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-rw-r--r--qc_app/__init__.py48
-rw-r--r--qc_app/base_routes.py29
-rw-r--r--qc_app/check_connections.py28
-rw-r--r--qc_app/db/__init__.py8
-rw-r--r--qc_app/db/averaging.py23
-rw-r--r--qc_app/db/datasets.py133
-rw-r--r--qc_app/db/platforms.py25
-rw-r--r--qc_app/db/populations.py54
-rw-r--r--qc_app/db/species.py22
-rw-r--r--qc_app/db/tissues.py50
-rw-r--r--qc_app/db_utils.py46
-rw-r--r--qc_app/dbinsert.py397
-rw-r--r--qc_app/entry.py127
-rw-r--r--qc_app/errors.py29
-rw-r--r--qc_app/files.py26
-rw-r--r--qc_app/input_validation.py27
-rw-r--r--qc_app/jobs.py130
-rw-r--r--qc_app/parse.py175
-rw-r--r--qc_app/samples.py354
-rw-r--r--qc_app/static/css/custom-bootstrap.css23
-rw-r--r--qc_app/static/css/styles.css7
-rw-r--r--qc_app/static/css/two-column-with-separator.css27
-rw-r--r--qc_app/static/images/CITGLogo.pngbin11962 -> 0 bytes
-rw-r--r--qc_app/static/js/select_platform.js70
-rw-r--r--qc_app/static/js/upload_progress.js97
-rw-r--r--qc_app/static/js/upload_samples.js132
-rw-r--r--qc_app/static/js/utils.js10
-rw-r--r--qc_app/templates/base.html51
-rw-r--r--qc_app/templates/cli-output.html8
-rw-r--r--qc_app/templates/continue_from_create_dataset.html52
-rw-r--r--qc_app/templates/continue_from_create_study.html52
-rw-r--r--qc_app/templates/data_review.html85
-rw-r--r--qc_app/templates/dbupdate_error.html12
-rw-r--r--qc_app/templates/dbupdate_hidden_fields.html29
-rw-r--r--qc_app/templates/errors_display.html47
-rw-r--r--qc_app/templates/final_confirmation.html47
-rw-r--r--qc_app/templates/flash_messages.html25
-rw-r--r--qc_app/templates/http-error.html18
-rw-r--r--qc_app/templates/index.html81
-rw-r--r--qc_app/templates/insert_error.html32
-rw-r--r--qc_app/templates/insert_progress.html46
-rw-r--r--qc_app/templates/insert_success.html19
-rw-r--r--qc_app/templates/job_progress.html40
-rw-r--r--qc_app/templates/no_such_job.html14
-rw-r--r--qc_app/templates/parse_failure.html26
-rw-r--r--qc_app/templates/parse_results.html30
-rw-r--r--qc_app/templates/rqtl2/create-geno-dataset-success.html55
-rw-r--r--qc_app/templates/rqtl2/create-probe-dataset-success.html59
-rw-r--r--qc_app/templates/rqtl2/create-probe-study-success.html49
-rw-r--r--qc_app/templates/rqtl2/create-tissue-success.html106
-rw-r--r--qc_app/templates/rqtl2/index.html36
-rw-r--r--qc_app/templates/rqtl2/no-such-job.html13
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-error.html39
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-results.html24
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-status.html20
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-error.html120
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-results.html66
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-status.html41
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-success.html37
-rw-r--r--qc_app/templates/rqtl2/select-geno-dataset.html144
-rw-r--r--qc_app/templates/rqtl2/select-population.html136
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html191
-rw-r--r--qc_app/templates/rqtl2/select-probeset-study-id.html143
-rw-r--r--qc_app/templates/rqtl2/select-tissue.html115
-rw-r--r--qc_app/templates/rqtl2/summary-info.html65
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html276
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html33
-rw-r--r--qc_app/templates/samples/select-population.html99
-rw-r--r--qc_app/templates/samples/select-species.html30
-rw-r--r--qc_app/templates/samples/upload-failure.html27
-rw-r--r--qc_app/templates/samples/upload-progress.html22
-rw-r--r--qc_app/templates/samples/upload-samples.html139
-rw-r--r--qc_app/templates/samples/upload-success.html18
-rw-r--r--qc_app/templates/select_dataset.html161
-rw-r--r--qc_app/templates/select_platform.html82
-rw-r--r--qc_app/templates/select_species.html92
-rw-r--r--qc_app/templates/select_study.html108
-rw-r--r--qc_app/templates/stdout_output.html8
-rw-r--r--qc_app/templates/unhandled_exception.html21
-rw-r--r--qc_app/templates/upload_progress_indicator.html35
-rw-r--r--qc_app/templates/worker_failure.html24
-rw-r--r--qc_app/upload/__init__.py7
-rw-r--r--qc_app/upload/rqtl2.py1157
83 files changed, 0 insertions, 6609 deletions
diff --git a/qc_app/__init__.py b/qc_app/__init__.py
deleted file mode 100644
index 3ee8aa0..0000000
--- a/qc_app/__init__.py
+++ /dev/null
@@ -1,48 +0,0 @@
-"""The Quality-Control Web Application entry point"""
-import os
-import logging
-from pathlib import Path
-
-from flask import Flask, request
-
-from .entry import entrybp
-from .upload import upload
-from .parse import parsebp
-from .samples import samples
-from .base_routes import base
-from .dbinsert import dbinsertbp
-from .errors import register_error_handlers
-
-def override_settings_with_envvars(
- app: Flask, ignore: tuple[str, ...]=tuple()) -> None:
- """Override settings in `app` with those in ENVVARS"""
- for setting in (key for key in app.config if key not in ignore):
- app.config[setting] = os.environ.get(setting) or app.config[setting]
-
-
-def create_app():
- """The application factory"""
- app = Flask(__name__)
- app.config.from_pyfile(
- Path(__file__).parent.joinpath("default_settings.py"))
- if "QCAPP_CONF" in os.environ:
- app.config.from_envvar("QCAPP_CONF") # Override defaults with instance path
-
- override_settings_with_envvars(app, ignore=tuple())
-
- if "QCAPP_SECRETS" in os.environ:
- app.config.from_envvar("QCAPP_SECRETS")
-
- # setup jinja2 symbols
- app.jinja_env.globals.update(request_url=lambda : request.url)
-
- # setup blueprints
- app.register_blueprint(base, url_prefix="/")
- app.register_blueprint(entrybp, url_prefix="/")
- app.register_blueprint(parsebp, url_prefix="/parse")
- app.register_blueprint(upload, url_prefix="/upload")
- app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
- app.register_blueprint(samples, url_prefix="/samples")
-
- register_error_handlers(app)
- return app
diff --git a/qc_app/base_routes.py b/qc_app/base_routes.py
deleted file mode 100644
index 9daf439..0000000
--- a/qc_app/base_routes.py
+++ /dev/null
@@ -1,29 +0,0 @@
-"""Basic routes required for all pages"""
-import os
-from flask import Blueprint, send_from_directory
-
-base = Blueprint("base", __name__)
-
-def appenv():
- """Get app's guix environment path."""
- return os.environ.get("GN_UPLOADER_ENVIRONMENT")
-
-@base.route("/bootstrap/<path:filename>")
-def bootstrap(filename):
- """Fetch bootstrap files."""
- return send_from_directory(
- appenv(), f"share/genenetwork2/javascript/bootstrap/{filename}")
-
-
-@base.route("/jquery/<path:filename>")
-def jquery(filename):
- """Fetch jquery files."""
- return send_from_directory(
- appenv(), f"share/genenetwork2/javascript/jquery/{filename}")
-
-
-@base.route("/node-modules/<path:filename>")
-def node_modules(filename):
- """Fetch node-js modules."""
- return send_from_directory(
- appenv(), f"lib/node_modules/{filename}")
diff --git a/qc_app/check_connections.py b/qc_app/check_connections.py
deleted file mode 100644
index ceccc32..0000000
--- a/qc_app/check_connections.py
+++ /dev/null
@@ -1,28 +0,0 @@
-"""Check the various connection used in the application"""
-import sys
-import traceback
-
-import redis
-import MySQLdb
-
-from qc_app.db_utils import database_connection
-
-def check_redis(uri: str):
- "Check the redis connection"
- try:
- with redis.Redis.from_url(uri) as rconn:
- rconn.ping()
- except redis.exceptions.ConnectionError as conn_err:
- print(conn_err, file=sys.stderr)
- print(traceback.format_exc(), file=sys.stderr)
- sys.exit(1)
-
-def check_db(uri: str):
- "Check the mysql connection"
- try:
- with database_connection(uri) as dbconn: # pylint: disable=[unused-variable]
- pass
- except MySQLdb.OperationalError as op_err:
- print(op_err, file=sys.stderr)
- print(traceback.format_exc(), file=sys.stderr)
- sys.exit(1)
diff --git a/qc_app/db/__init__.py b/qc_app/db/__init__.py
deleted file mode 100644
index 36e93e8..0000000
--- a/qc_app/db/__init__.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""Database functions"""
-from .species import species, species_by_id
-from .populations import (
- save_population,
- population_by_id,
- populations_by_species,
- population_by_species_and_id)
-from .datasets import geno_datasets_by_species_and_population
diff --git a/qc_app/db/averaging.py b/qc_app/db/averaging.py
deleted file mode 100644
index 62bbe67..0000000
--- a/qc_app/db/averaging.py
+++ /dev/null
@@ -1,23 +0,0 @@
-"""Functions for db interactions for averaging methods"""
-from typing import Optional
-
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def averaging_methods(conn: mdb.Connection) -> tuple[dict, ...]:
- """Fetch all available averaging methods"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM AvgMethod")
- return tuple(dict(row) for row in cursor.fetchall())
-
-def averaging_method_by_id(
- conn: mdb.Connection, averageid: int) -> Optional[dict]:
- """Fetch the averaging method by its ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM AvgMethod WHERE Id=%s",
- (averageid,))
- result = cursor.fetchone()
- if bool(result):
- return dict(result)
-
- return None
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
deleted file mode 100644
index 767ec41..0000000
--- a/qc_app/db/datasets.py
+++ /dev/null
@@ -1,133 +0,0 @@
-"""Functions for accessing the database relating to datasets."""
-from datetime import date
-from typing import Optional
-
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def geno_datasets_by_species_and_population(
- conn: mdb.Connection,
- speciesid: int,
- populationid: int) -> tuple[dict, ...]:
- """Retrieve all genotypes datasets by species and population"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT gf.* FROM InbredSet AS iset INNER JOIN GenoFreeze AS gf "
- "ON iset.InbredSetId=gf.InbredSetId "
- "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
- {"sid": speciesid, "pid": populationid})
- return tuple(dict(row) for row in cursor.fetchall())
-
-def geno_dataset_by_id(conn: mdb.Connection, dataset_id) -> Optional[dict]:
- """Retrieve genotype dataset by ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s", (dataset_id,))
- _dataset = cursor.fetchone()
- return dict(_dataset) if bool(_dataset) else None
-
-def probeset_studies_by_species_and_population(
- conn: mdb.Connection,
- speciesid: int,
- populationid: int) -> tuple[dict, ...]:
- """Retrieve all probesets"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT pf.* FROM InbredSet AS iset INNER JOIN ProbeFreeze AS pf "
- "ON iset.InbredSetId=pf.InbredSetId "
- "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
- {"sid": speciesid, "pid": populationid})
- return tuple(dict(row) for row in cursor.fetchall())
-
-def probeset_datasets_by_study(conn: mdb.Connection,
- studyid: int) -> tuple[dict, ...]:
- """Retrieve all probeset databases by study."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s",
- (studyid,))
- return tuple(dict(row) for row in cursor.fetchall())
-
-def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]:
- """Retrieve ProbeSet study by ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s", (studyid,))
- _study = cursor.fetchone()
- return dict(_study) if bool(_study) else None
-
-def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
- populationid: int,
- platformid: int,
- tissueid: int,
- studyname: str,
- studyfullname: str = "",
- studyshortname: str = ""):
- """Create a new ProbeSet study."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- studydata = {
- "platid": platformid,
- "tissueid": tissueid,
- "name": studyname,
- "fname": studyfullname or studyname,
- "sname": studyshortname,
- "today": date.today().isoformat(),
- "popid": populationid
- }
- cursor.execute(
- """
- INSERT INTO ProbeFreeze(
- ChipId, TissueId, Name, FullName, ShortName, CreateTime,
- InbredSetId
- ) VALUES (
- %(platid)s, %(tissueid)s, %(name)s, %(fname)s, %(sname)s,
- %(today)s, %(popid)s
- )
- """,
- studydata)
- studyid = cursor.lastrowid
- cursor.execute("UPDATE ProbeFreeze SET ProbeFreezeId=%s WHERE Id=%s",
- (studyid, studyid))
- return {**studydata, "studyid": studyid}
-
-def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
- studyid: int,
- averageid: int,
- datasetname: str,
- datasetfullname: str,
- datasetshortname: str="",
- public: bool = True,
- datascale="log2") -> dict:
- """Create a new ProbeSet dataset."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- dataset = {
- "studyid": studyid,
- "averageid": averageid,
- "name2": datasetname,
- "fname": datasetfullname,
- "name": datasetshortname,
- "sname": datasetshortname,
- "today": date.today().isoformat(),
- "public": 2 if public else 0,
- "authorisedusers": "williamslab",
- "datascale": datascale
- }
- cursor.execute(
- """
- INSERT INTO ProbeSetFreeze(
- ProbeFreezeId, AvgId, Name, Name2, FullName, ShortName,
- CreateTime, public, AuthorisedUsers, DataScale)
- VALUES(
- %(studyid)s, %(averageid)s, %(name)s, %(name2)s, %(fname)s,
- %(sname)s, %(today)s, %(public)s, %(authorisedusers)s,
- %(datascale)s)
- """,
- dataset)
- return {**dataset, "datasetid": cursor.lastrowid}
-
-def probeset_dataset_by_id(conn: mdb.Connection, datasetid) -> Optional[dict]:
- """Fetch a ProbeSet dataset by its ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s", (datasetid,))
- result = cursor.fetchone()
- if bool(result):
- return dict(result)
-
- return None
diff --git a/qc_app/db/platforms.py b/qc_app/db/platforms.py
deleted file mode 100644
index cb527a7..0000000
--- a/qc_app/db/platforms.py
+++ /dev/null
@@ -1,25 +0,0 @@
-"""Handle db interactions for platforms."""
-from typing import Optional
-
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def platforms_by_species(
- conn: mdb.Connection, speciesid: int) -> tuple[dict, ...]:
- """Retrieve platforms by the species"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s "
- "ORDER BY GeneChipName ASC",
- (speciesid,))
- return tuple(dict(row) for row in cursor.fetchall())
-
-def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
- """Retrieve a platform by its ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM GeneChip WHERE Id=%s",
- (platformid,))
- result = cursor.fetchone()
- if bool(result):
- return dict(result)
-
- return None
diff --git a/qc_app/db/populations.py b/qc_app/db/populations.py
deleted file mode 100644
index 4485e52..0000000
--- a/qc_app/db/populations.py
+++ /dev/null
@@ -1,54 +0,0 @@
-"""Functions for accessing the database relating to species populations."""
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def population_by_id(conn: mdb.Connection, population_id) -> dict:
- """Get the grouping/population by id."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
- (population_id,))
- return cursor.fetchone()
-
-def population_by_species_and_id(
- conn: mdb.Connection, species_id, population_id) -> dict:
- """Retrieve a population by its identifier and species."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s",
- (species_id, population_id))
- return cursor.fetchone()
-
-def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
- "Retrieve group (InbredSet) information from the database."
- with conn.cursor(cursorclass=DictCursor) as cursor:
- query = "SELECT * FROM InbredSet WHERE SpeciesId=%s"
- cursor.execute(query, (speciesid,))
- return tuple(cursor.fetchall())
-
- return tuple()
-
-def save_population(conn: mdb.Connection, population_details: dict) -> dict:
- """Save the population details to the db."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "INSERT INTO InbredSet("
- "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
- "MenuOrderId, Description"
- ") "
- "VALUES ("
- "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
- "%(FullName)s, %(MenuOrderId)s, %(Description)s"
- ")",
- {
- "MenuOrderId": 0,
- "InbredSetId": 0,
- **population_details
- })
- new_id = cursor.lastrowid
- cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
- (new_id, new_id))
- return {
- **population_details,
- "Id": new_id,
- "InbredSetId": new_id,
- "population_id": new_id
- }
diff --git a/qc_app/db/species.py b/qc_app/db/species.py
deleted file mode 100644
index 653e59b..0000000
--- a/qc_app/db/species.py
+++ /dev/null
@@ -1,22 +0,0 @@
-"""Database functions for species."""
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def species(conn: mdb.Connection) -> tuple:
- "Retrieve the species from the database."
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
- "FullName FROM Species")
- return tuple(cursor.fetchall())
-
- return tuple()
-
-def species_by_id(conn: mdb.Connection, speciesid) -> dict:
- "Retrieve the species from the database by id."
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
- "FullName FROM Species WHERE SpeciesId=%s",
- (speciesid,))
- return cursor.fetchone()
diff --git a/qc_app/db/tissues.py b/qc_app/db/tissues.py
deleted file mode 100644
index 9fe7bab..0000000
--- a/qc_app/db/tissues.py
+++ /dev/null
@@ -1,50 +0,0 @@
-"""Handle db interactions for tissue."""
-from typing import Union, Optional
-
-import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
-
-def all_tissues(conn: mdb.Connection) -> tuple[dict, ...]:
- """All available tissue."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM Tissue ORDER BY TissueName")
- return tuple(dict(row) for row in cursor.fetchall())
-
-
-def tissue_by_id(conn: mdb.Connection, tissueid) -> Optional[dict]:
- """Retrieve a tissue by its ID"""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM Tissue WHERE Id=%s", (tissueid,))
- result = cursor.fetchone()
- if bool(result):
- return dict(result)
-
- return None
-
-
-def create_new_tissue(
- conn: mdb.Connection,
- name: str,
- shortname: str,
- birnlexid: Optional[str] = None,
- birnlexname: Optional[str] = None
-) -> dict[str, Union[int, str, None]]:
- """Add a new tissue, organ or biological material to the database."""
- with conn.cursor() as cursor:
- cursor.execute(
- "INSERT INTO "
- "Tissue(TissueName, Name, Short_Name, BIRN_lex_ID, BIRN_lex_Name) "
- "VALUES (%s, %s, %s, %s, %s)",
- (name, name, shortname, birnlexid, birnlexname))
- tissueid = cursor.lastrowid
- cursor.execute("UPDATE Tissue SET TissueId=%s WHERE Id=%s",
- (tissueid, tissueid))
- return {
- "Id": tissueid,
- "TissueId": tissueid,
- "TissueName": name,
- "Name": name,
- "Short_Name": shortname,
- "BIRN_lex_ID": birnlexid,
- "BIRN_lex_Name": birnlexname
- }
diff --git a/qc_app/db_utils.py b/qc_app/db_utils.py
deleted file mode 100644
index ef26398..0000000
--- a/qc_app/db_utils.py
+++ /dev/null
@@ -1,46 +0,0 @@
-"""module contains all db related stuff"""
-import logging
-import traceback
-import contextlib
-from urllib.parse import urlparse
-from typing import Any, Tuple, Optional, Iterator, Callable
-
-import MySQLdb as mdb
-from redis import Redis
-from flask import current_app as app
-
-def parse_db_url(db_url) -> Tuple:
- """
- Parse SQL_URI configuration variable.
- """
- parsed_db = urlparse(db_url)
- return (parsed_db.hostname, parsed_db.username,
- parsed_db.password, parsed_db.path[1:], parsed_db.port)
-
-
-@contextlib.contextmanager
-def database_connection(db_url: Optional[str] = None) -> Iterator[mdb.Connection]:
- """function to create db connector"""
- host, user, passwd, db_name, db_port = parse_db_url(
- db_url or app.config["SQL_URI"])
- connection = mdb.connect(
- host, user, passwd, db_name, port=(db_port or 3306))
- try:
- yield connection
- connection.commit()
- except mdb.Error as _mdb_err:
- logging.error(traceback.format_exc())
- connection.rollback()
- finally:
- connection.close()
-
-def with_db_connection(func: Callable[[mdb.Connection], Any]) -> Any:
- """Call `func` with a MySQDdb database connection."""
- with database_connection(app.config["SQL_URI"]) as conn:
- return func(conn)
-
-def with_redis_connection(func: Callable[[Redis], Any]) -> Any:
- """Call `func` with a redis connection."""
- redisuri = app.config["REDIS_URL"]
- with Redis.from_url(redisuri, decode_responses=True) as rconn:
- return func(rconn)
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
deleted file mode 100644
index ef08423..0000000
--- a/qc_app/dbinsert.py
+++ /dev/null
@@ -1,397 +0,0 @@
-"Handle inserting data into the database"
-import os
-import json
-from typing import Union
-from functools import reduce
-from datetime import datetime
-
-from redis import Redis
-from MySQLdb.cursors import DictCursor
-from flask import (
- flash, request, url_for, Blueprint, redirect, render_template,
- current_app as app)
-
-from qc_app.db_utils import with_db_connection, database_connection
-from qc_app.db import species, species_by_id, populations_by_species
-
-from . import jobs
-
-dbinsertbp = Blueprint("dbinsert", __name__)
-
-def render_error(error_msg):
- "Render the generic error page"
- return render_template("dbupdate_error.html", error_message=error_msg), 400
-
-def make_menu_items_grouper(grouping_fn=lambda item: item):
- "Build function to be used to group menu items."
- def __grouper__(acc, row):
- grouping = grouping_fn(row[2])
- row_values = (row[0].strip(), row[1].strip())
- if acc.get(grouping) is None:
- return {**acc, grouping: (row_values,)}
- return {**acc, grouping: (acc[grouping] + (row_values,))}
- return __grouper__
-
-def genechips():
- "Retrieve the genechip information from the database"
- def __organise_by_species__(acc, chip):
- speciesid = chip["SpeciesId"]
- if acc.get(speciesid) is None:
- return {**acc, speciesid: (chip,)}
- return {**acc, speciesid: acc[speciesid] + (chip,)}
-
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC")
- return reduce(__organise_by_species__, cursor.fetchall(), {})
-
- return {}
-
-def platform_by_id(genechipid:int) -> Union[dict, None]:
- "Retrieve the gene platform by id"
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT * FROM GeneChip WHERE GeneChipId=%s",
- (genechipid,))
- return cursor.fetchone()
-
-def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
- "Retrieve the studies by the related species and gene platform"
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- query = (
- "SELECT Species.SpeciesId, ProbeFreeze.* "
- "FROM Species INNER JOIN InbredSet "
- "ON Species.SpeciesId=InbredSet.SpeciesId "
- "INNER JOIN ProbeFreeze "
- "ON InbredSet.InbredSetId=ProbeFreeze.InbredSetId "
- "WHERE Species.SpeciesId = %s "
- "AND ProbeFreeze.ChipId = %s")
- cursor.execute(query, (speciesid, genechipid))
- return tuple(cursor.fetchall())
-
- return tuple()
-
-def organise_groups_by_family(acc:dict, group:dict) -> dict:
- "Organise the group (InbredSet) information by the group field"
- family = group["Family"]
- if acc.get(family):
- return {**acc, family: acc[family] + (group,)}
- return {**acc, family: (group,)}
-
-def tissues() -> tuple:
- "Retrieve type (Tissue) information from the database."
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM Tissue ORDER BY Name")
- return tuple(cursor.fetchall())
-
- return tuple()
-
-@dbinsertbp.route("/platform", methods=["POST"])
-def select_platform():
- "Select the platform (GeneChipId) used for the data."
- job_id = request.form["job_id"]
- with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
- database_connection(app.config["SQL_URI"]) as conn):
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
- if job:
- filename = job["filename"]
- filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
- if os.path.exists(filepath):
- default_species = 1
- gchips = genechips()
- return render_template(
- "select_platform.html", filename=filename,
- filetype=job["filetype"], totallines=int(job["currentline"]),
- default_species=default_species, species=species(conn),
- genechips=gchips[default_species],
- genechips_data=json.dumps(gchips))
- return render_error(f"File '{filename}' no longer exists.")
- return render_error(f"Job '{job_id}' no longer exists.")
- return render_error("Unknown error")
-
-@dbinsertbp.route("/study", methods=["POST"])
-def select_study():
- "View to select/create the study (ProbeFreeze) associated with the data."
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
-
- speciesid = form["species"]
- genechipid = form["genechipid"]
-
- the_studies = studies_by_species_and_platform(speciesid, genechipid)
- the_groups = reduce(
- organise_groups_by_family,
- with_db_connection(
- lambda conn: populations_by_species(conn, speciesid)),
- {})
- return render_template(
- "select_study.html", filename=form["filename"],
- filetype=form["filetype"], totallines=form["totallines"],
- species=speciesid, genechipid=genechipid, studies=the_studies,
- groups=the_groups, tissues = tissues(),
- selected_group=int(form.get("inbredsetid", -13)),
- selected_tissue=int(form.get("tissueid", -13)))
- except AssertionError as aserr:
- return render_error(f"Missing data: {aserr.args[0]}")
-
-@dbinsertbp.route("/create-study", methods=["POST"])
-def create_study():
- "Create a new study (ProbeFreeze)."
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
- assert form.get("studyname"), "study name"
- assert form.get("inbredsetid"), "group"
- assert form.get("tissueid"), "type/tissue"
-
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- values = (
- form["genechipid"],
- form["tissueid"],
- form["studyname"],
- form.get("studyfullname", ""),
- form.get("studyshortname", ""),
- datetime.now().date().strftime("%Y-%m-%d"),
- form["inbredsetid"])
- query = (
- "INSERT INTO ProbeFreeze("
- "ChipId, TissueId, Name, FullName, ShortName, CreateTime, "
- "InbredSetId"
- ") VALUES (%s, %s, %s, %s, %s, %s, %s)")
- cursor.execute(query, values)
- new_studyid = cursor.lastrowid
- cursor.execute(
- "UPDATE ProbeFreeze SET ProbeFreezeId=%s WHERE Id=%s",
- (new_studyid, new_studyid))
- flash("Study created successfully", "alert-success")
- return render_template(
- "continue_from_create_study.html",
- filename=form["filename"], filetype=form["filetype"],
- totallines=form["totallines"], species=form["species"],
- genechipid=form["genechipid"], studyid=new_studyid)
- except AssertionError as aserr:
- flash(f"Missing data: {aserr.args[0]}", "alert-error")
- return redirect(url_for("dbinsert.select_study"), code=307)
-
-def datasets_by_study(studyid:int) -> tuple:
- "Retrieve datasets associated with a study with the ID `studyid`."
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s"
- cursor.execute(query, (studyid,))
- return tuple(cursor.fetchall())
-
- return tuple()
-
-def averaging_methods() -> tuple:
- "Retrieve averaging methods from database"
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM AvgMethod")
- return tuple(cursor.fetchall())
-
- return tuple()
-
-def dataset_datascales() -> tuple:
- "Retrieve datascales from database"
- with database_connection() as conn:
- with conn.cursor() as cursor:
- cursor.execute(
- 'SELECT DISTINCT DataScale FROM ProbeSetFreeze '
- 'WHERE DataScale IS NOT NULL AND DataScale != ""')
- return tuple(
- item for item in
- (res[0].strip() for res in cursor.fetchall())
- if (item is not None and item != ""))
-
- return tuple()
-
-@dbinsertbp.route("/dataset", methods=["POST"])
-def select_dataset():
- "Select the dataset to add the file contents against"
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
- assert form.get("studyid"), "study"
-
- studyid = form["studyid"]
- datasets = datasets_by_study(studyid)
- return render_template(
- "select_dataset.html", **{**form, "studyid": studyid},
- datasets=datasets, avgmethods=averaging_methods(),
- datascales=dataset_datascales())
- except AssertionError as aserr:
- return render_error(f"Missing data: {aserr.args[0]}")
-
-@dbinsertbp.route("/create-dataset", methods=["POST"])
-def create_dataset():
- "Select the dataset to add the file contents against"
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
- assert form.get("studyid"), "study"
- assert form.get("avgid"), "averaging method"
- assert form.get("datasetname2"), "Dataset Name 2"
- assert form.get("datasetfullname"), "Dataset Full Name"
- assert form.get("datasetshortname"), "Dataset Short Name"
- assert form.get("datasetpublic"), "Dataset public specification"
- assert form.get("datasetconfidentiality"), "Dataset confidentiality"
- assert form.get("datasetdatascale"), "Dataset Datascale"
-
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- datasetname = form["datasetname"]
- cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Name=%s",
- (datasetname,))
- results = cursor.fetchall()
- if bool(results):
- flash("A dataset with that name already exists.",
- "alert-error")
- return redirect(url_for("dbinsert.select_dataset"), code=307)
- values = (
- form["studyid"], form["avgid"],
- datasetname, form["datasetname2"],
- form["datasetfullname"], form["datasetshortname"],
- datetime.now().date().strftime("%Y-%m-%d"),
- form["datasetpublic"], form["datasetconfidentiality"],
- "williamslab", form["datasetdatascale"])
- query = (
- "INSERT INTO ProbeSetFreeze("
- "ProbeFreezeId, AvgID, Name, Name2, FullName, "
- "ShortName, CreateTime, OrderList, public, "
- "confidentiality, AuthorisedUsers, DataScale) "
- "VALUES"
- "(%s, %s, %s, %s, %s, %s, %s, NULL, %s, %s, %s, %s)")
- cursor.execute(query, values)
- new_datasetid = cursor.lastrowid
- return render_template(
- "continue_from_create_dataset.html",
- filename=form["filename"], filetype=form["filetype"],
- species=form["species"], genechipid=form["genechipid"],
- studyid=form["studyid"], datasetid=new_datasetid,
- totallines=form["totallines"])
- except AssertionError as aserr:
- flash(f"Missing data {aserr.args[0]}", "alert-error")
- return redirect(url_for("dbinsert.select_dataset"), code=307)
-
-def study_by_id(studyid:int) -> Union[dict, None]:
- "Get a study by its Id"
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT * FROM ProbeFreeze WHERE Id=%s",
- (studyid,))
- return cursor.fetchone()
-
-def dataset_by_id(datasetid:int) -> Union[dict, None]:
- "Retrieve a dataset by its id"
- with database_connection() as conn:
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- ("SELECT AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.* "
- "FROM ProbeSetFreeze INNER JOIN AvgMethod "
- "ON ProbeSetFreeze.AvgId=AvgMethod.AvgMethodId "
- "WHERE ProbeSetFreeze.Id=%s"),
- (datasetid,))
- return cursor.fetchone()
-
-def selected_keys(original: dict, keys: tuple) -> dict:
- "Return a new dict from the `original` dict with only `keys` present."
- return {key: value for key,value in original.items() if key in keys}
-
-@dbinsertbp.route("/final-confirmation", methods=["POST"])
-def final_confirmation():
- "Preview the data before triggering entry into the database"
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
- assert form.get("studyid"), "study"
- assert form.get("datasetid"), "dataset"
-
- speciesid = form["species"]
- genechipid = form["genechipid"]
- studyid = form["studyid"]
- datasetid=form["datasetid"]
- return render_template(
- "final_confirmation.html", filename=form["filename"],
- filetype=form["filetype"], totallines=form["totallines"],
- species=speciesid, genechipid=genechipid, studyid=studyid,
- datasetid=datasetid, the_species=selected_keys(
- with_db_connection(lambda conn: species_by_id(conn, speciesid)),
- ("SpeciesName", "Name", "MenuName")),
- platform=selected_keys(
- platform_by_id(genechipid),
- ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")),
- study=selected_keys(
- study_by_id(studyid), ("Name", "FullName", "ShortName")),
- dataset=selected_keys(
- dataset_by_id(datasetid),
- ("AvgMethodName", "Name", "Name2", "FullName", "ShortName",
- "DataScale")))
- except AssertionError as aserr:
- return render_error(f"Missing data: {aserr.args[0]}")
-
-@dbinsertbp.route("/insert-data", methods=["POST"])
-def insert_data():
- "Trigger data insertion"
- form = request.form
- try:
- assert form.get("filename"), "filename"
- assert form.get("filetype"), "filetype"
- assert form.get("species"), "species"
- assert form.get("genechipid"), "platform"
- assert form.get("studyid"), "study"
- assert form.get("datasetid"), "dataset"
-
- filename = form["filename"]
- filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
- redisurl = app.config["REDIS_URL"]
- if os.path.exists(filepath):
- with Redis.from_url(redisurl, decode_responses=True) as rconn:
- job = jobs.launch_job(
- jobs.data_insertion_job(
- rconn, filepath, form["filetype"], form["totallines"],
- form["species"], form["genechipid"], form["datasetid"],
- app.config["SQL_URI"], redisurl,
- app.config["JOBS_TTL_SECONDS"]),
- redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors")
-
- return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"]))
- return render_error(f"File '{filename}' no longer exists.")
- except AssertionError as aserr:
- return render_error(f"Missing data: {aserr.args[0]}")
-
-@dbinsertbp.route("/status/<job_id>", methods=["GET"])
-def insert_status(job_id: str):
- "Retrieve status of data insertion."
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
-
- if job:
- job_status = job["status"]
- if job_status == "success":
- return render_template("insert_success.html", job=job)
- if job["status"] == "error":
- return render_template("insert_error.html", job=job)
- return render_template("insert_progress.html", job=job)
- return render_template("no_such_job.html", job_id=job_id), 400
diff --git a/qc_app/entry.py b/qc_app/entry.py
deleted file mode 100644
index f2db878..0000000
--- a/qc_app/entry.py
+++ /dev/null
@@ -1,127 +0,0 @@
-"""Entry-point module"""
-import os
-import mimetypes
-from typing import Tuple
-from zipfile import ZipFile, is_zipfile
-
-from werkzeug.utils import secure_filename
-from flask import (
- flash,
- request,
- url_for,
- redirect,
- Blueprint,
- render_template,
- current_app as app,
- send_from_directory)
-
-from qc_app.db import species
-from qc_app.db_utils import with_db_connection
-
-entrybp = Blueprint("entry", __name__)
-
-@entrybp.route("/favicon.ico", methods=["GET"])
-def favicon():
- """Return the favicon."""
- return send_from_directory(os.path.join(app.root_path, "static"),
- "images/CITGLogo.png",
- mimetype="image/png")
-
-
-def errors(rqst) -> Tuple[str, ...]:
- """Return a tuple of the errors found in the request `rqst`. If no error is
- found, then an empty tuple is returned."""
- def __filetype_error__():
- return (
- ("Invalid file type provided.",)
- if rqst.form.get("filetype") not in ("average", "standard-error")
- else tuple())
-
- def __file_missing_error__():
- return (
- ("No file was uploaded.",)
- if ("qc_text_file" not in rqst.files or
- rqst.files["qc_text_file"].filename == "")
- else tuple())
-
- def __file_mimetype_error__():
- text_file = rqst.files["qc_text_file"]
- return (
- (
- ("Invalid file! Expected a tab-separated-values file, or a zip "
- "file of the a tab-separated-values file."),)
- if text_file.mimetype not in (
- "text/plain", "text/tab-separated-values",
- "application/zip")
- else tuple())
-
- return (
- __filetype_error__() +
- (__file_missing_error__() or __file_mimetype_error__()))
-
-def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
- """Check the uploaded zip file for errors."""
- zfile_errors: Tuple[str, ...] = tuple()
- if is_zipfile(filepath):
- with ZipFile(filepath, "r") as zfile:
- infolist = zfile.infolist()
- if len(infolist) != 1:
- zfile_errors = zfile_errors + (
- ("Expected exactly one (1) member file within the uploaded zip "
- f"file. Got {len(infolist)} member files."),)
- if len(infolist) == 1 and infolist[0].is_dir():
- zfile_errors = zfile_errors + (
- ("Expected a member text file in the uploaded zip file. Got a "
- "directory/folder."),)
-
- if len(infolist) == 1 and not infolist[0].is_dir():
- zfile.extract(infolist[0], path=upload_dir)
- mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}")
- if mime[0] != "text/tab-separated-values":
- zfile_errors = zfile_errors + (
- ("Expected the member text file in the uploaded zip file to"
- " be a tab-separated file."),)
-
- return zfile_errors
-
-@entrybp.route("/", methods=["GET"])
-def index():
- """Load the landing page"""
- return render_template("index.html")
-
-@entrybp.route("/upload", methods=["GET", "POST"])
-def upload_file():
- """Enables uploading the files"""
- if request.method == "GET":
- return render_template(
- "select_species.html", species=with_db_connection(species))
-
- upload_dir = app.config["UPLOAD_FOLDER"]
- request_errors = errors(request)
- if request_errors:
- for error in request_errors:
- flash(error, "alert-danger error-expr-data")
- return redirect(url_for("entry.upload_file"))
-
- filename = secure_filename(request.files["qc_text_file"].filename)
- if not os.path.exists(upload_dir):
- os.mkdir(upload_dir)
-
- filepath = os.path.join(upload_dir, filename)
- request.files["qc_text_file"].save(os.path.join(upload_dir, filename))
-
- zip_errors = zip_file_errors(filepath, upload_dir)
- if zip_errors:
- for error in zip_errors:
- flash(error, "alert-danger error-expr-data")
- return redirect(url_for("entry.upload_file"))
-
- return redirect(url_for("parse.parse",
- speciesid=request.form["speciesid"],
- filename=filename,
- filetype=request.form["filetype"]))
-
-@entrybp.route("/data-review", methods=["GET"])
-def data_review():
- """Provide some help on data expectations to the user."""
- return render_template("data_review.html")
diff --git a/qc_app/errors.py b/qc_app/errors.py
deleted file mode 100644
index 3e7c893..0000000
--- a/qc_app/errors.py
+++ /dev/null
@@ -1,29 +0,0 @@
-"""Application error handling."""
-import traceback
-from werkzeug.exceptions import HTTPException
-
-import MySQLdb as mdb
-from flask import Flask, request, render_template, current_app as app
-
-def handle_general_exception(exc: Exception):
- """Handle generic exceptions."""
- trace = traceback.format_exc()
- app.logger.error(
- "Error (%s.%s): Generic unhandled exception!! (URI: %s)\n%s",
- exc.__class__.__module__, exc.__class__.__name__, request.url, trace)
- return render_template("unhandled_exception.html", trace=trace), 500
-
-def handle_http_exception(exc: HTTPException):
- """Handle HTTP exceptions."""
- app.logger.error(
- "HTTP Error %s: %s", exc.code, exc.description, exc_info=True)
- return render_template("http-error.html",
- request_url=request.url,
- exc=exc,
- trace=traceback.format_exception(exc)), exc.code
-
-def register_error_handlers(appl: Flask):
- """Register top-level error/exception handlers."""
- appl.register_error_handler(Exception, handle_general_exception)
- appl.register_error_handler(HTTPException, handle_http_exception)
- appl.register_error_handler(mdb.MySQLError, handle_general_exception)
diff --git a/qc_app/files.py b/qc_app/files.py
deleted file mode 100644
index b163612..0000000
--- a/qc_app/files.py
+++ /dev/null
@@ -1,26 +0,0 @@
-"""Utilities to deal with uploaded files."""
-import hashlib
-from pathlib import Path
-from datetime import datetime
-from flask import current_app
-
-from werkzeug.utils import secure_filename
-from werkzeug.datastructures import FileStorage
-
-def save_file(fileobj: FileStorage, upload_dir: Path) -> Path:
- """Save the uploaded file and return the path."""
- assert bool(fileobj), "Invalid file object!"
- hashed_name = hashlib.sha512(
- f"{fileobj.filename}::{datetime.now().isoformat()}".encode("utf8")
- ).hexdigest()
- filename = Path(secure_filename(hashed_name)) # type: ignore[arg-type]
- if not upload_dir.exists():
- upload_dir.mkdir()
-
- filepath = Path(upload_dir, filename)
- fileobj.save(filepath)
- return filepath
-
-def fullpath(filename: str):
- """Get a file's full path. This makes use of `flask.current_app`."""
- return Path(current_app.config["UPLOAD_FOLDER"], filename).absolute()
diff --git a/qc_app/input_validation.py b/qc_app/input_validation.py
deleted file mode 100644
index 9abe742..0000000
--- a/qc_app/input_validation.py
+++ /dev/null
@@ -1,27 +0,0 @@
-"""Input validation utilities"""
-from typing import Any
-
-def is_empty_string(value: str) -> bool:
- """Check whether as string is empty"""
- return (isinstance(value, str) and value.strip() == "")
-
-def is_empty_input(value: Any) -> bool:
- """Check whether user provided an empty value."""
- return (value is None or is_empty_string(value))
-
-def is_integer_input(value: Any) -> bool:
- """
- Check whether user provided a value that can be parsed into an integer.
- """
- def __is_int__(val, base):
- try:
- int(val, base=base)
- except ValueError:
- return False
- return True
- return isinstance(value, int) or (
- (not is_empty_input(value)) and (
- isinstance(value, str) and (
- __is_int__(value, 10)
- or __is_int__(value, 8)
- or __is_int__(value, 16))))
diff --git a/qc_app/jobs.py b/qc_app/jobs.py
deleted file mode 100644
index 21889da..0000000
--- a/qc_app/jobs.py
+++ /dev/null
@@ -1,130 +0,0 @@
-"""Handle jobs"""
-import os
-import sys
-import shlex
-import subprocess
-from uuid import UUID, uuid4
-from datetime import timedelta
-from typing import Union, Optional
-
-from redis import Redis
-from flask import current_app as app
-
-JOBS_PREFIX = "JOBS"
-
-class JobNotFound(Exception):
- """Raised if we try to retrieve a non-existent job."""
-
-def jobsnamespace():
- """
- Return the jobs namespace prefix. It depends on app configuration.
-
- Calling this function outside of an application context will cause an
- exception to be raised. It is mostly a convenience utility to use within the
- application.
- """
- return f"{app.config['GNQC_REDIS_PREFIX']}:{JOBS_PREFIX}"
-
-def job_key(namespaceprefix: str, jobid: Union[str, UUID]) -> str:
- """Build the key by appending it to the namespace prefix."""
- return f"{namespaceprefix}:{jobid}"
-
-def raise_jobnotfound(rprefix:str, jobid: Union[str,UUID]):
- """Utility to raise a `NoSuchJobError`"""
- raise JobNotFound(f"Could not retrieve job '{jobid}' from '{rprefix}.")
-
-def error_filename(jobid, error_dir):
- "Compute the path of the file where errors will be dumped."
- return f"{error_dir}/job_{jobid}.error"
-
-def initialise_job(# pylint: disable=[too-many-arguments]
- rconn: Redis, rprefix: str, jobid: str, command: list, job_type: str,
- ttl_seconds: int = 86400, extra_meta: Optional[dict] = None) -> dict:
- "Initialise a job 'object' and put in on redis"
- the_job = {
- "jobid": jobid, "command": shlex.join(command), "status": "pending",
- "percent": 0, "job-type": job_type, **(extra_meta or {})
- }
- rconn.hset(job_key(rprefix, jobid), mapping=the_job)
- rconn.expire(
- name=job_key(rprefix, jobid), time=timedelta(seconds=ttl_seconds))
- return the_job
-
-def build_file_verification_job(#pylint: disable=[too-many-arguments]
- redis_conn: Redis,
- dburi: str,
- redisuri: str,
- speciesid: int,
- filepath: str,
- filetype: str,
- ttl_seconds: int):
- "Build a file verification job"
- jobid = str(uuid4())
- command = [
- sys.executable, "-m", "scripts.validate_file",
- dburi, redisuri, jobsnamespace(), jobid,
- "--redisexpiry", str(ttl_seconds),
- str(speciesid), filetype, filepath,
- ]
- return initialise_job(
- redis_conn, jobsnamespace(), jobid, command, "file-verification",
- ttl_seconds, {
- "filetype": filetype,
- "filename": os.path.basename(filepath), "percent": 0
- })
-
-def data_insertion_job(# pylint: disable=[too-many-arguments]
- redis_conn: Redis, filepath: str, filetype: str, totallines: int,
- speciesid: int, platformid: int, datasetid: int, databaseuri: str,
- redisuri: str, ttl_seconds: int) -> dict:
- "Build a data insertion job"
- jobid = str(uuid4())
- command = [
- sys.executable, "-m", "scripts.insert_data", filetype, filepath,
- speciesid, platformid, datasetid, databaseuri, redisuri
- ]
- return initialise_job(
- redis_conn, jobsnamespace(), jobid, command, "data-insertion",
- ttl_seconds, {
- "filename": os.path.basename(filepath), "filetype": filetype,
- "totallines": totallines
- })
-
-def launch_job(the_job: dict, redisurl: str, error_dir):
- """Launch a job in the background"""
- if not os.path.exists(error_dir):
- os.mkdir(error_dir)
-
- jobid = the_job["jobid"]
- with open(error_filename(jobid, error_dir),
- "w",
- encoding="utf-8") as errorfile:
- subprocess.Popen( # pylint: disable=[consider-using-with]
- [sys.executable, "-m", "scripts.worker", redisurl, jobsnamespace(),
- jobid],
- stderr=errorfile,
- env={"PYTHONPATH": ":".join(sys.path)})
-
- return the_job
-
-def job(rconn: Redis, rprefix: str, jobid: Union[str,UUID]):
- "Retrieve the job"
- thejob = (rconn.hgetall(job_key(rprefix, jobid)) or
- raise_jobnotfound(rprefix, jobid))
- return thejob
-
-def update_status(
- rconn: Redis, rprefix: str, jobid: Union[str, UUID], status: str):
- """Update status of job in redis."""
- rconn.hset(name=job_key(rprefix, jobid), key="status", value=status)
-
-def update_stdout_stderr(rconn: Redis,
- rprefix: str,
- jobid: Union[str, UUID],
- bytes_read: bytes,
- stream: str):
- "Update the stdout/stderr keys according to the value of `stream`."
- thejob = job(rconn, rprefix, jobid)
- contents = thejob.get(stream, '')
- new_contents = contents + bytes_read.decode("utf-8")
- rconn.hset(name=job_key(rprefix, jobid), key=stream, value=new_contents)
diff --git a/qc_app/parse.py b/qc_app/parse.py
deleted file mode 100644
index d20f6f0..0000000
--- a/qc_app/parse.py
+++ /dev/null
@@ -1,175 +0,0 @@
-"""File parsing module"""
-import os
-
-import jsonpickle
-from redis import Redis
-from flask import flash, request, url_for, redirect, Blueprint, render_template
-from flask import current_app as app
-
-from quality_control.errors import InvalidValue, DuplicateHeading
-
-from qc_app import jobs
-from qc_app.dbinsert import species_by_id
-from qc_app.db_utils import with_db_connection
-
-parsebp = Blueprint("parse", __name__)
-
-def isinvalidvalue(item):
- """Check whether item is of type InvalidValue"""
- return isinstance(item, InvalidValue)
-
-def isduplicateheading(item):
- """Check whether item is of type DuplicateHeading"""
- return isinstance(item, DuplicateHeading)
-
-@parsebp.route("/parse", methods=["GET"])
-def parse():
- """Trigger file parsing"""
- errors = False
- speciesid = request.args.get("speciesid")
- filename = request.args.get("filename")
- filetype = request.args.get("filetype")
- if speciesid is None:
- flash("No species selected", "alert-error error-expr-data")
- errors = True
- else:
- try:
- speciesid = int(speciesid)
- species = with_db_connection(
- lambda con: species_by_id(con, speciesid))
- if not bool(species):
- flash("No such species.", "alert-error error-expr-data")
- errors = True
- except ValueError:
- flash("Invalid speciesid provided. Expected an integer.",
- "alert-error error-expr-data")
- errors = True
-
- if filename is None:
- flash("No file provided", "alert-error error-expr-data")
- errors = True
-
- if filetype is None:
- flash("No filetype provided", "alert-error error-expr-data")
- errors = True
-
- if filetype not in ("average", "standard-error"):
- flash("Invalid filetype provided", "alert-error error-expr-data")
- errors = True
-
- if filename:
- filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
- if not os.path.exists(filepath):
- flash("Selected file does not exist (any longer)",
- "alert-error error-expr-data")
- errors = True
-
- if errors:
- return redirect(url_for("entry.upload_file"))
-
- redisurl = app.config["REDIS_URL"]
- with Redis.from_url(redisurl, decode_responses=True) as rconn:
- job = jobs.launch_job(
- jobs.build_file_verification_job(
- rconn, app.config["SQL_URI"], redisurl,
- speciesid, filepath, filetype,
- app.config["JOBS_TTL_SECONDS"]),
- redisurl,
- f"{app.config['UPLOAD_FOLDER']}/job_errors")
-
- return redirect(url_for("parse.parse_status", job_id=job["jobid"]))
-
-@parsebp.route("/status/<job_id>", methods=["GET"])
-def parse_status(job_id: str):
- "Retrieve the status of the job"
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- try:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
- except jobs.JobNotFound as _exc:
- return render_template("no_such_job.html", job_id=job_id), 400
-
- error_filename = jobs.error_filename(
- job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
- if os.path.exists(error_filename):
- stat = os.stat(error_filename)
- if stat.st_size > 0:
- return redirect(url_for("parse.fail", job_id=job_id))
-
- job_id = job["jobid"]
- progress = float(job["percent"])
- status = job["status"]
- filename = job.get("filename", "uploaded file")
- errors = jsonpickle.decode(
- job.get("errors", jsonpickle.encode(tuple())))
- if status in ("success", "aborted"):
- return redirect(url_for("parse.results", job_id=job_id))
-
- if status == "parse-error":
- return redirect(url_for("parse.fail", job_id=job_id))
-
- app.jinja_env.globals.update(
- isinvalidvalue=isinvalidvalue,
- isduplicateheading=isduplicateheading)
- return render_template(
- "job_progress.html",
- job_id = job_id,
- job_status = status,
- progress = progress,
- message = job.get("message", ""),
- job_name = f"Parsing '{filename}'",
- errors=errors)
-
-@parsebp.route("/results/<job_id>", methods=["GET"])
-def results(job_id: str):
- """Show results of parsing..."""
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
-
- if job:
- filename = job["filename"]
- errors = jsonpickle.decode(job.get("errors", jsonpickle.encode(tuple())))
- app.jinja_env.globals.update(
- isinvalidvalue=isinvalidvalue,
- isduplicateheading=isduplicateheading)
- return render_template(
- "parse_results.html",
- errors=errors,
- job_name = f"Parsing '{filename}'",
- user_aborted = job.get("user_aborted"),
- job_id=job["jobid"])
-
- return render_template("no_such_job.html", job_id=job_id)
-
-@parsebp.route("/fail/<job_id>", methods=["GET"])
-def fail(job_id: str):
- """Handle parsing failure"""
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
-
- if job:
- error_filename = jobs.error_filename(
- job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
- if os.path.exists(error_filename):
- stat = os.stat(error_filename)
- if stat.st_size > 0:
- return render_template(
- "worker_failure.html", job_id=job_id)
-
- return render_template("parse_failure.html", job=job)
-
- return render_template("no_such_job.html", job_id=job_id)
-
-@parsebp.route("/abort", methods=["POST"])
-def abort():
- """Handle user request to abort file processing"""
- job_id = request.form["job_id"]
-
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
-
- if job:
- rconn.hset(name=jobs.job_key(jobs.jobsnamespace(), job_id),
- key="user_aborted",
- value=int(True))
-
- return redirect(url_for("parse.parse_status", job_id=job_id))
diff --git a/qc_app/samples.py b/qc_app/samples.py
deleted file mode 100644
index 804f262..0000000
--- a/qc_app/samples.py
+++ /dev/null
@@ -1,354 +0,0 @@
-"""Code regarding samples"""
-import os
-import sys
-import csv
-import uuid
-from pathlib import Path
-from typing import Iterator
-
-import MySQLdb as mdb
-from redis import Redis
-from MySQLdb.cursors import DictCursor
-from flask import (
- flash,
- request,
- url_for,
- redirect,
- Blueprint,
- render_template,
- current_app as app)
-
-from functional_tools import take
-
-from qc_app import jobs
-from qc_app.files import save_file
-from qc_app.input_validation import is_integer_input
-from qc_app.db_utils import (
- with_db_connection,
- database_connection,
- with_redis_connection)
-from qc_app.db import (
- species_by_id,
- save_population,
- population_by_id,
- populations_by_species,
- species as fetch_species)
-
-samples = Blueprint("samples", __name__)
-
-@samples.route("/upload/species", methods=["GET", "POST"])
-def select_species():
- """Select the species."""
- if request.method == "GET":
- return render_template("samples/select-species.html",
- species=with_db_connection(fetch_species))
-
- index_page = redirect(url_for("entry.upload_file"))
- species_id = request.form.get("species_id")
- if bool(species_id):
- species_id = int(species_id)
- species = with_db_connection(
- lambda conn: species_by_id(conn, species_id))
- if bool(species):
- return redirect(url_for(
- "samples.select_population", species_id=species_id))
- flash("Invalid species selected!", "alert-error")
- flash("You need to select a species", "alert-error")
- return index_page
-
-@samples.route("/upload/species/<int:species_id>/create-population",
- methods=["POST"])
-def create_population(species_id: int):
- """Create new grouping/population."""
- if not is_integer_input(species_id):
- flash("You did not provide a valid species. Please select one to "
- "continue.",
- "alert-danger")
- return redirect(url_for("samples.select_species"))
- species = with_db_connection(lambda conn: species_by_id(conn, species_id))
- if not bool(species):
- flash("Species with given ID was not found.", "alert-danger")
- return redirect(url_for("samples.select_species"))
-
- species_page = redirect(url_for("samples.select_species"), code=307)
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- pop_name = request.form.get("inbredset_name", "").strip()
- pop_fullname = request.form.get("inbredset_fullname", "").strip()
-
- if not bool(species):
- flash("Invalid species!", "alert-error error-create-population")
- return species_page
- if (not bool(pop_name)) or (not bool(pop_fullname)):
- flash("You *MUST* provide a grouping/population name",
- "alert-error error-create-population")
- return species_page
-
- pop = save_population(conn, {
- "SpeciesId": species["SpeciesId"],
- "Name": pop_name,
- "InbredSetName": pop_fullname,
- "FullName": pop_fullname,
- "Family": request.form.get("inbredset_family") or None,
- "Description": request.form.get("description") or None
- })
-
- flash("Grouping/Population created successfully.", "alert-success")
- return redirect(url_for("samples.upload_samples",
- species_id=species_id,
- population_id=pop["population_id"]))
-
-@samples.route("/upload/species/<int:species_id>/population",
- methods=["GET", "POST"])
-def select_population(species_id: int):
- """Select from existing groupings/populations."""
- if not is_integer_input(species_id):
- flash("You did not provide a valid species. Please select one to "
- "continue.",
- "alert-danger")
- return redirect(url_for("samples.select_species"))
- species = with_db_connection(lambda conn: species_by_id(conn, species_id))
- if not bool(species):
- flash("Species with given ID was not found.", "alert-danger")
- return redirect(url_for("samples.select_species"))
-
- if request.method == "GET":
- return render_template(
- "samples/select-population.html",
- species=species,
- populations=with_db_connection(
- lambda conn: populations_by_species(conn, species_id)))
-
- population_page = redirect(url_for(
- "samples.select_population", species_id=species_id), code=307)
- _population_id = request.form.get("inbredset_id")
- if not is_integer_input(_population_id):
- flash("You did not provide a valid population. Please select one to "
- "continue.",
- "alert-danger")
- return population_page
- population = with_db_connection(
- lambda conn: population_by_id(conn, _population_id))
- if not bool(population):
- flash("Invalid grouping/population!",
- "alert-error error-select-population")
- return population_page
-
- return redirect(url_for("samples.upload_samples",
- species_id=species_id,
- population_id=_population_id),
- code=307)
-
-def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs) -> Iterator[dict]:
- """Read the samples file."""
- with open(filepath, "r", encoding="utf-8") as inputfile:
- reader = csv.DictReader(
- inputfile,
- fieldnames=(
- None if firstlineheading
- else ("Name", "Name2", "Symbol", "Alias")),
- delimiter=separator,
- quotechar=kwargs.get("quotechar", '"'))
- for row in reader:
- yield row
-
-def save_samples_data(conn: mdb.Connection,
- speciesid: int,
- file_data: Iterator[dict]):
- """Save the samples to DB."""
- data = ({**row, "SpeciesId": speciesid} for row in file_data)
- total = 0
- with conn.cursor() as cursor:
- while True:
- batch = take(data, 5000)
- if len(batch) == 0:
- break
- cursor.executemany(
- "INSERT INTO Strain(Name, Name2, SpeciesId, Symbol, Alias) "
- "VALUES("
- " %(Name)s, %(Name2)s, %(SpeciesId)s, %(Symbol)s, %(Alias)s"
- ") ON DUPLICATE KEY UPDATE Name=Name",
- batch)
- total += len(batch)
- print(f"\tSaved {total} samples total so far.")
-
-def cross_reference_samples(conn: mdb.Connection,
- species_id: int,
- population_id: int,
- strain_names: Iterator[str]):
- """Link samples to their population."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute(
- "SELECT MAX(OrderId) AS loid FROM StrainXRef WHERE InbredSetId=%s",
- (population_id,))
- last_order_id = (cursor.fetchone()["loid"] or 10)
- total = 0
- while True:
- batch = take(strain_names, 5000)
- if len(batch) == 0:
- break
- params_str = ", ".join(["%s"] * len(batch))
- ## This query is slow -- investigate.
- cursor.execute(
- "SELECT s.Id FROM Strain AS s LEFT JOIN StrainXRef AS sx "
- "ON s.Id = sx.StrainId WHERE s.SpeciesId=%s AND s.Name IN "
- f"({params_str}) AND sx.StrainId IS NULL",
- (species_id,) + tuple(batch))
- strain_ids = (sid["Id"] for sid in cursor.fetchall())
- params = tuple({
- "pop_id": population_id,
- "strain_id": strain_id,
- "order_id": last_order_id + (order_id * 10),
- "mapping": "N",
- "pedigree": None
- } for order_id, strain_id in enumerate(strain_ids, start=1))
- cursor.executemany(
- "INSERT INTO StrainXRef( "
- " InbredSetId, StrainId, OrderId, Used_for_mapping, PedigreeStatus"
- ")"
- "VALUES ("
- " %(pop_id)s, %(strain_id)s, %(order_id)s, %(mapping)s, "
- " %(pedigree)s"
- ")",
- params)
- last_order_id += (len(params) * 10)
- total += len(batch)
- print(f"\t{total} total samples cross-referenced to the population "
- "so far.")
-
-def build_sample_upload_job(# pylint: disable=[too-many-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 [])
-
-@samples.route("/upload/species/<int:species_id>/populations/<int:population_id>/samples",
- methods=["GET", "POST"])
-def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
- """Upload the samples."""
- samples_uploads_page = redirect(url_for("samples.upload_samples",
- species_id=species_id,
- population_id=population_id))
- if not is_integer_input(species_id):
- flash("You did not provide a valid species. Please select one to "
- "continue.",
- "alert-danger")
- return redirect(url_for("samples.select_species"))
- species = with_db_connection(lambda conn: species_by_id(conn, species_id))
- if not bool(species):
- flash("Species with given ID was not found.", "alert-danger")
- return redirect(url_for("samples.select_species"))
-
- if not is_integer_input(population_id):
- flash("You did not provide a valid population. Please select one "
- "to continue.",
- "alert-danger")
- return redirect(url_for("samples.select_population",
- species_id=species_id),
- code=307)
- population = with_db_connection(
- lambda conn: population_by_id(conn, int(population_id)))
- if not bool(population):
- flash("Invalid grouping/population!", "alert-error")
- return redirect(url_for("samples.select_population",
- species_id=species_id),
- code=307)
-
- if request.method == "GET" or request.files.get("samples_file") is None:
- return render_template("samples/upload-samples.html",
- species=species,
- population=population)
-
- try:
- samples_file = save_file(request.files["samples_file"],
- Path(app.config["UPLOAD_FOLDER"]))
- except AssertionError:
- flash("You need to provide a file with the samples data.",
- "alert-error")
- return samples_uploads_page
-
- firstlineheading = (request.form.get("first_line_heading") == "on")
-
- separator = request.form.get("separator", ",")
- if separator == "other":
- separator = request.form.get("other_separator", ",")
- if not bool(separator):
- flash("You need to provide a separator character.", "alert-error")
- return samples_uploads_page
-
- quotechar = (request.form.get("field_delimiter", '"') or '"')
-
- redisuri = app.config["REDIS_URL"]
- with Redis.from_url(redisuri, decode_responses=True) as rconn:
- the_job = jobs.launch_job(
- jobs.initialise_job(
- rconn,
- jobs.jobsnamespace(),
- str(uuid.uuid4()),
- build_sample_upload_job(
- species["SpeciesId"],
- population["InbredSetId"],
- samples_file,
- separator,
- firstlineheading,
- quotechar),
- "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(
- "samples.upload_status", job_id=the_job["jobid"]))
-
-@samples.route("/upload/status/<uuid:job_id>", methods=["GET"])
-def upload_status(job_id: uuid.UUID):
- """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)
-
- if status == "error":
- return redirect(url_for("samples.upload_failure", job_id=job_id))
-
- error_filename = Path(jobs.error_filename(
- job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors"))
- if error_filename.exists():
- stat = os.stat(error_filename)
- if stat.st_size > 0:
- return redirect(url_for(
- "samples.upload_failure", job_id=job_id))
-
- return render_template(
- "samples/upload-progress.html",
- job=job) # maybe also handle this?
-
- return render_template("no_such_job.html", job_id=job_id), 400
-
-@samples.route("/upload/failure/<uuid:job_id>", methods=["GET"])
-def upload_failure(job_id: uuid.UUID):
- """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", job=job)
diff --git a/qc_app/static/css/custom-bootstrap.css b/qc_app/static/css/custom-bootstrap.css
deleted file mode 100644
index 67f1199..0000000
--- a/qc_app/static/css/custom-bootstrap.css
+++ /dev/null
@@ -1,23 +0,0 @@
-/** Customize some bootstrap selectors **/
-.btn {
- text-transform: capitalize;
-}
-
-.navbar-inverse {
- background-color: #336699;
- border-color: #080808;
- color: #FFFFFF;
- background-image: none;
-}
-
-.navbar-inverse .navbar-nav>li>a {
- color: #FFFFFF;
-}
-
-.navbar-nav > li > a {
- padding: 5px;
-}
-
-.navbar {
- min-height: 30px;
-}
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
deleted file mode 100644
index a88c229..0000000
--- a/qc_app/static/css/styles.css
+++ /dev/null
@@ -1,7 +0,0 @@
-.heading {
- text-transform: capitalize;
-}
-
-label {
- text-transform: capitalize;
-}
diff --git a/qc_app/static/css/two-column-with-separator.css b/qc_app/static/css/two-column-with-separator.css
deleted file mode 100644
index b6efd46..0000000
--- a/qc_app/static/css/two-column-with-separator.css
+++ /dev/null
@@ -1,27 +0,0 @@
-.two-column-with-separator {
- display: grid;
- grid-template-columns: 9fr 1fr 9fr;
-}
-
-.two-col-sep-col1 {
- grid-column: 1 / 2;
-}
-
-.two-col-sep-separator {
- grid-column: 2 / 3;
- text-align: center;
- color: #FE3535;
- font-weight: bolder;
-}
-
-.two-col-sep-col2 {
- grid-column: 3 / 4;
-}
-
-.two-col-sep-col1, .two-col-sep-col2 {
- border-style: solid;
- border-color: #FE3535;
- border-width: 1px;
- border-radius: 2em;
- padding: 2em 3em 2em 3em;
-}
diff --git a/qc_app/static/images/CITGLogo.png b/qc_app/static/images/CITGLogo.png
deleted file mode 100644
index ae99fed..0000000
--- a/qc_app/static/images/CITGLogo.png
+++ /dev/null
Binary files differ
diff --git a/qc_app/static/js/select_platform.js b/qc_app/static/js/select_platform.js
deleted file mode 100644
index 4fdd865..0000000
--- a/qc_app/static/js/select_platform.js
+++ /dev/null
@@ -1,70 +0,0 @@
-function radio_column(chip) {
- col = document.createElement("td");
- radio = document.createElement("input");
- radio.setAttribute("type", "radio");
- radio.setAttribute("name", "genechipid");
- radio.setAttribute("value", chip["GeneChipId"]);
- radio.setAttribute("required", "required");
- col.appendChild(radio);
- return col;
-}
-
-function setup_genechips(genechip_data) {
- columns = ["GeneChipId", "GeneChipName"]
- submit_button = document.querySelector(
- "#select-platform-form button[type='submit']");
- elt = document.getElementById(
- "genechips-table").getElementsByTagName("tbody")[0];
- remove_children(elt);
- if((genechip_data === undefined) || genechip_data.length === 0) {
- row = document.createElement("tr");
- col = document.createElement("td");
- col.setAttribute("colspan", "3");
- text = document.createTextNode("No chips found for selected species");
- col.appendChild(text);
- row.appendChild(col);
- elt.appendChild(row);
- submit_button.setAttribute("disabled", true);
- return false;
- }
-
- submit_button.removeAttribute("disabled")
- genechip_data.forEach(chip => {
- row = document.createElement("tr");
- row.appendChild(radio_column(chip));
- columns.forEach(column => {
- col = document.createElement("td");
- content = document.createTextNode(chip[column]);
- col.appendChild(content);
- row.appendChild(col);
- });
- elt.appendChild(row);
- });
-}
-
-function genechips() {
- return JSON.parse(
- document.getElementById("select-platform-form").getAttribute(
- "data-genechips"));
-}
-
-function update_genechips(event) {
- genec = genechips();
-
- species_elt = document.getElementById("species");
-
- if(event.target == species_elt) {
- setup_genechips(genec[species_elt.value.toLowerCase()]);
- }
-}
-
-function select_row_radio(row) {
- radio = row.getElementsByTagName(
- "td")[0].getElementsByTagName(
- "input")[0];
- if(radio === undefined) {
- return false;
- }
- radio.setAttribute("checked", "checked");
- return true;
-}
diff --git a/qc_app/static/js/upload_progress.js b/qc_app/static/js/upload_progress.js
deleted file mode 100644
index 9638b36..0000000
--- a/qc_app/static/js/upload_progress.js
+++ /dev/null
@@ -1,97 +0,0 @@
-function make_processing_indicator(elt) {
- var count = 0;
- return function() {
- var message = "Finalising upload and saving file: "
- if(count > 5) {
- count = 1;
- }
- for(i = 0; i < count; i++) {
- message = message + ".";
- }
- elt.innerHTML = message
- count = count + 1
- };
-}
-
-function make_progress_updater(file, indicator_elt) {
- var progress_bar = indicator_elt.querySelector("#progress-bar");
- var progress_text = indicator_elt.querySelector("#progress-text");
- var extra_text = indicator_elt.querySelector("#progress-extra-text");
- return function(event) {
- if(event.loaded <= file.size) {
- var percent = Math.round((event.loaded / file.size) * 100);
- progress_bar.value = percent
- progress_text.innerHTML = "Uploading: " + percent + "%";
- extra_text.setAttribute("class", "hidden")
- }
-
- if(event.loaded == event.total) {
- progress_bar.value = 100;
- progress_text.innerHTML = "Uploaded: 100%";
- extra_text.setAttribute("class", null);
- intv = setInterval(make_processing_indicator(extra_text), 400);
- setTimeout(function() {clearTimeout(intv);}, 20000);
- }
- };
-}
-
-function setup_cancel_upload(request, indicator_elt) {
- document.getElementById("btn-cancel-upload").addEventListener(
- "click", function(event) {
- event.preventDefault();
- request.abort();
- });
-}
-
-function setup_request(file, progress_indicator_elt) {
- var request = new XMLHttpRequest();
- var updater = make_progress_updater(file, progress_indicator_elt);
- request.upload.addEventListener("progress", updater);
- request.onload = function(event) {
- document.location.assign(request.responseURL);
- };
- setup_cancel_upload(request, progress_indicator_elt)
- return request;
-}
-
-function selected_filetype(radios) {
- for(idx = 0; idx < radios.length; idx++) {
- if(radios[idx].checked) {
- return radios[idx].value;
- }
- }
-}
-
-function make_data_uploader(setup_formdata) {
- return function(event) {
- event.preventDefault();
-
- var pindicator = document.getElementById("upload-progress-indicator");
-
- var form = event.target;
- var the_file = form.querySelector("input[type='file']").files[0];
- if(the_file === undefined) {
- form.querySelector("input[type='file']").parentElement.setAttribute(
- "class", "invalid-input");
- error_elt = form.querySelector("#no-file-error");
- if(error_elt !== undefined) {
- error_elt.setAttribute("style", "display: block;");
- }
- return false;
- }
- var formdata = setup_formdata(form);
-
- document.getElementById("progress-filename").innerHTML = the_file.name;
- var request = setup_request(the_file, pindicator);
- request.open(form.getAttribute("method"), form.getAttribute("action"));
- request.send(formdata);
- return false;
- }
-}
-
-
-function setup_upload_handlers(formid, datauploader) {
- console.info("Setting up the upload handlers.")
- upload_form = document.getElementById(formid);
- upload_form.addEventListener("submit", datauploader);
-}
diff --git a/qc_app/static/js/upload_samples.js b/qc_app/static/js/upload_samples.js
deleted file mode 100644
index aed536f..0000000
--- a/qc_app/static/js/upload_samples.js
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Read the file content and set the `data-preview-content` attribute on the
- * file element
- */
-function read_first_n_lines(event,
- fileelement,
- numlines,
- firstlineheading = true) {
- var thefile = fileelement.files[0];
- var reader = new FileReader();
- reader.addEventListener("load", (event) => {
- var filecontent = event.target.result.split(
- "\n").slice(
- 0, (numlines + (firstlineheading ? 1 : 0))).map(
- (line) => {return line.trim("\r");});
- fileelement.setAttribute(
- "data-preview-content", JSON.stringify(filecontent));
- display_preview(event);
- })
- reader.readAsText(thefile);
-}
-
-function remove_rows(preview_table) {
- var table_body = preview_table.getElementsByTagName("tbody")[0];
- while(table_body.children.length > 0) {
- table_body.removeChild(table_body.children.item(0));
- }
-}
-
-/*
- * Display error row
- */
-function display_error_row(preview_table, error_message) {
- remove_rows(preview_table);
- row = document.createElement("tr");
- cell = document.createElement("td");
- cell.setAttribute("colspan", 4);
- cell.innerHTML = error_message;
- row.appendChild(cell);
- preview_table.getElementsByTagName("tbody")[0].appendChild(row);
-}
-
-function strip(str, chars) {
- var end = str.length;
- var start = 0
- for(var j = str.length; j > 0; j--) {
- if(!chars.includes(str[j - 1])) {
- break;
- }
- end = end - 1;
- }
- for(var i = 0; i < end; i++) {
- if(!chars.includes(str[i])) {
- break;
- }
- start = start + 1;
- }
- return str.slice(start, end);
-}
-
-function process_preview_data(preview_data, separator, delimiter) {
- return preview_data.map((line) => {
- return line.split(separator).map((field) => {
- return strip(field, delimiter);
- });
- });
-}
-
-function render_preview(preview_table, preview_data) {
- remove_rows(preview_table);
- var table_body = preview_table.getElementsByTagName("tbody")[0];
- preview_data.forEach((line) => {
- var row = document.createElement("tr");
- line.forEach((field) => {
- var cell = document.createElement("td");
- cell.innerHTML = field;
- row.appendChild(cell);
- });
- table_body.appendChild(row);
- });
-}
-
-/*
- * Display a preview of the data, relying on the user's selection.
- */
-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;
- if(separator === "other") {
- 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 firstlineheading = document.getElementById("chk:heading").checked;
-
- var fileelement = document.getElementById("file:samples");
- var preview_data = JSON.parse(
- fileelement.getAttribute("data-preview-content") || "[]");
- if(preview_data.length == 0) {
- display_error_row(
- data_preview_table,
- "No file data to preview. Check that file is provided.");
- }
-
- render_preview(data_preview_table, process_preview_data(
- preview_data.slice(0 + (firstlineheading ? 1 : 0)),
- separator,
- delimiter));
-}
-
-document.getElementById("chk:heading").addEventListener(
- "change", display_preview);
-document.getElementById("select:separator").addEventListener(
- "change", display_preview);
-document.getElementById("txt:separator").addEventListener(
- "keyup", display_preview);
-document.getElementById("txt:delimiter").addEventListener(
- "keyup", display_preview);
-document.getElementById("file:samples").addEventListener(
- "change", (event) => {
- read_first_n_lines(event,
- document.getElementById("file:samples"),
- 30,
- document.getElementById("chk:heading").checked);
- });
diff --git a/qc_app/static/js/utils.js b/qc_app/static/js/utils.js
deleted file mode 100644
index 045dd47..0000000
--- a/qc_app/static/js/utils.js
+++ /dev/null
@@ -1,10 +0,0 @@
-function remove_children(element) {
- Array.from(element.children).forEach(child => {
- element.removeChild(child);
- });
-}
-
-function trigger_change_event(element) {
- evt = new Event("change");
- element.dispatchEvent(evt);
-}
diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html
deleted file mode 100644
index eb5e6b7..0000000
--- a/qc_app/templates/base.html
+++ /dev/null
@@ -1,51 +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>GN Uploader: {%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.bootstrap',
- filename='css/bootstrap-theme.min.css')}}" />
-
-
- <link rel="shortcut icon" type="image/png" sizes="64x64"
- href="{{url_for('static', filename='images/CITGLogo.png')}}" />
-
- <link rel="stylesheet" type="text/css" href="/static/css/custom-bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
-
- {%block css%}{%endblock%}
- </head>
-
- <body>
- <div class="navbar navbar-inverse navbar-static-top pull-left"
- role="navigation"
- style="width: 100%;min-width: 850px;white-space: nowrap;">
- <div class="container-fluid" style="width: 100%">
- <ul class="nav navbar-nav">
- <li><a href="/" style="font-weight: bold">GN Uploader</a></li>
- <li>
- <a href="{{gnuri or 'https://genenetwork.org'}}">GeneNetwork</a>
- </li>
- </ul>
- </div>
- </div>
- <div class="container">
- {%block contents%}{%endblock%}
- </div>
-
- <script src="{{url_for('base.jquery',
- filename='jquery.min.js')}}"></script>
- <script src="{{url_for('base.bootstrap',
- filename='js/bootstrap.min.js')}}"></script>
- {%block javascript%}{%endblock%}
- </body>
-</html>
diff --git a/qc_app/templates/cli-output.html b/qc_app/templates/cli-output.html
deleted file mode 100644
index 33fb73b..0000000
--- a/qc_app/templates/cli-output.html
+++ /dev/null
@@ -1,8 +0,0 @@
-{%macro cli_output(job, stream)%}
-
-<h4>{{stream | upper}} Output</h4>
-<div class="cli-output">
- <pre>{{job.get(stream, "")}}</pre>
-</div>
-
-{%endmacro%}
diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html
deleted file mode 100644
index 03bb49c..0000000
--- a/qc_app/templates/continue_from_create_dataset.html
+++ /dev/null
@@ -1,52 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Create Study{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: create study</h2>
-
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend>continue with new dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, datasetid=datasetid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- <legend>Select from existing dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, datasetid=datasetid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">go back</button>
- </form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/continue_from_create_study.html b/qc_app/templates/continue_from_create_study.html
deleted file mode 100644
index 34e6e5e..0000000
--- a/qc_app/templates/continue_from_create_study.html
+++ /dev/null
@@ -1,52 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Create Study{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: create study</h2>
-
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend>continue with new study</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- <legend>Select from existing study</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">go back</button>
- </form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/data_review.html b/qc_app/templates/data_review.html
deleted file mode 100644
index b7528fd..0000000
--- a/qc_app/templates/data_review.html
+++ /dev/null
@@ -1,85 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Review{%endblock%}
-
-{%block contents%}
-<h1 class="heading">data review</h1>
-
-<div class="row">
- <h2 id="data-concerns">Data Concerns</h2>
- <p>The following are some of the requirements that the data in your file
- <strong>MUST</strong> fulfil before it is considered valid for this system:
- </p>
-
- <ol>
- <li>File headings
- <ul>
- <li>The first row in the file should contains the headings. The number of
- headings in this first row determines the number of columns expected for
- all other lines in the file.</li>
- <li>Each heading value in the first row MUST appear in the first row
- <strong>ONE AND ONLY ONE</strong> time</li>
- <li>The sample/cases (previously 'strains') headers in your first row will be
- against those in the <a href="https://genenetwork.org"
- title="Link to the GeneNetwork service">
- GeneNetwork</a> database.<br />
- <small class="text-muted">
- If you encounter an error saying your sample(s)/case(s) do not exist
- in the GeneNetwork database, then you will have to use the
- <a href="{{url_for('samples.select_species')}}"
- title="Upload samples/cases feature">Upload Samples/Cases</a>
- option on this system to upload them.
- </small>
- </ul>
- </li>
-
- <li>Data
- <ol>
- <li><strong>NONE</strong> of the data cells/fields is allowed to be empty.
- All fields/cells <strong>MUST</strong> contain a value.</li>
- <li>The first column of the data rows will be considered a textual field,
- holding the "identifier" for that row<li>
- <li>Except for the first column/field for each data row,
- <strong>NONE</strong> of the data columns/cells/fields should contain
- spurious characters like `eeeee`, `5.555iloveguix`, etc...<br />
- All of them should be decimal values</li>
- <li>decimal numbers must conform to the following criteria:
- <ul>
- <li>when checking an average file decimal numbers must have exactly three
- decimal places to the right of the decimal point.</li>
- <li>when checking a standard error file decimal numbers must have six or
- greater decimal places to the right of the decimal point.</li>
- <li>there must be a number to the left side of the decimal place
- (e.g. 0.55555 is allowed but .55555 is not).</li>
- </ul>
- </li>
- </ol>
- </li>
- </ol>
-</div>
-
-
-<div class="row">
- <h2 id="file-types">Supported File Types</h2>
- We support the following file types:
-
- <ul>
- <li>Tab-Separated value files (.tsv)
- <ul>
- <li>The <strong>TAB</strong> character is used to separate the fields of each
- column</li>
- <li>The values of each field <strong>ARE NOT</strong> quoted.</li>
- <li>Here is an
- <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv">
- example file</a> with a single data row.</li>
- </ul>
- </li>
- <li>.txt files: Content has the same format as .tsv file above</li>
- <li>.zip files: each zip file should contain
- <strong>ONE AND ONLY ONE</strong> file of the .tsv or .txt type above.
- <br />Any zip file with more than one file is invalid, and so is an empty
- zip file.</li>
- </ul>
-
-</div>
-{%endblock%}
diff --git a/qc_app/templates/dbupdate_error.html b/qc_app/templates/dbupdate_error.html
deleted file mode 100644
index e1359d2..0000000
--- a/qc_app/templates/dbupdate_error.html
+++ /dev/null
@@ -1,12 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}DB Update Error{%endblock%}
-
-{%block contents%}
-<h1 class="heading">database update error</h2>
-
-<p class="alert-danger">
- <strong>Database Update Error</strong>: {{error_message}}
-</p>
-
-{%endblock%}
diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/qc_app/templates/dbupdate_hidden_fields.html
deleted file mode 100644
index ccbc299..0000000
--- a/qc_app/templates/dbupdate_hidden_fields.html
+++ /dev/null
@@ -1,29 +0,0 @@
-{%macro hidden_fields(filename, filetype):%}
-
-<!-- {{kwargs}}: mostly for accessing the kwargs in macro -->
-
-<input type="hidden" name="filename" value="{{filename}}" />
-<input type="hidden" name="filetype" value="{{filetype}}" />
-{%if kwargs.get("totallines")%}
-<input type="hidden" name="totallines" value="{{kwargs['totallines']}}" />
-{%endif%}
-{%if kwargs.get("species"):%}
-<input type="hidden" name="species" value="{{kwargs['species']}}" />
-{%endif%}
-{%if kwargs.get("genechipid"):%}
-<input type="hidden" name="genechipid" value="{{kwargs['genechipid']}}" />
-{%endif%}
-{%if kwargs.get("inbredsetid"):%}
-<input type="hidden" name="inbredsetid" value="{{kwargs['inbredsetid']}}" />
-{%endif%}
-{%if kwargs.get("tissueid"):%}
-<input type="hidden" name="tissueid" value="{{kwargs['tissueid']}}" />
-{%endif%}
-{%if kwargs.get("studyid"):%}
-<input type="hidden" name="studyid" value="{{kwargs['studyid']}}" />
-{%endif%}
-{%if kwargs.get("datasetid"):%}
-<input type="hidden" name="datasetid" value="{{kwargs['datasetid']}}" />
-{%endif%}
-
-{%endmacro%}
diff --git a/qc_app/templates/errors_display.html b/qc_app/templates/errors_display.html
deleted file mode 100644
index 715cfcf..0000000
--- a/qc_app/templates/errors_display.html
+++ /dev/null
@@ -1,47 +0,0 @@
-{%macro errors_display(errors, no_error_msg, error_message, complete)%}
-
-{%if errors | length == 0 %}
-<span {%if complete%}class="alert-success"{%endif%}>{{no_error_msg}}</span>
-{%else %}
-<p class="alert-danger">{{error_message}}</p>
-
-<table class="table reports-table">
- <thead>
- <tr>
- <th>line number</th>
- <th>column(s)</th>
- <th>error</th>
- <th>error message</th>
- </tr>
- </thead>
-
- <tbody>
- {%for error in errors%}
- <tr>
- <td>{{error["line"]}}</td>
- <td>
- {%if isinvalidvalue(error):%}
- {{error.column}}
- {%elif isduplicateheading(error): %}
- {{error.columns}}
- {%else: %}
- -
- {%endif %}
- </td>
- <td>
- {%if isinvalidvalue(error):%}
- Invalid Value
- {%elif isduplicateheading(error): %}
- Duplicate Header
- {%else%}
- Inconsistent Columns
- {%endif %}
- </td>
- <td>{{error["message"]}}</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-{%endif%}
-
-{%endmacro%}
diff --git a/qc_app/templates/final_confirmation.html b/qc_app/templates/final_confirmation.html
deleted file mode 100644
index 0727fc8..0000000
--- a/qc_app/templates/final_confirmation.html
+++ /dev/null
@@ -1,47 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Confirmation{%endblock%}
-
-{%macro display_item(item_name, item_data):%}
-<li>
- <strong>{{item_name}}</strong>
- {%if item_data%}
- <ul>
- {%for term,value in item_data.items():%}
- <li><strong>{{term}}:</strong> {{value}}</li>
- {%endfor%}
- </ul>
- {%endif%}
-</li>
-{%endmacro%}
-
-{%block contents%}
-<h2 class="heading">Final Confirmation</h2>
-
-<div class="two-col-sep-col1">
- <p><strong>Selected Data</strong></p>
- <ul>
- <li><strong>File</strong>
- <ul>
- <li><strong>Filename</strong>: {{filename}}</li>
- <li><strong>File Type</strong>: {{filetype}}</li>
- </ul>
- </li>
- {{display_item("Species", the_species)}}
- {{display_item("Platform", platform)}}
- {{display_item("Study", study)}}
- {{display_item("Dataset", dataset)}}
- </ul>
-</div>
-
-<form method="POST" action="{{url_for('dbinsert.insert_data')}}">
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid,datasetid=datasetid, totallines=totallines)}}
- <fieldset>
- <input type="submit" class="btn btn-primary" value="confirm" />
- </fieldset>
-</form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/flash_messages.html b/qc_app/templates/flash_messages.html
deleted file mode 100644
index b7af178..0000000
--- a/qc_app/templates/flash_messages.html
+++ /dev/null
@@ -1,25 +0,0 @@
-{%macro flash_all_messages()%}
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-{%endmacro%}
-
-{%macro flash_messages(filter_class)%}
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- {%if filter_class in category%}
- <li class="{{category}}">{{message}}</li>
- {%endif%}
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-{%endmacro%}
diff --git a/qc_app/templates/http-error.html b/qc_app/templates/http-error.html
deleted file mode 100644
index 374fb86..0000000
--- a/qc_app/templates/http-error.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}HTTP Error: {{exc.code}}{%endblock%}
-
-{%block contents%}
-<h1>{{exc.code}}: {{exc.description}}</h1>
-
-<div class="row">
- <p>
- You attempted to access {{request_url}} which failed with the following
- error:
- </p>
-</div>
-
-<div class="row">
- <pre>{{"\n".join(trace)}}</pre>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
deleted file mode 100644
index 89d2ae9..0000000
--- a/qc_app/templates/index.html
+++ /dev/null
@@ -1,81 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<div class="row">
- <h1 class="heading">data upload</h1>
-
- <div class="explainer">
- <p>Each of the sections below gives you a different option for data upload.
- Please read the documentation for each section carefully to understand what
- each section is about.</p>
- </div>
-</div>
-
-<div class="row">
- <h2 class="heading">R/qtl2 Bundles</h2>
-
- <div class="explainer">
- <p>This feature combines and extends the two upload methods below. Instead of
- uploading one item at a time, the R/qtl2 bundle you upload can contain both
- the genotypes data (samples/individuals/cases and their data) and the
- expression data.</p>
- <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
- of the methods below can handle.</p>
-
- <a href="{{url_for('upload.rqtl2.select_species')}}"
- title="Upload a zip bundle of R/qtl2 files">
- <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
- </div>
-</div>
-
-
-<div class="row">
- <h2 class="heading">Expression Data</h2>
-
- <div class="explainer">
- <p>This feature enables you to upload expression data. It expects the data to
- be in <strong>tab-separated values (TSV)</strong> files. The data should be
- a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
- list of the <em>phenotypes</em> and the first row is a list of
- <em>samples/cases</em>.</p>
-
- <p>If you haven't done so please go to this page to learn the requirements for
- file formats and helpful suggestions to enter your data in a fast and easy
- way.</p>
-
- <ol>
- <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
- with our system requirements. (
- <a href="{{url_for('entry.data_review')}}#data-concerns"
- title="Details for the data expectations.">Help</a>
- )</li>
- <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
- <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
- files (<a href="{{url_for('entry.data_review')}}#file-types"
- title="Details for the data expectations.">Help</a>)</li>
- </ol>
- </div>
-
- <a href="{{url_for('entry.upload_file')}}"
- title="Upload your expression data"
- class="btn btn-primary">upload expression data</a>
-</div>
-
-<div class="row">
- <h2 class="heading">samples/cases</h2>
-
- <div class="explainer">
- <p>For the expression data above, you need the samples/cases in your file to
- already exist in the GeneNetwork database. If there are any samples that do
- not already exist the upload of the expression data will fail.</p>
- <p>This section gives you the opportunity to upload any missing samples</p>
- </div>
-
- <a href="{{url_for('samples.select_species')}}"
- title="Upload samples/cases/individuals for your data"
- class="btn btn-primary">upload Samples/Cases</a>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/insert_error.html b/qc_app/templates/insert_error.html
deleted file mode 100644
index 5301288..0000000
--- a/qc_app/templates/insert_error.html
+++ /dev/null
@@ -1,32 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Insertion Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Insertion Failure</h1>
-
-<div class="row">
- <p>
- There was an error inserting data into the database
- </p>
-
- <p>
- Please notify the developers of this issue when you encounter it,
- providing the information below.
- </p>
-
- <h4>Debugging Information</h4>
-
- <ul>
- <li><strong>job id</strong>: {{job["jobid"]}}</li>
- </ul>
-</div>
-
-<div class="row">
- <h4>STDERR Output</h4>
- <pre class="cli-output">
- {{job["stderr"]}}
- </pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/insert_progress.html b/qc_app/templates/insert_progress.html
deleted file mode 100644
index 52177d6..0000000
--- a/qc_app/templates/insert_progress.html
+++ /dev/null
@@ -1,46 +0,0 @@
-{%extends "base.html"%}
-{%from "stdout_output.html" import stdout_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}</h1>
-
-<div class="row">
- <form>
- <div class="form-group">
- <label for="job_status" class="form-label">status:</label>
- <span class="form-text">{{job_status}}: {{message}}</span>
- </div>
-
-{%if job.get("stdout", "").split("\n\n") | length < 3 %}
-{%set lines = 0%}
-{%else%}
-{%set lines = (job.get("stdout", "").split("\n\n") | length / 3) %}
-{%endif%}
-{%set totallines = job.get("totallines", lines+3) | int %}
-{%if totallines > 1000 %}
-{%set fraction = ((lines*1000)/totallines) %}
-{%else%}
-{%set fraction = (lines/totallines)%}
-{%endif%}
-
- <div class="form-group">
- <label for="job_{{job_id}}" class="form-label">inserting: </label>
- <progress id="jobs_{{job_id}}"
- value="{{(fraction)}}"
- class="form-control">{{fraction*100}}</progress>
- <span class="form-text text-muted">
- {{"%.2f" | format(fraction * 100 | float)}}%</span>
- </div>
- </form>
-</div>
-
-
-{{stdout_output(job)}}
-
-{%endblock%}
diff --git a/qc_app/templates/insert_success.html b/qc_app/templates/insert_success.html
deleted file mode 100644
index 7e1fa8d..0000000
--- a/qc_app/templates/insert_success.html
+++ /dev/null
@@ -1,19 +0,0 @@
-{%extends "base.html"%}
-{%from "stdout_output.html" import stdout_output%}
-
-{%block title%}Insertion Success{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Insertion Success</h1>
-
-<div class="row">
-<p>Data inserted successfully!</p>
-
-<p>The following queries were run:</p>
-</div>
-
-<div class="row">
- {{stdout_output(job)}}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html
deleted file mode 100644
index 1af0763..0000000
--- a/qc_app/templates/job_progress.html
+++ /dev/null
@@ -1,40 +0,0 @@
-{%extends "base.html"%}
-{%from "errors_display.html" import errors_display%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}</h2>
-
-<div class="row">
- <form action="{{url_for('parse.abort')}}" method="POST">
- <legend class="heading">Status</legend>
- <div class="form-group">
- <label for="job_status" class="form-label">status:</label>
- <span class="form-text">{{job_status}}: {{message}}</span><br />
- </div>
-
- <div class="form-group">
- <label for="job_{{job_id}}" class="form-label">parsing: </label>
- <progress id="job_{{job_id}}"
- value="{{progress/100}}"
- class="form-control">
- {{progress}}</progress>
- <span class="form-text text-muted">{{"%.2f" | format(progress)}}%</span>
- </div>
-
- <input type="hidden" name="job_id" value="{{job_id}}" />
-
- <button type="submit" class="btn btn-danger">Abort</button>
- </form>
-</div>
-
-<div class="row">
- {{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/no_such_job.html b/qc_app/templates/no_such_job.html
deleted file mode 100644
index 42a2d48..0000000
--- a/qc_app/templates/no_such_job.html
+++ /dev/null
@@ -1,14 +0,0 @@
-{%extends "base.html"%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5;url={{url_for('entry.upload_file')}}">
-{%endblock%}
-
-{%block title%}No Such Job{%endblock%}
-
-{%block contents%}
-<h1 class="heading">No Such Job: {{job_id}}</h2>
-
-<p>No job, with the id '<em>{{job_id}}</em>' was found!</p>
-
-{%endblock%}
diff --git a/qc_app/templates/parse_failure.html b/qc_app/templates/parse_failure.html
deleted file mode 100644
index 31f6be8..0000000
--- a/qc_app/templates/parse_failure.html
+++ /dev/null
@@ -1,26 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Worker Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Worker Failure</h1>
-
-<p>
- There was an error while parsing your file.
-</p>
-
-<p>
- Please notify the developers of this issue when you encounter it,
- providing the information below.
-</p>
-
-<h4>Debugging Information</h4>
-
-<ul>
- <li><strong>job id</strong>: {{job["job_id"]}}</li>
- <li><strong>filename</strong>: {{job["filename"]}}</li>
- <li><strong>line number</strong>: {{job["line_number"]}}</li>
- <li><strong>Progress</strong>: {{job["percent"]}} %</li>
-</ul>
-
-{%endblock%}
diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html
deleted file mode 100644
index e2bf7f0..0000000
--- a/qc_app/templates/parse_results.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "errors_display.html" import errors_display%}
-
-{%block title%}Parse Results{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}: parse results</h2>
-
-{%if user_aborted%}
-<span class="alert-warning">Job aborted by the user</span>
-{%endif%}
-
-{{errors_display(errors, "No errors found in the file", "We found the following errors", True)}}
-
-{%if errors | length == 0 and not user_aborted %}
-<form method="post" action="{{url_for('dbinsert.select_platform')}}">
- <input type="hidden" name="job_id" value="{{job_id}}" />
- <input type="submit" value="update database" class="btn btn-primary" />
-</form>
-{%endif%}
-
-{%if errors | length > 0 or user_aborted %}
-<br />
-<a href="{{url_for('entry.upload_file')}}" title="Back to index page."
- class="btn btn-primary">
- Go back
-</a>
-{%endif%}
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html
deleted file mode 100644
index 1b50221..0000000
--- a/qc_app/templates/rqtl2/create-geno-dataset-success.html
+++ /dev/null
@@ -1,55 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="explainer">
- <p>You successfully created the genotype dataset with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{geno_dataset.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{geno_dataset.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{geno_dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{geno_dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{geno_dataset.today}}</dd>
-
- <dt>Public?</dt>
- <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
- </dl>
- </p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">select from existing genotype datasets</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id"
- value="{{geno_dataset.id}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html
deleted file mode 100644
index 790d174..0000000
--- a/qc_app/templates/rqtl2/create-probe-dataset-success.html
+++ /dev/null
@@ -1,59 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Dataset</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet dataset with the following
- information.
- <dl>
- <dt>Averaging Method</dt>
- <dd>{{avgmethod.Name}}</dd>
-
- <dt>ID</dt>
- <dd>{{dataset.datasetid}}</dd>
-
- <dt>Name</dt>
- <dd>{{dataset.name2}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{dataset.today}}</dd>
-
- <dt>DataScale</dt>
- <dd>{{dataset.datascale}}</dd>
- </dl>
- </p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet dataset</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{study.Id}}" />
- <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html
deleted file mode 100644
index d0ee508..0000000
--- a/qc_app/templates/rqtl2/create-probe-study-success.html
+++ /dev/null
@@ -1,49 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Study</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet study with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{study.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{study.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{study.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{study.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{study.today}}</dd>
- </dl>
- </p>
-
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet study</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{study.studyid}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/create-tissue-success.html b/qc_app/templates/rqtl2/create-tissue-success.html
deleted file mode 100644
index 5f2c5a0..0000000
--- a/qc_app/templates/rqtl2/create-tissue-success.html
+++ /dev/null
@@ -1,106 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Tissue</h2>
-
-<div class="row">
- <p>You have successfully added a new tissue, organ or biological material with
- the following details:</p>
-</div>
-
-<div class="row">
- {{flash_all_messages()}}
-
- <form id="frm-create-tissue-display"
- method="POST"
- action="#">
- <legend class="heading">Create Tissue</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
-
- <div class="form-group">
- <label>Name</label>
- <label>{{tissue.TissueName}}</label>
- </div>
-
- <div class="form-group">
- <label>Short Name</label>
- <label>{{tissue.Short_Name}}</label>
- </div>
-
- {%if tissue.BIRN_lex_ID%}
- <div class="form-group">
- <label>BIRN Lex ID</label>
- <label>{{tissue.BIRN_lex_ID}}</label>
- </div>
- {%endif%}
-
- {%if tissue.BIRN_lex_Name%}
- <div class="form-group">
- <label>BIRN Lex Name</label>
- <label>{{tissue.BIRN_lex_Name}}</label>
- </div>
- {%endif%}
- </form>
-
- <div id="action-buttons"
- style="width:65ch;display:inline-grid;column-gap:5px;">
-
- <form id="frm-create-tissue-success-continue"
- method="POST"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- style="display: inline; width: 100%; grid-column: 1 / 2;
- padding-top: 0.5em; text-align: center; border: none;
- background-color: inherit;">
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
- </div>
-</div>
-
-<div class="row">
- <p style="display:inline;width:100%;grid-column:2/3;text-align:center;
- color:#336699;font-weight:bold;">
- OR
- </p>
-</div>
-
-<div class="row">
- <form id="frm-create-tissue-success-select-existing"
- method="POST"
- action="{{url_for('upload.rqtl2.select_tissue',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- style="display: inline; width: 100%; grid-column: 3 / 4;
- padding-top: 0.5em; text-align: center; border: none;
- background-color: inherit;">
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
-
- <button type="submit" class="btn btn-primary">
- select from existing tissues</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/index.html b/qc_app/templates/rqtl2/index.html
deleted file mode 100644
index f3329c2..0000000
--- a/qc_app/templates/rqtl2/index.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 data upload</h1>
-
-<h2>R/qtl2 Upload</h2>
-
-<form method="POST" action="{{url_for('upload.rqtl2.select_species')}}"
- id="frm-rqtl2-upload">
- <legend class="heading">upload R/qtl2 bundle</legend>
- {{flash_messages("error-rqtl2")}}
-
- <div class="form-group">
- <label for="select:species" class="form-label">Species</label>
- <select id="select:species"
- name="species_id"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for spec in species%}
- <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
- {%endfor%}
- </select>
- <small class="form-text text-muted">
- Data that you upload to the system should belong to a know species.
- Here you can select the species that you wish to upload data for.
- </small>
- </div>
-
- <button type="submit" class="btn btn-primary" />submit</button>
-</form>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/no-such-job.html b/qc_app/templates/rqtl2/no-such-job.html
deleted file mode 100644
index b17004f..0000000
--- a/qc_app/templates/rqtl2/no-such-job.html
+++ /dev/null
@@ -1,13 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: No Such Job</h2>
-
-<p class="alert-danger">No job with ID {{jobid}} was found.</p>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-error.html b/qc_app/templates/rqtl2/rqtl2-job-error.html
deleted file mode 100644
index 9817518..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-error.html
+++ /dev/null
@@ -1,39 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<div class="explainer">
- <p>The processing of the R/qtl2 bundle you uploaded has failed. We have
- provided some information below to help you figure out what the problem
- could be.</p>
- <p>If you find that you cannot figure out what the problem is on your own,
- please contact the team running the system for assistance, providing the
- following details:
- <ul>
- <li>R/qtl2 bundle you uploaded</li>
- <li>This URL: <strong>{{request_url()}}</strong></li>
- <li>(maybe) a screenshot of this page</li>
- </ul>
- </p>
-</div>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-<h4>Log</h4>
-<div class="cli-output">
- {%for msg in messages%}
- {{msg}}<br />
- {%endfor%}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-results.html b/qc_app/templates/rqtl2/rqtl2-job-results.html
deleted file mode 100644
index 4ecd415..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-results.html
+++ /dev/null
@@ -1,24 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<div class="explainer">
- <p>The processing of the R/qtl2 bundle you uploaded has completed
- successfully.</p>
- <p>You should now be able to use GeneNetwork to run analyses on your data.</p>
-</div>
-
-<h4>Log</h4>
-<div class="cli-output">
- {%for msg in messages%}
- {{msg}}<br />
- {%endfor%}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-status.html b/qc_app/templates/rqtl2/rqtl2-job-status.html
deleted file mode 100644
index e896f88..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-status.html
+++ /dev/null
@@ -1,20 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="3">
-{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
deleted file mode 100644
index 90e8887..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ /dev/null
@@ -1,120 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
-
-{%macro errors_table(tableid, errors)%}
-<table id="{{tableid}}" class="table error-table">
- <caption>{{caption}}</caption>
- <thead>
- <tr>
- <th>Line</th>
- <th>Column</th>
- <th>Value</th>
- <th>Message</th>
- </tr>
- </thead>
- <tbody>
- {%for error in errors%}
- <tr>
- <td>{{error.line}}</td>
- <td>{{error.column}}</td>
- <td>{{error.value}}</td>
- <td>{{error.message}}</td>
- </tr>
- {%else%}
- <tr>
- <td colspan="4">No errors to display here.</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-{%endmacro%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job Error</h1>
-
-<div class="explainer">
- <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p>
- <p>We list below some of the errors that need to be fixed before the data can
- be uploaded onto GeneNetwork.</p>
-</div>
-
-{%if errorsgeneric | length > 0%}
-<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3>
-<div class="explainer">
- We found the following generic errors in your R/qtl2 bundle:
-</div>
-
-<h3>Missing Files</h3>
-<div class="explainer">
- <p>These files are listed in the bundle's control file, but do not actually
- exist in the bundle</p>
-</div>
-<table id="tbl-errors-missing-files" class="table error-table">
- <thead>
- <tr>
- <th>Control File Key</th>
- <th>Bundle File Name</th>
- <th>Message</th>
- </tr>
- </thead>
- <tbody>
- {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%}
- <tr>
- <td>{{error.controlfilekey}}</td>
- <td>{{error.filename}}</td>
- <td>{{error.message}}</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-
-<h3>Other Generic Errors</h3>
-{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}}
-{%endif%}
-
-{%if errorsgeno | length > 0%}
-<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'geno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
-{%endif%}
-
-{%if errorspheno | length > 0%}
-<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'pheno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
-{%endif%}
-
-{%if errorsphenose | length > 0%}
-<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'phenose' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
-{%endif%}
-
-{%if errorsphenocovar | length > 0%}
-<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
-</div>
-{{errorsphenocovar}}
-{%endif%}
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
deleted file mode 100644
index 59bc8cd..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
+++ /dev/null
@@ -1,66 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}R/qtl2 bundle: QC job results{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job results</h1>
-
-<div class="row">
- <p>The R/qtl2 bundle you uploaded has passed all automated quality-control
- checks successfully.</p>
- <p>You may now continue to load the data into GeneNetwork for the bundle, with
- the following details:</p>
-</div>
-
-<div class="row">
- <form id="form-qc-job-results"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.Id)}}"
- method="POST">
- <div class="form-group">
- <legend>Species</legend>
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <span class="form-label">Name</span>
- <span class="form-text">{{species.Name | capitalize}}</span>
-
- <span class="form-label">Scientific</span>
- <span class="form-text">{{species.FullName | capitalize}}</span>
- </div>
-
- <div class="form-group">
- <legend>population</legend>
- <input type="hidden" name="population_id" value="{{population.Id}}" />
-
- <span class="form-label">Name</span>
- <span class="form-text">{{population.InbredSetName}}</span>
-
- <span class="form-label">Full Name</span>
- <span class="form-text">{{population.FullName}}</span>
-
- <span class="form-label">Genetic Type</span>
- <span class="form-text">{{population.GeneticType}}</span>
-
- <span class="form-label">Description</span>
- <span class="form-text">{{population.Description or "-"}}</span>
- </div>
-
- <div class="form-group">
- <legend>R/qtl2 Bundle File</legend>
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" />
- <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" />
-
- <span class="form-label">Original Name</span>
- <span class="form-text">{{rqtl2bundleorig}}</span>
-
- <span class="form-label">Internal Name</span>
- <span class="form-text">{{rqtl2bundle[0:25]}}&hellip;</span>
- </div>
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html b/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
deleted file mode 100644
index f4a6266..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
+++ /dev/null
@@ -1,41 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="3">
-{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job status</h1>
-
-{%if geno_percent%}
-<p>
- <h2>Checking 'geno' file:</h2>
- <progress id="prg-geno-checking" value="{{geno_percent}}" max="100">
- {{geno_percent}}%</progress>
- {{geno_percent}}%</p>
-{%endif%}
-
-{%if pheno_percent%}
-<p>
- <h2>Checking 'pheno' file:</h2>
- <progress id="prg-pheno-checking" value="{{pheno_percent}}" max="100">
- {{pheno_percent}}%</progress>
- {{pheno_percent}}%</p>
-{%endif%}
-
-{%if phenose_percent%}
-<p>
- <h2>Checking 'phenose' file:</h2>
- <progress id="prg-phenose-checking" value="{{phenose_percent}}" max="100">
- {{phenose_percent}}%</progress>
- {{phenose_percent}}%</p>
-{%endif%}
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
deleted file mode 100644
index 2861a04..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
+++ /dev/null
@@ -1,37 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%}
-
-{%block contents%}
-<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2>
-
-<div class="row">
- <p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control
- checks successfully, and is now ready for uploading into the database.</p>
- <p>Click "Continue" below to proceed.</p>
-</div>
-
-<!--
- The "action" on this form takes us to the next step, where we can
- select all the other data necessary to enter the data into the database.
- -->
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- {{flash_all_messages()}}
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
deleted file mode 100644
index 873f9c3..0000000
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ /dev/null
@@ -1,144 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="row">
- <p>Your R/qtl2 files bundle contains a "geno" specification. You will
- therefore need to select from one of the existing Genotype datasets or
- create a new one.</p>
- <p>This is the dataset where your data will be organised under.</p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_geno_dataset',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">select from existing genotype datasets</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- {{flash_messages("error-rqtl2-select-geno-dataset")}}
-
- <div class="form-group">
- <legend>Datasets</legend>
- <label for="select:geno-datasets" class="form-label">Dataset</label>
- <select id="select:geno-datasets"
- name="geno-dataset-id"
- required="required"
- {%if datasets | length == 0%}
- disabled="disabled"
- {%endif%}
- class="form-control"
- aria-describedby="help-geno-dataset-select-dataset">
- <option value="">Select dataset</option>
- {%for dset in datasets%}
- <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
- {%endfor%}
- </select>
- <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
- Select from the existing genotype datasets for species
- {{species.SpeciesName}} ({{species.FullName}}).
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">select dataset</button>
- </form>
-</div>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.create_geno_dataset',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">create a new genotype dataset</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- {{flash_messages("error-rqtl2-create-geno-dataset")}}
-
- <div class="form-group">
- <label for="txt:dataset-name" class="form-label">Name</label>
- <input type="text"
- id="txt:dataset-name"
- name="dataset-name"
- maxlength="100"
- required="required"
- class="form-control"
- aria-describedby="help-geno-dataset-name" />
- <span id="help-geno-dataset-name" class="form-text text-muted">
- Provide the new name for the genotype dataset, e.g. "BXDGeno"
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt:dataset-fullname" class="form-label">Full Name</label>
- <input type="text"
- id="txt:dataset-fullname"
- name="dataset-fullname"
- required="required"
- maxlength="100"
- class="form-control"
- aria-describedby="help-geno-dataset-fullname" />
-
- <span id="help-geno-dataset-fullname" class="form-text text-muted">
- Provide a longer name that better describes the genotype dataset, e.g.
- "BXD Genotypes"
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt:dataset-shortname" class="form-label">Short Name</label>
- <input type="text"
- id="txt:dataset-shortname"
- name="dataset-shortname"
- maxlength="100"
- class="form-control"
- aria-describedby="help-geno-dataset-shortname" />
-
- <span id="help-geno-dataset-shortname" class="form-text text-muted">
- Provide a short name for the genotype dataset. This is optional. If not
- provided, we'll default to the same value as the "Name" above.
- </span>
- </div>
-
- <div class="form-group">
- <input type="checkbox"
- id="chk:dataset-public"
- name="dataset-public"
- checked="checked"
- class="form-check"
- aria-describedby="help-geno-datasent-public" />
- <label for="chk:dataset-public" class="form-check-label">Public?</label>
-
- <span id="help-geno-dataset-public" class="form-text text-muted">
- Specify whether the dataset will be available publicly. Check to make the
- dataset publicly available and uncheck to limit who can access the dataset.
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">create new dataset</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-population.html b/qc_app/templates/rqtl2/select-population.html
deleted file mode 100644
index 37731f0..0000000
--- a/qc_app/templates/rqtl2/select-population.html
+++ /dev/null
@@ -1,136 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div class="explainer">
- <p>The data is organised in a hierarchical form, beginning with
- <em>species</em> at the very top. Under <em>species</em> the data is
- organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
- (In some really old documents/systems, you might see this referred to as
- <em>InbredSet</em>.)</p>
- <p>In this section, you get to define what population your data is to be
- organised by.</p>
-</div>
-
-<form method="POST"
- action="{{url_for('upload.rqtl2.select_population', species_id=species.SpeciesId)}}">
- <legend class="heading">select grouping/population</legend>
- {{flash_messages("error-select-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <label for="select:inbredset" class="form-label">population</label>
- <select id="select:inbredset"
- name="inbredset_id"
- required="required"
- class="form-control">
- <option value="">Select a grouping/population</option>
- {%for pop in populations%}
- <option value="{{pop.InbredSetId}}">
- {{pop.InbredSetName}} ({{pop.FullName}})</option>
- {%endfor%}
- </select>
- <span class="form-text text-muted">If you are adding data to an already existing
- population, simply pick the population from this drop-down selector. If
- you cannot find your population from this list, try the form below to
- create a new one..</span>
- </div>
-
- <button type="submit" class="btn btn-primary" />select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST"
- action="{{url_for('upload.rqtl2.create_population', species_id=species.SpeciesId)}}">
- <legend class="heading">create new grouping/population</legend>
- {{flash_messages("error-create-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <legend class="heading">mandatory</legend>
-
- <div class="form-group">
- <label for="txt:inbredset-name" class="form-label">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- maxlength="30"
- placeholder="Enter grouping/population name"
- class="form-control" />
- <span class="form-text text-muted">This is a short name that identifies the
- population. Useful for menus, and quick scanning.</span>
- </div>
-
- <div class="form-group">
- <label for="txt:" class="form-label">full name</label>
- <input id="txt:inbredset-fullname"
- name="inbredset_fullname"
- type="text"
- required="required"
- maxlength="100"
- placeholder="Enter the grouping/population's full name"
- class="form-control" />
- <span class="form-text text-muted">This can be the same as the name above, or can
- be longer. Useful for documentation, and human communication.</span>
- </div>
- </div>
-
- <div class="form-group">
- <legend class="heading">optional</legend>
-
- <div class="form-group">
- <label for="num:public" class="form-label">public?</label>
- <select id="num:public"
- name="public"
- class="form-control">
- <option value="0">0 - Only accessible to authorised users</option>
- <option value="1">1 - Publicly accessible to all users</option>
- <option value="2" selected>
- 2 - Publicly accessible to all users</option>
- </select>
- <span class="form-text text-muted">This determines whether the
- population/grouping will appear on the menus for users.</span>
- </div>
-
- <div class="form-group">
- <label for="txt:inbredset-family" class="form-label">family</label>
- <input id="txt:inbredset-family"
- name="inbredset_family"
- type="text"
- placeholder="I am not sure what this is about."
- class="form-control" />
- <span class="form-text text-muted">I do not currently know what this is about.
- This is a failure on my part to figure out what this is and provide a
- useful description. Please feel free to remind me.</span>
- </div>
-
- <div class="form-group">
- <label for="txtarea:" class="form-label">Description</label>
- <textarea id="txtarea:description"
- name="description"
- rows="5"
- placeholder="Enter a description of this grouping/population"
- class="form-control"></textarea>
- <span class="form-text text-muted">
- A long-form description of what the population consists of. Useful for
- humans.</span>
- </div>
- </div>
-
- <button type="submit" class="btn btn-primary" />
- create grouping/population</button>
-</form>
-
-{%endblock%}
-
-
-{%block javascript%}
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
deleted file mode 100644
index 26f52ed..0000000
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ /dev/null
@@ -1,191 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
-
-<div class="row">
- <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
- file(s). This data needs to be organised under a dataset.</p>
- <p>This page gives you the ability to do that.</p>
-</div>
-
-{%if datasets | length > 0%}
-<div class="row">
- <form method="POST"
- action="{{url_for('upload.rqtl2.select_probeset_dataset',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-dataset">
- <legend class="heading">Select from existing ProbeSet datasets</legend>
- {{flash_messages("error-rqtl2")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
-
- <div class="form-group">
- <label class="form-label" for="select:probe-dataset">Dataset</label>
- <select id="select:probe-dataset"
- name="probe-dataset-id"
- required="required"
- {%if datasets | length == 0%}disabled="disabled"{%endif%}
- class="form-control"
- aria-describedby="help-probe-dataset">
- <option value="">Select a dataset</option>
- {%for dataset in datasets%}
- <option value={{dataset.Id}}>
- {{dataset.Name}}
- {%if dataset.FullName%}
- -- ({{dataset.FullName}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span id="help-probe-dataset" class="form-text text-muted">
- Select from existing ProbeSet datasets.</span>
- </div>
-
- <button type="submit" class="btn btn-primary" />select dataset</button>
-</form>
-</div>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-{%endif%}
-
-<div class="row">
- <p>Create an entirely new ProbeSet dataset for your data.</p>
-</div>
-
-<div class="row">
- <form method="POST"
- action="{{url_for('upload.rqtl2.create_probeset_dataset',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-dataset">
- <legend class="heading">Create a new ProbeSet dataset</legend>
- {{flash_messages("error-rqtl2-create-probeset-dataset")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
-
- <div class="form-group">
- <label class="form-label" for="select:average">averaging method</label>
- <select id="select:average"
- name="averageid"
- required="required"
- class="form-control"
- aria-describedby="help-average">
- <option value="">Select averaging method</option>
- {%for avgmethod in avgmethods%}
- <option value="{{avgmethod.Id}}">
- {{avgmethod.Name}}
- {%if avgmethod.Normalization%}
- ({{avgmethod.Normalization}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span id="help-average" class="form-text text-muted">
- Select the averaging method used for your data.
- </span>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="txt:datasetname">Name</label>
- <input type="text" id="txt:datasetname" name="datasetname"
- required="required"
- maxlength="40"
- title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)"
- class="form-control"
- aria-describedby="help-dataset-name" />
-
- <span id="help-dataset-name" class="form-text text-muted">
- Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
- is mandatory <strong>MUST</strong> be provided.
- </span>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="txt:datasetfullname">Full Name</label>
- <input type="text" id="txt:datasetfullname" name="datasetfullname"
- required="required"
- maxlength="100"
- title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)"
- class="form-control"
- aria-describedby="help-dataset-fullname" />
-
- <span id="help-dataset-fullname" class="form-text text-muted">
- Provide a longer, more descriptive name for the dataset e.g.
- "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
- <strong>MUST</strong> be provided.
- </span>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="txt:datasetshortname">Short Name</label>
- <input type="text" id="txt:datasetshortname" name="datasetshortname"
- maxlength="100"
- title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)"
- class="form-control"
- aria-describedby="help-dataset-shortname" />
-
- <span id="help-dataset-shortname" class="form-text text-muted">
- Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
- This is optional.
- </span>
- </div>
-
- <div class="form-check">
- <input type="checkbox" id="chk:public" name="datasetpublic"
- checked="checked"
- title="Whether or not the dataset is accessible by the general public."
- class="form-check-input"
- aria-describedby="help-public" />
- <label class="form-check-label" for="chk:datasetpublic">Public?</label>
-
- <span id="help-public" class="form-text text-muted">
- Check to specify that the dataset will be publicly available. Uncheck to
- limit access to the dataset.
- </span>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="select:datasetdatascale">Data Scale</label>
- <select id="select:datasetdatascale"
- name="datasetdatascale"
- required="required"
- class="form-control"
- aria-describedby="help-dataset-datascale">
- <option value="log2" selected="selected">log2</option>
- <option value="z_score">z_score</option>
- <option value="log2_ratio">log2_ratio</option>
- <option value="linear">linear</option>
- <option value="linear_positive">linear_positive</option>
- </select>
-
- <span id="help-dataset-datascale" class="form-text text-muted">
- Select from a list of scaling methods.
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">create dataset</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
deleted file mode 100644
index b9bf52e..0000000
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ /dev/null
@@ -1,143 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages %}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Phenotype(ProbeSet) Study</h2>
-
-<div class="row">
- <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
- file(s). This data needs to be organised under a study.</p>
- <p>In this page, you can either select from a existing dataset:</p>
-
- <form method="POST"
- action="{{url_for('upload.rqtl2.select_probeset_study',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-study">
- <legend class="heading">Select from existing ProbeSet studies</legend>
- {{flash_messages("error-rqtl2-select-probeset-study")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
-
- <div>
- <label for="select:probe-study" class="form-label">Study</label>
- <select id="select:probe-study"
- name="probe-study-id"
- required="required"
- aria-describedby="help-select-probeset-study"
- {%if studies | length == 0%}disabled="disabled"{%endif%}
- class="form-control">
- <option value="">Select a study</option>
- {%for study in studies%}
- <option value={{study.Id}}>
- {{study.Name}}
- {%if study.FullName%}
- -- ({{study.FullName}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
- <small id="help-select-probeset-study" class="form-text text-muted">
- Select from existing ProbeSet studies.
- </small>
- </div>
-
- <button type="submit" class="btn btn-primary">select study</button>
- </form>
-</div>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-
-<div class="row">
-
- <p>Create a new ProbeSet dataset below:</p>
-
- <form method="POST"
- action="{{url_for('upload.rqtl2.create_probeset_study',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-study">
- <legend class="heading">Create new ProbeSet study</legend>
-
- {{flash_messages("error-rqtl2-create-probeset-study")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
-
- <div>
- <label for="select:platform" class="form-label">Platform</label>
- <select id="select:platform"
- name="platformid"
- required="required"
- aria-describedby="help-select-platform"
- {%if platforms | length == 0%}disabled="disabled"{%endif%}
- class="form-control">
- <option value="">Select a platform</option>
- {%for platform in platforms%}
- <option value="{{platform.GeneChipId}}">
- {{platform.GeneChipName}} ({{platform.Name}})
- </option>
- {%endfor%}
- </select>
- <small id="help-select-platform" class="form-text text-muted">
- Select from a list of known genomics platforms.
- </small>
- </div>
-
- <div class="form-group">
- <label for="txt:studyname" class="form-label">Study name</label>
- <input type="text" id="txt:studyname" name="studyname"
- placeholder="Name of the study. (Required)"
- required="required"
- maxlength="100"
- class="form-control" />
- <span class="form-text text-muted" id="help-study-name">
- Provide a name for the study.</span>
- </div>
-
- <div class="form-group">
- <label for="txt:studyfullname" class="form-label">Full Study Name</label>
- <input type="text"
- id="txt:studyfullname"
- name="studyfullname"
- placeholder="Longer name of the study. (Optional)"
- maxlength="100"
- class="form-control" />
- <span class="form-text text-muted" id="help-study-full-name">
- Provide a longer, more descriptive name for the study. This is optional
- and you can leave it blank.
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt:studyshortname" class="form-label">Short Study Name</label>
- <input type="text"
- id="txt:studyshortname"
- name="studyshortname"
- placeholder="Shorter name of the study. (Optional)"
- maxlength="100"
- class="form-control" />
- <span class="form-text text-muted" id="help-study-short-name">
- Provide a shorter name for the study. This is optional and you can leave
- it blank.
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">create study</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-tissue.html b/qc_app/templates/rqtl2/select-tissue.html
deleted file mode 100644
index 34e1758..0000000
--- a/qc_app/templates/rqtl2/select-tissue.html
+++ /dev/null
@@ -1,115 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Tissue</h2>
-
-<div class="row">
- <p>The data you are uploading concerns a tissue, cell, organ, or other
- biological material used in an experiment.</p>
- <p>Select the appropriate biological material below</p>
-</div>
-
-{%if tissues | length > 0%}
-<div class="row">
- <form method="POST"
- action="{{url_for('upload.rqtl2.select_tissue',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:select-probeset-dataset">
- <legend class="heading">Select from existing ProbeSet datasets</legend>
- {{flash_messages("error-select-tissue")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
-
- <div class="form-group">
- <label class="form-label" for="select-tissue">Tissue</label>
- <select id="select-tissue"
- name="tissueid"
- required="required"
- {%if tissues | length == 0%}disabled="disabled"{%endif%}
- class="form-control"
- aria-describedby="help-select-tissue">
- <option value="">Select a tissue</option>
- {%for tissue in tissues%}
- <option value={{tissue.Id}}>
- {{tissue.Name}}
- {%if tissue.Short_Name%}
- -- ({{tissue.Short_Name}})
- {%endif%}
- </option>
- {%endfor%}
- </select>
-
- <span id="help-select-tissue" class="form-text text-muted">
- Select from existing biological material.</span>
- </div>
-
- <button type="submit" class="btn btn-primary">use selected</button>
- </form>
-</div>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-{%endif%}
-
-<div class="row">
- <p>If you cannot find the biological material in the drop-down above, add it
- to the system below.</p>
-
- <form method="POST"
- action="{{url_for('upload.rqtl2.create_tissue',
- species_id=species.SpeciesId, population_id=population.Id)}}"
- id="frm:create-probeset-dataset">
- <legend class="heading">Add new tissue, organ or biological material</legend>
- {{flash_messages("error-create-tissue")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
-
- <div class="form-group">
- <label class="form-label" for="tissue-name">name</label>
- <input type="text"
- id="txt-tissuename"
- name="tissuename"
- required="required"
- title = "A name to identify the tissue, organ or biological material."
- class="form-control"
- aria-describedby="help-tissue-name" />
-
- <span class="form-text text-muted" id="help-tissue-name">
- A name to identify the tissue, organ or biological material.
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt-shortname" class="form-label">short name</label>
- <input type="text" id="txt-tissueshortname" name="tissueshortname"
- required="required"
- maxlength="7"
- title="A short name (e.g. 'Mam') for the biological material."
- class="form-control"
- aria-describedby="help-tissue-short-name" />
-
- <span class="form-text text-muted" id="help-tissue-short-name">
- Provide a short name for the tissue, organ or biological material used in
- the experiment.
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary" />add new material</button>
-</form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
deleted file mode 100644
index 1be87fa..0000000
--- a/qc_app/templates/rqtl2/summary-info.html
+++ /dev/null
@@ -1,65 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Summary</h2>
-
-<div class="row">
- <p>This is the information you have provided to accompany the R/qtl2 bundle
- you have uploaded. Please verify the information is correct before
- proceeding.</p>
-</div>
-
-<div class="row">
- <dl>
- <dt>Species</dt>
- <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
-
- <dt>Population</dt>
- <dd>{{population.InbredSetName}}</dd>
-
- {%if geno_dataset%}
- <dt>Genotype Dataset</dt>
- <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
- {%endif%}
-
- {%if tissue%}
- <dt>Tissue</dt>
- <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd>
- {%endif%}
-
- {%if probe_study%}
- <dt>ProbeSet Study</dt>
- <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
- {%endif%}
-
- {%if probe_dataset%}
- <dt>ProbeSet Dataset</dt>
- <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
- {%endif%}
- </dl>
-</div>
-
-<div class="row">
- <form id="frm:confirm-rqtl2bundle-details"
- action="{{url_for('upload.rqtl2.confirm_bundle_details',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet dataset</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
- <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
deleted file mode 100644
index 07c240f..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ /dev/null
@@ -1,276 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "upload_progress_indicator.html" import upload_progress_indicator%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-{%macro rqtl2_file_help()%}
-<span class="form-text text-muted">
- <p>
- Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle
- contains exactly one control file and the corresponding files mentioned in
- the control file.
- </p>
- <p>
- The control file can be either a YAML or JSON file. <em>ALL</em> other data
- files in the zip bundle should be CSV files.
- </p>
- <p>See the
- <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
- target="_blank">
- R/qtl2 file format specifications
- </a>
- for more details.
- </p>
-</span>
-{%endmacro%}
-{{upload_progress_indicator()}}
-
-<div id="resumable-file-display-template"
- class="panel panel-info"
- style="display: none">
- <div class="panel-heading"></div>
- <div class="panel-body"></div>
-</div>
-
-
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<div id="resumable-drop-area"
- style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;">
- <p>
- <a id="resumable-browse-button" href="#"
- class="btn btn-info">Browse</a>
- </p>
- <p class="form-text text-muted">
- You can drag and drop your file here, or click the browse button.
- Click on the file to remove it.
- </p>
- {{rqtl2_file_help()}}
- <div id="resumable-selected-files"
- style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div>
- <div id="resumable-class-buttons" style="text-align: right;">
- <button id="resumable-upload-button"
- class="btn btn-primary"
- style="display: none">start upload</button>
- <button id="resumable-cancel-upload-button"
- class="btn btn-danger"
- style="display: none">cancel upload</button>
- </div>
- <div id="resumable-progress-bar" class="progress" style="display: none">
- <div class="progress-bar"
- role="progress-bar"
- aria-valuenow="60"
- aria-valuemin="0"
- aria-valuemax="100"
- style="width: 0%;">
- Uploading: 60%
- </div>
- </div>
-</div>
-
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data"
- data-resumable-target="{{url_for(
- 'upload.rqtl2.upload_rqtl2_bundle_chunked_post',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}">
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
-
- {{flash_all_messages()}}
-
- <div class="form-group">
- <legend class="heading">file upload</legend>
- <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label>
- <input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file"
- accept="application/zip, .zip"
- required="required"
- class="form-control" />
- {{rqtl2_file_help()}}
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- data-toggle="modal"
- data-target="#upload-progress-indicator">upload R/qtl2 bundle</button>
-</form>
-
-{%endblock%}
-
-{%block javascript%}
-<script src="{{url_for('base.node_modules',
- filename='resumablejs/resumable.js')}}"></script>
-<script type="text/javascript" src="/static/js/upload_progress.js"></script>
-<script type="text/javascript">
- function readBinaryFile(file) {
- return new Promise((resolve, reject) => {
- var _reader = new FileReader();
- _reader.onload = (event) => {resolve(_reader.result);};
- _reader.readAsArrayBuffer(file);
- });
- }
-
- function computeFileChecksum(file) {
- return readBinaryFile(file)
- .then((content) => {
- return window.crypto.subtle.digest(
- "SHA-256", new Uint8Array(content));
- }).then((digest) => {
- return Uint8ArrayToHex(new Uint8Array(digest))
- });
- }
-
- function Uint8ArrayToHex(arr) {
- var toHex = (val) => {
- _hex = val.toString(16);
- if(_hex.length < 2) {
- return "0" + val;
- }
- return _hex;
- };
- _hexstr = ""
- arr.forEach((val) => {_hexstr += toHex(val)});
- return _hexstr
- }
-
- var r = Resumable({
- target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"),
- fileType: ["zip"],
- maxFiles: 1,
- forceChunkSize: true,
- generateUniqueIdentifier: (file, event) => {
- return computeFileChecksum(file).then((checksum) => {
- var _relativePath = (file.webkitRelativePath
- || file.relativePath
- || file.fileName
- || file.name);
- return checksum + "-" + _relativePath.replace(
- /[^a-zA-Z0-9_-]/img, "");
- });
- }
- });
-
- if(r.support) {
- //Hide form and display drag&drop UI
- $("#frm-upload-rqtl2-bundle").css("display", "none");
- $("#resumable-drop-area").css("display", "block");
-
- // Define UI elements for browse and drag&drop
- r.assignDrop(document.getElementById("resumable-drop-area"));
- r.assignBrowse(document.getElementById("resumable-browse-button"));
-
- // Event handlers
-
- function display_files(files) {
- displayArea = $("#resumable-selected-files")
- displayArea.empty();
- files.forEach((file) => {
- var displayElement = $(
- "#resumable-file-display-template").clone();
- displayElement.removeAttr("id");
- displayElement.css("display", "");
- displayElement.find(".panel-heading").text(file.fileName);
- list = $("<ul></ul>");
- list.append($("<li><strong>Name</strong>: "
- + (file.name
- || file.fileName
- || file.relativePath
- || file.webkitRelativePath)
- + "</li>"));
- list.append($("<li><strong>Size</strong>: "
- + (file.size / (1024*1024)).toFixed(2)
- + " MB</li>"));
- list.append($("<li><strong>Unique Identifier</strong>: "
- + file.uniqueIdentifier + "</li>"));
- list.append($("<li><strong>Mime</strong>: "
- + file.file.type
- + "</li>"));
- displayElement.find(".panel-body").append(list);
- displayElement.appendTo("#resumable-selected-files");
- });
- }
-
- r.on("filesAdded", function(files) {
- display_files(files);
- $("#resumable-upload-button").css("display", "");
- $("#resumable-upload-button").on("click", (event) => {
- r.upload();
- });
- });
-
- r.on("uploadStart", (event) => {
- $("#resumable-upload-button").css("display", "none");
- $("#resumable-cancel-upload-button").css("display", "");
- $("#resumable-cancel-upload-button").on("click", (event) => {
- r.files.forEach((file) => {
- if(file.isUploading()) {
- file.abort();
- }
- });
- $("#resumable-cancel-upload-button").css("display", "none");
- $("#resumable-upload-button").on("click", (event) => {
- r.files.forEach((file) => {file.retry();});
- });
- $("#resumable-upload-button").css("display", "");
- });
- });
-
- r.on("progress", () => {
- var progress = (r.progress() * 100).toFixed(2);
- var pbar = $("#resumable-progress-bar > .progress-bar");
- $("#resumable-progress-bar").css("display", "");
- pbar.css("width", progress+"%");
- pbar.attr("aria-valuenow", progress);
- pbar.text("Uploading: " + progress + "%");
- })
-
- r.on("fileSuccess", (file, message) => {
- if(message != "OK") {
- var uri = (window.location.protocol
- + "//"
- + window.location.host
- + message);
- window.location.replace(uri);
- }
- });
-
- r.on("error", (message, file) => {
- filename = (file.webkitRelativePath
- || file.relativePath
- || file.fileName
- || file.name);
- jsonmsg = JSON.parse(message);
- alert("There was an error while uploading your file '"
- + filename
- + "'. The error message was:\n\n\t"
- + jsonmsg.error
- + " ("
- + jsonmsg.statuscode
- + "): " + jsonmsg.message);
- })
- } else {
- setup_upload_handlers(
- "frm-upload-rqtl2-bundle", make_data_uploader(
- function (form) {
- var formdata = new FormData();
- formdata.append(
- "species_id",
- form.querySelector('input[name="species_id"]').value);
- formdata.append(
- "population_id",
- form.querySelector('input[name="population_id"]').value);
- formdata.append(
- "rqtl2_bundle_file",
- form.querySelector("#file-rqtl2-bundle").files[0]);
- return formdata;
- }));
- }
-</script>
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
deleted file mode 100644
index 93b1dc9..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ /dev/null
@@ -1,33 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<div class="row">
- <p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p>
- <p>The next step is to select the various extra information we need to figure
- out what to do with the data. You will select/create the relevant studies
- and/or datasets to organise the data in the steps that follow.</p>
- <p>Click "Continue" below to proceed.</p>
-
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- {{flash_all_messages()}}
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html
deleted file mode 100644
index da19ddc..0000000
--- a/qc_app/templates/samples/select-population.html
+++ /dev/null
@@ -1,99 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div>
- <p>We organise the samples/cases/strains in a hierarchichal form, starting
- with <strong>species</strong> at the very top. Under species, we have a
- grouping in terms of the relevant population
- (e.g. Inbred populations, cell tissue, etc.)</p>
-</div>
-
-<form method="POST" action="{{url_for('samples.select_population',
- species_id=species.SpeciesId)}}">
- <legend class="heading">select grouping/population</legend>
- {{flash_messages("error-select-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <label for="select:inbredset" class="form-label">grouping/population</label>
- <select id="select:inbredset"
- name="inbredset_id"
- required="required"
- class="form-control">
- <option value="">Select a grouping/population</option>
- {%for pop in populations%}
- <option value="{{pop.InbredSetId}}">
- {{pop.InbredSetName}} ({{pop.FullName}})</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST" action="{{url_for('samples.create_population',
- species_id=species.SpeciesId)}}">
- <legend class="heading">create new grouping/population</legend>
- {{flash_messages("error-create-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <div class="form-group">
- <legend>mandatory</legend>
-
- <label for="txt:inbredset-name" class="form-label">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- placeholder="Enter grouping/population name"
- class="form-control" />
-
- <label for="txt:" class="form-label">full name</label>
- <input id="txt:inbredset-fullname"
- name="inbredset_fullname"
- type="text"
- required = "required"
- placeholder="Enter the grouping/population's full name"
- class="form-control" />
- </div>
- <div class="form-group">
- <legend>Optional</legend>
-
- <label for="num:public" class="form-label">public?</label>
- <input id="num:public"
- name="public"
- type="number"
- min="0" max="2" value="2"
- class="form-control" />
-
- <label for="txt:inbredset-family" class="form-label">family</label>
- <input id="txt:inbredset-family"
- name="inbredset_family"
- type="text"
- placeholder="I am not sure what this is about."
- class="form-control" />
-
- <label for="txtarea:" class="form-label">Description</label>
- <textarea id="txtarea:description"
- name="description"
- rows="5"
- placeholder="Enter a description of this grouping/population"
- class="form-control"></textarea>
- </div>
-
- <button type="submit" class="btn btn-primary">create grouping/population</button>
-</form>
-
-{%endblock%}
-
-
-{%block javascript%}
-{%endblock%}
diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html
deleted file mode 100644
index edadc61..0000000
--- a/qc_app/templates/samples/select-species.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h2 class="heading">upload samples/cases</h2>
-
-<p>We need to know what species your data belongs to.</p>
-
-{{flash_all_messages()}}
-
-<form method="POST" action="{{url_for('samples.select_species')}}">
- <legend class="heading">upload samples</legend>
- <div class="form-group">
- <label for="select_species02" class="form-label">Species</label>
- <select id="select_species02"
- name="species_id"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for spec in species%}
- <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">submit</button>
-</form>
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-failure.html b/qc_app/templates/samples/upload-failure.html
deleted file mode 100644
index 09e2ecf..0000000
--- a/qc_app/templates/samples/upload-failure.html
+++ /dev/null
@@ -1,27 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Samples Upload Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>There was a failure attempting to upload the samples.</p>
-
-<p>Here is some information to help with debugging the issue. Provide this
- information to the developer/maintainer.</p>
-
-<h3>Debugging Information</h3>
-<ul>
- <li><strong>job id</strong>: {{job.job_id}}</li>
- <li><strong>status</strong>: {{job.status}}</li>
- <li><strong>job type</strong>: {{job["job-type"]}}</li>
-</ul>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-progress.html b/qc_app/templates/samples/upload-progress.html
deleted file mode 100644
index 7bb02be..0000000
--- a/qc_app/templates/samples/upload-progress.html
+++ /dev/null
@@ -1,22 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>saving to database...</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html
deleted file mode 100644
index e62de57..0000000
--- a/qc_app/templates/samples/upload-samples.html
+++ /dev/null
@@ -1,139 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload Samples{%endblock%}
-
-{%block css%}{%endblock%}
-
-{%block contents%}
-<h1 class="heading">upload samples</h1>
-
-{{flash_messages("alert-success")}}
-
-<p>You can now upload a character-separated value (CSV) file that contains
- details about your samples. The CSV file should have the following fields:
- <dl>
- <dt>Name</dt>
- <dd>The primary name for the sample</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. Can be an empty field.</dd>
-
- <dt>Alias</dt>
- <dd>An alias for the sample. Can be an empty field.</dd>
- </dl>
-</p>
-
-<form id="form-samples"
- method="POST"
- action="{{url_for('samples.upload_samples',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- enctype="multipart/form-data">
- <legend class="heading">upload samples</legend>
-
- <div class="form-group">
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <label class="form-label">species:</label>
- <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span>
- </div>
-
- <div class="form-group">
- <input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" />
- <label class="form-label">grouping/population:</label>
- <span class="form-text">{{population.Name}} [{{population.FullName}}]</span>
- </div>
-
- <div class="form-group">
- <label for="file-samples" class="form-label">select file</label>
- <input type="file" name="samples_file" id="file:samples"
- accept="text/csv, text/tab-separated-values"
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="select:separator" class="form-label">field separator</label>
- <select id="select:separator"
- name="separator"
- required="required"
- class="form-control">
- <option value="">Select separator for your file: (default is comma)</option>
- <option value="&#x0009;">TAB</option>
- <option value="&#x0020;">Space</option>
- <option value=",">Comma</option>
- <option value=";">Semicolon</option>
- <option value="other">Other</option>
- </select>
- <input id="txt:separator"
- type="text"
- name="other_separator"
- class="form-control" />
- <small class="form-text text-muted">
- If you select '<strong>Other</strong>' for the field separator value,
- enter the character that separates the fields in your CSV file in the form
- field below.
- </small>
- </div>
-
- <div class="form-group form-check">
- <input id="chk:heading"
- type="checkbox"
- name="first_line_heading"
- class="form-check-input" />
- <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
- columns.
- </small>
- </div>
-
- <div class="form-group">
- <label for="txt:delimiter" class="form-label">field delimiter</label>
- <input id="txt:delimiter"
- type="text"
- name="field_delimiter"
- maxlength="1"
- class="form-control" />
- <small class="form-text text-muted">
- If there is a character delimiting the string texts within particular
- fields in your CSV, provide the character here. This can be left blank if
- no such delimiters exist in your file.
- </small>
- </div>
-
- <button type="submit"
- class="btn btn-primary">upload samples file</button>
-</form>
-
-<table id="tbl:samples-preview" class="table">
- <caption class="heading">preview content</caption>
-
- <thead>
- <tr>
- <th>Name</th>
- <th>Name2</th>
- <th>Symbol</th>
- <th>Alias</th>
- </tr>
- </thead>
-
- <tbody>
- <tr id="default-row">
- <td colspan="4">
- Please make some selections to preview the data.</td>
- </tr>
- </tbody>
-</table>
-
-{%endblock%}
-
-
-{%block javascript%}
-<script src="/static/js/upload_samples.js" type="text/javascript"></script>
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-success.html b/qc_app/templates/samples/upload-success.html
deleted file mode 100644
index cb745c3..0000000
--- a/qc_app/templates/samples/upload-success.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>Successfully uploaded the samples.</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
deleted file mode 100644
index 2f07de8..0000000
--- a/qc_app/templates/select_dataset.html
+++ /dev/null
@@ -1,161 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select dataset</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
- id="select-dataset-form" class="two-col-sep-col1">
- <legend class="heading">choose existing dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <div class="form-group">
- <label for="datasetid" class="form-label">dataset:</label>
- <select id="datasetid" name="datasetid" class="form-control"
- {%if datasets | length == 0:%}
- disabled="disabled"
- {%endif%}>
- {%for dataset in datasets:%}
- <option value="{{dataset['Id']}}">
- [{{dataset["Name"]}}] - {{dataset["FullName"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary"
- {%if datasets | length == 0:%}
- disabled="disabled"
- {%endif%} />update database</button>
-</form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" id="create-dataset-form"
- action="{{url_for('dbinsert.create_dataset')}}"
- class="two-col-sep-col2">
- <legend class="heading">create new dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- {%with messages = get_flashed_messages(with_categories=true)%}
- {%if messages:%}
- <ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
- </ul>
- {%endif%}
- {%endwith%}
-
- <div class="form-group">
- <label for="avgid" class="form-label">average:</label>
- <select id="avgid" name="avgid" required="required" class="form-control">
- <option value="">Select averaging method</option>
- {%for method in avgmethods:%}
- <option value="{{method['AvgMethodId']}}"
- {%if avgid is defined and method['AvgMethodId'] | int == avgid | int%}
- selected="selected"
- {%endif%}>
- {{method["Name"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <label for="datasetname" class="form-label">name:</label>
- <input id="datasetname" name="datasetname" type="text"
- class="form-control"
- {%if datasetname is defined %}
- value="{{datasetname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetname2" class="form-label">name 2:</label>
- <input id="datasetname2" name="datasetname2" type="text"
- required="required" class="form-control"
- {%if datasetname2 is defined %}
- value="{{datasetname2}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetfullname" class="form-label">full name:</label>
- <input id="datasetfullname" name="datasetfullname" type="text"
- required="required" class="form-control"
- {%if datasetfullname is defined %}
- value="{{datasetfullname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetshortname" class="form-label">short name:</label>
- <input id="datasetshortname" name="datasetshortname" type="text"
- required="required" class="form-control"
- {%if datasetshortname is defined %}
- value="{{datasetshortname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetpublic" class="form-label">public:</label>
- <input id="datasetpublic" name="datasetpublic" type="number"
- required="required" min="0" max="2"
- {%if datasetpublic is defined %}
- value="{{datasetpublic | int}}"
- {%else%}
- value="0"
- {%endif%}
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="datasetconfidentiality">confidentiality:</label>
- <input id="datasetconfidentiality" name="datasetconfidentiality"
- type="number" required="required" min="0" max="2"
- {%if datasetconfidentiality is defined %}
- value="{{datasetconfidentiality | int}}"
- {%else%}
- value="0"
- {%endif%}
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="datasetdatascale" class="form-label">data scale:</label>
- <select id="datasetdatascale" name="datasetdatascale" class="form-control">
- <option value="">None</option>
- {%for dscale in datascales:%}
- <option value="{{dscale}}"
- {%if datasetdatascale is defined and dscale == datasetdatascale%}
- selected="selected"
- {%elif dscale == "log2":%}
- selected="selected"
- {%endif%}>
- {{dscale}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">create new dataset</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html
deleted file mode 100644
index d9bc68f..0000000
--- a/qc_app/templates/select_platform.html
+++ /dev/null
@@ -1,82 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select platform</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}">
- <input type="hidden" name="filename" value="{{filename}}" />
- <input type="hidden" name="filetype" value="{{filetype}}" />
- <input type="hidden" name="totallines" value="{{totallines}}" />
-
- <div class="form-group">
- <label for="species" class="form-label">species</label>
- <select id="species" name="species" class="form-control">
- {%for row in species:%}
- <option value="{{row['SpeciesId']}}"
- {%if row["Name"] == default_species:%}
- selected="selected"
- {%endif%}>
- {{row["MenuName"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <table id="genechips-table" class="table">
- <caption>select platform</caption>
- <thead>
- <tr>
- <th>Select</th>
- <th>GeneChip ID</th>
- <th>GeneChip Name</th>
- </tr>
- </thead>
-
- <tbody>
- {%for chip in genechips:%}
- <tr>
- <td>
- <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
- required="required" />
- </td>
- <td>{{chip["GeneChipId"]}}</td>
- <td>{{chip["GeneChipName"]}}</td>
- </tr>
- {%else%}
- <tr>
- <td colspan="5">No chips found for selected species</td>
- </tr>
- {%endfor%}
- </tbody>
- </table>
-
- <button type="submit" class="btn btn-primary">submit platform</button>
- </form>
-</div>
-{%endblock%}
-
-{%block javascript%}
-<script type="text/javascript" src="/static/js/utils.js"></script>
-<script type="text/javascript" src="/static/js/select_platform.js"></script>
-<script type="text/javascript">
- document.getElementById(
- "species").addEventListener("change", update_genechips);
- document.getElementById(
- "genechips-table").getElementsByTagName(
- "tbody")[0].addEventListener(
- "click",
- function(event) {
- if(event.target.tagName.toLowerCase() == "td") {
- return select_row_radio(event.target.parentElement);
- }
- if(event.target.tagName.toLowerCase() == "td") {
- return select_row_radio(event.target);
- }
- return false;
- });
-</script>
-{%endblock%}
diff --git a/qc_app/templates/select_species.html b/qc_app/templates/select_species.html
deleted file mode 100644
index 3b1a8a9..0000000
--- a/qc_app/templates/select_species.html
+++ /dev/null
@@ -1,92 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-{%from "upload_progress_indicator.html" import upload_progress_indicator%}
-
-{%block title%}expression data: select species{%endblock%}
-
-{%block contents%}
-{{upload_progress_indicator()}}
-
-<h2 class="heading">expression data: select species</h2>
-
-<div class="row">
- <form action="{{url_for('entry.upload_file')}}"
- method="POST"
- enctype="multipart/form-data"
- id="frm-upload-expression-data">
- <legend class="heading">upload expression data</legend>
- {{flash_messages("error-expr-data")}}
-
- <div class="form-group">
- <label for="select_species01" class="form-label">Species</label>
- <select id="select_species01"
- name="speciesid"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for aspecies in species%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <legend class="heading">file type</legend>
-
- <div class="form-check">
- <input type="radio" name="filetype" value="average" id="filetype_average"
- required="required" class="form-check-input" />
- <label for="filetype_average" class="form-check-label">average</label>
- </div>
-
- <div class="form-check">
- <input type="radio" name="filetype" value="standard-error"
- id="filetype_standard_error" required="required"
- class="form-check-input" />
- <label for="filetype_standard_error" class="form-check-label">
- standard error
- </label>
- </div>
- </div>
-
- <div class="form-group">
- <span id="no-file-error" class="alert-danger" style="display: none;">
- No file selected
- </span>
- <label for="file_upload" class="form-label">select file</label>
- <input type="file" name="qc_text_file" id="file_upload"
- accept="text/plain, text/tab-separated-values, application/zip"
- class="form-control"/>
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- data-toggle="modal"
- data-target="#upload-progress-indicator">upload file</button>
- </form>
-</div>
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript" src="static/js/upload_progress.js"></script>
-<script type="text/javascript">
- function setup_formdata(form) {
- var formdata = new FormData();
- formdata.append(
- "speciesid",
- form.querySelector("#select_species01").value)
- formdata.append(
- "qc_text_file",
- form.querySelector("input[type='file']").files[0]);
- formdata.append(
- "filetype",
- selected_filetype(
- Array.from(form.querySelectorAll("input[type='radio']"))));
- return formdata;
- }
-
- setup_upload_handlers(
- "frm-upload-expression-data", make_data_uploader(setup_formdata));
-</script>
-{%endblock%}
diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html
deleted file mode 100644
index 648ad4c..0000000
--- a/qc_app/templates/select_study.html
+++ /dev/null
@@ -1,108 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select study</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend class="heading">Select from existing study</legend>
- {{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
- totallines=totallines)}}
-
- <div class="form-group">
- <label class="form-label" for="study">study:</label>
- <select id="study" name="studyid" class="form-control">
- {%for study in studies:%}
- <option value="{{study['Id']}}">{{study["Name"]}}</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- {%if studies | length == 0:%}
- disabled="disabled"
- {%endif%} />submit selected study</button>
-</form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.create_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- {%with messages = get_flashed_messages(with_categories=true)%}
- {%if messages:%}
- <ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
- </ul>
- {%endif%}
- {%endwith%}
- <legend class="heading">Create new study</legend>
- {{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
- totallines=totallines)}}
-
- <div class="form-group">
- <label class="form-label" for="studyname">name:</label>
- <input type="text" id="studyname" name="studyname" class="form-control"
- required="required"
- {%if studyname:%}
- value="{{studyname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label class="form-label" for="group">group:</label>
- <select id="group" name="inbredsetid" class="form-control"
- required="required">
- <option value="">Select group</option>
- {%for family in groups:%}
- <optgroup label="{{family}}">
- {%for group in groups[family]:%}
- <option value="{{group['InbredSetId']}}"
- {%if group["InbredSetId"] == selected_group:%}
- selected="selected"
- {%endif%}>
- {{group["FullName"]}}
- </option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="tissue">tissue:</label>
- <select id="tissue" name="tissueid" class="form-control"
- required="required">
- <option value="">Select type</option>
- {%for tissue in tissues:%}
- <option value="{{tissue['TissueId']}}"
- {%if tissue["TissueId"] == selected_tissue:%}
- selected="selected"
- {%endif%}>
- {{tissue["Name"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">create study</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/stdout_output.html b/qc_app/templates/stdout_output.html
deleted file mode 100644
index 85345a9..0000000
--- a/qc_app/templates/stdout_output.html
+++ /dev/null
@@ -1,8 +0,0 @@
-{%macro stdout_output(job)%}
-
-<h4>STDOUT Output</h4>
-<div class="cli-output">
- <pre>{{job.get("stdout", "")}}</pre>
-</div>
-
-{%endmacro%}
diff --git a/qc_app/templates/unhandled_exception.html b/qc_app/templates/unhandled_exception.html
deleted file mode 100644
index 6e6a051..0000000
--- a/qc_app/templates/unhandled_exception.html
+++ /dev/null
@@ -1,21 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}System Error{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<p>
- An error has occured, and your request has been aborted. Please notify the
- administrator to try and get this sorted.
-</p>
-<p>
- Provide the following information to help the administrator figure out and fix
- the issue:<br />
- <hr /><br />
- {{trace}}
- <hr /><br />
-</p>
-{%endblock%}
diff --git a/qc_app/templates/upload_progress_indicator.html b/qc_app/templates/upload_progress_indicator.html
deleted file mode 100644
index e274e83..0000000
--- a/qc_app/templates/upload_progress_indicator.html
+++ /dev/null
@@ -1,35 +0,0 @@
-{%macro upload_progress_indicator()%}
-<div id="upload-progress-indicator" class="modal fade" tabindex="-1" role="dialog">
- <div class="modal-dialog" role="document">
- <div class="modal-content">
- <div class="modal-header">
- <h3 class="modal-title">Uploading file</h3>
- </div>
-
- <div class="modal-body">
- <form id="frm-cancel-upload" style="border-style: none;">
- <div class="form-group">
- <span id="progress-filename" class="form-text">No file selected!</span>
- <progress id="progress-bar" value="0" max="100" class="form-control">
- 0</progress>
- </div>
-
- <div class="form-group">
- <span class="form-text text-muted" id="progress-text">
- Uploading 0%</span>
- <span class="form-text text-muted" id="progress-extra-text">
- Processing</span>
- </div>
- </form>
- </div>
-
- <div class="modal-footer">
- <button id="btn-cancel-upload"
- type="button"
- class="btn btn-danger"
- data-dismiss="modal">Cancel</button>
- </div>
- </div>
- </div>
-</div>
-{%endmacro%}
diff --git a/qc_app/templates/worker_failure.html b/qc_app/templates/worker_failure.html
deleted file mode 100644
index b65b140..0000000
--- a/qc_app/templates/worker_failure.html
+++ /dev/null
@@ -1,24 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Worker Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Worker Failure</h1>
-
-<p>
- There was a critical failure launching the job to parse your file.
- This is our fault and (probably) has nothing to do with the file you uploaded.
-</p>
-
-<p>
- Please notify the developers of this issue when you encounter it,
- providing the link to this page, or the information below.
-</p>
-
-<h4>Debugging Information</h4>
-
-<ul>
- <li><strong>job id</strong>: {{job_id}}</li>
-</ul>
-
-{%endblock%}
diff --git a/qc_app/upload/__init__.py b/qc_app/upload/__init__.py
deleted file mode 100644
index 5f120d4..0000000
--- a/qc_app/upload/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-"""Package handling upload of files."""
-from flask import Blueprint
-
-from .rqtl2 import rqtl2
-
-upload = Blueprint("upload", __name__)
-upload.register_blueprint(rqtl2, url_prefix="/rqtl2")
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
deleted file mode 100644
index 51d8321..0000000
--- a/qc_app/upload/rqtl2.py
+++ /dev/null
@@ -1,1157 +0,0 @@
-"""Module to handle uploading of R/qtl2 bundles."""#pylint: disable=[too-many-lines]
-import sys
-import json
-import traceback
-from pathlib import Path
-from datetime import date
-from uuid import UUID, uuid4
-from functools import partial
-from zipfile import ZipFile, is_zipfile
-from typing import Union, Callable, Optional
-
-import MySQLdb as mdb
-from redis import Redis
-from MySQLdb.cursors import DictCursor
-from werkzeug.utils import secure_filename
-from flask import (
- flash,
- escape,
- request,
- jsonify,
- url_for,
- redirect,
- Response,
- Blueprint,
- render_template,
- current_app as app)
-
-from r_qtl import r_qtl2
-
-from qc_app import jobs
-from qc_app.files import save_file, fullpath
-from qc_app.dbinsert import species as all_species
-from qc_app.db_utils import with_db_connection, database_connection
-
-from qc_app.db.platforms import platform_by_id, platforms_by_species
-from qc_app.db.averaging import averaging_methods, averaging_method_by_id
-from qc_app.db.tissues import all_tissues, tissue_by_id, create_new_tissue
-from qc_app.db import (
- species_by_id,
- save_population,
- populations_by_species,
- population_by_species_and_id,)
-from qc_app.db.datasets import (
- geno_dataset_by_id,
- geno_datasets_by_species_and_population,
-
- probeset_study_by_id,
- probeset_create_study,
- probeset_dataset_by_id,
- probeset_create_dataset,
- probeset_datasets_by_study,
- probeset_studies_by_species_and_population)
-
-rqtl2 = Blueprint("rqtl2", __name__)
-
-@rqtl2.route("/", methods=["GET", "POST"])
-@rqtl2.route("/select-species", methods=["GET", "POST"])
-def select_species():
- """Select the species."""
- if request.method == "GET":
- return render_template("rqtl2/index.html", species=with_db_connection(all_species))
-
- species_id = request.form.get("species_id")
- species = with_db_connection(
- lambda conn: species_by_id(conn, species_id))
- if bool(species):
- return redirect(url_for(
- "upload.rqtl2.select_population", species_id=species_id))
- flash("Invalid species or no species selected!", "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_species"))
-
-
-@rqtl2.route("/upload/species/<int:species_id>/select-population",
- methods=["GET", "POST"])
-def select_population(species_id: int):
- """Select/Create the population to organise data under."""
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- if not bool(species):
- flash("Invalid species selected!", "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_species"))
-
- if request.method == "GET":
- return render_template(
- "rqtl2/select-population.html",
- species=species,
- populations=populations_by_species(conn, species_id))
-
- population = population_by_species_and_id(
- conn, species["SpeciesId"], request.form.get("inbredset_id"))
- if not bool(population):
- flash("Invalid Population!", "alert-error error-rqtl2")
- return redirect(
- url_for("upload.rqtl2.select_population", pgsrc="error"),
- code=307)
-
- return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
- species_id=species["SpeciesId"],
- population_id=population["InbredSetId"]))
-
-
-@rqtl2.route("/upload/species/<int:species_id>/create-population",
- methods=["POST"])
-def create_population(species_id: int):
- """Create a new population for the given species."""
- population_page = redirect(url_for("upload.rqtl2.select_population",
- species_id=species_id))
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- population_name = request.form.get("inbredset_name", "").strip()
- population_fullname = request.form.get("inbredset_fullname", "").strip()
- if not bool(species):
- flash("Invalid species!", "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_species"))
- if not bool(population_name):
- flash("Invalid Population Name!", "alert-error error-rqtl2")
- return population_page
- if not bool(population_fullname):
- flash("Invalid Population Full Name!", "alert-error error-rqtl2")
- return population_page
- new_population = save_population(conn, {
- "SpeciesId": species["SpeciesId"],
- "Name": population_name,
- "InbredSetName": population_fullname,
- "FullName": population_fullname,
- "Family": request.form.get("inbredset_family") or None,
- "Description": request.form.get("description") or None
- })
-
- flash("Population created successfully.", "alert-success")
- return redirect(
- url_for("upload.rqtl2.upload_rqtl2_bundle",
- species_id=species_id,
- population_id=new_population["population_id"],
- pgsrc="create-population"),
- code=307)
-
-
-class __RequestError__(Exception): #pylint: disable=[invalid-name]
- """Internal class to avoid pylint's `too-many-return-statements` error."""
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle"),
- methods=["GET", "POST"])
-def upload_rqtl2_bundle(species_id: int, population_id: int):
- """Allow upload of R/qtl2 bundle."""
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- population = population_by_species_and_id(
- conn, species["SpeciesId"], population_id)
- if not bool(species):
- flash("Invalid species!", "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_species"))
- if not bool(population):
- flash("Invalid Population!", "alert-error error-rqtl2")
- return redirect(
- url_for("upload.rqtl2.select_population", pgsrc="error"),
- code=307)
- if request.method == "GET" or (
- request.method == "POST"
- and bool(request.args.get("pgsrc"))):
- return render_template("rqtl2/upload-rqtl2-bundle-step-01.html",
- species=species,
- population=population)
-
- 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"]))
- except AssertionError:
- app.logger.debug(traceback.format_exc())
- flash("Please provide a valid R/qtl2 zip bundle.",
- "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
- species_id=species_id,
- population_id=population_id))
-
- if not is_zipfile(str(the_file)):
- app.logger.debug("The file is not a zip file.")
- raise __RequestError__("Invalid file! Expected a zip file.")
-
- jobid = trigger_rqtl2_bundle_qc(
- species_id,
- population_id,
- the_file,
- request.files["rqtl2_bundle_file"].filename)#type: ignore[arg-type]
- return redirect(url_for(
- "upload.rqtl2.rqtl2_bundle_qc_status", jobid=jobid))
-
-
-def trigger_rqtl2_bundle_qc(
- species_id: int,
- population_id: int,
- rqtl2bundle: Path,
- originalfilename: str
-) -> UUID:
- """Trigger QC on the R/qtl2 bundle."""
- redisuri = app.config["REDIS_URL"]
- with Redis.from_url(redisuri, decode_responses=True) as rconn:
- jobid = uuid4()
- redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"]
- jobs.launch_job(
- jobs.initialise_job(
- rconn,
- jobs.jobsnamespace(),
- str(jobid),
- [sys.executable, "-m", "scripts.qc_on_rqtl2_bundle",
- app.config["SQL_URI"], app.config["REDIS_URL"],
- jobs.jobsnamespace(), str(jobid), str(species_id),
- str(population_id), "--redisexpiry",
- str(redis_ttl_seconds)],
- "rqtl2-bundle-qc-job",
- redis_ttl_seconds,
- {"job-metadata": json.dumps({
- "speciesid": species_id,
- "populationid": population_id,
- "rqtl2-bundle-file": str(rqtl2bundle.absolute()),
- "original-filename": originalfilename})}),
- redisuri,
- f"{app.config['UPLOAD_FOLDER']}/job_errors")
- return jobid
-
-
-def chunk_name(uploadfilename: str, chunkno: int) -> str:
- """Generate chunk name from original filename and chunk number"""
- if uploadfilename == "":
- raise ValueError("Name cannot be empty!")
- if chunkno < 1:
- raise ValueError("Chunk number must be greater than zero")
- return f"{secure_filename(uploadfilename)}_part_{chunkno:05d}"
-
-
-def chunks_directory(uniqueidentifier: str) -> Path:
- """Compute the directory where chunks are temporarily stored."""
- if uniqueidentifier == "":
- raise ValueError("Unique identifier cannot be empty!")
- return Path(app.config["UPLOAD_FOLDER"], f"tempdir_{uniqueidentifier}")
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle-chunked"),
- methods=["GET"])
-def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"]
- species_id: int,
- population_id: int
-):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that provides a way
- for testing whether all the chunks have been uploaded and to assist with
- resuming a failed upload.
- """
- fileid = request.args.get("resumableIdentifier", type=str) or ""
- filename = request.args.get("resumableFilename", type=str) or ""
- chunk = request.args.get("resumableChunkNumber", type=int) or 0
- if not(fileid or filename or chunk):
- return jsonify({
- "message": "At least one required query parameter is missing.",
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- if Path(chunks_directory(fileid),
- chunk_name(filename, chunk)).exists():
- return "OK"
-
- return jsonify({
- "message": f"Chunk {chunk} was not found.",
- "error": "NotFound",
- "statuscode": 404
- }), 404
-
-
-def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path:
- """Merge the chunks into a single file."""
- with open(targetfile, "ab") as _target:
- for chunkfile in chunkpaths:
- with open(chunkfile, "rb") as _chunkdata:
- _target.write(_chunkdata.read())
-
- chunkfile.unlink()
- return targetfile
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle-chunked"),
- methods=["POST"])
-def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that allows large
- files to be uploaded in chunks.
-
- This should hopefully speed up uploads, and if done right, even enable
- resumable uploads
- """
- _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0
- _chunk = request.form.get("resumableChunkNumber", default=1, type=int)
- _uploadfilename = request.form.get(
- "resumableFilename", default="", type=str) or ""
- _fileid = request.form.get(
- "resumableIdentifier", default="", type=str) or ""
- _targetfile = Path(app.config["UPLOAD_FOLDER"], _fileid)
-
- if _targetfile.exists():
- return jsonify({
- "message": (
- "A file with a similar unique identifier has previously been "
- "uploaded and possibly is/has being/been processed."),
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- try:
- # save chunk data
- chunks_directory(_fileid).mkdir(exist_ok=True, parents=True)
- request.files["file"].save(Path(chunks_directory(_fileid),
- chunk_name(_uploadfilename, _chunk)))
-
- # Check whether upload is complete
- chunkpaths = tuple(
- Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk))
- for _achunk in range(1, _totalchunks+1))
- if all(_file.exists() for _file in chunkpaths):
- # merge_files and clean up chunks
- __merge_chunks__(_targetfile, chunkpaths)
- chunks_directory(_fileid).rmdir()
- jobid = trigger_rqtl2_bundle_qc(
- species_id, population_id, _targetfile, _uploadfilename)
- return url_for(
- "upload.rqtl2.rqtl2_bundle_qc_status", jobid=jobid)
- except Exception as exc:# pylint: disable=[broad-except]
- msg = "Error processing uploaded file chunks."
- app.logger.error(msg, exc_info=True, stack_info=True)
- return jsonify({
- "message": msg,
- "error": type(exc).__name__,
- "error-description": " ".join(str(arg) for arg in exc.args),
- "error-trace": traceback.format_exception(exc)
- }), 500
-
- return "OK"
-
-
-@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>",
- methods=["GET", "POST"])
-def rqtl2_bundle_qc_status(jobid: UUID):
- """Check the status of the QC jobs."""
- with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
- database_connection(app.config["SQL_URI"]) as dbconn):
- try:
- thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid)
- messagelistname = thejob.get("log-messagelist")
- logmessages = (rconn.lrange(messagelistname, 0, -1)
- if bool(messagelistname) else [])
- jobstatus = thejob["status"]
- if jobstatus == "error":
- return render_template("rqtl2/rqtl2-qc-job-error.html",
- job=thejob,
- errorsgeneric=json.loads(
- thejob.get("errors-generic", "[]")),
- errorsgeno=json.loads(
- thejob.get("errors-geno", "[]")),
- errorspheno=json.loads(
- thejob.get("errors-pheno", "[]")),
- errorsphenose=json.loads(
- thejob.get("errors-phenose", "[]")),
- errorsphenocovar=json.loads(
- thejob.get("errors-phenocovar", "[]")),
- messages=logmessages)
- if jobstatus == "success":
- jobmeta = json.loads(thejob["job-metadata"])
- species = species_by_id(dbconn, jobmeta["speciesid"])
- return render_template(
- "rqtl2/rqtl2-qc-job-results.html",
- species=species,
- population=population_by_species_and_id(
- dbconn, species["SpeciesId"], jobmeta["populationid"]),
- rqtl2bundle=Path(jobmeta["rqtl2-bundle-file"]).name,
- rqtl2bundleorig=jobmeta["original-filename"])
-
- def compute_percentage(thejob, filetype) -> Union[str, None]:
- if f"{filetype}-linecount" in thejob:
- return "100"
- if f"{filetype}-filesize" in thejob:
- percent = ((int(thejob.get(f"{filetype}-checked", 0))
- /
- int(thejob.get(f"{filetype}-filesize", 1)))
- * 100)
- return f"{percent:.2f}"
- return None
-
- return render_template(
- "rqtl2/rqtl2-qc-job-status.html",
- job=thejob,
- geno_percent=compute_percentage(thejob, "geno"),
- pheno_percent=compute_percentage(thejob, "pheno"),
- phenose_percent=compute_percentage(thejob, "phenose"),
- messages=logmessages)
- except jobs.JobNotFound:
- return render_template("rqtl2/no-such-job.html", jobid=jobid)
-
-
-def redirect_on_error(flaskroute, **kwargs):
- """Utility to redirect on error"""
- return redirect(url_for(flaskroute, **kwargs, pgsrc="error"),
- code=(307 if request.method == "POST" else 302))
-
-
-def check_species(conn: mdb.Connection, formargs: dict) -> Optional[
- tuple[str, Response]]:
- """
- Check whether the 'species_id' value is provided, and whether a
- corresponding species exists in the database.
-
- Maybe give the function a better name..."""
- speciespage = redirect_on_error("upload.rqtl2.select_species")
- if "species_id" not in formargs:
- return "You MUST provide the Species identifier.", speciespage
-
- if not bool(species_by_id(conn, formargs["species_id"])):
- return "No species with the provided identifier exists.", speciespage
-
- return None
-
-
-def check_population(conn: mdb.Connection,
- formargs: dict,
- species_id) -> Optional[tuple[str, Response]]:
- """
- Check whether the 'population_id' value is provided, and whether a
- corresponding population exists in the database.
-
- Maybe give the function a better name..."""
- poppage = redirect_on_error(
- "upload.rqtl2.select_species", species_id=species_id)
- if "population_id" not in formargs:
- return "You MUST provide the Population identifier.", poppage
-
- if not bool(population_by_species_and_id(
- conn, species_id, formargs["population_id"])):
- return "No population with the provided identifier exists.", poppage
-
- return None
-
-
-def check_r_qtl2_bundle(formargs: dict,
- species_id,
- population_id) -> Optional[tuple[str, Response]]:
- """Check for the existence of the R/qtl2 bundle."""
- fileuploadpage = redirect_on_error("upload.rqtl2.upload_rqtl2_bundle",
- species_id=species_id,
- population_id=population_id)
- if not "rqtl2_bundle_file" in formargs:
- return (
- "You MUST provide a R/qtl2 zip bundle for upload.", fileuploadpage)
-
- if not Path(fullpath(formargs["rqtl2_bundle_file"])).exists():
- return "No R/qtl2 bundle with the given name exists.", fileuploadpage
-
- return None
-
-
-def check_geno_dataset(conn: mdb.Connection,
- formargs: dict,
- species_id,
- population_id) -> Optional[tuple[str, Response]]:
- """Check for the Genotype dataset."""
- genodsetpg = redirect_on_error("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id)
- if not bool(formargs.get("geno-dataset-id")):
- return (
- "You MUST provide a valid Genotype dataset identifier", genodsetpg)
-
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
- (formargs["geno-dataset-id"],))
- results = cursor.fetchall()
- if not bool(results):
- return ("No genotype dataset with the provided identifier exists.",
- genodsetpg)
- if len(results) > 1:
- return (
- "Data corruption: More than one genotype dataset with the same "
- "identifier.",
- genodsetpg)
-
- return None
-
-def check_tissue(
- conn: mdb.Connection,formargs: dict) -> Optional[tuple[str, Response]]:
- """Check for tissue/organ/biological material."""
- selectdsetpg = redirect_on_error("upload.rqtl2.select_dataset_info",
- species_id=formargs["species_id"],
- population_id=formargs["population_id"])
- if not bool(formargs.get("tissueid", "").strip()):
- return ("No tissue/organ/biological material provided.", selectdsetpg)
-
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM Tissue WHERE Id=%s",
- (formargs["tissueid"],))
- results = cursor.fetchall()
- if not bool(results):
- return ("No tissue/organ with the provided identifier exists.",
- selectdsetpg)
-
- if len(results) > 1:
- return (
- "Data corruption: More than one tissue/organ with the same "
- "identifier.",
- selectdsetpg)
-
- return None
-
-
-def check_probe_study(conn: mdb.Connection,
- formargs: dict,
- species_id,
- population_id) -> Optional[tuple[str, Response]]:
- """Check for the ProbeSet study."""
- dsetinfopg = redirect_on_error("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id)
- if not bool(formargs.get("probe-study-id")):
- return "No probeset study was selected!", dsetinfopg
-
- if not bool(probeset_study_by_id(conn, formargs["probe-study-id"])):
- return ("No probeset study with the provided identifier exists",
- dsetinfopg)
-
- return None
-
-
-def check_probe_dataset(conn: mdb.Connection,
- formargs: dict,
- species_id,
- population_id) -> Optional[tuple[str, Response]]:
- """Check for the ProbeSet dataset."""
- dsetinfopg = redirect_on_error("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id)
- if not bool(formargs.get("probe-dataset-id")):
- return "No probeset dataset was selected!", dsetinfopg
-
- if not bool(probeset_dataset_by_id(conn, formargs["probe-dataset-id"])):
- return ("No probeset dataset with the provided identifier exists",
- dsetinfopg)
-
- return None
-
-
-def with_errors(endpointthunk: Callable, *checkfns):
- """Run 'endpointthunk' with error checking."""
- formargs = {**dict(request.args), **dict(request.form)}
- errors = tuple(item for item in (_fn(formargs=formargs) for _fn in checkfns)
- if item is not None)
- if len(errors) > 0:
- flash(errors[0][0], "alert-error error-rqtl2")
- return errors[0][1]
-
- return endpointthunk()
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/select-geno-dataset"),
- methods=["POST"])
-def select_geno_dataset(species_id: int, population_id: int):
- """Select from existing geno datasets."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- geno_dset = geno_datasets_by_species_and_population(
- conn, species_id, population_id)
- if not bool(geno_dset):
- flash("No genotype dataset was provided!",
- "alert-error error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_geno_dataset",
- species_id=species_id,
- population_id=population_id,
- pgsrc="error"),
- code=307)
-
- flash("Genotype accepted", "alert-success error-rqtl2")
- return redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="upload.rqtl2.select_geno_dataset"),
- code=307)
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population, conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/create-geno-dataset"),
- methods=["POST"])
-def create_geno_dataset(species_id: int, population_id: int):
- """Create a new geno dataset."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- sgeno_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="error"),
- code=307)
- errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset"
- if not bool(request.form.get("dataset-name")):
- flash("You must provide the dataset name", errorclasses)
- return sgeno_page
- if not bool(request.form.get("dataset-fullname")):
- flash("You must provide the dataset full name", errorclasses)
- return sgeno_page
- public = 2 if request.form.get("dataset-public") == "on" else 0
-
- with conn.cursor(cursorclass=DictCursor) as cursor:
- datasetname = request.form["dataset-name"]
- new_dataset = {
- "name": datasetname,
- "fname": request.form.get("dataset-fullname"),
- "sname": request.form.get("dataset-shortname") or datasetname,
- "today": date.today().isoformat(),
- "pub": public,
- "isetid": population_id
- }
- cursor.execute("SELECT * FROM GenoFreeze WHERE Name=%s",
- (datasetname,))
- results = cursor.fetchall()
- if bool(results):
- flash(
- f"A genotype dataset with name '{escape(datasetname)}' "
- "already exists.",
- errorclasses)
- return redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="error"),
- code=307)
- cursor.execute(
- "INSERT INTO GenoFreeze("
- "Name, FullName, ShortName, CreateTime, public, InbredSetId"
- ") "
- "VALUES("
- "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s"
- ")",
- new_dataset)
- flash("Created dataset successfully.", "alert-success")
- return render_template(
- "rqtl2/create-geno-dataset-success.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
- rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
- geno_dataset={**new_dataset, "id": cursor.lastrowid})
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population, conn=conn, species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/select-tissue"),
- methods=["POST"])
-def select_tissue(species_id: int, population_id: int):
- """Select from existing tissues."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- if not bool(request.form.get("tissueid", "").strip()):
- flash("Invalid tissue selection!",
- "alert-error error-select-tissue error-rqtl2")
-
- return redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="upload.rqtl2.select_geno_dataset"),
- code=307)
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/create-tissue"),
- methods=["POST"])
-def create_tissue(species_id: int, population_id: int):
- """Add new tissue, organ or biological material to the system."""
- form = request.form
- datasetinfopage = redirect(
- url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="upload.rqtl2.select_geno_dataset"),
- code=307)
- with database_connection(app.config["SQL_URI"]) as conn:
- tissuename = form.get("tissuename", "").strip()
- tissueshortname = form.get("tissueshortname", "").strip()
- if not bool(tissuename):
- flash("Organ/Tissue name MUST be provided.",
- "alert-error error-create-tissue error-rqtl2")
- return datasetinfopage
-
- if not bool(tissueshortname):
- flash("Organ/Tissue short name MUST be provided.",
- "alert-error error-create-tissue error-rqtl2")
- return datasetinfopage
-
- try:
- tissue = create_new_tissue(conn, tissuename, tissueshortname)
- flash("Tissue created successfully!", "alert-success")
- return render_template(
- "rqtl2/create-tissue-success.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
- rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
- geno_dataset=geno_dataset_by_id(
- conn,
- int(request.form["geno-dataset-id"])),
- tissue=tissue)
- except mdb.IntegrityError as _ierr:
- flash("Tissue/Organ with that short name already exists!",
- "alert-error error-create-tissue error-rqtl2")
- return datasetinfopage
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/select-probeset-study"),
- methods=["POST"])
-def select_probeset_study(species_id: int, population_id: int):
- """Select or create a probeset study."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id),
- code=307)
- if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
- flash("Invalid study selected!", "alert-error error-rqtl2")
- return summary_page
-
- return summary_page
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_tissue, conn=conn),
- partial(check_probe_study,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/select-probeset-dataset"),
- methods=["POST"])
-def select_probeset_dataset(species_id: int, population_id: int):
- """Select or create a probeset dataset."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id),
- code=307)
- if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
- flash("Invalid study selected!", "alert-error error-rqtl2")
- return summary_page
-
- return summary_page
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_tissue, conn=conn),
- partial(check_probe_study,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_probe_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/create-probeset-study"),
- methods=["POST"])
-def create_probeset_study(species_id: int, population_id: int):
- """Create a new probeset study."""
- errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-study"
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- form = request.form
- dataset_info_page = redirect(
- url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id),
- code=307)
-
- if not (bool(form.get("platformid")) and
- bool(platform_by_id(conn, int(form["platformid"])))):
- flash("Invalid platform selected.", errorclasses)
- return dataset_info_page
-
- if not (bool(form.get("tissueid")) and
- bool(tissue_by_id(conn, int(form["tissueid"])))):
- flash("Invalid tissue selected.", errorclasses)
- return dataset_info_page
-
- studyname = form["studyname"]
- try:
- study = probeset_create_study(
- conn, population_id, int(form["platformid"]), int(form["tissueid"]),
- studyname, form.get("studyfullname") or "",
- form.get("studyshortname") or "")
- except mdb.IntegrityError as _ierr:
- flash(f"ProbeSet study with name '{escape(studyname)}' already "
- "exists.",
- errorclasses)
- return dataset_info_page
- return render_template(
- "rqtl2/create-probe-study-success.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
- rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
- geno_dataset=geno_dataset_by_id(
- conn,
- int(request.form["geno-dataset-id"])),
- study=study)
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_tissue, conn=conn))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/create-probeset-dataset"),
- methods=["POST"])
-def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
- """Create a new probeset dataset."""
- errorclasses = "alert-error error-rqtl2 error-rqtl2-create-probeset-dataset"
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():#pylint: disable=[too-many-return-statements]
- form = request.form
- summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id),
- code=307)
- if not bool(form.get("averageid")):
- flash("Averaging method not selected!", errorclasses)
- return summary_page
- if not bool(form.get("datasetname")):
- flash("Dataset name not provided!", errorclasses)
- return summary_page
- if not bool(form.get("datasetfullname")):
- flash("Dataset full name not provided!", errorclasses)
- return summary_page
-
- tissue = tissue_by_id(conn, form.get("tissueid", "").strip())
-
- study = probeset_study_by_id(conn, int(form["probe-study-id"]))
- if not bool(study):
- flash("Invalid ProbeSet study provided!", errorclasses)
- return summary_page
-
- avgmethod = averaging_method_by_id(conn, int(form["averageid"]))
- if not bool(avgmethod):
- flash("Invalid averaging method provided!", errorclasses)
- return summary_page
-
- try:
- dset = probeset_create_dataset(conn,
- int(form["probe-study-id"]),
- int(form["averageid"]),
- form["datasetname"],
- form["datasetfullname"],
- form["datasetshortname"],
- form["datasetpublic"] == "on",
- form.get(
- "datasetdatascale", "log2"))
- except mdb.IntegrityError as _ierr:
- app.logger.debug("Possible integrity error: %s", traceback.format_exc())
- flash(("IntegrityError: The data you provided has some errors: "
- f"{_ierr.args}"),
- errorclasses)
- return summary_page
- except Exception as _exc:# pylint: disable=[broad-except]
- app.logger.debug("Error creating ProbeSet dataset: %s",
- traceback.format_exc())
- flash(("There was a problem creating your dataset. Please try "
- "again."),
- errorclasses)
- return summary_page
- return render_template(
- "rqtl2/create-probe-dataset-success.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
- rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
- geno_dataset=geno_dataset_by_id(
- conn,
- int(request.form["geno-dataset-id"])),
- tissue=tissue,
- study=study,
- avgmethod=avgmethod,
- dataset=dset)
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_tissue, conn=conn),
- partial(check_probe_study,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/dataset-info"),
- methods=["POST"])
-def select_dataset_info(species_id: int, population_id: int):
- """
- If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
- dataset the genotypes belong to.
- """
- form = request.form
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- species = species_by_id(conn, species_id)
- population = population_by_species_and_id(
- conn, species_id, population_id)
- thefile = fullpath(form["rqtl2_bundle_file"])
- with ZipFile(str(thefile), "r") as zfile:
- cdata = r_qtl2.control_data(zfile)
-
- geno_dataset = geno_dataset_by_id(
- conn,form.get("geno-dataset-id", "").strip())
- if "geno" in cdata and not bool(form.get("geno-dataset-id")):
- return render_template(
- "rqtl2/select-geno-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- datasets=geno_datasets_by_species_and_population(
- conn, species_id, population_id))
-
- tissue = tissue_by_id(conn, form.get("tissueid", "").strip())
- if "pheno" in cdata and not bool(tissue):
- return render_template(
- "rqtl2/select-tissue.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- studies=probeset_studies_by_species_and_population(
- conn, species_id, population_id),
- platforms=platforms_by_species(conn, species_id),
- tissues=all_tissues(conn))
-
- probeset_study = probeset_study_by_id(
- conn, form.get("probe-study-id", "").strip())
- if "pheno" in cdata and not bool(probeset_study):
- return render_template(
- "rqtl2/select-probeset-study-id.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- studies=probeset_studies_by_species_and_population(
- conn, species_id, population_id),
- platforms=platforms_by_species(conn, species_id),
- tissue=tissue)
- probeset_study = probeset_study_by_id(
- conn, int(form["probe-study-id"]))
-
- probeset_dataset = probeset_dataset_by_id(
- conn, form.get("probe-dataset-id", "").strip())
- if "pheno" in cdata and not bool(probeset_dataset):
- return render_template(
- "rqtl2/select-probeset-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- probe_study=probeset_study,
- tissue=tissue,
- datasets=probeset_datasets_by_study(
- conn, int(form["probe-study-id"])),
- avgmethods=averaging_methods(conn))
-
- return render_template("rqtl2/summary-info.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- tissue=tissue,
- probe_study=probeset_study,
- probe_dataset=probeset_dataset)
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/confirm-bundle-details"),
- methods=["POST"])
-def confirm_bundle_details(species_id: int, population_id: int):
- """Confirm the details and trigger R/qtl2 bundle processing..."""
- redisuri = app.config["REDIS_URL"]
- with (database_connection(app.config["SQL_URI"]) as conn,
- Redis.from_url(redisuri, decode_responses=True) as rconn):
- def __thunk__():
- redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"]
- jobid = str(uuid4())
- _job = jobs.launch_job(
- jobs.initialise_job(
- rconn,
- jobs.jobsnamespace(),
- jobid,
- [
- sys.executable, "-m", "scripts.process_rqtl2_bundle",
- app.config["SQL_URI"], app.config["REDIS_URL"],
- jobs.jobsnamespace(), jobid, "--redisexpiry",
- str(redis_ttl_seconds)],
- "R/qtl2 Bundle Upload",
- redis_ttl_seconds,
- {
- "bundle-metadata": json.dumps({
- "speciesid": species_id,
- "populationid": population_id,
- "rqtl2-bundle-file": str(fullpath(
- request.form["rqtl2_bundle_file"])),
- "geno-dataset-id": request.form.get(
- "geno-dataset-id", ""),
- "probe-study-id": request.form.get(
- "probe-study-id", ""),
- "probe-dataset-id": request.form.get(
- "probe-dataset-id", ""),
- **({
- "platformid": probeset_study_by_id(
- conn,
- int(request.form["probe-study-id"]))["ChipId"]
- } if bool(request.form.get("probe-study-id")) else {})
- })
- }),
- redisuri,
- f"{app.config['UPLOAD_FOLDER']}/job_errors")
-
- return redirect(url_for("upload.rqtl2.rqtl2_processing_status",
- jobid=jobid))
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population,
- conn=conn,
- species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id),
- partial(check_geno_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_probe_study,
- conn=conn,
- species_id=species_id,
- population_id=population_id),
- partial(check_probe_dataset,
- conn=conn,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route("/status/<uuid:jobid>")
-def rqtl2_processing_status(jobid: UUID):
- """Retrieve the status of the job processing the uploaded R/qtl2 bundle."""
- with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- try:
- thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid)
-
- messagelistname = thejob.get("log-messagelist")
- logmessages = (rconn.lrange(messagelistname, 0, -1)
- if bool(messagelistname) else [])
-
- if thejob["status"] == "error":
- return render_template(
- "rqtl2/rqtl2-job-error.html", job=thejob, messages=logmessages)
- if thejob["status"] == "success":
- return render_template("rqtl2/rqtl2-job-results.html",
- job=thejob,
- messages=logmessages)
-
- return render_template(
- "rqtl2/rqtl2-job-status.html", job=thejob, messages=logmessages)
- except jobs.JobNotFound as _exc:
- return render_template("rqtl2/no-such-job.html", jobid=jobid)