + str(population["Id"]), + str(dataset["Id"]), + app.config["AUTH_SERVER_URL"], + token["access_token"]] + _cmd, + "delete-phenotypes", + extra_meta={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "success_handler": ( + "uploader.phenotypes.views." + "delete_phenotypes_success_handler") + }, + external_id=session.logged_in_user_id()) + ).then( + lambda _job: gnlibs_jobs.launch_job( + _job, + _jobs_db, + Path(f"{uploads_dir(app)}/job_errors"), + worker_manager="gn_libs.jobs.launcher", + loglevel=_loglevel) + ).either(__handle_error__, proceed_to_job_status) + case _: + _phenos: tuple[dict, ...] = tuple() + if len(xref_ids) > 0: + _phenos = dataset_phenotypes( + conn, population["Id"], dataset["Id"], xref_ids=xref_ids) + + return render_template( + "phenotypes/confirm-delete-phenotypes.html", + species=species, + population=population, + dataset=dataset, + phenotypes=_phenos) diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py index 97d4854..bb5066e 100644 --- a/uploader/population/rqtl2.py +++ b/uploader/population/rqtl2.py @@ -134,7 +134,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): try: app.logger.debug("Files in the form: %s", request.files) the_file = save_file(request.files["rqtl2_bundle_file"], - Path(app.config["UPLOAD_FOLDER"])) + Path(app.config["UPLOADS_DIRECTORY"])) except AssertionError: app.logger.debug(traceback.format_exc()) flash("Please provide a valid R/qtl2 zip bundle.", @@ -185,7 +185,7 @@ def trigger_rqtl2_bundle_qc( "rqtl2-bundle-file": str(rqtl2bundle.absolute()), "original-filename": originalfilename})}), redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") + f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return jobid @@ -895,7 +895,7 @@ def confirm_bundle_details(species_id: int, population_id: int): }) }), redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") + f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return redirect(url_for("expression-data.rqtl2.rqtl2_processing_status", jobid=jobid)) diff --git a/uploader/population/views.py b/uploader/population/views.py index a6e2358..795ce81 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -11,8 +11,6 @@ from flask import (flash, Blueprint, current_app as app) -from uploader.sui import sui_template - from uploader.samples.views import samplesbp from uploader.flask_extensions import url_for from uploader.oauth2.client import oauth2_post @@ -157,7 +155,7 @@ def create_population(species_id: int): "FullName": population_fullname, "InbredSetCode": request.form.get("population_code") or None, "Description": request.form.get("population_description") or None, - "Family": request.form.get("population_family").strip() or None, + "Family": request.form.get("population_family", "").strip() or None, "MappingMethodId": request.form.get("population_mapping_method_id"), "GeneticType": request.form.get("population_genetic_type") or None }) @@ -244,5 +242,4 @@ def view_population(species_id: int, population_id: int): dataset_phenotypes(conn, population["Id"], _dataset["Id"])) } - return render_template(sui_template("populations/view-population.html"), - **_kwargs) + return render_template("populations/view-population.html", **_kwargs) diff --git a/uploader/publications/datatables.py b/uploader/publications/datatables.py index e07fafd..8b3d4a0 100644 --- a/uploader/publications/datatables.py +++ b/uploader/publications/datatables.py @@ -13,7 +13,7 @@ def fetch_publications( search: Optional[str] = None, offset: int = 0, limit: int = -1 -) -> tuple[dict, int, int, int]: +) -> tuple[tuple[dict, ...], int, int, int]: """Fetch publications from the database.""" _query = "SELECT * FROM Publication" _count_query = "SELECT COUNT(*) FROM Publication" diff --git a/uploader/publications/misc.py b/uploader/publications/misc.py index fca6f71..f0ff9c7 100644 --- a/uploader/publications/misc.py +++ b/uploader/publications/misc.py @@ -4,10 +4,10 @@ def publications_differences( filedata: tuple[dict, ...], dbdata: tuple[dict, ...], - pubmedid2pubidmap: tuple[dict, ...] + pubmedid2pubidmap: dict[int, int] ) -> tuple[dict, ...]: """Compute the differences between file data and db data""" - diff = tuple() + diff: tuple[dict, ...] = tuple() for filerow, dbrow in zip( sorted(filedata, key=lambda item: ( item["phenotype_id"], item["xref_id"])), diff --git a/uploader/publications/models.py b/uploader/publications/models.py index dcfa02b..d913144 100644 --- a/uploader/publications/models.py +++ b/uploader/publications/models.py @@ -101,6 +101,20 @@ def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict: return dict(_res) if _res else {} +def fetch_publications_by_ids( + conn: Connection, publications_ids: tuple[int, ...] +) -> tuple[dict, ...]: + """Fetch publications with the given IDs.""" + if len(publications_ids) == 0: + return tuple() + + with conn.cursor(cursorclass=DictCursor) as cursor: + paramstr = ", ".join(["%s"] * len(publications_ids)) + cursor.execute(f"SELECT * FROM Publication WHERE Id IN ({paramstr})", + tuple(publications_ids)) + return tuple(dict(row) for row in cursor.fetchall()) + + def fetch_publication_phenotypes( conn: Connection, publication_id: int) -> Iterable[dict]: """Fetch all phenotypes linked to this publication.""" diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py index 2531c4a..15bf701 100644 --- a/uploader/publications/pubmed.py +++ b/uploader/publications/pubmed.py @@ -1,5 +1,6 @@ """Module to interact with NCBI's PubMed""" import logging +from typing import Optional import requests from lxml import etree @@ -40,7 +41,7 @@ def __pages__(pagination: etree.Element) -> str: )) if start is not None else "" -def __abstract__(article: etree.Element) -> str: +def __abstract__(article: etree.Element) -> Optional[str]: abstract = article.find("Abstract/AbstractText") return abstract.text if abstract is not None else None diff --git a/uploader/publications/views.py b/uploader/publications/views.py index 4ec832f..89e9f5d 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -1,5 +1,6 @@ """Endpoints for publications""" import json +import datetime from gn_libs.mysqldb import database_connection from flask import ( @@ -82,13 +83,24 @@ def view_publication(publication_id: int): @require_login def create_publication(): """Create a new publication.""" + _get_args = { + key: request.args[key] + for key in ("species_id", "population_id", "dataset_id", "return_to") + if bool(request.args.get(key)) + } + if request.method == "GET": - return render_template("publications/create-publication.html") + now = datetime.datetime.now() + return render_template( + "publications/create-publication.html", + get_args=_get_args, + current_year=now.year, + current_month=now.strftime("%B")) form = request.form authors = form.get("publication-authors").encode("utf8") if authors is None or authors == "": flash("The publication's author(s) MUST be provided!", "alert alert-danger") - return redirect(url_for("publications.create", **request.args)) + return redirect(url_for("publications.create")) with database_connection(app.config["SQL_URI"]) as conn: publications = create_new_publications(conn, ({ @@ -106,7 +118,7 @@ def create_publication(): return redirect(url_for( request.args.get("return_to") or "publications.view_publication", publication_id=publications[0]["publication_id"], - **request.args)) + **_get_args)) flash("Publication creation failed!", "alert alert-danger") app.logger.debug("Failed to create the new publication.", exc_info=True) @@ -130,14 +142,14 @@ def edit_publication(publication_id: int): _pub = update_publications(conn, ({ "publication_id": publication_id, "pubmed_id": form.get("pubmed-id") or None, - "abstract": form.get("publication-abstract").encode("utf8") or None, - "authors": form.get("publication-authors").encode("utf8"), - "title": form.get("publication-title").encode("utf8") or None, - "journal": form.get("publication-journal").encode("utf8") or None, - "volume": form.get("publication-volume").encode("utf8") or None, - "pages": form.get("publication-pages").encode("utf8") or None, + "abstract": (form.get("publication-abstract") or "").encode("utf8") or None, + "authors": (form.get("publication-authors") or "").encode("utf8"), + "title": (form.get("publication-title") or "").encode("utf8") or None, + "journal": (form.get("publication-journal") or "").encode("utf8") or None, + "volume": (form.get("publication-volume") or "").encode("utf8") or None, + "pages": (form.get("publication-pages") or "").encode("utf8") or None, "month": (form.get("publication-month") or "").encode("utf8").capitalize() or None, - "year": form.get("publication-year").encode("utf8") or None + "year": (form.get("publication-year") or "").encode("utf8") or None },)) if not _pub: @@ -171,7 +183,8 @@ def delete_publication(publication_id: int): flash("Cannot delete publication with linked phenotypes!", "alert-warning") return redirect(url_for( - "publications.view_publication", publication_id=publication_id)) + "publications.view_publication", + publication_id=publication_id)) if request.method == "GET": return render_template( @@ -182,4 +195,4 @@ def delete_publication(publication_id: int): delete_publications(conn, (publication,)) flash("Deleted the publication successfully.", "alert-success") - return render_template("publications/delete-publication-success.html") + return redirect(url_for("publications.index")) diff --git a/uploader/request_checks.py b/uploader/request_checks.py index f1d8027..84935f9 100644 --- a/uploader/request_checks.py +++ b/uploader/request_checks.py @@ -2,14 +2,20 @@ These are useful for reusability, and hence maintainability of the code. """ +import logging + +from typing import Callable from functools import wraps -from gn_libs.mysqldb import database_connection +from gn_libs.mysqldb import Connection, database_connection from flask import flash, url_for, redirect, current_app as app from uploader.species.models import species_by_id from uploader.population.models import population_by_species_and_id +logger = logging.getLogger(__name__) + + def with_species(redirect_uri: str): """Ensure the species actually exists.""" def __decorator__(function): @@ -28,7 +34,7 @@ def with_species(redirect_uri: str): "alert-danger") return redirect(url_for(redirect_uri)) except ValueError as _verr: - app.logger.debug( + logger.debug( "Exception converting value to integer: %s", kwargs.get("species_id"), exc_info=True) @@ -63,7 +69,7 @@ def with_population(species_redirect_uri: str, redirect_uri: str): "alert-danger") return select_population_uri except ValueError as _verr: - app.logger.debug( + logger.debug( "Exception converting value to integer: %s", kwargs.get("population_id"), exc_info=True) @@ -73,3 +79,45 @@ def with_population(species_redirect_uri: str, redirect_uri: str): return function(**{**kwargs, "population": population}) return __with_population__ return __decorator__ + + +def with_dataset( + species_redirect_uri: str, + population_redirect_uri: str, + redirect_uri: str, + dataset_by_id: Callable[ + [Connection, int, int, int], + dict] +): + """Ensure the dataset actually exists.""" + def __decorator__(func): + @wraps(func) + @with_population(species_redirect_uri, population_redirect_uri) + def __with_dataset__(**kwargs): + try: + _spcid = int(kwargs["species_id"]) + _popid = int(kwargs["population_id"]) + _dsetid = int(kwargs.get("dataset_id")) + select_dataset_uri = redirect(url_for( + redirect_uri, species_id=_spcid, population_id=_popid)) + if not bool(_dsetid): + flash("You need to select a valid 'dataset_id' value.", + "alert-danger") + return select_dataset_uri + with database_connection(app.config["SQL_URI"]) as conn: + dataset = dataset_by_id(conn, _spcid, _popid, _dsetid) + if not bool(dataset): + flash("You must select a valid dataset.", + "alert-danger") + return select_dataset_uri + except ValueError as _verr: + logger.debug( + "Exception converting 'dataset_id' to integer: %s", + kwargs.get("dataset_id"), + exc_info=True) + flash("Expected 'dataset_id' value to be an integer." + "alert-danger") + return select_dataset_uri + return func(**{**kwargs, "dataset": dataset}) + return __with_dataset__ + return __decorator__ diff --git a/uploader/route_utils.py b/uploader/route_utils.py index 4449475..426d7eb 100644 --- a/uploader/route_utils.py +++ b/uploader/route_utils.py @@ -56,22 +56,24 @@ def generic_select_population( def redirect_to_next(default: dict): """Redirect to the next uri if specified, else redirect to default.""" assert "uri" in default, "You must provide at least the 'uri' value." - try: - next_page = base64_decode_to_dict(request.args.get("next")) - _uri = next_page["uri"] - next_page.pop("uri") - return redirect(url_for(_uri, **next_page)) - except (TypeError, JSONDecodeError) as _err: - logger.debug("We could not decode the next value '%s'", - next_page, - exc_info=True) + _next = request.args.get("next") or "" + if bool(_next): + try: + next_page = base64_decode_to_dict(_next) + _uri = next_page["uri"] + next_page.pop("uri") + return redirect(url_for(_uri, **next_page)) + except (TypeError, JSONDecodeError) as _err: + logger.debug("We could not decode the next value '%s'", + next_page, + exc_info=True) return redirect(url_for( default["uri"], **{key:value for key,value in default.items() if key != "uri"})) -def build_next_argument(uri: str, **kwargs) -> str: +def build_next_argument(uri: str, **kwargs) -> bytes: """Build the `next` URI argument from provided details.""" dumps_keywords = ( "skipkeys", "ensure_ascii", "check_circular", "allow_nan", "cls", diff --git a/uploader/samples/views.py b/uploader/samples/views.py index f8baf7e..2a09f8e 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -1,17 +1,19 @@ """Code regarding samples""" -import os import sys import uuid +import logging from pathlib import Path -from redis import Redis from flask import (flash, request, redirect, Blueprint, current_app as app) -from uploader import jobs +from gn_libs import jobs +from gn_libs import sqlite3 + +from uploader import session from uploader.files import save_file from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer @@ -23,8 +25,7 @@ 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) + database_connection) from .models import samples_by_species_and_population @@ -96,22 +97,6 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u activelink="list-samples") -def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments] - speciesid: int, - populationid: int, - samplesfile: Path, - separator: str, - firstlineheading: bool, - quotechar: str): - """Define the async command to run the actual samples data upload.""" - return [ - sys.executable, "-m", "scripts.insert_samples", app.config["SQL_URI"], - str(speciesid), str(populationid), str(samplesfile.absolute()), - separator, f"--redisuri={app.config['REDIS_URL']}", - f"--quotechar={quotechar}" - ] + (["--firstlineheading"] if firstlineheading else []) - - @samplesbp.route("<int:species_id>/populations/<int:population_id>/upload-samples", methods=["GET", "POST"]) @require_login @@ -153,7 +138,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma try: samples_file = save_file(request.files["samples_file"], - Path(app.config["UPLOAD_FOLDER"])) + Path(app.config["UPLOADS_DIRECTORY"])) except AssertionError: flash("You need to provide a file with the samples data.", "alert-error") @@ -170,102 +155,50 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma quotechar = (request.form.get("field_delimiter", '"') or '"') - redisuri = app.config["REDIS_URL"] - with Redis.from_url(redisuri, decode_responses=True) as rconn: - #T0DO: Add a QC step here — what do we check? - # 1. Does any sample in the uploaded file exist within the database? - # If yes, what is/are its/their species and population? - # 2. If yes 1. above, provide error with notes on which species and - # populations already own the samples. - the_job = jobs.launch_job( + _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + with sqlite3.connection(_jobs_db) as conn: + job = jobs.launch_job( jobs.initialise_job( - rconn, - jobs.jobsnamespace(), + conn, str(uuid.uuid4()), - build_sample_upload_job( - species["SpeciesId"], - population["InbredSetId"], - samples_file, + [ + sys.executable, "-m", "scripts.insert_samples", + app.config["SQL_URI"], + str(species["SpeciesId"]), + str(population["InbredSetId"]), + str(samples_file.absolute()), separator, - firstlineheading, - quotechar), + f"--quotechar={quotechar}" + ] + (["--firstlineheading"] if firstlineheading else []), "samples_upload", - app.config["JOBS_TTL_SECONDS"], - {"job_name": f"Samples Upload: {samples_file.name}"}), - redisuri, - f"{app.config['UPLOAD_FOLDER']}/job_errors") - return redirect(url_for( - "species.populations.samples.upload_status", - species_id=species_id, - population_id=population_id, - job_id=the_job["jobid"])) - - -@samplesbp.route("<int:species_id>/populations/<int:population_id>/" - "upload-samples/status/<uuid:job_id>", - methods=["GET"]) -@require_login -@with_population(species_redirect_uri="species.populations.samples.index", - redirect_uri="species.populations.samples.select_population") -def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] - """Check on the status of a samples upload job.""" - job = with_redis_connection(lambda rconn: jobs.job( - rconn, jobs.jobsnamespace(), job_id)) - if job: - status = job["status"] - if status == "success": - return render_template("samples/upload-success.html", - job=job, - species=species, - population=population,) - - if status == "error": - return redirect(url_for( - "species.populations.samples.upload_failure", - species_id=species["SpeciesId"], - population_id=population["Id"], - job_id=job_id)) - - error_filename = Path(jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) - if error_filename.exists(): - stat = os.stat(error_filename) - if stat.st_size > 0: - return redirect(url_for( - "samples.upload_failure", job_id=job_id)) - - return render_template("samples/upload-progress.html", - species=species, - population=population, - job=job) # maybe also handle this? - - return render_template("no_such_job.html", - job_id=job_id, - species=species, - population=population), 400 - - -@samplesbp.route("<int:species_id>/populations/<int:population_id>/" - "upload-samples/failure/<uuid:job_id>", - methods=["GET"]) -@require_login -@with_population(species_redirect_uri="species.populations.samples.index", - redirect_uri="species.populations.samples.select_population") -def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] - """Display the errors of the samples upload failure.""" - job = with_redis_connection(lambda rconn: jobs.job( - rconn, jobs.jobsnamespace(), job_id)) - if not bool(job): - return render_template("no_such_job.html", job_id=job_id), 400 - - error_filename = Path(jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) - if error_filename.exists(): - stat = os.stat(error_filename) - if stat.st_size > 0: - return render_template("worker_failure.html", job_id=job_id) - - return render_template("samples/upload-failure.html", - species=species, - population=population, - job=job) + extra_meta={ + "job_name": f"Samples Upload: {samples_file.name}", + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "success_handler": ( + "uploader.samples.views.samples_upload_success_handler") + }, + external_id=session.logged_in_user_id()), + _jobs_db, + Path(f"{app.config['UPLOADS_DIRECTORY']}/job_errors").absolute(), + loglevel=logging.getLevelName( + app.logger.getEffectiveLevel()).lower()) + return redirect( + url_for("background-jobs.job_status", job_id=job["job_id"])) + + +def samples_upload_success_handler(job): + """Handler for background jobs: Successful upload of samples""" + return return_to_samples_list_view_handler( + job, "Samples uploaded successfully.") + + +def return_to_samples_list_view_handler(job, msg): + """Handler for background jobs: Return to list_samples page.""" + flash(msg, "alert alert-success") + return redirect(url_for( + "species.populations.samples." + "list_samples", + species_id=job["metadata"]["species_id"], + population_id=job["metadata"]["population_id"], + job_id=job["job_id"])) diff --git a/uploader/session.py b/uploader/session.py index 5af5827..9872ceb 100644 --- a/uploader/session.py +++ b/uploader/session.py @@ -1,12 +1,15 @@ """Deal with user sessions""" +import logging from uuid import UUID, uuid4 from datetime import datetime from typing import Any, Optional, TypedDict +from flask import session from authlib.jose import KeySet -from flask import request, session from pymonad.either import Left, Right, Either +logger = logging.getLogger(__name__) + class UserDetails(TypedDict): """Session information relating specifically to the user.""" @@ -22,8 +25,6 @@ class SessionInfo(TypedDict): session_id: UUID user: UserDetails anon_id: UUID - user_agent: str - ip_addr: str masquerade: Optional[UserDetails] auth_server_jwks: Optional[dict[str, Any]] @@ -66,9 +67,6 @@ def session_info() -> SessionInfo: "logged_in": False }, "anon_id": anon_id, - "user_agent": request.headers.get("User-Agent"), - "ip_addr": request.environ.get("HTTP_X_FORWARDED_FOR", - request.remote_addr), "masquerading": None })) @@ -91,6 +89,17 @@ def user_details() -> UserDetails: """Retrieve user details.""" return session_info()["user"] + +def logged_in_user_id() -> Optional[UUID]: + """Get user id for logged in user. If user has not logged in, return None.""" + return user_token().then( + lambda _tok: user_details() + ).then( + lambda _user: Either(_user["user_id"], + (None, _user["email"] != "anon@ymous.user")) + ).either(lambda _err: None, lambda uid: uid) + + def user_token() -> Either: """Retrieve the user token.""" return session_info()["user"]["token"] diff --git a/uploader/species/views.py b/uploader/species/views.py index 9b14d01..4bfa7ae 100644 --- a/uploader/species/views.py +++ b/uploader/species/views.py @@ -8,8 +8,6 @@ from flask import (flash, Blueprint, current_app as app) -from uploader.sui import sui_template - from uploader.population import popbp from uploader.platforms import platformsbp from uploader.flask_extensions import url_for @@ -56,7 +54,7 @@ def view_species(species_id: int): species_id=species_id, population_id=population["Id"])) return render_template( - sui_template("species/view-species.html"), + "species/view-species.html", species=species, activelink="view-species", populations=populations_by_species(conn, species["SpeciesId"])) diff --git a/uploader/static/css/layout-common.css b/uploader/static/css/layout-common.css index 36a5735..9c9d034 100644 --- a/uploader/static/css/layout-common.css +++ b/uploader/static/css/layout-common.css @@ -1,3 +1,21 @@ * { box-sizing: border-box; } + +body { + display: grid; + grid-gap: 1em; +} + +#header { + margin: -0.7em; /* Fill entire length of screen */ + /* Define layout for the children elements */ + display: grid; +} + +#header #header-nav { + /* Place it in the parent element */ + grid-column-start: 1; + grid-column-end: 2; + display: flex; +} diff --git a/uploader/static/css/layout-large.css b/uploader/static/css/layout-large.css index 8abd2dd..c1950b1 100644 --- a/uploader/static/css/layout-large.css +++ b/uploader/static/css/layout-large.css @@ -1,8 +1,6 @@ @media screen and (min-width: 20.1in) { body { - display: grid; grid-template-columns: 7fr 3fr; - grid-gap: 1em; } #header { @@ -12,7 +10,7 @@ /* Define layout for the children elements */ display: grid; - grid-template-columns: 8fr 2fr; + grid-template-columns: 1fr 9fr; } #header #header-text { @@ -45,6 +43,8 @@ grid-column-start: 1; grid-column-end: 3; padding: 0 3px; + + margin: -0.3em -0.7em 0 -0.7em; } #main #main-content { @@ -52,6 +52,7 @@ grid-column-start: 1; grid-column-end: 2; + overflow-x: auto; } #main #sidebar-content { diff --git a/uploader/static/css/layout-medium.css b/uploader/static/css/layout-medium.css index 2cca711..a29411d 100644 --- a/uploader/static/css/layout-medium.css +++ b/uploader/static/css/layout-medium.css @@ -1,8 +1,6 @@ @media screen and (width > 8in) and (max-width: 20in) { body { - display: grid; grid-template-columns: 65fr 35fr; - grid-gap: 1em; } #header { @@ -12,7 +10,7 @@ /* Define layout for the children elements */ display: grid; - grid-template-columns: 8fr 2fr; + grid-template-columns: 2fr 8fr; } #header #header-text { @@ -51,10 +49,10 @@ /* Place it in the parent element */ grid-column-start: 1; grid-column-end: 2; - grid-gap: 5px; /* Define layout for the children elements */ max-width: 100%; + overflow-x: auto; } #main #sidebar-content { diff --git a/uploader/static/css/layout-small.css b/uploader/static/css/layout-small.css index 80a3759..87dd910 100644 --- a/uploader/static/css/layout-small.css +++ b/uploader/static/css/layout-small.css @@ -2,7 +2,7 @@ body { display: grid; grid-template-columns: 1fr; - grid-template-rows: 1fr 2fr 7fr; + grid-template-rows: 1fr 90fr; grid-gap: 1em; } @@ -31,6 +31,11 @@ grid-column-end: 2; } + #header #header-nav ul { + display: grid; + grid-template-columns: 1fr; + } + #main { /* Place it in the parent element */ grid-column-start: 1; @@ -38,7 +43,7 @@ display: grid; /* Define layout for the children elements */ - grid-template-rows: 1.5em 80% 20%; + grid-template-rows: 1fr 80fr 20fr; grid-template-columns: 1fr; } @@ -51,6 +56,7 @@ #main #main-content { grid-row-start: 2; grid-row-end: 3; + overflow-x: auto; } #main #sidebar-content { diff --git a/uploader/static/css/theme.css b/uploader/static/css/theme.css index 2acce5f..6f5cb0c 100644 --- a/uploader/static/css/theme.css +++ b/uploader/static/css/theme.css @@ -8,24 +8,27 @@ body { #header { background-color: #336699; color: #FFFFFF; - border-radius: 3px; min-height: 30px; + border-bottom: solid black 1px; } #header #header-nav .nav li a { /* Content styling */ color: #FFFFFF; - background: #4477AA; - border: solid 5px #336699; - border-radius: 5px; font-size: 0.7em; text-align: center; padding: 1px 7px; + text-decoration: none; } #main #breadcrumbs { - border-radius:3px; text-align: center; + background-color: #D5D5D5; + padding: 0 1em 0 1em; +} + +#main #breadcrumbs .breadcrumb { + padding-top: 0.5em; } #main #main-content { @@ -34,7 +37,7 @@ body { } #main #sidebar-content { - background: #EEEEEE; + background: #FEFEFE; border-radius: 5px; padding: 10px 5px; @@ -56,6 +59,10 @@ body { text-transform: capitalize; } +label { + text-transform: Capitalize; +} + input[type="search"] { border-radius: 5px; } @@ -74,8 +81,22 @@ table.dataTable tbody tr.selected td { background-color: #ffee99 !important; } -.form-group { +#frm-add-phenotypes .form-group { margin-bottom: 2em; padding-bottom: 0.2em; - border-bottom: solid gray 1px; + border-bottom: solid #A9A9A9 1px; +} + + +.breadcrumb-item { + text-transform: Capitalize; +} + +.breadcrumb-item a { + text-decoration: none; +} + +.table thead tr th { + text-align: center; + vertical-align: middle; } diff --git a/uploader/static/images/frontpage_banner.png b/uploader/static/images/frontpage_banner.png Binary files differnew file mode 100644 index 0000000..d25e1c9 --- /dev/null +++ b/uploader/static/images/frontpage_banner.png diff --git a/uploader/static/js/datatables.js b/uploader/static/js/datatables.js index 82fd696..bfcda2a 100644 --- a/uploader/static/js/datatables.js +++ b/uploader/static/js/datatables.js @@ -11,13 +11,36 @@ var addTableLength = (menuList, lengthToAdd, dataLength) => { var defaultLengthMenu = (data) => { menuList = [] - var lengths = [10, 25, 50, 100, 1000, data.length]; + var lengths = [10, 25, 50, 100, 1000]; + if(data.length > 1000) { + lengths.push(data.length) + } lengths.forEach((len) => { menuList = addTableLength(menuList, len, data.length); }); return menuList; }; +var setRowCheckableProperty = (node, state) => { + /** + * Set a row's (`node`) checkbox's or radio button's checked state to the + * boolean value `state`. + **/ + if(typeof(state) == "boolean") { + var pseudoclass = state == false ? ":checked" : ":not(:checked)"; + var checkable = ( + $(node).find(`input[type="checkbox"]${pseudoclass}`)[0] + || + $(node).find(`input[type="radio"]${pseudoclass}`)[0]); + $(checkable).prop("checked", state); + } else { + throw new Error("`state` *MUST* be a boolean value.") + } +}; + +var setRowChecked = (node) => {setRowCheckableProperty(node, true);}; +var setRowUnchecked = (node) => {setRowCheckableProperty(node, false);}; + var buildDataTable = (tableId, data = [], columns = [], userSettings = {}) => { var defaultSettings = { responsive: true, @@ -35,35 +58,40 @@ var buildDataTable = (tableId, data = [], columns = [], userSettings = {}) => { 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); - } - } + drawCallback: function (settings) { + var api = this.api(); + api.rows({selected: true}).nodes().each((node, index) => { + setRowChecked(node); + }); + api.rows({selected: false}).nodes().each((node, index) => { + setRowUnchecked(node); }); } } var theDataTable = $(tableId).DataTable({ ...defaultSettings, - ...userSettings + ...userSettings, + ...(data.length == 0 ? {} : {data: data}), + ...(columns.length == 0 ? {} : {columns: columns}) }); - 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("select", (event, datatable, type, indexes) => { + datatable + .rows(indexes) + .nodes() + .each((node, index) => { + setRowChecked(node); + }); }); - theDataTable.on("deselect", (event, datatable, type, cell, originalEvent) => { - datatable.rows({selected: false}).nodes().each((node, index) => { - $(node).find(".chk-row-select").prop("checked", false) - }); + theDataTable.on("deselect", (event, datatable, type, indexes) => { + datatable + .rows(indexes) + .nodes() + .each(function(node, index) { + setRowUnchecked(node); + }); }); + + theDataTable.selectAll = () => {theDataTable.rows().select()}; + theDataTable.deselectAll = () => {theDataTable.rows().deselect()}; return theDataTable; }; diff --git a/uploader/static/js/files.js b/uploader/static/js/files.js index 0bde6f7..7532df3 100644 --- a/uploader/static/js/files.js +++ b/uploader/static/js/files.js @@ -84,7 +84,8 @@ var errorHandler = makeResumableHandler("error"); var markResumableDragAndDropElement = (resumable, fileinput, droparea, browsebutton) => { if(resumable.support) { //Hide file input element and display drag&drop UI - add_class(fileinput, "visually-hidden"); + add_class( + fileinput.closest(".non-resumable-elements"), "visually-hidden"); remove_class(droparea, "visually-hidden"); // Define UI elements for browse and drag&drop @@ -96,7 +97,7 @@ var markResumableDragAndDropElement = (resumable, fileinput, droparea, browsebut }; -var makeResumableElement = (targeturi, fileinput, droparea, uploadbutton, filetype) => { +var makeResumableElement = (targeturi, droparea, filetype) => { var resumable = Resumable({ target: targeturi, fileType: filetype, @@ -116,3 +117,255 @@ var makeResumableElement = (targeturi, fileinput, droparea, uploadbutton, filety return resumable; }; + + +var CSVFilesMetadata = () => { + return { + "separator": $("#txt-file-separator").val(), + "comment_char": $( + "#txt-file-comment-character").val(), + "na_strings": $("#txt-file-na").val() + } +}; + + +var updatePreview = (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 comment_chars = formdata + .comment_char + .split(" ") + .map((v) => {return v.trim();}) + .filter((v) => {return Boolean(v);}); + var navalues = formdata + .na_strings + .split(" ") + .map((v) => {return v.trim();}) + .filter((v) => {return Boolean(v);}); + filedata.forEach((line) => { + if(comment_chars.includes(line[0]) || linenum >= numrows) { + return false; + } + var row = $("<tr></tr>"); + line.split(formdata.separator) + .map((field) => { + var value = field.trim(); + if(navalues.includes(value)) { + return "[NO-VALUE]"; + } + 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"), "visually-hidden"); + } else { + remove_class(table.find(".data-row-template"), "visually-hidden"); + } +}; + + +var makePreviewUpdater = (preview_table, preview_rows) => { + return (data) => { + updatePreview( + preview_table, + data, + CSVFilesMetadata(), + preview_rows); + }; +}; + + +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, "visually-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, "visually-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, "visually-hidden"); + remove_class(cancel_button, "visually-hidden"); + add_class(browse_button, "visually-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, "visually-hidden"); + remove_class(retry_button, "visually-hidden"); + remove_class(browse_button, "visually-hidden"); + }); +}; + + +var startUpload = (browse_button, retry_button, cancel_button) => { + return (event) => { + remove_class(cancel_button, "visually-hidden"); + add_class(retry_button, "visually-hidden"); + add_class(browse_button, "visually-hidden"); + }; +}; + + +var makeFormSubmitter = function (form, processForm, num_files) { + var uploaded_files = new Set(); + + return function (new_file) { + uploaded_files.add(new_file); + if(uploaded_files.size === num_files) { + if(form.length !== 1) { + // TODO: Handle error somehow? + alert("The form was not provided. Bailing!"); + return false; + } + + $.ajax({ + "url": form.attr("action"), + "type": "POST", + "data": processForm(form[0], uploaded_files),// `uploaded_files` changes with each file added -- check this and fix. + "beforeSend": function(xhr) { + xhr.setRequestHeader("Accept", "application/json"); + }, + "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, submitForm) => { + return (file, message) => { + submitForm({...JSON.parse(message), "file-input-name": file_input_name}); + }; +}; + + +var uploadError = (submitButton) => { + return (message, file) => { + submitButton.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, submitForm, filetypes=["csv", "tsv", "txt"], preview_rows=5 +) => { + 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"), + $("#" + resumable_element_id), + filetypes), + file_input, + $("#" + 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, + 100, + [makePreviewUpdater( + $("#" + preview_table_id), + preview_rows)]) + }); + }), + startUpload($("#" + resumable_element_id + "-browse-button"), + $("#" + resumable_element_id + "-retry-button"), + $("#" + resumable_element_id + "-cancel-button"))), + uploadSuccess(file_input.attr("name"), submitForm)), + uploadError(submit_button)); + + /** Setup progress indicator **/ + progressHandler( + r, + indicateProgress(r, $("#" + resumable_element_id + "-progress-bar"))); + + return r; +}; diff --git a/uploader/static/js/upload_samples.js b/uploader/static/js/upload_samples.js index aed536f..1c25a1d 100644 --- a/uploader/static/js/upload_samples.js +++ b/uploader/static/js/upload_samples.js @@ -87,20 +87,20 @@ function display_preview(event) { var data_preview_table = document.getElementById("tbl:samples-preview"); remove_rows(data_preview_table); - var separator = document.getElementById("select:separator").value; + var separator = document.getElementById("select-separator").value; if(separator === "other") { - separator = document.getElementById("txt:separator").value; + separator = document.getElementById("txt-separator").value; } if(separator == "") { display_error_row(data_preview_table, "Please provide a separator."); return false; } - var delimiter = document.getElementById("txt:delimiter").value; + var delimiter = document.getElementById("txt-delimiter").value; - var firstlineheading = document.getElementById("chk:heading").checked; + var firstlineheading = document.getElementById("chk-heading").checked; - var fileelement = document.getElementById("file:samples"); + var fileelement = document.getElementById("file-samples"); var preview_data = JSON.parse( fileelement.getAttribute("data-preview-content") || "[]"); if(preview_data.length == 0) { @@ -115,18 +115,18 @@ function display_preview(event) { delimiter)); } -document.getElementById("chk:heading").addEventListener( +document.getElementById("chk-heading").addEventListener( "change", display_preview); -document.getElementById("select:separator").addEventListener( +document.getElementById("select-separator").addEventListener( "change", display_preview); -document.getElementById("txt:separator").addEventListener( +document.getElementById("txt-separator").addEventListener( "keyup", display_preview); -document.getElementById("txt:delimiter").addEventListener( +document.getElementById("txt-delimiter").addEventListener( "keyup", display_preview); -document.getElementById("file:samples").addEventListener( +document.getElementById("file-samples").addEventListener( "change", (event) => { read_first_n_lines(event, - document.getElementById("file:samples"), + document.getElementById("file-samples"), 30, - document.getElementById("chk:heading").checked); + document.getElementById("chk-heading").checked); }); diff --git a/uploader/static/js/utils.js b/uploader/static/js/utils.js index 1b31661..62d3662 100644 --- a/uploader/static/js/utils.js +++ b/uploader/static/js/utils.js @@ -28,7 +28,8 @@ var remove_class = (element, classvalue) => { var add_class = (element, classvalue) => { remove_class(element, classvalue); - element.attr("class", (element.attr("class") || "") + " " + classvalue); + element.attr("class", + ((element.attr("class") || "") + " " + classvalue).trim()); }; $(".not-implemented").click((event) => { diff --git a/uploader/sui.py b/uploader/sui.py deleted file mode 100644 index 8eb863d..0000000 --- a/uploader/sui.py +++ /dev/null @@ -1,8 +0,0 @@ -"""Utilities for streamlined UI. This is a temporary module.""" -from flask import request - -def sui_template(template_path: str) -> str: - """Return the streamlined UI template for given template path.""" - _sui="sui-" if request.args.get("streamlined_ui") else "" - _parts = template_path.split("/") - return "/".join(_parts[:-1] + [f"{_sui}{_parts[-1]}"]) diff --git a/uploader/templates/background-jobs/base.html b/uploader/templates/background-jobs/base.html new file mode 100644 index 0000000..7201207 --- /dev/null +++ b/uploader/templates/background-jobs/base.html @@ -0,0 +1,10 @@ +{%extends "base.html"%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('background-jobs.list_jobs')}}"> + background jobs + </a> +</li> +{%endblock%} diff --git a/uploader/templates/background-jobs/default-success-page.html b/uploader/templates/background-jobs/default-success-page.html deleted file mode 100644 index 5732456..0000000 --- a/uploader/templates/background-jobs/default-success-page.html +++ /dev/null @@ -1,17 +0,0 @@ -{%extends "phenotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Background Jobs: Success{%endblock%} - -{%block pagetitle%}Background Jobs: Success{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - <p>Job <strong>{{job.job_id}}</strong>, - {%if job.get("metadata", {}).get("job-type")%} - of type '<em>{{job.metadata["job-type"]}}</em> - {%endif%}' completed successfully.</p> -</div> -{%endblock%} diff --git a/uploader/templates/background-jobs/delete-job.html b/uploader/templates/background-jobs/delete-job.html new file mode 100644 index 0000000..242c775 --- /dev/null +++ b/uploader/templates/background-jobs/delete-job.html @@ -0,0 +1,61 @@ +{%extends "background-jobs/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "background-jobs/macro-display-job-details.html" import display_job_details%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('background-jobs.job_summary', job_id=job.job_id)}}"> + summary + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">background jobs: delete?</h2> + + <p class="text-danger">Are you sure you want to delete the job below?</p> + + {{display_job_details(job, display_datetime)}} +</div> + +<div class="row"> + <form id="frm-delete-job" + method="POST" + action="{{url_for('background-jobs.delete_single', job_id=job.job_id)}}"> + <div class="row"> + <div class="col"> + <input type="submit" + class="btn btn-info" + value="cancel" + name="btn-confirm-delete" /> + </div> + <div class="col"> + <input type="submit" + class="btn btn-danger" + value="delete" + name="btn-confirm-delete" /> + </div> + </div> + </form> +</div> +{%endblock%} + + +{%block sidebarcontents%} +<div class="row"> + <h6 class="subheading">What is this?</h6> +</div> +<div class="row"> + <p>Confirm whether or not you want to delete job + <strong>{{job.job_id}}</strong>.</p> +</div> +{{super()}} +{%endblock%} diff --git a/uploader/templates/background-jobs/job-status.html b/uploader/templates/background-jobs/job-status.html new file mode 100644 index 0000000..2e75c6d --- /dev/null +++ b/uploader/templates/background-jobs/job-status.html @@ -0,0 +1,45 @@ +{%extends "background-jobs/base.html"%} +{%from "background-jobs/macro-display-job-details.html" import display_job_details%} + +{%from "flash_messages.html" import flash_all_messages%} + +{%block extrameta%} +<meta http-equiv="refresh" content="5" /> +{%endblock%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">job status</h2> + + {{display_job_details(job, display_datetime)}} +</div> + +<div class="row"> + <div class="col"> + <a href="{{url_for('background-jobs.stop_job', job_id=job.job_id)}}" + title="Stop/Kill this job." + class="btn btn-danger">stop job</a> + </div> +</div> + +<div class="row"> + <h3 class="subheading">STDOUT</h3> + <div style="max-width: 40em; overflow: scroll"> + <pre>{{job["stdout"]}}</pre> + </div> +</div> + +<div class="row"> + <h3 class="subheading">STDERR</h3> + <div style="max-width: 40em; overflow: scroll"> + <pre>{{job["stderr"]}}</pre> + </div> +</div> + +{%endblock%} diff --git a/uploader/templates/background-jobs/job-summary.html b/uploader/templates/background-jobs/job-summary.html new file mode 100644 index 0000000..ef9ef6c --- /dev/null +++ b/uploader/templates/background-jobs/job-summary.html @@ -0,0 +1,75 @@ +{%extends "background-jobs/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "background-jobs/macro-display-job-details.html" import display_job_details%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('background-jobs.job_summary', job_id=job.job_id)}}"> + summary + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">background jobs: summary</h2> + + {{display_job_details(job, display_datetime)}} +</div> + +<div class="row"> + {%if view_under_construction%} + <div class="col"> + <a href="#" + class="btn btn-info not-implemented" + title="Update the expiry date and time for this job.">update expiry</a> + </div> + + {%if job.metadata.status in ("stopped",)%} + <div class="col"> + <a href="#" + class="btn btn-warning not-implemented" + title="Create a new copy of this job, and run the copy.">Run Copy</a> + </div> + {%endif%} + {%endif%} + + <div class="col"> + <a href="{{url_for('background-jobs.delete_single', job_id=job.job_id)}}" + class="btn btn-danger" + title="Delete this job.">delete</a> + </div> +</div> + +<div class="row"> + <h3 class="subheading">Script Errors and Logging</h3> + <div style="max-width: 40em; overflow: scroll"> + <pre>{{job["stderr"]}}</pre> + </div> +</div> + +<div class="row"> + <h3 class="subheading">Script Output</h3> + <div style="max-width: 40em; overflow: scroll"> + <pre>{{job["stdout"]}}</pre> + </div> +</div> +{%endblock%} + + +{%block sidebarcontents%} +<div class="row"> + <h6 class="subheading">What is this?</h6> +</div> +<div class="row"> + <p>This page shows the results of running job '{{job.job_id}}'.</p> +</div> +{{super()}} +{%endblock%} diff --git a/uploader/templates/background-jobs/list-jobs.html b/uploader/templates/background-jobs/list-jobs.html new file mode 100644 index 0000000..c16b850 --- /dev/null +++ b/uploader/templates/background-jobs/list-jobs.html @@ -0,0 +1,79 @@ +{%extends "background-jobs/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"><h2 class="heading">Background Jobs</h2></div> + +<div class="row"> + <div class="table-responsive"> + <table class="table"> + <thead> + <tr class="table-primary"> + <th>Type</th> + <th>Created</th> + <th title="Date and time past which the job's details will be deleted from the system."> + Expires</th> + <th>Status</th> + <th>Actions</th> + </tr> + </thead> + + <tbody> + {%for job in jobs%} + <tr> + <td>{{job.metadata["job-type"]}}</td> + <td>{{display_datetime(job.created)}}</td> + <td title="Date and time past which the job's details will be deleted from the system."> + {{display_datetime(job.expires)}} + </td> + <td {%if job.metadata.status == "completed"%} + class="fw-bold text-capitalize text-success" + {%elif job.metadata.status == "error"%} + class="fw-bold text-capitalize text-danger" + {%elif job.metadata.status == "stopped"%} + class="fw-bold text-capitalize text-warning" + {%else%} + class="fw-bold text-capitalize text-info" + {%endif%}> + <div> + {{job.metadata.status}} + </div> + </td> + <td> + <a href="{{url_for('background-jobs.job_summary', job_id=job.job_id)}}" + class="btn btn-info" + title="View more detailed information about this job."> + view summary</a> + </td> + </tr> + {%else%} + <tr> + <td colspan="5"> + You do not have any jobs you have run in the background.</td> + </tr> + {%endfor%} + </tbody> + </table> + </div> +</div> +{%endblock%} + + +{%block sidebarcontents%} +<div class="row"> + <h6 class="subheading">What is this?</h6> +</div> +<div class="row"> + <p>The table lists the jobs that are running in the background, that you + started.</p> + <p>You can use the tools provided on this page to manage the jobs, and to view + each job's details.</p> +</div> +{{super()}} +{%endblock%} diff --git a/uploader/templates/background-jobs/macro-display-job-details.html b/uploader/templates/background-jobs/macro-display-job-details.html new file mode 100644 index 0000000..82e33c0 --- /dev/null +++ b/uploader/templates/background-jobs/macro-display-job-details.html @@ -0,0 +1,29 @@ +{%macro display_job_details(job, display_datetime)%} +<table class="table"> + <thead> + </thead> + + <tbody> + <tr> + <th class="table-primary">Job ID</th> + <td>{{job.job_id}}</td> + </tr> + <tr> + <th class="table-primary">Type</th> + <td>{{job.metadata["job-type"]}}</td> + </tr> + <tr> + <th class="table-primary">Created</th> + <td>{{display_datetime(job.created)}}</td> + </tr> + <tr> + <th class="table-primary">Expires</th> + <td>{{display_datetime(job.expires)}}</td> + </tr> + <tr> + <th class="table-primary">Status</th> + <td>{{job.metadata.status}}</td> + </tr> + </tbody> +</table> +{%endmacro%} diff --git a/uploader/templates/background-jobs/stop-job.html b/uploader/templates/background-jobs/stop-job.html new file mode 100644 index 0000000..fc190ac --- /dev/null +++ b/uploader/templates/background-jobs/stop-job.html @@ -0,0 +1,61 @@ +{%extends "background-jobs/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "background-jobs/macro-display-job-details.html" import display_job_details%} + +{%block title%}Background Jobs{%endblock%} + +{%block pagetitle%}Background Jobs{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('background-jobs.job_summary', job_id=job.job_id)}}"> + summary + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2 class="heading">background jobs: stop?</h2> + + <p class="text-danger">Are you sure you want to stop the job below?</p> + + {{display_job_details(job, display_datetime)}} +</div> + +<div class="row"> + <form id="frm-stop-job" + method="POST" + action="{{url_for('background-jobs.stop_job', job_id=job.job_id)}}"> + <div class="row"> + <div class="col"> + <input type="submit" + class="btn btn-info" + value="cancel" + name="btn-confirm-stop" /> + </div> + <div class="col"> + <input type="submit" + class="btn btn-danger" + value="stop" + name="btn-confirm-stop" /> + </div> + </div> + </form> +</div> +{%endblock%} + + +{%block sidebarcontents%} +<div class="row"> + <h6 class="subheading">What is this?</h6> +</div> +<div class="row"> + <p>Confirm whether or not you want to stop job + <strong>{{job.job_id}}</strong>.</p> +</div> +{{super()}} +{%endblock%} diff --git a/uploader/templates/background-jobs/sui-default-success-page.html b/uploader/templates/background-jobs/sui-default-success-page.html deleted file mode 100644 index 5732456..0000000 --- a/uploader/templates/background-jobs/sui-default-success-page.html +++ /dev/null @@ -1,17 +0,0 @@ -{%extends "phenotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Background Jobs: Success{%endblock%} - -{%block pagetitle%}Background Jobs: Success{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - <p>Job <strong>{{job.job_id}}</strong>, - {%if job.get("metadata", {}).get("job-type")%} - of type '<em>{{job.metadata["job-type"]}}</em> - {%endif%}' completed successfully.</p> -</div> -{%endblock%} diff --git a/uploader/templates/base.html b/uploader/templates/base.html index d521ccb..ae4ecef 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -16,7 +16,11 @@ <link rel="stylesheet" type="text/css" href="{{url_for('base.datatables', filename='css/dataTables.bootstrap5.min.css')}}" /> - <link rel="stylesheet" type="text/css" href="/static/css/styles.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-common.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-large.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-medium.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/layout-small.css" /> + <link rel="stylesheet" type="text/css" href="/static/css/theme.css" /> {%block css%}{%endblock%} @@ -26,14 +30,32 @@ <header id="header"> <span id="header-text">GeneNetwork</span> <nav id="header-nav"> - <ul class="nav justify-content-end"> + <ul class="nav"> + {%if user_logged_in()%} + <li> + <a href="{{url_for('background-jobs.list_jobs')}}" + title="User's background jobs."> + <!-- https://icons.getbootstrap.com/icons/back/ --> + <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-back" viewBox="0 0 16 16"> + <path d="M0 2a2 2 0 0 1 2-2h8a2 2 0 0 1 2 2v2h2a2 2 0 0 1 2 2v8a2 2 0 0 1-2 2H6a2 2 0 0 1-2-2v-2H2a2 2 0 0 1-2-2zm2-1a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1z"/> + </svg> + Background jobs + </a> + </li> + <li> - {%if user_logged_in()%} <a href="{{url_for('oauth2.logout')}}" title="Log out of the system"> + <!-- https://icons.getbootstrap.com/icons/file-person/ --> + <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-file-person" viewBox="0 0 16 16"> + <path d="M12 1a1 1 0 0 1 1 1v10.755S12 11 8 11s-5 1.755-5 1.755V2a1 1 0 0 1 1-1zM4 0a2 2 0 0 0-2 2v12a2 2 0 0 0 2 2h8a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2z"/> + <path d="M8 10a3 3 0 1 0 0-6 3 3 0 0 0 0 6"/> + </svg> <span class="glyphicon glyphicon-user"></span> - {{user_email()}} Sign Out</a> - {%else%} + Sign Out ({{user_email()}})</a> + </li> + {%else%} + <li> <a href="{{authserver_authorise_uri()}}" title="Log in to the system">Sign In</a> {%endif%} @@ -42,91 +64,29 @@ </nav> </header> - <aside id="nav-sidebar"> - <ul class="nav flex-column"> - <li {%if activemenu=="home"%}class="activemenu"{%endif%}> - <a href="{{url_for('base.index')}}" >Home</a></li> - <li {%if activemenu=="publications"%}class="activemenu"{%endif%}> - <a href="{{url_for('publications.index')}}" - title="View and manage publications.">Publications</a></li> - <li {%if activemenu=="species"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.list_species')}}" - title="View and manage species information.">Species</a></li> - <li {%if activemenu=="platforms"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.platforms.index')}}" - title="View and manage species platforms.">Sequencing Platforms</a></li> - <li {%if activemenu=="populations"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.populations.index')}}" - title="View and manage species populations.">Populations</a></li> - <li {%if activemenu=="samples"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.populations.samples.index')}}" - title="Upload population samples.">Samples</a></li> - <li {%if activemenu=="genotypes"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.populations.genotypes.index')}}" - title="Upload Genotype data.">Genotype Data</a></li> - <!-- - TODO: Maybe include menus here for managing studies and dataset or - maybe have the studies/datasets managed under their respective - sections, e.g. "Publish*" studies/datasets under the "Phenotypes" - section, "ProbeSet*" studies/datasets under the "Expression Data" - sections, etc. - --> - <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.populations.phenotypes.index')}}" - title="Upload phenotype data.">Phenotype Data</a></li> - <!-- - <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> - <a href="{{url_for('species.populations.expression-data.index')}}" - title="Upload expression data." - class="not-implemented">Expression Data</a></li> - <li {%if activemenu=="individuals"%}class="activemenu"{%endif%}> - <a href="#" - class="not-implemented" - title="Upload individual data.">Individual Data</a></li> - <li {%if activemenu=="rna-seq"%}class="activemenu"{%endif%}> - <a href="#" - class="not-implemented" - title="Upload RNA-Seq data.">RNA-Seq Data</a></li> - <li {%if activemenu=="async-jobs"%}class="activemenu"{%endif%}> - <a href="#" - class="not-implemented" - title="View and manage the backgroud jobs you have running"> - Background Jobs</a></li> - --> - </ul> - </aside> <main id="main" class="main"> + <nav id="breadcrumbs" aria-label="breadcrumb"> + <ol class="breadcrumb"> + {%block breadcrumbs%} + <li class="breadcrumb-item"> + <a href="{{url_for('base.index')}}">Home</a></li> + {%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 id="all-content"> - <div id="main-content"> + <div id="main-content"> {%block contents%}{%endblock%} </div> - <div id="sidebar-content"> + + <div id="sidebar-content"> {%block sidebarcontents%}{%endblock%} </div> - </div> </main> + + <script type="text/javascript" src="/static/js/debug.js"></script> <!-- Core dependencies --> diff --git a/uploader/templates/cli-output.html b/uploader/templates/cli-output.html index 64b1a9a..9cff09d 100644 --- a/uploader/templates/cli-output.html +++ b/uploader/templates/cli-output.html @@ -1,7 +1,7 @@ {%macro cli_output(job, stream)%} <h4 class="subheading">{{stream | upper}} Output</h4> -<div class="cli-output" style="max-height: 10em; overflow: auto;"> +<div class="cli-output" style="overflow: auto;"> <pre>{{job.get(stream, "")}}</pre> </div> diff --git a/uploader/templates/genotypes/add-genotypes-records-base.html b/uploader/templates/genotypes/add-genotypes-records-base.html new file mode 100644 index 0000000..bf3812f --- /dev/null +++ b/uploader/templates/genotypes/add-genotypes-records-base.html @@ -0,0 +1,39 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block contents%} + +<div class="row"> + <form id="frm-add-genotypes-records" + method="POST" + enctype="multipart/form-data" + action="{{url_for( + 'species.populations.genotypes.add_genotype_records', + species_id=species.SpeciesId, population_id=population.Id, + dataset_id=dataset.Id)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> + <legend>Add New Genotype Records</legend> + + {%block frm_add_genotypes_records_elements%}{%endblock%} + + <div class="form-group"> + <input type="submit" + value="upload genotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + <h2 class="heading" id="page-documentation">Help</h2> + {%block page_documentation%}{%endblock%} +</div> +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/genotypes/add-genotypes-records-csv.html b/uploader/templates/genotypes/add-genotypes-records-csv.html new file mode 100644 index 0000000..6ebc005 --- /dev/null +++ b/uploader/templates/genotypes/add-genotypes-records-csv.html @@ -0,0 +1,147 @@ +{%extends "genotypes/add-genotypes-records-base.html"%} +{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} +{%from "macro-csv-fields.html" import display_csv_fields%} +{%from "macro-csv-fields.html" import add_csv_fields_event_handlers%} +{%from "macro-csv-fields.html" import display_csv_fields_documentation%} +{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} + +{%block frm_add_genotypes_records_elements%} +<div class="form-text help-block"> + <p>You can add new genotype records here.</p> +</div> + +<div class="border rounded p-3 mb-3" role="group" aria-labelledby="file-inputs-group-label"> + <div id="file-inputs-group-label" class="fw-bold mb-2">File Details</div> + {{display_csv_fields()}} + + <div class="form-group"> + <div class="non-resumable-elements"> + <div class="row mb-3"> + <label for="finput-genotypes-records-file" class="col-sm-2 col-form-label"> + genotypes records</label> + <div class="col-sm-10"> + <input id="finput-genotypes-records-file" + name="genotypes-records-file" + class="form-control" + type="file" + data-preview-table="tbl-preview-geno-records" + required="required" /> + </div> + <span class="form-text text-muted"> + Provide a file that contains only the genotypes records, + <a href="#docs-file-genotypes-records-csv" + title="Documentation of the genotypes records file format."> + the documentation for the expected format of the file</a>.</span> + </div> + </div> + {{display_resumable_elements( + "resumable-genotypes-records-file", + "Genotypes records", + '<p>Drag and drop the CSV file here, that contains the genotype records you + want to add.</p> + + <p>Please see the + <a href="#docs-file-genotypes-records" + title="Documentation of the genotypes records data file format."> + "Genotypes records" documentation</a> section below for more + information on the expected format of the file provided here.</p>')}} + {{display_preview_table("tbl-preview-geno-records", "genotypes records")}} + </div> +</div> +{%endblock%} + +{%block page_documentation%} +{{super()}} + +<h3 class="sub-heading">CSV file metadata</h3> +{{display_csv_fields_documentation()}} +{%endblock%} + +{%block javascript%} +{{super()}} + +<script src="{{url_for('base.node_modules', + filename='resumablejs/resumable.js')}}"></script> +<script src="/static/js/files.js"></script> + +{{add_csv_fields_event_handlers()}} + +<script type="text/javascript"> + $(function(evt) { + var NUM_READ_LINES = 100; + var NUM_PREVIEW_ROWS = 10; + + $("#finput-genotypes-records-file").on("change", function(event) { + readFirstNLines( + event.target.files[0], + NUM_READ_LINES, + [makePreviewUpdater($("#tbl-preview-geno-records"))]); + }); + + var r = makeResumableObject( + form_id="frm-add-genotypes-records", + file_input_id="finput-genotypes-records-file", + resumable_element_id="resumable-genotypes-records-file", + preview_table_id="tbl-preview-geno-records", + makeFormSubmitter( + $("#frm-add-genotypes-records"), + function(form, uploaded_files) { + 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; + }, + 1), + filetypes=["csv", "tsv", "txt", "geno"], + preview_rows=NUM_PREVIEW_ROWS); + + var handler_update_previews = function(event) { + var preview_table = $("#tbl-preview-geno-records"); + var file_input = $("#finput-genotypes-records-file"); + if(file_input[0].files.length > 0) { + readFirstNLines( + file_input[0].files[0], + NUM_READ_LINES, + [makePreviewUpdater(preview_table, NUM_PREVIEW_ROWS)]); + } + + if(typeof(r) !== "undefined") { + if(r.files.length > 0) { + readFirstNLines( + r.files[0].file, + NUM_READ_LINES, + [makePreviewUpdater(preview_table, NUM_PREVIEW_ROWS)]); + } + } + }; + + [ + "#txt-file-separator", + "#txt-file-comment-character", + "#txt-file-na" + ].forEach((elementid) => { + $(elementid).on("change", handler_update_previews); + }); + + $("#frm-add-genotypes-records input[type=submit]").on("click", function(event) { + event.preventDefault(); + var submit_button = event.target; + submit_button.setAttribute("disabled", "disabled"); + r.upload(); + + try { + var filename = r.files[0].name; + } catch (error) { + window.alert("You MUST provide a file before attempting to upload."); + submit_button.removeAttribute("disabled"); + } + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html index 7d61312..c2abc63 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -1,23 +1,23 @@ {%extends "populations/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} +{%from "genotypes/macro-display-dataset-card.html" import display_dataset_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="genotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if population is mapping%} - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}"> - {%if dataset is defined and dataset is mapping%} - {{dataset.Name}} - {%else%} - Genotypes - {%endif%}</a> - {%else%} - <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> - {%endif%} +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.genotypes.index', + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + genotype + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} + + +{%block sidebarcontents%} +{%if dataset is defined and dataset is not none%} +{{display_dataset_card(species, population, dataset)}} +{%else%} +{{display_sui_population_card(species, population)}} +{%endif%} {%endblock%} diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html index 10331c1..7f435a1 100644 --- a/uploader/templates/genotypes/create-dataset.html +++ b/uploader/templates/genotypes/create-dataset.html @@ -35,13 +35,13 @@ id="txt-geno-dataset-name" name="geno-dataset-name" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" + readonly="readonly" /> <small class="form-text text-muted"> <p>This is a short representative, but constrained name for the genotype - dataset.<br /> - The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens - and underscores. Any other character will cause the name to be - rejected.</p></small> + dataset. It is used internally by GeneNetwork.</p> + </small> </div> <div class="form-group"> @@ -50,7 +50,8 @@ id="txt-geno-dataset-fullname" name="geno-dataset-fullname" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}} Genotypes" /> <small class="form-text text-muted"> <p>This is a longer, more descriptive name for your dataset.</p></small> </div> @@ -61,7 +62,8 @@ <input type="text" id="txt-geno-dataset-shortname" name="geno-dataset-shortname" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" /> <small class="form-text text-muted"> <p>A short name for your dataset. If you leave this field blank, the short name will be set to the same value as the diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html index b50ebc5..1c3483d 100644 --- a/uploader/templates/genotypes/index.html +++ b/uploader/templates/genotypes/index.html @@ -1,32 +1,200 @@ {%extends "genotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-select-species.html" import select_species_form%} {%block title%}Genotypes{%endblock%} {%block pagetitle%}Genotypes{%endblock%} - {%block contents%} {{flash_all_messages()}} + +{%if dataset is defined and dataset is not none%} + +<div class="row"> + <h2>Genotype Data</h2> + + <div class="row"> + <div class="col"> + <p> + <a href="{{url_for( + 'species.populations.genotypes.add_genotype_records', + species_id=species.SpeciesId, population_id=population.Id, + dataset_id=dataset.Id)}}" + class="btn btn-primary"> + Add genotype records + </a> + </p> + </div> + </div> + + <div class="table-responsive"> + <table id="tbl-genotype-records" class="table compact stripe cell-border"> + <thead> + <tr> + <th title="">#</th> + <th title="">Index</th> + <th title="Locus of marker on the chromosome">Locus</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of marker in centimorgans">cM</th> + <th title="Physical location of marker in megabasepairs">Mb</th> + {%for sample in samples%} + <th title="Data for sample {{sample}}">{{sample}}</th> + {%endfor%} + </tr> + </thead> + + <tbody> + {%for record in genotype_records%} + <tr> + <td> + <input type="checkbox" + id="chk-geno-record-{{record.Id}}" + name="geno_record_id" + value="{{record.Id}}" /> + </td> + <td>{{record.index}}</td> + <td>{{record.Name}}</td> + <td>{{record.Chr}}</td> + <td>{{record.cM}}</td> + <td>{{record.Mb}}</td> + {%for sample in samples%} + <td>{{record.data[sample]}}</td> + {%endfor%} + </tr> + {%else%} + <tr> + <td colspan="6" class="text-info"> + There are no records + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> +</div> + <div class="row"> - <p> - This section allows you to upload genotype information for your experiments, - in the case that you have not previously done so. - </p> - <p> - We'll need to link the genotypes to the species and population, so do please - go ahead and select those in the next two steps. - </p> + <h2>Genotype Encoding</h2> + <p>The numerical values in the table above are mapped from the following allele symbols:</p> + + <table class="table"> + <thead> + <tr> + <th>Allele Type</th> + <th>Allele Symbol</th> + <th>Mapped To</th> + </tr> + </thead> + + <tbody> + {%for row in genocode%} + <tr> + <td {%if row.AlleleType == 'mat'%} + title="Maternal allele" + {%elif row.AlleleType == "pat"%} + title="Paternal allele" + {%elif row.AlleleType == "het"%} + title="Heterozygous allele" + {%else%} + title="Unknown allele" + {%endif%}> + {{row.AlleleType}}</td> + <td>{{row.AlleleSymbol}}</td> + <td>{{row.DatabaseValue if row.DatabaseValue is not none}}</td> + </tr> + {%else%} + <tr> + <td colspan="3" class="text-info"> + There is no genotype encoding defined for this data. + </td> + </tr> + {%endfor%} + </tbody> + </table> </div> +{%else%} + <div class="row"> - {{select_species_form(url_for("species.populations.genotypes.index"), - species)}} + <p>We need to create a dataset to hold the genotype information for this + species/population, before we can proceed to upload the genotype data.</p> + <p>Please click the button below to create the dataset.</p> + + <div class="col"> + <a href="{{url_for('species.populations.genotypes.create_dataset', species_id=species.SpeciesId, population_id=population.Id)}}" + class="btn btn-primary">create genotype dataset</a> + </div> </div> + +{%endif%} + {%endblock%} + {%block javascript%} -<script type="text/javascript" src="/static/js/species.js"></script> +<script type="text/javascript"> + $(function() { + var genoRecordsUrl = "{{url_for('species.populations.genotypes.index', species_id=species.SpeciesId, population_id=population.Id)}}"; + + var dtGenotypeRecords = false; + fetch(genoRecordsUrl, { + method: "POST", + headers: { + "Accept": "application/json", + "Content-Type": "application/json" + }, + body: JSON.stringify({}) + }) + .then(response => response.json()) + .then(recordsData => { + var records = recordsData.genotype_records; + var samples = recordsData.samples_order; + var columns = [ + { + data: function(record) { + return `<input type="checkbox"` + + `id="chk-geno-record-` + record.Id + `"` + + `name="geno_record_id"` + + `value="` + record.Id + `"` + + ` />`; + } + }, + {data: "index"}, + {data: "Name"}, + {data: "Chr"}, + {data: "cM"}, + {data: "Mb"} + ].concat(samples.map((sample) => { + return {data: (record) => record.data[sample]}; + })); + + dtGenotypeRecords = buildDataTable( + "#tbl-genotype-records", + [], + columns, + { + serverSide: true, + ajax: { + url: genoRecordsUrl, + dataSrc: "genotype_records", + recordsTotal: "total_genotype_records", + recordsFiltered: "fetched_genotype_records" + }, + paging: true, + scroller: true, + scrollY: "50vh", + scrollCollapse: false, + layout: { + top: "info", + topStart: null, + topEnd: null, + bottom: null, + bottomStart: null, + bottomEnd: null + } + }); + }); + }); +</script> {%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html deleted file mode 100644 index 0f074fd..0000000 --- a/uploader/templates/genotypes/list-genotypes.html +++ /dev/null @@ -1,149 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-display-population-card.html" import display_population_card%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - -{%block lvl4_breadcrumbs%} -<li {%if activelink=="list-genotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}">List genotypes</a> -</li> -{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - <h2>Genetic Markers</h2> - <p>There are a total of {{total_markers}} currently registered genetic markers - for the "{{species.FullName}}" species. You can click - <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="View genetic markers for species '{{species.FullName}}"> - this link to view the genetic markers - </a>. - </p> -</div> - -<div class="row"> - <h2>Genotype Encoding</h2> - <p> - The genotype encoding used for the "{{population.FullName}}" population from - the "{{species.FullName}}" species is as shown in the table below. - </p> - <table class="table"> - - <thead> - <tr> - <th>Allele Type</th> - <th>Allele Symbol</th> - <th>Allele Value</th> - </tr> - </thead> - - <tbody> - {%for row in genocode%} - <tr> - <td>{{row.AlleleType}}</td> - <td>{{row.AlleleSymbol}}</td> - <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td> - </tr> - {%else%} - <tr> - <td colspan="7" class="text-info"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There is no explicit genotype encoding defined for this population. - </td> - </tr> - {%endfor%} - </tbody> - </table> - - {%if genocode | length < 1%} - <a href="#add-genotype-encoding" - title="Add a genotype encoding system for this population" - class="btn btn-primary not-implemented"> - add genotype encoding - </a> - {%endif%} -</div> - -<div class="row text-danger"> - <h3>Some Important Concepts to Consider/Remember</h3> - <ul> - <li>Reference vs. Non-reference alleles</li> - <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> - </ul> - <h3>Possible references</h3> - <ul> - <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> - <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> - </ul> -</div> - -<div class="row"> - <h2>Genotype Datasets</h2> - - <p>The genotype data is organised under various genotype datasets. You can - click on the link for the relevant dataset to view a little more information - about it.</p> - - {%if dataset is not none%} - <table class="table"> - <thead> - <tr> - <th>Name</th> - <th>Full Name</th> - </tr> - </thead> - - <tbody> - <tr> - <td>{{dataset.Name}}</td> - <td><a href="{{url_for('species.populations.genotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="View details regarding and manage dataset '{{dataset.FullName}}'"> - {{dataset.FullName}}</a></td> - </tr> - </tbody> - </table> - {%else%} - <p class="text-warning"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There is no genotype dataset defined for this population. - </p> - <p> - <a href="{{url_for('species.populations.genotypes.create_dataset', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." - class="btn btn-primary"> - create new genotype dataset</a></p> - {%endif%} -</div> -<div class="row text-warning"> - <p> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a - single genotype dataset. If there is more than one, the system apparently - fails in unpredictable ways. - </p> - <p>Fix this to allow multiple datasets, each with a different assembly from - all the rest.</p> -</div> -{%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/genotypes/list-markers.html b/uploader/templates/genotypes/list-markers.html index a705ae3..22189c7 100644 --- a/uploader/templates/genotypes/list-markers.html +++ b/uploader/templates/genotypes/list-markers.html @@ -1,20 +1,18 @@ {%extends "genotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} {%block title%}Genotypes: List Markers{%endblock%} {%block pagetitle%}Genotypes: List Markers{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="list-markers"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId, - population_id=population.Id)}}">List markers</a> + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + markers + </a> </li> {%endblock%} @@ -59,7 +57,7 @@ <table class="table"> <thead> <tr> - <th title="">#</th> + <th title="">Index</th> <th title="">Marker Name</th> <th title="Chromosome">Chr</th> <th title="Physical location of the marker in megabasepairs"> @@ -99,7 +97,3 @@ </div> {%endif%} {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/genotypes/macro-display-dataset-card.html b/uploader/templates/genotypes/macro-display-dataset-card.html new file mode 100644 index 0000000..2b197d4 --- /dev/null +++ b/uploader/templates/genotypes/macro-display-dataset-card.html @@ -0,0 +1,24 @@ +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%macro display_dataset_card(species, population, dataset)%} +{{display_sui_population_card(species, population)}} +<div class="row"> + <table class="table"> + <caption>Current genotype dataset</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{dataset.Name}}</td> + </tr> + <tr> + <th>Full Name</th> + <td>{{dataset.FullName}}</td> + </tr> + <tr> + <th>Short Name</th> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> +{%endmacro%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html deleted file mode 100644 index acdd063..0000000 --- a/uploader/templates/genotypes/select-population.html +++ /dev/null @@ -1,25 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} -{%from "populations/macro-select-population.html" import select_population_form%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}} -</div> -{%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} - -{%block javascript%} -<script type="text/javascript" src="/static/js/populations.js"></script> -{%endblock%} diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html index e7ceb36..d95a8e3 100644 --- a/uploader/templates/genotypes/view-dataset.html +++ b/uploader/templates/genotypes/view-dataset.html @@ -1,21 +1,17 @@ {%extends "genotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Genotypes: View Dataset{%endblock%} {%block pagetitle%}Genotypes: View Dataset{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="view-dataset"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.genotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, - dataset_id=dataset.Id)}}">view dataset</a> + dataset_id=dataset.Id)}}">dataset</a> </li> {%endblock%} @@ -50,12 +46,9 @@ <div class="row"> <h2>Genotype Data</h2> - <p class="text-danger"> - Provide link to enable uploading of genotype data here.</p> + <div class="col" style="margin-bottom: 3px;"> + <a href="#" class="btn btn-primary not-implemented">upload genotypes</a> + </div> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/index.html b/uploader/templates/index.html index aa1414e..6e9c777 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -1,107 +1,170 @@ {%extends "base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "macro-forms.html" import add_http_feature_flags%} {%block title%}Home{%endblock%} {%block pagetitle%}Home{%endblock%} -{%block contents%} - -<div class="row"> - {{flash_all_messages()}} - <div class="explainer"> - <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> - - <h2 class="heading">Getting Started</h2> - <p>The sections below explain the features of the system. Review this guide - to learn how to use the system.</p> - - {%block extrapageinfo%}{%endblock%} - - <h3 class="subheading">Species</h3> - - <p>GeneNetwork supports genetic studies across multiple species (e.g. mice - [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . - Here you can:</p> - <ul> - <li>View all species that are currently supported</li> - <li>Add new species not yet in the system</li> - </ul> - - <h3 class="subheading">Populations</h3> - - <p>A "population" refers to a specific subgroup within a species that you’re - studying (e.g., BXD mice). Here you can:</p> - <ul> - <li>View the populations that exist for a selected species</li> - <li>Add new populations of study for a selected species</li> - </ul> - - <h3 class="subheading">Samples</h3> +{%block extra_breadcrumbs%}{%endblock%} - <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> +{%block contents%} - <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> +{%macro add_form_buttons()%} +<div class="row form-buttons"> + <div class="col"> + <input type="submit" + class="btn btn-primary" + value="use selected species" /> + </div> + <div class="col"> + <a href="{{url_for('species.create_species', return_to='base.index')}}" + class="btn btn-outline-primary" + title="Add a new species to Genenetwork.">add a new Species</a> + </div> +</div> +{%endmacro%} - <p><strong>Requirement</strong>: Samples must already have been registered - in the system before uploading genotype data.</p> +<div class="row">{{flash_all_messages()}}</div> - <h3 class="subheading">Phenotype Data</h3> +{%if user_logged_in()%} - <p>Phenotypes are the visible traits or features of a living thing. For - example, phenotypes include:</p> +<div class="row"> + <ul class="nav nav-tabs" id="index-actions"> + <li class="nav-item presentation"> + <button class="nav-link active" + id="upload-data-tab" + data-bs-toggle="tab" + data-bs-target="#upload-data-content" + type="button" + role="tab" + aria-controls="upload-data-content" + aria-selected="false">Upload Data</button></li> + <li class="nav-item presentation"> + <button class="nav-link" + id="publications-tab" + data-bs-toggle="tab" + data-bs-target="#publications-content" + type="button" + role="tab" + aria-controls="publications-content" + aria-selected="true">Publications</button></li> + </ul> +</div> - <ul> - <li>Weight</li> - <li>Height</li> - <li>Color (such as the color of fur or eyes)</li> - </ul> +<div class="row"> + <div class="tab-content" id="upload-data-tabs-content"> + <div class="tab-pane fade show active" + id="upload-data-content" + role="tabpanel" + aria-labelledby="upload-data-content-tab"> + <h2 class="heading">Species</h2> + + <p>Select the species you want to work with.</p> + + <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal"> + {{add_http_feature_flags()}} + + {{add_form_buttons()}} + + {%if species | length != 0%} + <div style="margin-top:1em;"> + <table id="tbl-select-species" class="table compact stripe" + data-species-list='{{species | tojson}}'> + <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%} + + {{add_form_buttons()}} + + </form> + </div> + + <div class="tab-pane fade" + id="publications-content" + role="tabpanel" + aria-labelledby="publications-content-tab"> + <p>You can view, edit, and delete existing publications, as well as add + new ones, by clicking the button below.</p> + + <a href="{{url_for('publications.index')}}" + title="Manage publications." + class="btn btn-primary">manage publications</a> + </div> + </div> +</div> - <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> +{%else%} - <!-- +<div class="row"> + <img src="/static/images/frontpage_banner.png" + alt="Banner image showing the process flow a user would follow." /> +</div> - <h3 class="subheading">Expression Data</h3> +<div class="row"> + <p>The GeneNetwork Uploader (gn-uploader) lets you easily add new data to the + GeneNetwork System. It automatically checks your data for quality and walks + you through fixing any issues before submission.</p> +</div> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> +<div class="row"> + <div class="col"> + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system" + class="btn btn-primary">Sign in</a> + </div> +</div> +{%endif%} - <h3 class="subheading">Individual Data</h3> +{%endblock%} - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> - <h3 class="subheading">RNA-Seq Data</h3> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> - </div> - --> +{%block sidebarcontents%} +{%if view_under_construction%} +<div class="row"> + <p>The data in Genenetwork is related to one species or another. Use the form + provided to select from existing species, or click on the + "Create a New Species" button if you cannot find the species you want to + work with.</p> </div> +<div class="row"> + <form id="frm-quick-navigation"> + <legend>Quick Navigation</legend> + <div class="form-group"> + <label for="fqn-species-id">Species</label> + <select name="species_id"> + <option value="">Select species</option> + </select> + </div> + </form> +</div> +{%endif%} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> {%endblock%} diff --git a/uploader/templates/jobs/sui-job-error.html b/uploader/templates/jobs/sui-job-error.html deleted file mode 100644 index 1a839a6..0000000 --- a/uploader/templates/jobs/sui-job-error.html +++ /dev/null @@ -1,17 +0,0 @@ -{%extends "sui-base.html"%} - -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Background Jobs: Error{%endblock%} - -{%block pagetitle%}Background Jobs: Error{%endblock%} - -{%block contents%} - -<h1>Background Jobs: Error</h1> -<p>Job <strong>{{job["job_id"]}}</strong> failed!</p> -<p>The error details are in the "STDERR" section below.</p> - -<h2>STDERR</h2> -<pre>{{job["stderr"]}}</pre> -{%endblock%} diff --git a/uploader/templates/jobs/sui-job-not-found.html b/uploader/templates/jobs/sui-job-not-found.html deleted file mode 100644 index 96c8586..0000000 --- a/uploader/templates/jobs/sui-job-not-found.html +++ /dev/null @@ -1,11 +0,0 @@ -{%extends "sui-base.html"%} - -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Background Jobs{%endblock%} - -{%block pagetitle%}Background Jobs{%endblock%} - -{%block contents%} -<p>Could not find job with ID: {{job_id}}</p> -{%endblock%} diff --git a/uploader/templates/jobs/sui-job-status.html b/uploader/templates/jobs/sui-job-status.html deleted file mode 100644 index fc5e532..0000000 --- a/uploader/templates/jobs/sui-job-status.html +++ /dev/null @@ -1,24 +0,0 @@ -{%extends "sui-base.html"%} - -{%from "flash_messages.html" import flash_all_messages%} - -{%block extrameta%} -<meta http-equiv="refresh" content="5" /> -{%endblock%} - -{%block title%}Background Jobs{%endblock%} - -{%block pagetitle%}Background Jobs{%endblock%} - -{%block contents%} - -<p>Status: {{job["metadata"]["status"]}}</p> -<p>Job Type: {{job["metadata"]["job-type"]}}</p> - -<h2>STDOUT</h2> -<pre>{{job["stdout"]}}</pre> - -<h2>STDERR</h2> -<pre>{{job["stderr"]}}</pre> - -{%endblock%} diff --git a/uploader/templates/login.html b/uploader/templates/login.html deleted file mode 100644 index e76c644..0000000 --- a/uploader/templates/login.html +++ /dev/null @@ -1,12 +0,0 @@ -{%extends "index.html"%} - -{%block title%}Data Upload{%endblock%} - -{%block pagetitle%}log in{%endblock%} - -{%block extrapageinfo%} -<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-csv-fields.html b/uploader/templates/macro-csv-fields.html new file mode 100644 index 0000000..b58a6d0 --- /dev/null +++ b/uploader/templates/macro-csv-fields.html @@ -0,0 +1,139 @@ +{%macro display_csv_fields()%} +<div class="form-group"> + <div class="row mb-3"> + <label for="txt-file-separator" class="col-sm-3 col-form-label"> + File Separator</label> + <div class="col-sm-9"> + <div class="input-group"> + <input id="txt-file-separator" + name="file-separator" + type="text" + value="	" + class="form-control" + maxlength="1" /> + <span class="input-group-btn"> + <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button> + </span> + </div> + </div> + <span class="form-text text-muted"> + Provide the character that separates the fields in your file(s). It should + be the same character for all files (if more than one is provided).<br /> + A tab character will be assumed if you leave this field blank. See + <a href="#docs-file-separator" + title="Documentation for file-separator characters"> + documentation for more information</a>. + </span> + </div> +</div> + +<div class="form-group"> + <div class="row mb-3"> + <label for="txt-file-comment-character" class="col-sm-3 col-form-label">File Comment-Characters</label> + <div class="col-sm-9"> + <div class="input-group"> + <input id="txt-file-comment-character" + name="file-comment-character" + type="text" + value="#" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-comment-character" class="btn btn-info"> + Reset Default</button> + </span> + </div> + </div> + <span class="form-text text-muted"> + This specifies that lines that begin with the character(s) provided will be + considered comment lines and ignored in their entirety. See + <a href="#docs-file-comment-character" + title="Documentation for comment characters"> + documentation for more information</a>. + </span> + </div> +</div> + +<div class="form-group"> + <div class="row mb-3"> + <label for="txt-file-na" class="col-sm-3 col-form-label">File "No-Value" Indicators</label> + <div class="col-sm-9"> + <div class="input-group"> + <input id="txt-file-na" + name="file-na" + type="text" + value="- NA N/A" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button> + </span> + </div> + </div> + <span class="form-text text-muted"> + This specifies strings in your file indicate that there is no value for a + particular cell (a cell is where a column and row intersect). Provide a + space-separated list of strings if you have more than one way of + indicating no values. See + <a href="#docs-file-na" title="Documentation for no-value fields"> + documentation for more information</a>.</span> + </div> +</div> +{%endmacro%} + + +{%macro display_csv_fields_documentation()%} +<dl> + <dt id="docs-file-separator">File separator</dt> + <dd>The files you provide should be character-separated value (CSV) files. + We need to know what character you used to separate the values in your + file. Some common ones are the Tab character, the comma, etc.<br /> + Providing that information makes it possible for the system to parse and + process your files correctly.<br> + <strong>NOTE:</strong> All the files you upload MUST use the same + separator.</dd> + + <dt id="docs-file-comment-character">Comment characters</dt> + <dd>We support use of comment lines in your files. We only support one type + of comment style, the <em>line comment</em>.<br /> + This mean the comment begins at the start of the line, and the end of that + line indicates the end of that comment. If you have a really long comment, + then you need to break it across multiple lines, marking each line a + comment line.<br /> + The "comment character" is the character at the start of the line that + indicates that the line is a line comment.<br /> + You can provide more than one comment character, separated by spaces.</dd> + + <dt id="docs-file-na">No-Value indicator(s)</dt> + <dd>Data in the real world is messy, and in some cases, entirely absent. You + need to indicate, in your files, that a particular field did not have a + value, and once you do that, you then need to let the system know how you + mark such fields. Common ways of indicating "empty values" are, leaving + the field blank, using a character such as '-', or using strings like + "NA", "N/A", "NULL", etc.<br /> + Providing this information will help with parsing and processing such + no-value fields the correct way.</dd> +</dl> +{%endmacro%} + + +{%macro add_csv_fields_event_handlers()%} +<script type="text/javascript"> + $(function(evt) { + /* The reset buttons */ + $("#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"); + }); + }); +</script> +{%endmacro%} diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html index 9909c20..3207129 100644 --- a/uploader/templates/phenotypes/add-phenotypes-base.html +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -1,26 +1,13 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block contents%} +{{super()}} {{flash_all_messages()}} <div class="row"> @@ -42,8 +29,7 @@ {%block frm_add_phenotypes_elements%}{%endblock%} - <fieldset id="fldset-publication-info"> - <legend>Publication Information</legend> + <h4>Publication Information</h4> <input type="hidden" name="publication-id" id="txt-publication-id" /> <span class="form-text text-muted"> Select a publication for your data. <br /> @@ -57,7 +43,7 @@ <table id="tbl-select-publication" class="table compact stripe"> <thead> <tr> - <th>#</th> + <th>Index</th> <th>PubMed ID</th> <th>Title</th> <th>Authors</th> @@ -66,7 +52,6 @@ <tbody></tbody> </table> - </fieldset> <div class="form-group"> <input type="submit" @@ -83,6 +68,8 @@ {%endblock%} + + {%block javascript%} <script type="text/javascript"> $(function() { @@ -97,7 +84,8 @@ if(pub.PubMed_ID) { return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + `${pub.PubMed_ID}/" target="_blank" ` + - `title="Link to publication on NCBI.">` + + `title="Link to publication on NCBI. This will ` + + `open in a new tab.">` + `${pub.PubMed_ID}</a>`; } return ""; @@ -110,10 +98,7 @@ if(pub.Title) { title = pub.Title } - return `<a href="/publications/view/${pub.Id}" ` + - `target="_blank" ` + - `title="Link to view publication details">` + - `${title}</a>`; + return title; } }, { diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html index 67b56e3..79556cf 100644 --- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -1,7 +1,6 @@ {%extends "phenotypes/add-phenotypes-base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} {%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} @@ -9,19 +8,6 @@ {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block frm_add_phenotypes_documentation%} <p>This page will allow you to upload all the separate files that make up your phenotypes. Here, you will have to upload each separate file individually. If @@ -35,8 +21,7 @@ {%endblock%} {%block frm_add_phenotypes_elements%} -<fieldset id="fldset-file-metadata"> - <legend>File(s) Metadata</legend> + <h4>File(s) Metadata</h4> <div class="form-group"> <label for="txt-file-separator" class="form-label">File Separator</label> <div class="input-group"> @@ -103,12 +88,9 @@ <a href="#docs-file-na" title="Documentation for no-value fields"> documentation for more information</a>.</span> </div> -</fieldset> -<fieldset id="fldset-files"> <legend>Data File(s)</legend> - <fieldset id="fldset-descriptions-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-descriptions-transposed" @@ -159,10 +141,8 @@ {{display_preview_table( "tbl-preview-pheno-desc", "phenotype descriptions")}} </div> - </fieldset> - - <fieldset id="fldset-data-file"> + <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-data-transposed" @@ -210,11 +190,9 @@ on the expected format for the file provided here.</p>')}} {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}} </div> - </fieldset> {%if population.Family in families_with_se_and_n%} - <fieldset id="fldset-se-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-se-transposed" @@ -261,10 +239,8 @@ {{display_preview_table("tbl-preview-pheno-se", "standard errors")}} </div> - </fieldset> - <fieldset id="fldset-n-file"> <div class="form-group"> <div class="form-check"> <input id="chk-phenotype-n-transposed" @@ -311,8 +287,6 @@ {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} </div> - </fieldset> -</fieldset> {%endif%} {%endblock%} @@ -447,10 +421,6 @@ {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block more_javascript%} <script src="{{url_for('base.node_modules', @@ -495,7 +465,7 @@ .map((field) => { var value = field.trim(); if(navalues.includes(value)) { - return "⋘NUL⋙"; + return "[NO-VALUE]"; } return value; }) @@ -747,9 +717,7 @@ markResumableDragAndDropElement( makeResumableElement( the_form.attr("data-resumable-target"), - file_input.parent(), $("#" + resumable_element_id), - submit_button, ["csv", "tsv", "txt"]), file_input.parent(), $("#" + resumable_element_id), diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html index 898fc0c..4afd6ab 100644 --- a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -1,25 +1,11 @@ {%extends "phenotypes/add-phenotypes-base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block frm_add_phenotypes_documentation%} <p>Select the zip file bundle containing information on the phenotypes you wish to upload, then click the "Upload Phenotypes" button below to @@ -201,7 +187,3 @@ <em>phenotypes × individuals</em>.</p> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html index adbc012..5959422 100644 --- a/uploader/templates/phenotypes/base.html +++ b/uploader/templates/phenotypes/base.html @@ -1,19 +1,27 @@ {%extends "populations/base.html"%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if dataset is mapping%} +{%block breadcrumbs%} +{{super()}} +{%if dataset%} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.phenotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">{{dataset.Name}}</a> - {%else%} - <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a> - {%endif%} + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}"> + {{dataset["Name"]}} + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endif%} +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> +</div> +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_pheno_dataset_card(species, population, dataset)}} {%endblock%} diff --git a/uploader/templates/phenotypes/confirm-delete-phenotypes.html b/uploader/templates/phenotypes/confirm-delete-phenotypes.html new file mode 100644 index 0000000..3cf6e65 --- /dev/null +++ b/uploader/templates/phenotypes/confirm-delete-phenotypes.html @@ -0,0 +1,196 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Delete Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="view-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"><h2>Delete Phenotypes</h2></div> + +{%if phenotypes | length > 0%} +<div class="row"> + <p>You have requested to delete the following phenotypes:</p> +</div> + +<div class="row"> + <div class="col"> + <a id="btn-select-all-phenotypes" + href="#" + class="btn btn-info" + title="Select all phenotypes">select all</a> + </div> + <div class="col"> + <a id="btn-deselect-all-phenotypes" + href="#" + class="btn btn-warning" + title="Deselect all phenotypes">deselect all</a> + </div> +</div> + +<div class="row"> + <table id="tbl-delete-phenotypes" class="table"> + <thead> + <tr> + <th>Index</th> + <th>Record ID</th> + <th>Description</th> + </tr> + </thead> + <tbody> + {%for phenotype in phenotypes%} + <tr> + <td> + <input id="chk-xref-id-{{phenotype.xref_id}}" + name="xref_ids" + type="checkbox" + value="{{phenotype.xref_id}}" + class="chk-row-select" /> + </td> + <td>{{phenotype.xref_id}}</td> + <td>{{phenotype.Post_publication_description or + phenotype.Pre_publication_description or + phenotype.original_description}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> + +<div class="row"> + <form id="frm-delete-phenotypes-selected" + method="POST" + action="{{url_for('species.populations.phenotypes.delete_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <div class="row"> + <div class="col"> + <input class="btn btn-info" + type="submit" + title="Cancel delete and return to dataset page." + name="action" + value="cancel" /></div> + <div class="col"> + <input id="btn-delete-phenotypes-selected" + class="btn btn-danger" + type="submit" + title="Delete the selected phenotypes from this dataset." + name="action" + value="delete" /> + </div> + </div> + </form> +</div> +{%else%} +<div class="row"> + <p>You did not select any phenotypes to delete. Delete everything?</p> +</div> + +<div class="row"> + <form id="frm-delete-phenotypes-all" + method="POST" + action="{{url_for('species.populations.phenotypes.delete_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}"> + <div class="form-check"> + <input class="form-check-input" + type="checkbox" + name="confirm_delete_all_phenotypes" + id="chk-confirm-delete-all-phenotypes" /> + <label class="form-check-label" + for="chk-confirm-delete-all-phenotypes"> + delete all phenotypes?</label> + </div> + + <div class="row"> + <div class="col"> + <input class="btn btn-info" + type="submit" + title="Cancel delete and return to dataset page." + name="action" + value="cancel" /></div> + <div class="col"> + <input class="btn btn-danger" + type="submit" + title="Delete all phenotypes in this dataset." + name="action" + value="delete" /> + </div> + </div> + </form> +</div> +{%endif%} + +{%endblock%} + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var dt = buildDataTable( + "#tbl-delete-phenotypes", + data=[], + columns=[], + userSettings={ + responsive: true, + select: { + style: "os", + info: false + }, + initComplete: function(setting, json) { + var api = this.api(); + api.rows().select(); + api.rows({selected: true}).nodes().each((node, index) => { + setRowChecked(node); + }); + } + }); + + $("#btn-select-all-phenotypes").on("click", function(event) { + dt.selectAll(); + }); + + $("#btn-deselect-all-phenotypes").on("click", function(event) { + dt.deselectAll(); + }); + + $("#btn-delete-phenotypes-selected").on("click", function(event) { + event.preventDefault(); + form = $("#frm-delete-phenotypes-selected"); + form.find(".dynamically-added-element").remove(); + dt.rows({selected: true}).nodes().each(function(node, index) { + var xref_id = $(node) + .find('input[type="checkbox"]:checked') + .val(); + var chk = $('<input type="checkbox">'); + chk.attr("class", "dynamically-added-element"); + chk.attr("value", xref_id); + chk.attr("name", "xref_ids"); + chk.attr("style", "display: none"); + chk.prop("checked", true); + form.append(chk); + }); + form.append( + $('<input type="hidden" name="action" value="delete" />')); + form.submit(); + }) + }); +</script> +{%endblock%} + diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html index 19a2b34..9963953 100644 --- a/uploader/templates/phenotypes/create-dataset.html +++ b/uploader/templates/phenotypes/create-dataset.html @@ -48,7 +48,8 @@ {%else%} class="form-control" {%endif%} - required="required" /> + required="required" + readonly="readonly" /> <small class="form-text text-muted"> <p>A short representative name for the dataset.</p> <p>Recommended: Use the population name and append "Publish" at the end. @@ -66,7 +67,7 @@ <input id="txt-dataset-fullname" name="dataset-fullname" type="text" - value="{{original_formdata.get('dataset-fullname', '')}}" + value="{{original_formdata.get('dataset-fullname', '') or population.Name + ' Phenotypes'}}" {%if errors["dataset-fullname"] is defined%} class="form-control danger" {%else%} diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html index 115d6af..1b3ee9d 100644 --- a/uploader/templates/phenotypes/edit-phenotype.html +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -142,7 +142,7 @@ <table class="table table-striped table-responsive table-form-table"> <thead style="position: sticky; top: 0;"> <tr> - <th>#</th> + <th>Index</th> <th>Sample</th> <th>Value</th> {%if population.Family in families_with_se_and_n%} diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html index 257f726..951907f 100644 --- a/uploader/templates/phenotypes/job-status.html +++ b/uploader/templates/phenotypes/job-status.html @@ -2,7 +2,6 @@ {%from "cli-output.html" import cli_output%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block extrameta%} {%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} @@ -14,23 +13,13 @@ {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">View Datasets</a> -</li> -{%endblock%} - {%block contents%} {%if job%} -<h4 class="subheading">Progress</h4> +<div class="row"> + <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> + <h3 class="subheading">upload progress</h3> +</div> <div class="row" style="overflow:scroll;"> <p><strong>Process Status:</strong> {{job.status}}</p> {%if metadata%} @@ -63,10 +52,10 @@ <p> {%if errors | length == 0%} <a href="{{url_for('species.populations.phenotypes.review_job_data', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - job_id=job_id)}}" + 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%} @@ -80,14 +69,29 @@ {%endif%} </div> -<h4 class="subheading">Errors</h4> +<h3 class="subheading">upload errors</h3> +{%if errors | length == 0 %} <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%} +</div> +{%else%} +{%if errors | length > 0%} +<div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.download_errors', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" + class="btn btn-info" + title="Download the errors as a CSV file.">download errors CSV</a> + </div> +</div> +{%endif%} +<div class="row" style="max-height: 20em; overflow: scroll;"> <table class="table table-responsive"> <thead style="position: sticky; top: 0; background: white;"> <tr> @@ -122,7 +126,8 @@ {%endfor%} </tbody> </table> - {%endif%} +</div> +{%endif%} </div> <div class="row"> @@ -149,7 +154,3 @@ </div> {%endif%} {%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html index 645be16..1fb0e61 100644 --- a/uploader/templates/phenotypes/load-phenotypes-success.html +++ b/uploader/templates/phenotypes/load-phenotypes-success.html @@ -1,26 +1,14 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="load-phenotypes-success"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - {%block contents%} +{{super()}} + <div class="row"> <p>You have successfully loaded <!-- maybe indicate the number of phenotypes here? -->your @@ -34,9 +22,5 @@ </div> {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html index 5a4c422..6dffe9f 100644 --- a/uploader/templates/phenotypes/macro-display-preview-table.html +++ b/uploader/templates/phenotypes/macro-display-preview-table.html @@ -1,19 +1,11 @@ {%macro display_preview_table(tableid, filetype)%} -<div class="card"> - <div class="card-body"> - <h5 class="card-title">{{filetype | title}}: File Preview</h5> - <div class="card-text" style="overflow: scroll;"> - <table id="{{tableid}}" class="table table-condensed table-responsive"> - <thead> - <tr> - </tr> - <tbody> - <tr> - <td class="data-row-template text-info"></td> - </tr> - </tbody> - </table> - </div> - </div> +<div class="table-responsive" + style="max-width:39.2em;border-radius:5px;border: solid 1px;overflow-x: scroll;"> + <h5>{{filetype | title}}: File Preview</h5> + <table id="{{tableid}}" class="table"> + <thead><tr></tr></thead> + + <tbody></tbody> + </table> </div> {%endmacro%} diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html index 859df74..0e8f119 100644 --- a/uploader/templates/phenotypes/review-job-data.html +++ b/uploader/templates/phenotypes/review-job-data.html @@ -70,6 +70,9 @@ {%endif%} {%endfor%} </ul> +</div> + +<div class="row"> <form id="frm-review-phenotype-data" method="POST" @@ -78,10 +81,38 @@ population_id=population.Id, dataset_id=dataset.Id)}}"> <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> - <input type="submit" - value="continue" - class="btn btn-primary" /> + <div class="form-group"> + <label for="txt-data-name">data name</label> + <input type="text" + id="txt-data-name" + class="form-control" + name="data_name" + title="A short, descriptive name for this data." + placeholder="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + value="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + required="required"> + <span class="form-text text-muted"> + This is a short, descriptive name for the data. It is useful to humans, + enabling them identify what traits each data "resource" wraps around. + </span> + </div> + + {%if view_under_construction%} + <div class="form-group"> + <label for="txt-data-description">data description</label> + <textarea id="txt-data-description" + class="form-control" + name="data_description" + title="A longer description for this data." + rows="5"></textarea> + <span class="form-text text-muted"> + </span> + </div> + {%endif%} + + <button type="submit" class="btn btn-primary">continue</button> </form> + </div> {%else%} <div class="row"> @@ -104,10 +135,6 @@ {%endif%} {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block javascript%} <script type="text/javascript"> diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-base.html b/uploader/templates/phenotypes/sui-add-phenotypes-base.html deleted file mode 100644 index 1e71267..0000000 --- a/uploader/templates/phenotypes/sui-add-phenotypes-base.html +++ /dev/null @@ -1,155 +0,0 @@ -{%extends "phenotypes/sui-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block contents%} -{{super()}} -{{flash_all_messages()}} - -<div class="row"> - <form id="frm-add-phenotypes" - method="POST" - enctype="multipart/form-data" - action="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - use_bundle=use_bundle)}}" - data-resumable-target="{{url_for('files.resumable_upload_post')}}"> - <legend>Add New Phenotypes</legend> - - <div class="form-text help-block"> - {%block frm_add_phenotypes_documentation%}{%endblock%} - <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> - </div> - - {%block frm_add_phenotypes_elements%}{%endblock%} - - <fieldset id="fldset-publication-info"> - <legend>Publication Information</legend> - <input type="hidden" name="publication-id" id="txt-publication-id" /> - <span class="form-text text-muted"> - Select a publication for your data. <br /> - Can't find a publication you can use? Go ahead and - <a href="{{url_for( - 'publications.create_publication', - return_to='species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">create a new publication</a>.</span> - <table id="tbl-select-publication" class="table compact stripe"> - <thead> - <tr> - <th>#</th> - <th>PubMed ID</th> - <th>Title</th> - <th>Authors</th> - </tr> - </thead> - - <tbody></tbody> - </table> - </fieldset> - - <div class="form-group"> - <input type="submit" - value="upload phenotypes" - class="btn btn-primary" /> - </div> - </form> -</div> - -<div class="row"> - {%block page_documentation%}{%endblock%} -</div> - -{%endblock%} - - - - -{%block javascript%} -<script type="text/javascript"> - $(function() { - var publicationsDataTable = buildDataTable( - "#tbl-select-publication", - [], - [ - {data: "index"}, - { - searchable: true, - data: (pub) => { - if(pub.PubMed_ID) { - return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + - `${pub.PubMed_ID}/" target="_blank" ` + - `title="Link to publication on NCBI.">` + - `${pub.PubMed_ID}</a>`; - } - return ""; - } - }, - { - searchable: true, - data: (pub) => { - var title = "⸻"; - if(pub.Title) { - title = pub.Title - } - return `<a href="/publications/view/${pub.Id}" ` + - `target="_blank" ` + - `title="Link to view publication details">` + - `${title}</a>`; - } - }, - { - searchable: true, - data: (pub) => { - authors = pub.Authors.split(",").map( - (item) => {return item.trim();}); - if(authors.length > 1) { - return authors[0] + ", et. al."; - } - return authors[0]; - } - } - ], - { - serverSide: true, - ajax: { - url: "/publications/list", - dataSrc: "publications" - }, - select: "single", - paging: true, - scrollY: 700, - deferRender: true, - scroller: true, - scrollCollapse: true, - layout: { - topStart: "info", - topEnd: "search" - } - }); - publicationsDataTable.on("select", (event, datatable, type, indexes) => { - indexes.forEach((element, index, thearray) => { - let row = datatable.row(element).node(); - console.debug(datatable.row(element).data()); - $("#frm-add-phenotypes #txt-publication-id").val( - datatable.row(element).data().Id); - }); - }); - publicationsDataTable.on("deselect", (event, datatable, type, indexes) => { - indexes.forEach((element, index, thearray) => { - let row = datatable.row(element).node(); - $("#frm-add-phenotypes #txt-publication-id").val(null); - }); - }); - }); -</script> - -{%block more_javascript%}{%endblock%} -{%endblock%} diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html b/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html deleted file mode 100644 index 6038617..0000000 --- a/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html +++ /dev/null @@ -1,829 +0,0 @@ -{%extends "phenotypes/sui-add-phenotypes-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} -{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block frm_add_phenotypes_documentation%} -<p>This page will allow you to upload all the separate files that make up your - phenotypes. Here, you will have to upload each separate file individually. If - you want instead to upload all your files as a single ZIP file, - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - use_bundle=true)}}" - title="">click here</a>.</p> -{%endblock%} - -{%block frm_add_phenotypes_elements%} -<fieldset id="fldset-file-metadata"> - <legend>File(s) Metadata</legend> - <div class="form-group"> - <label for="txt-file-separator" class="form-label">File Separator</label> - <div class="input-group"> - <input id="txt-file-separator" - name="file-separator" - type="text" - value="	" - class="form-control" - maxlength="1" /> - <span class="input-group-btn"> - <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button> - </span> - </div> - <span class="form-text text-muted"> - Provide the character that separates the fields in your file(s). It should - be the same character for all files (if more than one is provided).<br /> - A tab character will be assumed if you leave this field blank. See - <a href="#docs-file-separator" - title="Documentation for file-separator characters"> - documentation for more information</a>. - </span> - </div> - - <div class="form-group"> - <label for="txt-file-comment-character" class="form-label">File Comment-Character</label> - <div class="input-group"> - <input id="txt-file-comment-character" - name="file-comment-character" - type="text" - value="#" - class="form-control" - maxlength="1" /> - <span class="input-group-btn"> - <button id="btn-reset-file-comment-character" class="btn btn-info"> - Reset Default</button> - </span> - </div> - <span class="form-text text-muted"> - This specifies that lines that begin with the character provided will be - considered comment lines and ignored in their entirety. See - <a href="#docs-file-comment-character" - title="Documentation for comment characters"> - documentation for more information</a>. - </span> - </div> - - <div class="form-group"> - <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label> - <div class="input-group"> - <input id="txt-file-na" - name="file-na" - type="text" - value="- NA N/A" - class="form-control" /> - <span class="input-group-btn"> - <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button> - </span> - </div> - <span class="form-text text-muted"> - This specifies strings in your file indicate that there is no value for a - particular cell (a cell is where a column and row intersect). Provide a - space-separated list of strings if you have more than one way of - indicating no values. See - <a href="#docs-file-na" title="Documentation for no-value fields"> - documentation for more information</a>.</span> - </div> -</fieldset> - -<fieldset id="fldset-files"> - <legend>Data File(s)</legend> - - <fieldset id="fldset-descriptions-file"> - <div class="form-group"> - <div class="form-check"> - <input id="chk-phenotype-descriptions-transposed" - name="phenotype-descriptions-transposed" - type="checkbox" - class="form-check-input" - style="border: solid #8EABF0" /> - <label for="chk-phenotype-descriptions-transposed" - class="form-check-label"> - Description file transposed?</label> - </div> - - <div class="non-resumable-elements"> - <label for="finput-phenotype-descriptions" class="form-label"> - Phenotype Descriptions</label> - <input id="finput-phenotype-descriptions" - name="phenotype-descriptions" - class="form-control" - type="file" - data-preview-table="tbl-preview-pheno-desc" - required="required" /> - <span class="form-text text-muted"> - Provide a file that contains only the phenotype descriptions, - <a href="#docs-file-phenotype-description" - title="Documentation of the phenotype data file format."> - the documentation for the expected format of the file</a>.</span> - </div> - {{display_resumable_elements( - "resumable-phenotype-descriptions", - "phenotype descriptions", - '<p>Drag and drop the CSV file that contains the descriptions of your - phenotypes here.</p> - - <p>The CSV file should be a matrix of - <strong>phenotypes × descriptions</strong> i.e. The first column - contains the phenotype names/identifiers whereas the first row is a list - of metadata fields like, "description", "units", etc.</p> - - <p>If the format is transposed (i.e. - <strong>descriptions × phenotypes</strong>) select the checkbox above. - </p> - - <p>Please see the - <a href="#docs-file-phenotype-description" - title="Documentation of the phenotype data file format."> - "Phenotypes Descriptions" documentation</a> section below for more - information on the expected format of the file provided here.</p>')}} - {{display_preview_table( - "tbl-preview-pheno-desc", "phenotype descriptions")}} - </div> - </fieldset> - - - <fieldset id="fldset-data-file"> - <div class="form-group"> - <div class="form-check"> - <input id="chk-phenotype-data-transposed" - name="phenotype-data-transposed" - type="checkbox" - class="form-check-input" - style="border: solid #8EABF0" /> - <label for="chk-phenotype-data-transposed" class="form-check-label"> - Data file transposed?</label> - </div> - - <div class="non-resumable-elements"> - <label for="finput-phenotype-data" class="form-label">Phenotype Data</label> - <input id="finput-phenotype-data" - name="phenotype-data" - class="form-control" - type="file" - data-preview-table="tbl-preview-pheno-data" - required="required" /> - <span class="form-text text-muted"> - Provide a file that contains only the phenotype data. See - <a href="#docs-file-phenotype-data" - title="Documentation of the phenotype data file format."> - the documentation for the expected format of the file</a>.</span> - </div> - - {{display_resumable_elements( - "resumable-phenotype-data", - "phenotype data", - '<p>Drag and drop a CSV file that contains the phenotypes numerical data - here. You can click the "Browse" button (below and to the right) to - select the file from your computer.</p> - - <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, - i.e. The first column contains the samples identifiers while the first - row is the list of phenotypes identifiers occurring in the phenotypes - descriptions file.</p> - - <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) - select the checkbox above.</p> - <p>Please see the - <a href="#docs-file-phenotype-data" - title="Documentation of the phenotype data file format."> - "Phenotypes Data" documentation</a> section below for more information - on the expected format for the file provided here.</p>')}} - {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}} - </div> - </fieldset> - - - {%if population.Family in families_with_se_and_n%} - <fieldset id="fldset-se-file"> - <div class="form-group"> - <div class="form-check"> - <input id="chk-phenotype-se-transposed" - name="phenotype-se-transposed" - type="checkbox" - class="form-check-input" - style="border: solid #8EABF0" /> - <label for="chk-phenotype-se-transposed" class="form-check-label"> - Standard-Errors file transposed?</label> - </div> - <div class="group non-resumable-elements"> - <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label> - <input id="finput-phenotype-se" - name="phenotype-se" - class="form-control" - type="file" - data-preview-table="tbl-preview-pheno-se" - required="required" /> - <span class="form-text text-muted"> - Provide a file that contains only the standard errors for the phenotypes, - computed from the data above.</span> - </div> - - {{display_resumable_elements( - "resumable-phenotype-se", - "standard errors", - '<p>Drag and drop a CSV file that contains the phenotypes standard-errors - data here. You can click the "Browse" button (below and to the right) to - select the file from your computer.</p> - - <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, - i.e. The first column contains the samples identifiers while the first - row is the list of phenotypes identifiers occurring in the phenotypes - descriptions file.</p> - - <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) - select the checkbox above.</p> - - <p>Please see the - <a href="#docs-file-phenotype-se" - title="Documentation of the phenotype data file format."> - "Phenotypes Data" documentation</a> section below for more information - on the expected format of the file provided here.</p>')}} - - {{display_preview_table("tbl-preview-pheno-se", "standard errors")}} - </div> - </fieldset> - - - <fieldset id="fldset-n-file"> - <div class="form-group"> - <div class="form-check"> - <input id="chk-phenotype-n-transposed" - name="phenotype-n-transposed" - type="checkbox" - class="form-check-input" - style="border: solid #8EABF0" /> - <label for="chk-phenotype-n-transposed" class="form-check-label"> - Counts file transposed?</label> - </div> - <div class="non-resumable-elements"> - <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label> - <input id="finput-phenotype-n" - name="phenotype-n" - class="form-control" - type="file" - data-preview-table="tbl-preview-pheno-n" - required="required" /> - <span class="form-text text-muted"> - Provide a file that contains only the number of samples/individuals used in - the computation of the standard errors above.</span> - </div> - - {{display_resumable_elements( - "resumable-phenotype-n", - "number of samples/individuals", - '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts - data here. You can click the "Browse" button (below and to the right) to - select the file from your computer.</p> - - <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>, - i.e. The first column contains the samples identifiers while the first - row is the list of phenotypes identifiers occurring in the phenotypes - descriptions file.</p> - - <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>) - select the checkbox above.</p> - - <p>Please see the - <a href="#docs-file-phenotype-se" - title="Documentation of the phenotype data file format."> - "Phenotypes Data" documentation</a> section below for more information - on the expected format of the file provided here.</p>')}} - - {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}} - </div> - </fieldset> -</fieldset> -{%endif%} -{%endblock%} - - -{%block page_documentation%} -<div class="row"> - <h2 class="heading" id="docs-help">Help</h2> - <h3 class="subheading">Common Features</h3> - <p>The following are the common expectations for <strong>ALL</strong> the - files provided in the form above: - <ul> - <li>The file <strong>MUST</strong> be character-separated values (CSV) - text file</li> - <li>The first row in the file <strong>MUST</strong> be a heading row, and - will be composed of the list identifiers for all of - samples/individuals/cases involved in your study.</li> - <li>The first column of data in the file <strong>MUST</strong> be the - identifiers for all of the phenotypes you wish to upload.</li> - </ul> - </p> - - <p>If you do not specify the separator character, then we will assume a - <strong>TAB</strong> character was used as your separator.</p> - - <p>We also assume you might include comments lines in your files. In that - case, if you do not specify what character denotes that a line in your files - is a comment line, we will assume the <strong>#</strong> character.<br /> - A comment <strong>MUST ALWAYS</strong> begin at the start of the line marked - with the comment character specified.</p> - - <h3 class="subheading" id="docs-file-metadata">File Metadata</h3> - <p>We request some details about your files to help us parse and process the - files correctly. The details we collect are:</p> - <dl> - <dt id="docs-file-separator">File separator</dt> - <dd>The files you provide should be character-separated value (CSV) files. - We need to know what character you used to separate the values in your - file. Some common ones are the Tab character, the comma, etc.<br /> - Providing that information makes it possible for the system to parse and - process your files correctly.<br> - <strong>NOTE:</strong> All the files you upload MUST use the same - separator.</dd> - - <dt id="docs-file-comment-character">Comment character</dt> - <dd>We support use of comment lines in your files. We only support one type - of comment style, the <em>line comment</em>.<br /> - This mean the comment begins at the start of the line, and the end of that - line indicates the end of that comment. If you have a really long comment, - then you need to break it across multiple lines, marking each line a - comment line.<br /> - The "comment character" is the character at the start of the line that - indicates that the line is a line comment.</dd> - - <dt id="docs-file-na">No-Value indicator(s)</dt> - <dd>Data in the real world is messy, and in some cases, entirely absent. You - need to indicate, in your files, that a particular field did not have a - value, and once you do that, you then need to let the system know how you - mark such fields. Common ways of indicating "empty values" are, leaving - the field blank, using a character such as '-', or using strings like - "NA", "N/A", "NULL", etc.<br /> - Providing this information will help with parsing and processing such - no-value fields the correct way.</dd> - </dl> - - <h3 class="subheading" id="docs-file-phenotype-description"> - file: Phenotypes Descriptions</h3> - <p>The data in this file is a matrix of <em>phenotypes × metadata-fields</em>. - Please note we use the term "metadata-fields" above loosely, due to lack of - a good word for this.</p> - <p>The file <strong>MUST</strong> have columns in this order: - <dl> - <dt>Phenotype Identifiers</dt> - <dd>These are the names/identifiers for your phenotypes. These - names/identifiers are the same ones you will have in all the other files you are - uploading.</dd> - - <dt>Descriptions</dt> - <dd>Each phenotype will need a description. Good description are necessary - to inform other people of what the data is about. Good description are - hard to construct, so we provide - <a href="https://info.genenetwork.org/faq.php#q-22" - title="How to write phenotype descriptions"> - advice on describing your phenotypes.</a></dd> - - <dt>Units</dt> - <dd>Each phenotype will need units for the measurements taken. If there are - none, then indicate the field is a no-value field.</dd> - </dl></p> - <p>You can add more columns after those three if you want to, but these 3 - <strong>MUST</strong> be present.</p> - <p>The file would, for example, look like the following:</p> - <code>id,description,units,…<br /> - pheno10001|Central nervous system, behavior, cognition; …|mg|…<br /> - pheno10002|Aging, metabolism, central nervous system: …|mg|…<br /> - ⋮<br /></code> - - <p><strong>Note 01</strong>: The first usable row is the heading row.</p> - <p><strong>Note 02: </strong>This example demonstrates a subtle issue that - could make your CSV file invalid — the choice of your field separator - character.<br > - In the example above, we use the pipe character (<code>|</code>) as our - field separator. This is because, if we follow the advice on how to write - good descriptions, then we cannot use the comma as our separator – if - we did, then our CSV file would be invalid because the system would have no - way to tell the difference between the comma as a field separator, and the - comma as a way to separate the "general category and ontology terms".</p> - - <h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3> - <span id="docs-file-phenotype-data"></span> - <span id="docs-file-phenotype-se"></span> - <span id="docs-file-phenotype-n"></span> - <p>The data is a matrix of <em>samples(or individuals) × phenotypes</em>, e.g.</p> - <code> - # num-cases: 2549 - # num-phenos: 13 - id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br /> - IND001,61.400002,49,62.5,55.099998,…<br /> - IND002,54.099998,50.099998,53.299999,55.099998,…<br /> - IND003,483,403,501,403,…<br /> - IND004,49.799999,45.5,62.900002,NA,…<br /> - ⋮<br /></code> - - <p>where <code>IND001,IND002,IND003,IND004,…</code> are the - samples/individuals/cases in your study, and - <code>pheno10001,pheno10002,pheno10004,pheno10004,…</code> are the - identifiers for your phenotypes.</p> - <p>The lines beginning with the "<em>#</em>" symbol (i.e. - <code># num-cases: 2549</code> and <code># num-phenos: 13</code> are comment - lines and will be ignored</p> - <p>In this example, the comma (,) is used as the file separator.</p> -</div> - -{%endblock%} - - -{%block 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"), "visually-hidden"); - } else { - remove_class(table.find(".data-row-template"), "visually-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[0].files.length > 0) { - readFirstNLines( - file_input[0].files[0], - 10, - [makePreviewUpdater(preview_table)]); - } - }); - - if(typeof(resumables) !== "undefined") { - resumables.forEach((resumable) => { - if(resumable.files.length > 0) { - readFirstNLines( - resumable.files[0].file, - 10, - [makePreviewUpdater(resumable.preview_table)]); - } - }); - } - }; - - [ - "#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, "visually-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, "visually-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, "visually-hidden"); - remove_class(cancel_button, "visually-hidden"); - add_class(browse_button, "visually-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, "visually-hidden"); - remove_class(retry_button, "visually-hidden"); - remove_class(browse_button, "visually-hidden"); - }); - }; - - - var startUpload = (browse_button, retry_button, cancel_button) => { - return (event) => { - remove_class(cancel_button, "visually-hidden"); - add_class(retry_button, "visually-hidden"); - add_class(browse_button, "visually-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"); - formdata.append("publication-id", $("#txt-publication-id").val()); - 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", "txt"]), - 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) => { - r = makeResumableObject(row[0], row[1], row[2], row[3]); - r.preview_table = $("#" + row[3]); - return r; - }).filter((val) => { - return Boolean(val); - }); - - $("#frm-add-phenotypes input[type=submit]").on("click", (event) => { - event.preventDefault(); - console.debug(); - if ($("#txt-publication-id").val() == "") { - alert("You MUST provide a publication for the phenotypes."); - return false; - } - // TODO: Check all the relevant files exist - // TODO: Verify that files are not duplicated - var filenames = []; - 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/sui-add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html deleted file mode 100644 index 29a8dea..0000000 --- a/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html +++ /dev/null @@ -1,189 +0,0 @@ -{%extends "phenotypes/sui-add-phenotypes-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block frm_add_phenotypes_documentation%} -<p>Select the zip file bundle containing information on the phenotypes you - wish to upload, then click the "Upload Phenotypes" button below to - upload the data.</p> -<p>If you wish to upload the files individually instead, - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="">click here</a>.</p> -<p>See the <a href="#section-file-formats">File Formats</a> section below - to get an understanding of what is expected of the bundle files you - upload.</p> -{%endblock%} - -{%block frm_add_phenotypes_elements%} -<div class="form-group"> - <label for="finput-phenotypes-bundle" class="form-label"> - Phenotypes Bundle</label> - <input type="file" - id="finput-phenotypes-bundle" - name="phenotypes-bundle" - accept="application/zip, .zip" - required="required" - class="form-control" /> -</div> -{%endblock%} - -{%block page_documentation%} -<div class="row"> - <h2 class="heading" id="section-file-formats">File Formats</h2> - <p>We accept an extended form of the - <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files" - title="R/qtl2 software input file format documentation"> - input files' format used with the R/qtl2 software</a> as a single ZIP - file</p> - <p>The files that are used for this feature are: - <ul> - <li>the <em>control</em> file</li> - <li><em>pheno</em> file(s)</li> - <li><em>phenocovar</em> file(s)</li> - <li><em>phenose</em> files(s)</li> - </ul> - </p> - <p>Other files within the bundle will be ignored, for this feature.</p> - <p>The following section will detail the expectations for each of the - different file types within the uploaded ZIP file bundle for phenotypes:</p> - - <h3 class="subheading">Control File</h3> - <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts - as the control file. This file can be: - <ul> - <li>a <em>JSON</em> file, or</li> - <li>a <em>YAML</em> file.</li> - </ul> - </p> - - <p>The control file is useful for defining things about the bundle such as:</p> - <ul> - <li>The field separator value (default: <code>sep: ','</code>). There can - only ever be one field separator and it <strong>MUST</strong> be the same - one for <strong>ALL</strong> files in the bundle.</li> - <li>The comment character (default: <code>comment.char: '#'</code>). Any - line that starts with this character will be considered a comment line and - be ignored in its entirety.</li> - <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You - can specify more than one code to indicate missing values, e.g. - <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li> - </ul> - - <h3 class="subheading"><em>pheno</em> File(s)</h3> - <p>These files are the main data files. You must have at least one of these - files in your bundle for it to be valid for this step.</p> - <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as - below:<br /> - <code> - id,10001,10002,10003,10004,…<br /> - BXD1,61.400002,54.099998,483,49.799999,…<br /> - BXD2,49,50.099998,403,45.5,…<br /> - BXD5,62.5,53.299999,501,62.900002,…<br /> - BXD6,53.099998,55.099998,403,NA,…<br /> - ⋮<br /></code> - </p> - <p>If the <code>pheno_transposed</code> value is set to <code>True</code>, - then the data will be a <em>phenotypes × individuals</em> matrix as in the - example below:<br /> - <code> - id,BXD1,BXD2,BXD5,BXD6,…<br /> - 10001,61.400002,49,62.5,53.099998,…<br /> - 10002,54.099998,50.099998,53.299999,55.099998,…<br /> - 10003,483,403,501,403,…<br /> - 10004,49.799999,45.5,62.900002,NA,…<br /> - ⋮ - </code> - </p> - - - <h3 class="subheading"><em>phenocovar</em> File(s)</h3> - <p>At least one phenotypes metadata file with the metadata values such as - descriptions, PubMed Identifier, publication titles (if present), etc.</p> - <p>The data in this/these file(s) is a matrix of - <em>phenotypes × phenotypes-covariates</em>. The first column is always the - phenotype names/identifiers — same as in the R/qtl2 format.</p> - <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p> - <p>This file <strong>MUST</strong> be present in the bundle, and have data for - the bundle to be considered valid by our system for this step.<br /> - In addition to that, the following are the fields that <strong>must be - present</strong>, and - have values, in the file before the file is considered valid: - <ul> - <li><em>description</em>: A description for each phenotype. Useful - for users to know what the phenotype is about.</li> - <li><em>units</em>: The units of measurement for the phenotype, - e.g. milligrams for brain weight, centimetres/millimetres for - tail-length, etc.</li> - </ul></p> - - <p>The following <em>optional</em> fields can also be provided: - <ul> - <li><em>pubmedid</em>: A PubMed Identifier for the publication where - the phenotype is published. If this field is not provided, the system will - assume your phenotype is not published.</li> - </ul> - </p> - <p>These files will be marked up in the control file with the - <code>phenocovar</code> key, as in the examples below: - <ol> - <li>JSON: single file<br /> - <code>{<br /> - ⋮,<br /> - "phenocovar": "your_covariates_file.csv",<br /> - ⋮<br /> - } - </code> - </li> - <li>JSON: multiple files<br /> - <code>{<br /> - ⋮,<br /> - "phenocovar": [<br /> - "covariates_file_01.csv",<br /> - "covariates_file_01.csv",<br /> - ⋮<br /> - ],<br /> - ⋮<br /> - } - </code> - </li> - <li>YAML: single file or<br /> - <code> - ⋮<br /> - phenocovar: your_covariates_file.csv<br /> - ⋮ - </code> - </li> - <li>YAML: multiple files<br /> - <code> - ⋮<br /> - phenocovar:<br /> - - covariates_file_01.csv<br /> - - covariates_file_02.csv<br /> - - covariates_file_03.csv<br /> - …<br /> - ⋮ - </code> - </li> - </ol> - </p> - - <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3> - <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are - not supported by the original R/qtl2 file format</p> - <p>We use these files to upload the standard errors (<em>phenose</em>) when - the data file (<em>pheno</em>) is average data. In that case, the - <em>phenonum</em> file(s) contains the number of individuals that were - involved when computing the averages.</p> - <p>Both types of files are matrices of <em>individuals × phenotypes</em> by - default. Like the related <em>pheno</em> files, if - <code>pheno_transposed: True</code>, then the file will be a matrix of - <em>phenotypes × individuals</em>.</p> -</div> -{%endblock%} diff --git a/uploader/templates/phenotypes/sui-base.html b/uploader/templates/phenotypes/sui-base.html deleted file mode 100644 index d7d980f..0000000 --- a/uploader/templates/phenotypes/sui-base.html +++ /dev/null @@ -1,25 +0,0 @@ -{%extends "populations/sui-base.html"%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%} - -{%block breadcrumbs%} -{{super()}} -<li class="breadcrumb-item"> - <a href="{{url_for('species.populations.phenotypes.view_dataset', - species_id=species['SpeciesId'], - population_id=population['Id'], - dataset_id=dataset['Id'])}}"> - {{dataset["Name"]}} - </a> -</li> -{%endblock%} - -{%block contents%} -<div class="row"> - <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> -</div> -{%endblock%} - - -{%block sidebarcontents%} -{{display_sui_pheno_dataset_card(species, population, dataset)}} -{%endblock%} diff --git a/uploader/templates/phenotypes/sui-job-status.html b/uploader/templates/phenotypes/sui-job-status.html deleted file mode 100644 index bca87d5..0000000 --- a/uploader/templates/phenotypes/sui-job-status.html +++ /dev/null @@ -1,140 +0,0 @@ -{%extends "phenotypes/sui-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%} - -{%block extrameta%} -{%if job and job.status not in ("success", "completed:success", "error", "completed:error")%} -<meta http-equiv="refresh" content="5" /> -{%endif%} -{%endblock%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block contents%} - -{%if job%} -<div class="row"> - <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2> - <h3 class="subheading">upload progress</h3> -</div> -<div class="row" style="overflow:scroll;"> - <p><strong>Process Status:</strong> {{job.status}}</p> - {%if metadata%} - <table class="table table-responsive"> - <thead> - <tr> - <th>File</th> - <th>Status</th> - <th>Lines Processed</th> - <th>Total Errors</th> - </tr> - </thead> - - <tbody> - {%for file,meta in metadata.items()%} - <tr> - <td>{{file}}</td> - <td>{{meta.status}}</td> - <td>{{meta.linecount}}</td> - <td>{{meta["total-errors"]}}</td> - </tr> - {%endfor%} - </tbody> - </table> - {%endif%} -</div> - -<div class="row"> - {%if job.status in ("completed:success", "success")%} - <p> - {%if errors | length == 0%} - <a href="{{url_for('species.populations.phenotypes.review_job_data', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - job_id=job_id)}}" - class="btn btn-primary" - title="Continue to process data">Continue</a> - {%else%} - <span class="text-muted" - disabled="disabled" - style="border: solid 2px;border-radius: 5px;padding: 0.3em;"> - Cannot continue due to errors. Please fix the errors first. - </span> - {%endif%} - </p> - {%endif%} -</div> - -<h3 class="subheading">upload errors</h3> -<div class="row" style="max-height: 20em; overflow: scroll;"> - {%if errors | length == 0 %} - <p class="text-info"> - <span class="glyphicon glyphicon-info-sign"></span> - No errors found so far - </p> - {%else%} - <table class="table table-responsive"> - <thead style="position: sticky; top: 0; background: white;"> - <tr> - <th>File</th> - <th>Row</th> - <th>Column</th> - <th>Value</th> - <th>Message</th> - </tr> - </thead> - - <tbody style="font-size: 0.9em;"> - {%for error in errors%} - <tr> - <td>{{error.filename}}</td> - <td>{{error.rowtitle}}</td> - <td>{{error.coltitle}}</td> - <td>{%if error.cellvalue is not none and error.cellvalue | length > 25%} - {{error.cellvalue[0:24]}}… - {%else%} - {{error.cellvalue}} - {%endif%} - </td> - <td> - {%if error.message | length > 250 %} - {{error.message[0:249]}}… - {%else%} - {{error.message}} - {%endif%} - </td> - </tr> - {%endfor%} - </tbody> - </table> - {%endif%} -</div> - -<div class="row"> - {{cli_output(job, "stdout")}} -</div> - -<div class="row"> - {{cli_output(job, "stderr")}} -</div> - -{%else%} -<div class="row"> - <h3 class="text-danger">No Such Job</h3> - <p>Could not find a job with the ID: {{job_id}}</p> - <p> - Please go back to - <a href="{{url_for('species.populations.phenotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="'{{dataset.Name}}' dataset page"> - the '{{dataset.Name}}' dataset page</a> - to upload new phenotypes or edit existing ones.</p> -</div> -{%endif%} -{%endblock%} diff --git a/uploader/templates/phenotypes/sui-load-phenotypes-success.html b/uploader/templates/phenotypes/sui-load-phenotypes-success.html deleted file mode 100644 index dff0682..0000000 --- a/uploader/templates/phenotypes/sui-load-phenotypes-success.html +++ /dev/null @@ -1,26 +0,0 @@ -{%extends "phenotypes/sui-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block contents%} -{{super()}} - -<div class="row"> - <p>You have successfully loaded - <!-- maybe indicate the number of phenotypes here? -->your - new phenotypes into the database.</p> - <!-- TODO: Maybe notify user that they have sole access. --> - <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. --> - <p>View your data - <a href="{{search_page_uri}}" - target="_blank">on GeneNetwork2</a>. - You might need to login to GeneNetwork2 to view specific traits.</p> -</div> -{%endblock%} - - -{%block more_javascript%}{%endblock%} diff --git a/uploader/templates/phenotypes/sui-review-job-data.html b/uploader/templates/phenotypes/sui-review-job-data.html deleted file mode 100644 index ea4183d..0000000 --- a/uploader/templates/phenotypes/sui-review-job-data.html +++ /dev/null @@ -1,121 +0,0 @@ -{%extends "phenotypes/sui-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 class="text-info"><strong> - The data has <em>NOT</em> been added/saved yet. Review the details below - and click "Continue" to save the data.</strong></p> - <p>The “<strong>{{dataset.FullName}}</strong>” dataset from the - “<strong>{{population.FullName}}</strong>” population of the - species “<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>” - will be updated as follows:</p> - - <ul> - {%if publication%} - <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes - are linked to the following publication: - <ul> - <li><strong>Publication Title:</strong> - {{publication.Title or "—"}}</li> - <li><strong>Author(s):</strong> - {{publication.Authors or "—"}}</li> - </ul> - </li> - {%endif%} - {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} - {%if summary.get(ftype, False)%} - <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> - {%endif%} - {%endfor%} - </ul> - - <form id="frm-review-phenotype-data" - method="POST" - action="{{url_for('species.populations.phenotypes.load_data_to_database', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}"> - <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> - <input type="submit" - value="continue" - class="btn btn-primary" /> - </form> -</div> -{%else%} -<div class="row"> - <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 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/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index c634a48..fc84757 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -1,7 +1,6 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Phenotypes{%endblock%} @@ -24,25 +23,12 @@ {{flash_all_messages()}} <div class="row"> - <p>The basic dataset details are:</p> - - <table class="table"> - <thead> - <tr> - <th>Name</th> - <th>Full Name</th> - <th>Short Name</th> - </tr> - </thead> + <h2>Phenotype Data</h2> - <tbody> - <tr> - <td>{{dataset.Name}}</td> - <td>{{dataset.FullName}}</td> - <td>{{dataset.ShortName}}</td> - </tr> - </tbody> - </table> + <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> <div class="row"> @@ -68,7 +54,7 @@ <input type="submit" title="Compute/Recompute the means for all phenotypes." class="btn btn-info" - value="(rec/c)ompute means" + value="compute means" id="submit-frm-recompute-phenotype-means" /> </form> </div> @@ -86,24 +72,29 @@ <input type="submit" title="Run/Rerun QTLReaper." class="btn btn-info" - value="(re)run QTLReaper" + value="run QTLReaper" id="submit-frm-rerun-qtlreaper" /> </form> </div> -</div> -<div class="row"> - <h2>Phenotype Data</h2> - - <p>Click on any of the phenotypes in the table below to view and edit that - phenotype's data.</p> - <p>Use the search to filter through all the phenotypes and find specific - phenotypes of interest.</p> + <div class="col"> + <form id="frm-delete-phenotypes" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.delete_phenotypes', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}"> + <input type="submit" + class="btn btn-danger" + id="btn-delete-phenotypes" + title="Delete phenotypes from this dataset. If no phenotypes are selected in the table, this will delete ALL the phenotypes." + value="delete phenotypes" /> + </form> + </div> </div> - -<div class="row"> - +<div class="row" style="margin-top: 0.5em;"> <table id="tbl-phenotypes-list" class="table compact stripe cell-border"> <thead> <tr> @@ -119,12 +110,10 @@ </div> {%endblock%} -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} - {%block javascript%} +<script type="text/javascript" src="/static/js/urls.js"></script> + <script type="text/javascript"> $(function() { var species_id = {{species.SpeciesId}}; @@ -151,21 +140,44 @@ var spcs_id = {{species.SpeciesId}}; var pop_id = {{population.Id}}; var dtst_id = {{dataset.Id}}; - return `<a href="/species/${spcs_id}` + + var url = buildURLFromCurrentURL( + (`/species/${spcs_id}` + `/populations/${pop_id}` + `/phenotypes/datasets/${dtst_id}` + - `/phenotype/${pheno.xref_id}` + - `" target="_blank">` + + `/phenotype/${pheno.xref_id}`)); + return `<a href="${url.toString()}" target="_blank">` + `${pheno.InbredSetCode}_${pheno.xref_id}` + `</a>`; - } + }, + title: "Record", + visible: true, + searchable: true }, { data: function(pheno) { return (pheno.Post_publication_description || pheno.Original_description || pheno.Pre_publication_description); - } + }, + title: "Description", + visible: true, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Title; + }, + title: "Publication Title", + visible: false, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Authors; + }, + title: "Authors", + visible: false, + searchable: true } ], { @@ -204,6 +216,33 @@ }); form.submit(); }); + + $("#btn-delete-phenotypes").on( + "click", + function(event) { + // Collect selected phenotypes for deletion, if any. + event.preventDefault(); + form = $("#frm-delete-phenotypes"); + form.find(".dynamically-added-element").remove(); + $("#tbl-phenotypes-list") + .DataTable() + .rows({selected: true}). + nodes().each(function(node, index) { + var parts = $(node) + .find(".chk-row-select") + .val() + .split("_"); + var xref_id = parts[parts.length - 1].trim(); + var chk = $('<input type="checkbox">'); + chk.attr("class", "dynamically-added-element"); + chk.attr("value", xref_id); + chk.attr("name", "xref_ids"); + chk.attr("style", "display: none"); + chk.prop("checked", true); + form.append(chk); + }); + form.submit(); + }); }); </script> {%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 75e3c1e..a59949e 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -1,25 +1,10 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="view-phenotype"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.view_phenotype', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - xref_id=xref_id)}}">View Phenotype</a> -</li> -{%endblock%} - {%block contents%} {{flash_all_messages()}} @@ -118,7 +103,7 @@ or "group:resource:delete-resource" in privileges%} <table class="table"> <thead> <tr> - <th>#</th> + <th>Index</th> <th>Sample</th> <th>Value</th> {%if has_se%} @@ -153,7 +138,3 @@ or "group:resource:delete-resource" in privileges%} </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html index dac965f..d4f3686 100644 --- a/uploader/templates/platforms/base.html +++ b/uploader/templates/platforms/base.html @@ -1,13 +1,17 @@ {%extends "species/base.html"%} +{%from "species/macro-display-species-card.html" import display_sui_species_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="platforms"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.platforms.index')}}"> - Sequencing Platforms</a> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species['SpeciesId'])}}"> + Platforms + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_species_card(species)}} {%endblock%} diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html index 0866d5e..3a62472 100644 --- a/uploader/templates/platforms/create-platform.html +++ b/uploader/templates/platforms/create-platform.html @@ -1,19 +1,15 @@ {%extends "platforms/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} {%block title%}Platforms — Create Platforms{%endblock%} -{%block pagetitle%}Platforms — Create Platforms{%endblock%} - -{%block lvl3_breadcrumbs%} -<li {%if activelink=="create-platform"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.platforms.create_platform', - species_id=species.SpeciesId)}}">create platform</a> + species_id=species['SpeciesId'])}}"> + Create + </a> </li> {%endblock%} @@ -118,7 +114,3 @@ </form> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html index a6bcfdc..db14745 100644 --- a/uploader/templates/platforms/list-platforms.html +++ b/uploader/templates/platforms/list-platforms.html @@ -1,6 +1,5 @@ {%extends "platforms/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} {%block title%}Platforms — List Platforms{%endblock%} @@ -87,7 +86,3 @@ {%endif%} </div> {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html index 9db8083..24cacc2 100644 --- a/uploader/templates/populations/base.html +++ b/uploader/templates/populations/base.html @@ -1,18 +1,20 @@ {%extends "species/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} -{%block lvl2_breadcrumbs%} -<li {%if activelink=="populations"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if population is mapping%} +{%block breadcrumbs%} +{{super()}} +{%if population%} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.view_population', - species_id=species.SpeciesId, - population_id=population.Id)}}">{{population.Name}}</a> - {%else%} - <a href="{{url_for('species.populations.index')}}">Populations</a> - {%endif%} + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + {{population["Name"]}} + </a> </li> -{%block lvl3_breadcrumbs%}{%endblock%} +{%endif%} +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} {%endblock%} diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index 007b6bf..d5359f5 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -1,20 +1,16 @@ {%extends "populations/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-select-species.html" import select_species_form%} -{%from "species/macro-display-species-card.html" import display_species_card%} {%block title%}Create Population{%endblock%} {%block pagetitle%}Create Population{%endblock%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="create-population"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}">create population</a> + species_id=species['SpeciesId'])}}"> + create population</a> </li> {%endblock%} @@ -263,7 +259,3 @@ </form> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index 6b5f1e0..f3040ea 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -43,7 +43,7 @@ {%macro display_sui_population_card(species, population)%} {{display_sui_species_card(species)}} - +{%if population%} <div class="row"> <table class="table"> <caption>Current population</caption> @@ -75,4 +75,5 @@ </tbody> </table> </div> +{%endif%} {%endmacro%} diff --git a/uploader/templates/populations/sui-base.html b/uploader/templates/populations/sui-base.html deleted file mode 100644 index 0ca5c59..0000000 --- a/uploader/templates/populations/sui-base.html +++ /dev/null @@ -1,12 +0,0 @@ -{%extends "species/sui-base.html"%} - -{%block breadcrumbs%} -{{super()}} -<li class="breadcrumb-item"> - <a href="{{url_for('species.populations.view_population', - species_id=species['SpeciesId'], - population_id=population['Id'])}}"> - {{population["Name"]}} - </a> -</li> -{%endblock%} diff --git a/uploader/templates/populations/sui-view-population.html b/uploader/templates/populations/sui-view-population.html deleted file mode 100644 index 6244f4d..0000000 --- a/uploader/templates/populations/sui-view-population.html +++ /dev/null @@ -1,267 +0,0 @@ -{%extends "populations/sui-base.html"%} -{%from "macro-step-indicator.html" import step_indicator%} -{%from "populations/macro-display-population-card.html" import display_sui_population_card%} - -{%block contents%} -<div class="row"> - <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> -</div> - -<div class="row"> - <ul class="nav nav-tabs" id="population-actions"> - <li class="nav-item presentation"> - <button class="nav-link" - id="samples-tab" - data-bs-toggle="tab" - data-bs-target="#samples-content" - type="button" - role="tab" - aria-controls="samples-content" - aria-selected="true">Samples</button></li> - <li class="nav-item presentation"> - <button class="nav-link active" - id="phenotypes-tab" - data-bs-toggle="tab" - data-bs-target="#phenotypes-content" - type="button" - role="tab" - aria-controls="phenotypes-content" - aria-selected="false">Phenotypes</button></li> - {%if view_under_construction%} - <li class="nav-item presentation"> - <button class="nav-link" - id="genotypes-tab" - data-bs-toggle="tab" - data-bs-target="#genotypes-content" - type="button" - role="tab" - aria-controls="genotypes-content" - aria-selected="false">Genotypes</button></li> - <li class="nav-item presentation"> - <button class="nav-link" - id="expression-data-tab" - data-bs-toggle="tab" - data-bs-target="#expression-data-content" - type="button" - role="tab" - aria-controls="expression-data-content" - aria-selected="false">Expression-Data</button></li> - {%endif%} - </ul> -</div> - -<div class="row"> - <div class="tab-content" id="populations-tabs-content"> - <div class="tab-pane fade" - id="samples-content" - role="tabpanel" - aria-labelledby="samples-content-tab"> - <p>Think of a <strong>"sample"</strong> as say a single case or individual - in the experiment. It could even be a single strain (where applicable). - </p> - <p>This is a convenience feature for when you want to upload phenotypes to - the system, but do not have the genotypes data ready yet.</p> - <a href="{{url_for('species.populations.samples.list_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="View and upload samples for population '{{population['Name']}}'" - class="btn btn-primary">Manage Samples</a> - </div> - - <div class="tab-pane fade show active" - id="phenotypes-content" - role="tabpanel" - aria-labelledby="phenotypes-content-tab"> - - <div class="row" style="margin-top: 0.3em;"> - <div class="col"> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="Upload phenotype data for population '{{population['Name']}}'" - class="btn btn-primary">Upload new Phenotypes</a> - </div> - <div class="col"> - <a href="#" - title="List all existing publications for this population." - class="btn btn-primary not-implemented">view publications</a> - <!-- Maybe, actually filter publications by population? --> - <!-- Provide other features for publications on loaded page. --> - </div> - </div> - - <div class="row" style="margin-top: 1em;"> - <h3> Phenotypes in Population "{{population.FullName}} ({{population.Name}})"</h3> - - <p>The table below lists the phenotypes that already exist for - population "<em>{{population.FullName}} ({{population.Name}})</em>" of - species "<em>{{species.FullName}} ({{species.Name}})</em>".</p> - - <div class="row phenotypes-list-actions"> - <div class="col"> - <form id="frm-recompute-phenotype-means" - method="POST" - action="{{url_for( - 'species.populations.phenotypes.recompute_means', - species_id=species['SpeciesId'], - population_id=population['Id'], - dataset_id=dataset['Id'])}}"> - <input id="submit-frm-recompute-phenotype-means" - class="btn btn-info" - type="submit" - title="Compute/Recompute the means for selected phenotypes (or all phenotypes if none selected)." - value="(Rec/C)ompute means" /> - </form> - </div> - <div class="col"> - <form id="frm-rerun-qtlreaper" - method="POST" - action="{{url_for( - 'species.populations.phenotypes.rerun_qtlreaper', - species_id=species['SpeciesId'], - population_id=population['Id'], - dataset_id=dataset['Id'])}}"> - <input id="submit-frm-rerun-qtlreaper" - class="btn btn-info" - type="submit" - title="Run/Rerun QTLReaper for selected phenotypes (or all phenotypes if none selected)." - value="(rer/r)un QTLReaper" /> - </form> - </div> - </div> - - <table id="tbl-phenotypes-list" class="table compact stripe cell-border"> - <thead> - <tr> - <th></th> - <th>Index</th> - <th>Record</th> - <th>Description</th> - </tr> - </thead> - - <tbody></tbody> - </table> - </div> - </div> - - <div class="tab-pane fade" - id="genotypes-content" - role="tabpanel" - aria-labelledby="genotypes-content-tab"> - <p>This allows you to upload the data that concerns your genotypes.</p> - <p>Any samples/individuals/cases/strains that do not already exist in the - system will be added. This does not delete any existing data.</p> - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Upload genotype information for the '{{population.FullName}}' population of the '{{species.FullName}}' species." - class="btn btn-primary">upload genotypes</a> - </div> - <div class="tab-pane fade" id="expression-data-content" role="tabpanel" aria-labelledby="expression-data-content-tab"> - <p>Upload expression data (mRNA data) for this population.</p> - <a href="#" title="" class="btn btn-primary">upload genotypes</a> - </div> - </div> -</div> -{%endblock%} - -{%block sidebarcontents%} -<div class="row"> - <p>Each tab presents a feature that's available at the population level. - Select the tab that allows you to continue with your task.</p> -</div> -{{display_sui_population_card(species, population)}} -{%endblock%} - - - - -{%block javascript%} -<script type="text/javascript" src="/static/js/urls.js"></script> - -<script type="text/javascript"> - $(function() { - /** JS to build list of phenotypes table. **/ - var species_id = {{species.SpeciesId}}; - var population_id = {{population.Id}}; - var dataset_id = {{dataset.Id}}; - var dataset_name = "{{dataset.Name}}"; - var data = {{phenotypes | tojson}}; - - var dtPhenotypesList = buildDataTable( - "#tbl-phenotypes-list", - data, - [ - { - data: function(pheno) { - return `<input type="checkbox" name="selected-phenotypes" ` - + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" ` - + `value="${pheno.InbredSetCode}_${pheno.xref_id}" ` - + `class="chk-row-select" />` - } - }, - {data: "sequence_number"}, - { - data: function(pheno, type, set, meta) { - var spcs_id = {{species.SpeciesId}}; - var pop_id = {{population.Id}}; - var dtst_id = {{dataset.Id}}; - var url = buildURLFromCurrentURL( - (`/species/${spcs_id}` + - `/populations/${pop_id}` + - `/phenotypes/datasets/${dtst_id}` + - `/phenotype/${pheno.xref_id}`)); - return `<a href="${url.toString()}" 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", - layout: { - top1Start: { - pageLength: { - text: "Show _MENU_ of _TOTAL_" - } - }, - topStart: "info", - top1End: null - }, - rowId: function(pheno) { - return `${pheno.InbredSetCode}_${pheno.xref_id}`; - } - }); - - - $("#submit-frm-rerun-qtlreaper").on( - "click", - function(event) { - // (Re)run the QTLReaper script for selected phenotypes. - event.preventDefault(); - var form = $("#frm-rerun-qtlreaper"); - form.find(".dynamically-added-element").remove(); - dtPhenotypesList.rows({selected: true}).nodes().each((node, index) => { - _cloned = $(node).find(".chk-row-select").clone(); - _cloned.removeAttr("id"); - _cloned.removeAttr("class"); - _cloned.attr("style", "display: none;"); - _cloned.attr("data-type", "dynamically-added-element"); - _cloned.attr("class", "dynamically-added-element checkbox"); - _cloned.prop("checked", true); - form.append(_cloned); - }); - form.submit(); - }); - }); -</script> -{%endblock%} diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index 3b9661b..6da4cd7 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -1,104 +1,135 @@ {%extends "populations/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-select-species.html" import select_species_form%} -{%from "species/macro-display-species-card.html" import display_species_card%} - -{%block title%}Populations{%endblock%} - -{%block pagetitle%}Populations{%endblock%} - -{%block lvl3_breadcrumbs%} -<li {%if activelink=="view-population"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.view_population', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}">view</a> -</li> -{%endblock%} - +{%from "macro-step-indicator.html" import step_indicator%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} {%block contents%} <div class="row"> - <h2>Population Details</h2> - - {{flash_all_messages()}} - - <dl> - <dt>Name</dt> - <dd>{{population.Name}}</dd> - - <dt>FullName</dt> - <dd>{{population.FullName}}</dd> - - <dt>Code</dt> - <dd>{{population.InbredSetCode}}</dd> - - <dt>Genetic Type</dt> - <dd>{{population.GeneticType}}</dd> - - <dt>Family</dt> - <dd>{{population.Family}}</dd> - - <dt>Information</dt> - <dd><a href="https://info.genenetwork.org/species/source.php?SpeciesName={{species.Name}}&InbredSetName={{population.Name}}" - title="Link to detailed information on this population." - target="_blank">Population Information</a></dd> - </dl> + <h2 class="heading">Population: {{population.FullName}} ({{population.Name}})</h2> </div> <div class="row"> - … maybe provide a way to organise populations in the same family here … + <ul class="nav nav-tabs" id="population-actions"> + <li class="nav-item presentation"> + <button class="nav-link" + id="samples-tab" + data-bs-toggle="tab" + data-bs-target="#samples-content" + type="button" + role="tab" + aria-controls="samples-content" + aria-selected="true">Samples</button></li> + <li class="nav-item presentation"> + <button class="nav-link active" + id="phenotypes-tab" + data-bs-toggle="tab" + data-bs-target="#phenotypes-content" + type="button" + role="tab" + aria-controls="phenotypes-content" + aria-selected="false">Phenotypes</button></li> + {%if view_under_construction%} + <li class="nav-item presentation"> + <button class="nav-link" + id="genotypes-tab" + data-bs-toggle="tab" + data-bs-target="#genotypes-content" + type="button" + role="tab" + aria-controls="genotypes-content" + aria-selected="false">Genotypes</button></li> + <li class="nav-item presentation"> + <button class="nav-link" + id="expression-data-tab" + data-bs-toggle="tab" + data-bs-target="#expression-data-content" + type="button" + role="tab" + aria-controls="expression-data-content" + aria-selected="false">Expression-Data</button></li> + {%endif%} + </ul> </div> <div class="row"> - <h3>Actions</h3> - - <p> - Click any of the following links to use this population in performing the - subsequent operations. - </p> - - <nav class="nav"> - <ul> - <li> - <a href="{{url_for('species.populations.samples.list_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage samples: Add new or delete existing."> - manage samples</a> - </li> - <li> - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage genotypes for {{species.FullName}}">Manage Genotypes</a> - </li> - <li> - <a href="{{url_for('species.populations.phenotypes.list_datasets', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage phenotype data.">manage phenotype data</a> - </li> - <li> - <a href="#" title="Manage expression data" - class="not-implemented">manage expression data</a> - </li> - <li> - <a href="#" title="Manage individual data" - class="not-implemented">manage individual data</a> - </li> - <li> - <a href="#" title="Manage RNA-Seq data" - class="not-implemented">manage RNA-Seq data</a> - </li> - </ul> - </nav> + <div class="tab-content" id="populations-tabs-content"> + <div class="tab-pane fade" + id="samples-content" + role="tabpanel" + aria-labelledby="samples-content-tab"> + <p>Think of a <strong>"sample"</strong> as say a single case or individual + in the experiment. It could even be a single strain (where applicable). + These are, effectively, identifiers for the organisms (plants, animals, + etc) that your data is collected from, and is about. + </p> + + <p>The samples should be uploaded before any of the other types of data + (genotype, phenotype, expression, etc.), or be bundled together with + them, since they all need references to the samples.</p> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View and upload samples for population '{{population['Name']}}'" + class="btn btn-primary">manage samples</a> + </div> + + <div class="tab-pane fade show active" + id="phenotypes-content" + role="tabpanel" + aria-labelledby="phenotypes-content-tab"> + + <div class="row" style="margin-top: 1em;"> + <p>Phenotype data measures the actual observable traits or + characteristics of an organism e.g. physical appearance, biochemical + properties, development, behaviour and/or disease states.</p> + <p>This section enables you to view existing and/or upload new phenotype + data.</p> + + <div class="row"> + <div class="col"> + <a href="{{url_for( + 'species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View and upload phenotype traits" + class="btn btn-primary">manage phenotypes</a> + </div> + </div> + </div> + </div> + + <div class="tab-pane fade" + id="genotypes-content" + role="tabpanel" + aria-labelledby="genotypes-content-tab"> + <p>Genotype data records specific genetic variations (e.g. single + nucleotide polymorphisms (SNPs)) present at particular locations in an + individual's (see "Samples" section) DNA.</p> + <p>Click the button below to view existing and/or upload new genotype data + for this population.</p> + <a href="{{url_for('species.populations.genotypes.index', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Upload genotype information for the '{{population.FullName}}' population of the '{{species.FullName}}' species." + class="btn btn-primary">manage genotypes</a> + </div> + <div class="tab-pane fade" id="expression-data-content" role="tabpanel" aria-labelledby="expression-data-content-tab"> + <p>Expression data is data measuring how much genes are turned on or active.</p> + <a href="#" title="" class="btn btn-primary">manage expression data</a> + </div> + </div> </div> {%endblock%} {%block sidebarcontents%} -{{display_species_card(species)}} +<div class="row"> + <p>Each tab presents a feature that's available at the population level. + Select the tab that allows you to continue with your task.</p> +</div> +{{super()}} +{%endblock%} + + + + +{%block javascript%} {%endblock%} diff --git a/uploader/templates/publications/base.html b/uploader/templates/publications/base.html index db80bfa..de0a350 100644 --- a/uploader/templates/publications/base.html +++ b/uploader/templates/publications/base.html @@ -1,12 +1,9 @@ {%extends "base.html"%} -{%block lvl1_breadcrumbs%} -<li {%if activelink=="publications"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('publications.index')}}">Publications</a> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('publications.index')}}" + title="Manage publications">Publications</a> </li> -{%block lvl2_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html index 3f828a9..da5889e 100644 --- a/uploader/templates/publications/create-publication.html +++ b/uploader/templates/publications/create-publication.html @@ -3,7 +3,13 @@ {%block title%}View Publication{%endblock%} -{%block pagetitle%}View Publication{%endblock%} +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('publications.create_publication', **get_args)}}" + title="Manage publications">create publication</a> +</li> +{%endblock%} {%block contents%} @@ -12,7 +18,7 @@ <div class="row"> <form id="frm-create-publication" method="POST" - action="{{url_for('publications.create_publication', **request.args)}}" + action="{{url_for('publications.create_publication', **get_args)}}" class="form-horizontal"> <div class="row mb-3"> @@ -85,22 +91,22 @@ class="col-sm-2 col-form-label"> Month</label> <div class="col-sm-4"> - <select class="form-control" + <select class="form-select" id="select-publication-month" name="publication-month"> <option value="">Select a month</option> - <option value="january">January</option> - <option value="february">February</option> - <option value="march">March</option> - <option value="april">April</option> - <option value="may">May</option> - <option value="june">June</option> - <option value="july">July</option> - <option value="august">August</option> - <option value="september">September</option> - <option value="october">October</option> - <option value="november">November</option> - <option value="december">December</option> + <option {%if current_month | lower == "january"%}selected="selected"{%endif%}value="january">January</option> + <option {%if current_month | lower == "february"%}selected="selected"{%endif%}value="february">February</option> + <option {%if current_month | lower == "march"%}selected="selected"{%endif%}value="march">March</option> + <option {%if current_month | lower == "april"%}selected="selected"{%endif%}value="april">April</option> + <option {%if current_month | lower == "may"%}selected="selected"{%endif%}value="may">May</option> + <option {%if current_month | lower == "june"%}selected="selected"{%endif%}value="june">June</option> + <option {%if current_month | lower == "july"%}selected="selected"{%endif%}value="july">July</option> + <option {%if current_month | lower == "august"%}selected="selected"{%endif%}value="august">August</option> + <option {%if current_month | lower == "september"%}selected="selected"{%endif%}value="september">September</option> + <option {%if current_month | lower == "october"%}selected="selected"{%endif%}value="october">October</option> + <option {%if current_month | lower == "november"%}selected="selected"{%endif%}value="november">November</option> + <option {%if current_month | lower == "december"%}selected="selected"{%endif%}value="december">December</option> </select> <span class="form-text text-muted">Month of publication</span> </div> @@ -113,7 +119,10 @@ id="txt-publication-year" name="publication-year" class="form-control" - min="1960" /> + min="1960" + max="{{current_year}}" + value="{{current_year or ''}}" + required="required" /> <span class="form-text text-muted">Year of publication</span> </div> </div> @@ -152,11 +161,14 @@ </div> </div> - <div class="row mb-3"> - <div class="col-sm-2"></div> - <div class="col-sm-8"> - <input type="submit" class="btn btn-primary" value="Add" /> - <input type="reset" class="btn btn-danger" /> + <div class="row"> + <div class="col"> + <input type="submit" + class="btn btn-primary" + value="create publication" /> + </div> + <div class="col"> + <input type="reset" class="btn btn-danger" value="reset form" /> </div> </div> diff --git a/uploader/templates/publications/delete-publication.html b/uploader/templates/publications/delete-publication.html index 0ac93ec..a9c8c7c 100644 --- a/uploader/templates/publications/delete-publication.html +++ b/uploader/templates/publications/delete-publication.html @@ -1,9 +1,16 @@ {%extends "publications/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%block title%}View Publication{%endblock%} +{%block title%}Delete Publication{%endblock%} -{%block pagetitle%}View Publication{%endblock%} +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('publications.delete_publication', + publication_id=publication.Id)}}" + title="Manage publications">delete publication</a> +</li> +{%endblock%} {%block contents%} diff --git a/uploader/templates/publications/edit-publication.html b/uploader/templates/publications/edit-publication.html index 97fa134..314a78c 100644 --- a/uploader/templates/publications/edit-publication.html +++ b/uploader/templates/publications/edit-publication.html @@ -1,9 +1,16 @@ {%extends "publications/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%block title%}View Publication{%endblock%} - -{%block pagetitle%}View Publication{%endblock%} +{%block title%}Edit Publication{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('publications.edit_publication', + publication_id=publication.Id)}}" + title="Edit the publication's details">edit publication</a> +</li> +{%endblock%} {%block contents%} diff --git a/uploader/templates/publications/index.html b/uploader/templates/publications/index.html index 369812b..eb2e81b 100644 --- a/uploader/templates/publications/index.html +++ b/uploader/templates/publications/index.html @@ -3,23 +3,29 @@ {%block title%}Publications{%endblock%} -{%block pagetitle%}Publications{%endblock%} - {%block contents%} {{flash_all_messages()}} <div class="row" style="padding-bottom: 1em;"> - <a href="{{url_for('publications.create_publication')}}" - class="btn btn-primary"> - add new publication</a> + <div class="col"> + <a href="{{url_for('publications.create_publication')}}" + class="btn btn-primary" + title="Create a new publication."> + add new publication</a> + </div> +</div> + +<div class="row"> + <p>Click on the title to view more details or to edit the information for that + publication.</p> </div> <div class="row"> <table id="tbl-list-publications" class="table compact stripe"> <thead> <tr> - <th>#</th> + <th>Index</th> <th>PubMed ID</th> <th>Title</th> <th>Authors</th> @@ -33,6 +39,8 @@ {%block javascript%} +<script type="text/javascript" src="/static/js/urls.js"></script> + <script type="text/javascript"> $(function() { var publicationsDataTable = buildDataTable( @@ -43,24 +51,25 @@ { searchable: true, data: (pub) => { - if(pub.PubMed_ID) { - return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + - `${pub.PubMed_ID}/" target="_blank" ` + - `title="Link to publication on NCBI.">` + - `${pub.PubMed_ID}</a>`; - } - return ""; + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; } }, { searchable: true, data: (pub) => { - var title = "⸻"; - if(pub.Title) { - title = pub.Title - } - return `<a href="/publications/view/${pub.Id}" ` + - `target="_blank" ` + + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + url=buildURLFromCurrentURL( + `/publications/view/${pub.Id}`); + return `<a href="${url}" target="_blank" ` + `title="Link to view publication details">` + `${title}</a>`; } @@ -68,12 +77,12 @@ { searchable: true, data: (pub) => { - authors = pub.Authors.split(",").map( - (item) => {return item.trim();}); - if(authors.length > 1) { - return authors[0] + ", et. al."; - } - return authors[0]; + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; } } ], diff --git a/uploader/templates/publications/view-publication.html b/uploader/templates/publications/view-publication.html index 0bd7bc5..01ccf1e 100644 --- a/uploader/templates/publications/view-publication.html +++ b/uploader/templates/publications/view-publication.html @@ -3,8 +3,6 @@ {%block title%}View Publication{%endblock%} -{%block pagetitle%}View Publication{%endblock%} - {%block contents%} {{flash_all_messages()}} diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html index 291782b..7fd5020 100644 --- a/uploader/templates/samples/base.html +++ b/uploader/templates/samples/base.html @@ -1,12 +1,25 @@ {%extends "populations/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="samples"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.samples.index')}}">Samples</a> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species['SpeciesId'], + population_id=population.Id)}}"> + Samples + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> +</div> +{%endblock%} + + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} {%endblock%} diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html index aed27c3..3aac984 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -1,53 +1,34 @@ {%extends "samples/base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "populations/macro-select-population.html" import select_population_form%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Samples — List Samples{%endblock%} -{%block pagetitle%}Samples — List Samples{%endblock%} - -{%block lvl4_breadcrumbs%} -<li {%if activelink=="list-samples"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.samples.list_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}">List</a> -</li> -{%endblock%} - {%block contents%} -{{flash_all_messages()}} +{{super()}} <div class="row"> - <p> - You selected the population "{{population.FullName}}" from the - "{{species.FullName}}" species. - </p> + <h3 class="subheading">manage samples</h3> + {{flash_all_messages()}} </div> <div class="row"> - <p> + <div class="col"> <a href="{{url_for('species.populations.samples.upload_samples', species_id=species.SpeciesId, population_id=population.Id)}}" title="Add samples for population '{{population.FullName}}' from species '{{species.FullName}}'." - class="btn btn-primary"> - add samples - </a> - </p> + class="btn btn-primary">add new samples</a> + </div> </div> {%if samples | length > 0%} <div class="row"> <p> - This population already has <strong>{{total_samples}}</strong> - samples/individuals entered. You can explore the list of samples in this - population in the table below. + Population "{{population.FullName}} ({{population.Name}})" already has + <strong>{{total_samples}}</strong> samples/individuals entered. You can + explore the list of samples in the table below. </p> </div> @@ -106,15 +87,6 @@ {%endfor%} </tbody> </table> - - <p> - <a href="#" - title="Delete samples from population '{{population.FullName}}' from species - '{{species.FullName}}'." - class="btn btn-danger not-implemented"> - delete all samples - </a> - </p> </div> {%else%} <div class="row"> @@ -124,7 +96,3 @@ {%endif%} {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html index 2cf8053..75192ec 100644 --- a/uploader/templates/samples/upload-failure.html +++ b/uploader/templates/samples/upload-failure.html @@ -1,6 +1,5 @@ {%extends "base.html"%} {%from "cli-output.html" import cli_output%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Samples Upload Failure{%endblock%} @@ -31,7 +30,3 @@ {{cli_output(job, "stderr")}} </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html index 677d457..38f931b 100644 --- a/uploader/templates/samples/upload-progress.html +++ b/uploader/templates/samples/upload-progress.html @@ -1,6 +1,5 @@ {%extends "samples/base.html"%} {%from "cli-output.html" import cli_output%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block extrameta%} <meta http-equiv="refresh" content="5"> @@ -25,7 +24,3 @@ </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html index 6422094..1f665a3 100644 --- a/uploader/templates/samples/upload-samples.html +++ b/uploader/templates/samples/upload-samples.html @@ -1,21 +1,16 @@ {%extends "samples/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-select-population.html" import select_population_form%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Samples — Upload Samples{%endblock%} -{%block pagetitle%}Samples — Upload Samples{%endblock%} - -{%block lvl4_breadcrumbs%} -<li {%if activelink=="uploade-samples"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.samples.upload_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}">List</a> + species_id=species['SpeciesId'], + population_id=population.Id)}}"> + Upload + </a> </li> {%endblock%} @@ -23,35 +18,6 @@ {{flash_all_messages()}} <div class="row"> - <p> - You can now upload the samples for the "{{population.FullName}}" population - from the "{{species.FullName}}" species here. - </p> - <p> - Upload a <strong>character-separated value (CSV)</strong> file that contains - details about your samples. The CSV file should have the following fields: - <dl> - <dt>Name</dt> - <dd>The primary name/identifier for the sample/individual.</dd> - - <dt>Name2</dt> - <dd>A secondary name for the sample. This can simply be the same as - <strong>Name</strong> above. This field <strong>MUST</strong> contain a - value.</dd> - - <dt>Symbol</dt> - <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for - species that have strains. This field can be left empty for species like - Humans that do not have strains..</dd> - - <dt>Alias</dt> - <dd>An alias for the sample. Can be an empty field, or take on the same - value as that of the Symbol.</dd> - </dl> - </p> -</div> - -<div class="row"> <form id="form-samples" method="POST" action="{{url_for('species.populations.samples.upload_samples', @@ -65,14 +31,17 @@ <div class="form-group"> <label for="file-samples" class="form-label">select file</label> - <input type="file" name="samples_file" id="file:samples" + <input type="file" name="samples_file" id="file-samples" accept="text/csv, text/tab-separated-values, text/plain" class="form-control" /> + <small class="form-text text-muted"> + See the <a href="#docs-samples-upload">documentation below</a> for + details on expected file format.</small> </div> <div class="form-group"> - <label for="select:separator" class="form-label">field separator</label> - <select id="select:separator" + <label for="select-separator" class="form-label">field separator</label> + <select id="select-separator" name="separator" required="required" class="form-control"> @@ -83,7 +52,7 @@ <option value=";">Semicolon</option> <option value="other">Other</option> </select> - <input id="txt:separator" + <input id="txt-separator" type="text" name="other_separator" class="form-control" /> @@ -95,11 +64,11 @@ </div> <div class="form-group form-check"> - <input id="chk:heading" + <input id="chk-heading" type="checkbox" name="first_line_heading" class="form-check-input" /> - <label for="chk:heading" class="form-check-label"> + <label for="chk-heading" class="form-check-label"> first line is a heading?</label> <small class="form-text text-muted"> Select this if the first line in your file contains headings for the @@ -108,8 +77,8 @@ </div> <div class="form-group"> - <label for="txt:delimiter" class="form-label">field delimiter</label> - <input id="txt:delimiter" + <label for="txt-delimiter" class="form-label">field delimiter</label> + <input id="txt-delimiter" type="text" name="field_delimiter" maxlength="1" @@ -149,10 +118,34 @@ </tbody> </table> </div> -{%endblock%} -{%block sidebarcontents%} -{{display_population_card(species, population)}} + + +<div class="row" id="docs-samples-upload"> + <h3 class="subheading">File Format</h3> + <p> + Upload a <strong>character-separated value (CSV)</strong> file that contains + details about your samples. The CSV file should have the following fields: + <dl> + <dt>Name</dt> + <dd>The primary name/identifier for the sample/individual.</dd> + + <dt>Name2</dt> + <dd>A secondary name for the sample. This can simply be the same as + <strong>Name</strong> above. This field <strong>MUST</strong> contain a + value.</dd> + + <dt>Symbol</dt> + <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for + species that have strains. This field can be left empty for species like + Humans that do not have strains..</dd> + + <dt>Alias</dt> + <dd>An alias for the sample. Can be an empty field, or take on the same + value as that of the Symbol.</dd> + </dl> + </p> +</div> {%endblock%} {%block javascript%} diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html index 881d466..d6318e9 100644 --- a/uploader/templates/samples/upload-success.html +++ b/uploader/templates/samples/upload-success.html @@ -1,6 +1,5 @@ {%extends "samples/base.html"%} {%from "cli-output.html" import cli_output%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Job Status{%endblock%} @@ -30,7 +29,3 @@ </div> {%endblock%} - -{%block sidebarcontents%} -{{display_population_card(species, population)}} -{%endblock%} diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html index f64f72b..3be79f0 100644 --- a/uploader/templates/species/base.html +++ b/uploader/templates/species/base.html @@ -1,17 +1,12 @@ {%extends "base.html"%} -{%block lvl1_breadcrumbs%} -<li {%if activelink=="species"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if species is mapping%} - <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}"> - {{species.Name}}</a> - {%else%} - <a href="{{url_for('species.list_species')}}">Species</a> - {%endif%} +{%block breadcrumbs%} +{{super()}} +{%if species%} +<li class="breadcrumb-item"> + <a href="{{url_for('species.view_species', species_id=species['SpeciesId'])}}"> + {{species["Name"]|title}} + </a> </li> -{%block lvl2_breadcrumbs%}{%endblock%} +{%endif%} {%endblock%} diff --git a/uploader/templates/species/sui-base.html b/uploader/templates/species/sui-base.html deleted file mode 100644 index f7b4fef..0000000 --- a/uploader/templates/species/sui-base.html +++ /dev/null @@ -1,10 +0,0 @@ -{%extends "sui-base.html"%} - -{%block breadcrumbs%} -{{super()}} -<li class="breadcrumb-item"> - <a href="{{url_for('species.view_species', species_id=species['SpeciesId'])}}"> - {{species["Name"]|title}} - </a> -</li> -{%endblock%} diff --git a/uploader/templates/species/sui-view-species.html b/uploader/templates/species/sui-view-species.html deleted file mode 100644 index 4b6402e..0000000 --- a/uploader/templates/species/sui-view-species.html +++ /dev/null @@ -1,127 +0,0 @@ -{%extends "species/sui-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-forms.html" import add_http_feature_flags%} -{%from "macro-step-indicator.html" import step_indicator%} -{%from "species/macro-display-species-card.html" import display_sui_species_card%} - -{%block title%}View Species{%endblock%} - -{%macro add_form_buttons()%} -<div class="row form-buttons"> - <div class="col"> - <input type="submit" - value="use selected population" - class="btn btn-primary" /> - </div> - - <div class="col"> - <a href="url_for('species.population.create_population', - species_id=species.SpeciesId, - return_to='species.view_species')" - title="Create a new population for species '{{species.Name}}'." - class="btn btn-outline-info"> - Create a new population - </a> - </div> -</div> -{%endmacro%} - - -{%block contents%} -<div class="row"> - <h2 class="heading">{{species.FullName}} ({{species.Name}})</h2> -</div> - -<div class "row"> - <ul class="nav nav-tabs" id="species-actions"> - <li class="nav-item presentation"> - <button class="nav-link active" - id="populations-tab" - data-bs-toggle="tab" - data-bs-target="#populations-content" - type="button" - role="tab" - aria-controls="populations-content" - aria-selected="true">Populations</button> - </li> - <li class="nav-item presentation"> - <button class="nav-link" - id="sequencing-platforms-tab" - data-bs-toggle="tab" - data-bs-target="#sequencing-platforms-content" - type="button" - role="tab" - aria-controls="sequencing-platforms-content" - aria-selected="true">Sequencing Platforms</button> - </li> - </ul> -</div> - -<div class="row"> - <div class="tab-content" id="species-tabs-content"> - <div class="tab-pane fade show active" - id="populations-content" - role="tabpanel" - aria-labelledby="populations-content-tab"> - <p>Data belonging to a particular species is further divided into one or more - populations for easier handling. Please select the population you want to work - with.</p> - - <form method="GET" - action="{{url_for('species.view_species', species_id=species.SpeciesId)}}" - class="form-horizontal"> - {{add_http_feature_flags()}} - {{add_form_buttons()}} - - {%if populations | length != 0%} - <div style="margin-top:0.3em;"> - <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> - - {%else%} - <p class="form-text"> - There are no populations currently defined for {{species['FullName']}} - ({{species['SpeciesName']}}).</p> - {%endif%} - - {{add_form_buttons()}} - - </form> - </div> - <div class="tab-pane fade" - id="sequencing-platforms-content" - role="tabpanel" - aria-labelledby="sequencing-platforms-content-tab"> - <p>Upload and manage the sequencing platforms for species - '{{species.Name | title}} ({{species.FullName}})' - <a href="{{url_for('species.platforms.list_platforms', - species_id=species.SpeciesId)}}" - title="Manage sequencing platforms for {{species.Name}}">here</a>. - </p> - </div> - </div> -</div> -{%endblock%} - -{%block sidebarcontents%} -<div class="row"> - <p>You can manage species' populations and sequencing platforms here. Select - the tab for the feature you wish to continue working on.</p> -</div> -{{display_sui_species_card(species)}} -{%endblock%} - - -{%block javascript%} -<script type="text/javascript" src="/static/js/populations.js"></script> -{%endblock%} diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html index 2d02f7e..81608fc 100644 --- a/uploader/templates/species/view-species.html +++ b/uploader/templates/species/view-species.html @@ -1,90 +1,127 @@ {%extends "species/base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "macro-forms.html" import add_http_feature_flags%} +{%from "macro-step-indicator.html" import step_indicator%} +{%from "species/macro-display-species-card.html" import display_sui_species_card%} {%block title%}View Species{%endblock%} -{%block pagetitle%}View Species{%endblock%} +{%macro add_form_buttons()%} +<div class="row form-buttons"> + <div class="col"> + <input type="submit" + value="use selected population" + class="btn btn-primary" /> + </div> + + <div class="col"> + <a href="{{url_for('species.populations.create_population', + species_id=species.SpeciesId, + return_to='species.view_species')}}" + title="Create a new population for species '{{species.Name}}'." + class="btn btn-outline-info"> + Create a new population + </a> + </div> +</div> +{%endmacro%} -{%block lvl2_breadcrumbs%} -<li {%if activelink=="view-species"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}">View</a> -</li> -{%endblock%} {%block contents%} -{{flash_all_messages()}} <div class="row"> - <h2>Details on species {{species.FullName}}</h2> + <h2 class="heading">{{species.FullName}} ({{species.Name}})</h2> +</div> - <dl> - <dt>Common Name</dt> - <dd>{{species.SpeciesName}}</dd> +<div class "row"> + <ul class="nav nav-tabs" id="species-actions"> + <li class="nav-item presentation"> + <button class="nav-link active" + id="populations-tab" + data-bs-toggle="tab" + data-bs-target="#populations-content" + type="button" + role="tab" + aria-controls="populations-content" + aria-selected="true">Populations</button> + </li> + <li class="nav-item presentation"> + <button class="nav-link" + id="sequencing-platforms-tab" + data-bs-toggle="tab" + data-bs-target="#sequencing-platforms-content" + type="button" + role="tab" + aria-controls="sequencing-platforms-content" + aria-selected="true">Sequencing Platforms</button> + </li> + </ul> +</div> - <dt>Scientific Name</dt> - <dd>{{species.FullName}}</dd> +<div class="row"> + <div class="tab-content" id="species-tabs-content"> + <div class="tab-pane fade show active" + id="populations-content" + role="tabpanel" + aria-labelledby="populations-content-tab"> + <p>Data belonging to a particular species is further divided into one or more + populations for easier handling. Please select the population you want to work + with.</p> - <dt>Taxonomy ID</dt> - <dd>{{species.TaxonomyId}}</dd> - </dl> + <form method="GET" + action="{{url_for('species.view_species', species_id=species.SpeciesId)}}" + class="form-horizontal"> + {{add_http_feature_flags()}} + {{add_form_buttons()}} - <h3>Actions</h3> + {%if populations | length != 0%} + <div style="margin-top:0.3em;"> + <table id="tbl-select-population" class="table compact stripe" + data-populations-list='{{populations | tojson}}'> + <thead> + <tr> + <th></th> + <th>Population</th> + </tr> + </thead> - <p> - You can proceed to perform any of the following actions for species - {{species.FullName}} - </p> + <tbody></tbody> + </table> + </div> - <ol> - <li> - <a href="{{url_for('species.populations.list_species_populations', - species_id=species.SpeciesId)}}" - title="Create/Edit populations for {{species.FullName}}"> - Manage populations</a> - </li> - <li> - <a href="{{url_for('species.platforms.list_platforms', - species_id=species.SpeciesId)}}" - title="Create/Edit sequencing platforms for {{species.FullName}}"> - Manage sequencing platforms</a> - </li> - </ol> + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).</p> + {%endif%} - + {{add_form_buttons()}} + + </form> + </div> + <div class="tab-pane fade" + id="sequencing-platforms-content" + role="tabpanel" + aria-labelledby="sequencing-platforms-content-tab"> + <p>Upload and manage the sequencing platforms for species + '{{species.Name | title}} ({{species.FullName}})' + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Manage sequencing platforms for {{species.Name}}">here</a>. + </p> + </div> + </div> </div> {%endblock%} {%block sidebarcontents%} -<div class="card"> - <div class="card-body"> - <h5 class="card-title">Species Extras</h5> - <div class="card-text"> - <p>Some extra internal-use details (mostly for UI concerns on GeneNetwork)</p> - <p> - <small> - If you do not understand what the following are about, simply ignore them - — - They have no bearing whatsoever on your data, or its analysis. - </small> - </p> - <dl> - <dt>Family</dt> - <dd>{{species.Family}}</dd> +<div class="row"> + <p>You can manage species' populations and sequencing platforms here. Select + the tab for the feature you wish to continue working on.</p> +</div> +{{display_sui_species_card(species)}} +{%endblock%} - <dt>FamilyOrderId</dt> - <dd>{{species.FamilyOrderId}}</dd> - <dt>OrderId</dt> - <dd>{{species.OrderId}}</dd> - </dl> - </div> - <a href="{{url_for('species.edit_species_extra', - species_id=species.SpeciesId)}}" - class="card-link" - title="Edit the species' internal-use details.">Edit</a> - </div> -</div> +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> {%endblock%} diff --git a/uploader/templates/sui-base.html b/uploader/templates/sui-base.html deleted file mode 100644 index 719a646..0000000 --- a/uploader/templates/sui-base.html +++ /dev/null @@ -1,103 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - - <head> - - <meta charset="UTF-8" /> - <meta application-name="GeneNetwork Quality-Control Application" /> - <meta name="viewport" content="width=device-width, initial-scale=1.0" /> - {%block extrameta%}{%endblock%} - - <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> - - <link rel="stylesheet" type="text/css" - href="{{url_for('base.bootstrap', - filename='css/bootstrap.min.css')}}" /> - <link rel="stylesheet" type="text/css" - href="{{url_for('base.datatables', - filename='css/dataTables.bootstrap5.min.css')}}" /> - <link rel="stylesheet" type="text/css" href="/static/css/layout-common.css" /> - <link rel="stylesheet" type="text/css" href="/static/css/layout-large.css" /> - <link rel="stylesheet" type="text/css" href="/static/css/layout-medium.css" /> - <link rel="stylesheet" type="text/css" href="/static/css/layout-small.css" /> - <link rel="stylesheet" type="text/css" href="/static/css/theme.css" /> - - {%block css%}{%endblock%} - - </head> - - <body> - <header id="header"> - <span id="header-text">GeneNetwork</span> - <nav id="header-nav"> - <ul class="nav justify-content-end"> - <li> - {%if user_logged_in()%} - <a href="{{url_for('oauth2.logout')}}" - title="Log out of the system"> - <span class="glyphicon glyphicon-user"></span> - {{user_email()}} Sign Out</a> - {%else%} - <a href="{{authserver_authorise_uri()}}" - title="Log in to the system">Sign In</a> - {%endif%} - </li> - </ul> - </nav> - </header> - - - <main id="main" class="main"> - <nav id="breadcrumbs" aria-label="breadcrumb"> - <ol class="breadcrumb"> - {%block breadcrumbs%} - <li class="breadcrumb-item"> - <a href="{{url_for('base.index')}}">Home</a></li> - {%endblock%} - </ol> - </nav> - - <div id="main-content"> - {%block contents%}{%endblock%} - </div> - - <div id="sidebar-content"> - {%block sidebarcontents%}{%endblock%} - </div> - </main> - - - - <script type="text/javascript" src="/static/js/debug.js"></script> - <!-- - Core dependencies - --> - <script src="{{url_for('base.jquery', - filename='jquery.min.js')}}"></script> - <script src="{{url_for('base.bootstrap', - filename='js/bootstrap.min.js')}}"></script> - - <!-- - DataTables dependencies - --> - <script type="text/javascript" - src="{{url_for('base.datatables', - filename='js/dataTables.min.js')}}"></script> - <script type="text/javascript" - src="{{url_for('base.datatables_extensions', - filename='scroller/js/dataTables.scroller.min.js')}}"></script> - <script type="text/javascript" - src="{{url_for('base.datatables_extensions', - filename='buttons/js/dataTables.buttons.min.js')}}"></script> - <script type="text/javascript" - src="{{url_for('base.datatables_extensions', - filename='select/js/dataTables.select.min.js')}}"></script> - - <!-- - local dependencies - --> - <script type="text/javascript" src="/static/js/utils.js"></script> - <script type="text/javascript" src="/static/js/datatables.js"></script> - {%block javascript%}{%endblock%} - </body> -</html> diff --git a/uploader/templates/sui-index.html b/uploader/templates/sui-index.html deleted file mode 100644 index 888823f..0000000 --- a/uploader/templates/sui-index.html +++ /dev/null @@ -1,123 +0,0 @@ -{%extends "sui-base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-forms.html" import add_http_feature_flags%} -{%from "macro-step-indicator.html" import step_indicator%} - -{%block title%}Home{%endblock%} - -{%block pagetitle%}Home{%endblock%} - -{%block extra_breadcrumbs%}{%endblock%} - -{%block contents%} - -{%macro add_form_buttons()%} -<div class="row form-buttons"> - <div class="col"> - <input type="submit" - class="btn btn-primary" - value="use selected species" /> - </div> - <div class="col"> - <a href="{{url_for('species.create_species', return_to='base.index')}}" - class="btn btn-outline-primary" - title="Create a new species.">Create a new Species</a> - </div> -</div> -{%endmacro%} - -<div class="row">{{flash_all_messages()}}</div> - -{%if user_logged_in()%} - -<div class="row"> - <div class="row"> - <h2 class="heading">Species</h2> - - <p>Select the species you want to work with.</p> - </div> -</div> - -<div class="row"> - <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal"> - {{add_http_feature_flags()}} - - {{add_form_buttons()}} - - {%if species | length != 0%} - <div style="margin-top:1em;"> - <table id="tbl-select-species" class="table compact stripe" - data-species-list='{{species | tojson}}'> - <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%} - - {{add_form_buttons()}} - - </form> -</div> - -{%else%} - -<div class="row"> - <p>The Genenetwork Uploader (<em>gn-uploader</em>) enables upload of new data - into the Genenetwork System. It provides Quality Control over data, and - guidance in case you data does not meet the standards for acceptance.</p> - <p> - <a href="{{authserver_authorise_uri()}}" - title="Sign in to the system" - class="btn btn-primary">Sign in</a> - to get started.</p> -</div> -{%endif%} - -{%endblock%} - - - -{%block sidebarcontents%} -<div class="row"> - <p>The data in Genenetwork is related to one species or another. Use the form - provided to select from existing species, or click on the - "Create a New Species" button if you cannot find the species you want to - work with.</p> -</div> -<div class="row"> - <form id="frm-quick-navigation"> - <legend>Quick Navigation</legend> - <div class="form-group"> - <label for="fqn-species-id">Species</label> - <select name="species_id"> - <option value="">Select species</option> - </select> - </div> - </form> -</div> -{%endblock%} - - -{%block javascript%} -<script type="text/javascript" src="/static/js/species.js"></script> -{%endblock%} diff --git a/uploader/ui.py b/uploader/ui.py index 1994056..41791c7 100644 --- a/uploader/ui.py +++ b/uploader/ui.py @@ -1,5 +1,5 @@ """Utilities to handle the UI""" -from flask import render_template as flask_render_template +from uploader.flask_extensions import render_template as flask_render_template def make_template_renderer(default): """Render template for species.""" |
