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authorFrederick Muriuki Muriithi2024-09-23 14:30:15 -0500
committerFrederick Muriuki Muriithi2024-09-23 16:35:39 -0500
commit4285cc10e24d6410206329ba079406e9aa21cc30 (patch)
tree70f785460b14731634d0a4bd93ad5bbb9c5ba833
parent0b37b9b3fa4fead86787a705713645fa14530a54 (diff)
downloadgn-uploader-4285cc10e24d6410206329ba079406e9aa21cc30.tar.gz
Move R/qtl2 upload code under the populations package.
-rw-r--r--uploader/expression_data/rqtl2.py1175
-rw-r--r--uploader/templates/populations/rqtl2/create-tissue-success.html (renamed from uploader/templates/rqtl2/create-tissue-success.html)0
-rw-r--r--uploader/templates/populations/rqtl2/index.html54
-rw-r--r--uploader/templates/populations/rqtl2/no-such-job.html (renamed from uploader/templates/rqtl2/no-such-job.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-job-error.html (renamed from uploader/templates/rqtl2/rqtl2-job-error.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-job-results.html (renamed from uploader/templates/rqtl2/rqtl2-job-results.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-job-status.html (renamed from uploader/templates/rqtl2/rqtl2-job-status.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html (renamed from uploader/templates/rqtl2/rqtl2-qc-job-error.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html (renamed from uploader/templates/rqtl2/rqtl2-qc-job-results.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html (renamed from uploader/templates/rqtl2/rqtl2-qc-job-status.html)0
-rw-r--r--uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html (renamed from uploader/templates/rqtl2/rqtl2-qc-job-success.html)0
-rw-r--r--uploader/templates/populations/rqtl2/select-geno-dataset.html69
-rw-r--r--uploader/templates/populations/rqtl2/select-population.html57
-rw-r--r--uploader/templates/populations/rqtl2/select-probeset-dataset.html (renamed from uploader/templates/rqtl2/select-probeset-dataset.html)0
-rw-r--r--uploader/templates/populations/rqtl2/select-probeset-study-id.html (renamed from uploader/templates/rqtl2/select-probeset-study-id.html)0
-rw-r--r--uploader/templates/populations/rqtl2/select-tissue.html (renamed from uploader/templates/rqtl2/select-tissue.html)0
-rw-r--r--uploader/templates/populations/rqtl2/summary-info.html (renamed from uploader/templates/rqtl2/summary-info.html)0
-rw-r--r--uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html (renamed from uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html)0
-rw-r--r--uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html (renamed from uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html)0
-rw-r--r--uploader/templates/rqtl2/create-geno-dataset-success.html55
-rw-r--r--uploader/templates/rqtl2/create-probe-dataset-success.html59
-rw-r--r--uploader/templates/rqtl2/create-probe-study-success.html49
-rw-r--r--uploader/templates/rqtl2/index.html36
-rw-r--r--uploader/templates/rqtl2/select-geno-dataset.html144
-rw-r--r--uploader/templates/rqtl2/select-population.html136
25 files changed, 180 insertions, 1654 deletions
diff --git a/uploader/expression_data/rqtl2.py b/uploader/expression_data/rqtl2.py
deleted file mode 100644
index a855699..0000000
--- a/uploader/expression_data/rqtl2.py
+++ /dev/null
@@ -1,1175 +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 uploader import jobs
-from uploader.files import save_file, fullpath
-from uploader.dbinsert import species as all_species
-from uploader.db_utils import with_db_connection, database_connection
-
-from uploader.authorisation import require_login
-from uploader.db.platforms import platform_by_id, platforms_by_species
-from uploader.db.averaging import averaging_methods, averaging_method_by_id
-from uploader.db.tissues import all_tissues, tissue_by_id, create_new_tissue
-from uploader.population.models import (save_population,
- populations_by_species,
- population_by_species_and_id)
-from uploader.species.models import species_by_id
-from uploader.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"])
-@require_login
-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(
- "expression-data.rqtl2.select_population", species_id=species_id))
- flash("Invalid species or no species selected!", "alert-error error-rqtl2")
- return redirect(url_for("expression-data.rqtl2.select_species"))
-
-
-@rqtl2.route("/upload/species/<int:species_id>/select-population",
- methods=["GET", "POST"])
-@require_login
-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("expression-data.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("expression-data.rqtl2.select_population", pgsrc="error"),
- code=307)
-
- return redirect(url_for("expression-data.rqtl2.upload_rqtl2_bundle",
- species_id=species["SpeciesId"],
- population_id=population["InbredSetId"]))
-
-
-@rqtl2.route("/upload/species/<int:species_id>/create-population",
- methods=["POST"])
-@require_login
-def create_population(species_id: int):
- """Create a new population for the given species."""
- population_page = redirect(url_for("expression-data.rqtl2.select_population",
- species_id=species_id))
- with database_connection(app.config["SQL_URI"]) as conn:
- species = species_by_id(conn, species_id)
- population_name = request.form.get("inbredset_name", "").strip()
- population_fullname = request.form.get("inbredset_fullname", "").strip()
- if not bool(species):
- flash("Invalid species!", "alert-error error-rqtl2")
- return redirect(url_for("expression-data.rqtl2.select_species"))
- if not bool(population_name):
- flash("Invalid Population Name!", "alert-error error-rqtl2")
- return population_page
- if not bool(population_fullname):
- flash("Invalid Population Full Name!", "alert-error error-rqtl2")
- return population_page
- new_population = save_population(conn, {
- "SpeciesId": species["SpeciesId"],
- "Name": population_name,
- "InbredSetName": population_fullname,
- "FullName": population_fullname,
- "Family": request.form.get("inbredset_family") or None,
- "Description": request.form.get("description") or None
- })
-
- flash("Population created successfully.", "alert-success")
- return redirect(
- url_for("expression-data.rqtl2.upload_rqtl2_bundle",
- species_id=species_id,
- population_id=new_population["population_id"],
- pgsrc="create-population"),
- code=307)
-
-
-class __RequestError__(Exception): #pylint: disable=[invalid-name]
- """Internal class to avoid pylint's `too-many-return-statements` error."""
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle"),
- methods=["GET", "POST"])
-@require_login
-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("expression-data.rqtl2.select_species"))
- if not bool(population):
- flash("Invalid Population!", "alert-error error-rqtl2")
- return redirect(
- url_for("expression-data.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("expression-data.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(
- "expression-data.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"])
-@require_login
-def upload_rqtl2_bundle_chunked_get(# pylint: disable=["unused-argument"]
- species_id: int,
- population_id: int
-):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that provides a way
- for testing whether all the chunks have been uploaded and to assist with
- resuming a failed expression-data.
- """
- fileid = request.args.get("resumableIdentifier", type=str) or ""
- filename = request.args.get("resumableFilename", type=str) or ""
- chunk = request.args.get("resumableChunkNumber", type=int) or 0
- if not(fileid or filename or chunk):
- return jsonify({
- "message": "At least one required query parameter is missing.",
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- if Path(chunks_directory(fileid),
- chunk_name(filename, chunk)).exists():
- return "OK"
-
- return jsonify({
- "message": f"Chunk {chunk} was not found.",
- "error": "NotFound",
- "statuscode": 404
- }), 404
-
-
-def __merge_chunks__(targetfile: Path, chunkpaths: tuple[Path, ...]) -> Path:
- """Merge the chunks into a single file."""
- with open(targetfile, "ab") as _target:
- for chunkfile in chunkpaths:
- with open(chunkfile, "rb") as _chunkdata:
- _target.write(_chunkdata.read())
-
- chunkfile.unlink()
- return targetfile
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle-chunked"),
- methods=["POST"])
-@require_login
-def upload_rqtl2_bundle_chunked_post(species_id: int, population_id: int):
- """
- Extension to the `upload_rqtl2_bundle` endpoint above that allows large
- files to be uploaded in chunks.
-
- This should hopefully speed up uploads, and if done right, even enable
- resumable uploads
- """
- _totalchunks = request.form.get("resumableTotalChunks", type=int) or 0
- _chunk = request.form.get("resumableChunkNumber", default=1, type=int)
- _uploadfilename = request.form.get(
- "resumableFilename", default="", type=str) or ""
- _fileid = request.form.get(
- "resumableIdentifier", default="", type=str) or ""
- _targetfile = Path(app.config["UPLOAD_FOLDER"], _fileid)
-
- if _targetfile.exists():
- return jsonify({
- "message": (
- "A file with a similar unique identifier has previously been "
- "uploaded and possibly is/has being/been processed."),
- "error": "BadRequest",
- "statuscode": 400
- }), 400
-
- try:
- # save chunk data
- chunks_directory(_fileid).mkdir(exist_ok=True, parents=True)
- request.files["file"].save(Path(chunks_directory(_fileid),
- chunk_name(_uploadfilename, _chunk)))
-
- # Check whether upload is complete
- chunkpaths = tuple(
- Path(chunks_directory(_fileid), chunk_name(_uploadfilename, _achunk))
- for _achunk in range(1, _totalchunks+1))
- if all(_file.exists() for _file in chunkpaths):
- # merge_files and clean up chunks
- __merge_chunks__(_targetfile, chunkpaths)
- chunks_directory(_fileid).rmdir()
- jobid = trigger_rqtl2_bundle_qc(
- species_id, population_id, _targetfile, _uploadfilename)
- return url_for(
- "expression-data.rqtl2.rqtl2_bundle_qc_status", jobid=jobid)
- except Exception as exc:# pylint: disable=[broad-except]
- msg = "Error processing uploaded file chunks."
- app.logger.error(msg, exc_info=True, stack_info=True)
- return jsonify({
- "message": msg,
- "error": type(exc).__name__,
- "error-description": " ".join(str(arg) for arg in exc.args),
- "error-trace": traceback.format_exception(exc)
- }), 500
-
- return "OK"
-
-
-@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>",
- methods=["GET", "POST"])
-@require_login
-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("expression-data.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(
- "expression-data.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("expression-data.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 expression-data.", 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("expression-data.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("expression-data.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("expression-data.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("expression-data.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"])
-@require_login
-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("expression-data.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("expression-data.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="expression-data.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"])
-@require_login
-def create_geno_dataset(species_id: int, population_id: int):
- """Create a new geno dataset."""
- with database_connection(app.config["SQL_URI"]) as conn:
- def __thunk__():
- sgeno_page = redirect(url_for("expression-data.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="error"),
- code=307)
- errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset"
- if not bool(request.form.get("dataset-name")):
- flash("You must provide the dataset name", errorclasses)
- return sgeno_page
- if not bool(request.form.get("dataset-fullname")):
- flash("You must provide the dataset full name", errorclasses)
- return sgeno_page
- public = 2 if request.form.get("dataset-public") == "on" else 0
-
- with conn.cursor(cursorclass=DictCursor) as cursor:
- datasetname = request.form["dataset-name"]
- new_dataset = {
- "name": datasetname,
- "fname": request.form.get("dataset-fullname"),
- "sname": request.form.get("dataset-shortname") or datasetname,
- "today": date.today().isoformat(),
- "pub": public,
- "isetid": population_id
- }
- cursor.execute("SELECT * FROM GenoFreeze WHERE Name=%s",
- (datasetname,))
- results = cursor.fetchall()
- if bool(results):
- flash(
- f"A genotype dataset with name '{escape(datasetname)}' "
- "already exists.",
- errorclasses)
- return redirect(url_for("expression-data.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="error"),
- code=307)
- cursor.execute(
- "INSERT INTO GenoFreeze("
- "Name, FullName, ShortName, CreateTime, public, InbredSetId"
- ") "
- "VALUES("
- "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s"
- ")",
- new_dataset)
- flash("Created dataset successfully.", "alert-success")
- return render_template(
- "rqtl2/create-geno-dataset-success.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
- rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
- geno_dataset={**new_dataset, "id": cursor.lastrowid})
-
- return with_errors(__thunk__,
- partial(check_species, conn=conn),
- partial(check_population, conn=conn, species_id=species_id),
- partial(check_r_qtl2_bundle,
- species_id=species_id,
- population_id=population_id))
-
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
- "/rqtl2-bundle/select-tissue"),
- methods=["POST"])
-@require_login
-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("expression-data.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="expression-data.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"])
-@require_login
-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("expression-data.rqtl2.select_dataset_info",
- species_id=species_id,
- population_id=population_id,
- pgsrc="expression-data.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"])
-@require_login
-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("expression-data.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"])
-@require_login
-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("expression-data.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"])
-@require_login
-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("expression-data.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"])
-@require_login
-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("expression-data.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"])
-@require_login
-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"])
-@require_login
-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("expression-data.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)
diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html
index d6fe154..d6fe154 100644
--- a/uploader/templates/rqtl2/create-tissue-success.html
+++ b/uploader/templates/populations/rqtl2/create-tissue-success.html
diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html
new file mode 100644
index 0000000..ec6ffb8
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/index.html
@@ -0,0 +1,54 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 data upload</h1>
+
+<h2>R/qtl2 Upload</h2>
+
+<div class="row">
+ <form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}"
+ id="frm-rqtl2-upload">
+ <legend class="heading">upload R/qtl2 bundle</legend>
+ {{flash_messages("error-rqtl2")}}
+
+ <div class="form-group">
+ <label for="select:species" class="form-label">Species</label>
+ <select id="select:species"
+ name="species_id"
+ required="required"
+ class="form-control">
+ <option value="">Select species</option>
+ {%for spec in species%}
+ <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
+ {%endfor%}
+ </select>
+ <small class="form-text text-muted">
+ Data that you upload to the system should belong to a know species.
+ Here you can select the species that you wish to upload data for.
+ </small>
+ </div>
+
+ <input type="submit" class="btn btn-primary" value="submit" />
+ </form>
+</div>
+
+<div class="row">
+ <h2 class="heading">R/qtl2 Bundles</h2>
+
+ <div class="explainer">
+ <p>This feature combines and extends the two upload methods below. Instead of
+ uploading one item at a time, the R/qtl2 bundle you upload can contain both
+ the genotypes data (samples/individuals/cases and their data) and the
+ expression data.</p>
+ <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
+ of the methods below can handle.</p>
+
+ <a href="{{url_for('expression-data.rqtl2.select_species')}}"
+ title="Upload a zip bundle of R/qtl2 files">
+ <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
+ </div>
+</div>
+{%endblock%}
diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html
index b17004f..b17004f 100644
--- a/uploader/templates/rqtl2/no-such-job.html
+++ b/uploader/templates/populations/rqtl2/no-such-job.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html
index 9817518..9817518 100644
--- a/uploader/templates/rqtl2/rqtl2-job-error.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-error.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html
index 4ecd415..4ecd415 100644
--- a/uploader/templates/rqtl2/rqtl2-job-results.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-results.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html
index e896f88..e896f88 100644
--- a/uploader/templates/rqtl2/rqtl2-job-status.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-status.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html
index 90e8887..90e8887 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html
index b3c3a8f..b3c3a8f 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html
index f4a6266..f4a6266 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-status.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html
index f126835..f126835 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html
diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..3233abc
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html
@@ -0,0 +1,69 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="row">
+ <p>Your R/qtl2 files bundle could contain a "geno" specification. You will
+ therefore need to select from one of the existing Genotype datasets or
+ create a new one.</p>
+ <p>This is the dataset where your data will be organised under.</p>
+</div>
+
+<div class="row">
+ <form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('expression-data.rqtl2.select_geno_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ <legend class="heading">select from existing genotype datasets</legend>
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+
+ {{flash_messages("error-rqtl2-select-geno-dataset")}}
+
+ <div class="form-group">
+ <legend>Datasets</legend>
+ <label for="select:geno-datasets" class="form-label">Dataset</label>
+ <select id="select:geno-datasets"
+ name="geno-dataset-id"
+ required="required"
+ {%if datasets | length == 0%}
+ disabled="disabled"
+ {%endif%}
+ class="form-control"
+ aria-describedby="help-geno-dataset-select-dataset">
+ <option value="">Select dataset</option>
+ {%for dset in datasets%}
+ <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
+ {%endfor%}
+ </select>
+ <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
+ Select from the existing genotype datasets for species
+ {{species.SpeciesName}} ({{species.FullName}}).
+ </span>
+ </div>
+
+ <button type="submit" class="btn btn-primary">select dataset</button>
+ </form>
+</div>
+
+<div class="row">
+ <p>If the genotype dataset you need does not currently exist for your dataset,
+ go the <a href="{{url_for(
+ 'species.populations.genotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ title="Create a new genotypes dataset for {{species.FullName}}">
+ genotypes page to create the genotype dataset</a></p>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html
new file mode 100644
index 0000000..ded425f
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/select-population.html
@@ -0,0 +1,57 @@
+{%extends "expression-data/index.html"%}
+{%from "flash_messages.html" import flash_messages%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
+
+{%block title%}Select Grouping/Population{%endblock%}
+
+{%block contents%}
+<h1 class="heading">Select grouping/population</h1>
+
+<div class="row">
+ <p>The data is organised in a hierarchical form, beginning with
+ <em>species</em> at the very top. Under <em>species</em> the data is
+ organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
+ (In some really old documents/systems, you might see this referred to as
+ <em>InbredSet</em>.)</p>
+ <p>In this section, you get to define what population your data is to be
+ organised by.</p>
+</div>
+
+<div class="row">
+ <form method="POST"
+ action="{{url_for('expression-data.rqtl2.select_population',
+ species_id=species.SpeciesId)}}">
+ <legend class="heading">select grouping/population</legend>
+ {{flash_messages("error-select-population")}}
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+
+ <div class="form-group">
+ <label for="select:inbredset" class="form-label">population</label>
+ <select id="select:inbredset"
+ name="inbredset_id"
+ required="required"
+ class="form-control">
+ <option value="">Select a grouping/population</option>
+ {%for pop in populations%}
+ <option value="{{pop.InbredSetId}}">
+ {{pop.InbredSetName}} ({{pop.FullName}})</option>
+ {%endfor%}
+ </select>
+ <span class="form-text text-muted">Select the population for your data from
+ the list below.</span>
+ </div>
+
+ <button type="submit" class="btn btn-primary" />select population</button>
+</form>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html
index 74f8f69..74f8f69 100644
--- a/uploader/templates/rqtl2/select-probeset-dataset.html
+++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html
diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
index e3fd9cc..e3fd9cc 100644
--- a/uploader/templates/rqtl2/select-probeset-study-id.html
+++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html
index fe3080a..fe3080a 100644
--- a/uploader/templates/rqtl2/select-tissue.html
+++ b/uploader/templates/populations/rqtl2/select-tissue.html
diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html
index 0adba2e..0adba2e 100644
--- a/uploader/templates/rqtl2/summary-info.html
+++ b/uploader/templates/populations/rqtl2/summary-info.html
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html
index 9d45c5f..9d45c5f 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html
index 8210ed0..8210ed0 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html
diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
deleted file mode 100644
index bb6d63d..0000000
--- a/uploader/templates/rqtl2/create-geno-dataset-success.html
+++ /dev/null
@@ -1,55 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="explainer">
- <p>You successfully created the genotype dataset with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{geno_dataset.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{geno_dataset.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{geno_dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{geno_dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{geno_dataset.today}}</dd>
-
- <dt>Public?</dt>
- <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
- </dl>
- </p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('expression-data.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">select from existing genotype datasets</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id"
- value="{{geno_dataset.id}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
deleted file mode 100644
index 03b75c7..0000000
--- a/uploader/templates/rqtl2/create-probe-dataset-success.html
+++ /dev/null
@@ -1,59 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Dataset</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet dataset with the following
- information.
- <dl>
- <dt>Averaging Method</dt>
- <dd>{{avgmethod.Name}}</dd>
-
- <dt>ID</dt>
- <dd>{{dataset.datasetid}}</dd>
-
- <dt>Name</dt>
- <dd>{{dataset.name2}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{dataset.today}}</dd>
-
- <dt>DataScale</dt>
- <dd>{{dataset.datascale}}</dd>
- </dl>
- </p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('expression-data.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet dataset</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{study.Id}}" />
- <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
deleted file mode 100644
index e293f6f..0000000
--- a/uploader/templates/rqtl2/create-probe-study-success.html
+++ /dev/null
@@ -1,49 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Study</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet study with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{study.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{study.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{study.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{study.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{study.today}}</dd>
- </dl>
- </p>
-
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('expression-data.rqtl2.select_dataset_info',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">Create ProbeSet study</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
- <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
- <input type="hidden" name="probe-study-id" value="{{study.studyid}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
deleted file mode 100644
index 8ce13bf..0000000
--- a/uploader/templates/rqtl2/index.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 data upload</h1>
-
-<h2>R/qtl2 Upload</h2>
-
-<form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}"
- id="frm-rqtl2-upload">
- <legend class="heading">upload R/qtl2 bundle</legend>
- {{flash_messages("error-rqtl2")}}
-
- <div class="form-group">
- <label for="select:species" class="form-label">Species</label>
- <select id="select:species"
- name="species_id"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for spec in species%}
- <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
- {%endfor%}
- </select>
- <small class="form-text text-muted">
- Data that you upload to the system should belong to a know species.
- Here you can select the species that you wish to upload data for.
- </small>
- </div>
-
- <button type="submit" class="btn btn-primary" />submit</button>
-</form>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
deleted file mode 100644
index 1db51e0..0000000
--- a/uploader/templates/rqtl2/select-geno-dataset.html
+++ /dev/null
@@ -1,144 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="row">
- <p>Your R/qtl2 files bundle contains a "geno" specification. You will
- therefore need to select from one of the existing Genotype datasets or
- create a new one.</p>
- <p>This is the dataset where your data will be organised under.</p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('expression-data.rqtl2.select_geno_dataset',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">select from existing genotype datasets</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- {{flash_messages("error-rqtl2-select-geno-dataset")}}
-
- <div class="form-group">
- <legend>Datasets</legend>
- <label for="select:geno-datasets" class="form-label">Dataset</label>
- <select id="select:geno-datasets"
- name="geno-dataset-id"
- required="required"
- {%if datasets | length == 0%}
- disabled="disabled"
- {%endif%}
- class="form-control"
- aria-describedby="help-geno-dataset-select-dataset">
- <option value="">Select dataset</option>
- {%for dset in datasets%}
- <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
- {%endfor%}
- </select>
- <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
- Select from the existing genotype datasets for species
- {{species.SpeciesName}} ({{species.FullName}}).
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">select dataset</button>
- </form>
-</div>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-
-<div class="row">
- <form id="frm-upload-rqtl2-bundle"
- action="{{url_for('expression-data.rqtl2.create_geno_dataset',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data">
- <legend class="heading">create a new genotype dataset</legend>
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
- <input type="hidden" name="rqtl2_bundle_file"
- value="{{rqtl2_bundle_file}}" />
-
- {{flash_messages("error-rqtl2-create-geno-dataset")}}
-
- <div class="form-group">
- <label for="txt:dataset-name" class="form-label">Name</label>
- <input type="text"
- id="txt:dataset-name"
- name="dataset-name"
- maxlength="100"
- required="required"
- class="form-control"
- aria-describedby="help-geno-dataset-name" />
- <span id="help-geno-dataset-name" class="form-text text-muted">
- Provide the new name for the genotype dataset, e.g. "BXDGeno"
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt:dataset-fullname" class="form-label">Full Name</label>
- <input type="text"
- id="txt:dataset-fullname"
- name="dataset-fullname"
- required="required"
- maxlength="100"
- class="form-control"
- aria-describedby="help-geno-dataset-fullname" />
-
- <span id="help-geno-dataset-fullname" class="form-text text-muted">
- Provide a longer name that better describes the genotype dataset, e.g.
- "BXD Genotypes"
- </span>
- </div>
-
- <div class="form-group">
- <label for="txt:dataset-shortname" class="form-label">Short Name</label>
- <input type="text"
- id="txt:dataset-shortname"
- name="dataset-shortname"
- maxlength="100"
- class="form-control"
- aria-describedby="help-geno-dataset-shortname" />
-
- <span id="help-geno-dataset-shortname" class="form-text text-muted">
- Provide a short name for the genotype dataset. This is optional. If not
- provided, we'll default to the same value as the "Name" above.
- </span>
- </div>
-
- <div class="form-group">
- <input type="checkbox"
- id="chk:dataset-public"
- name="dataset-public"
- checked="checked"
- class="form-check"
- aria-describedby="help-geno-datasent-public" />
- <label for="chk:dataset-public" class="form-check-label">Public?</label>
-
- <span id="help-geno-dataset-public" class="form-text text-muted">
- Specify whether the dataset will be available publicly. Check to make the
- dataset publicly available and uncheck to limit who can access the dataset.
- </span>
- </div>
-
- <button type="submit" class="btn btn-primary">create new dataset</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
deleted file mode 100644
index 7d27303..0000000
--- a/uploader/templates/rqtl2/select-population.html
+++ /dev/null
@@ -1,136 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div class="explainer">
- <p>The data is organised in a hierarchical form, beginning with
- <em>species</em> at the very top. Under <em>species</em> the data is
- organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
- (In some really old documents/systems, you might see this referred to as
- <em>InbredSet</em>.)</p>
- <p>In this section, you get to define what population your data is to be
- organised by.</p>
-</div>
-
-<form method="POST"
- action="{{url_for('expression-data.rqtl2.select_population', species_id=species.SpeciesId)}}">
- <legend class="heading">select grouping/population</legend>
- {{flash_messages("error-select-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <label for="select:inbredset" class="form-label">population</label>
- <select id="select:inbredset"
- name="inbredset_id"
- required="required"
- class="form-control">
- <option value="">Select a grouping/population</option>
- {%for pop in populations%}
- <option value="{{pop.InbredSetId}}">
- {{pop.InbredSetName}} ({{pop.FullName}})</option>
- {%endfor%}
- </select>
- <span class="form-text text-muted">If you are adding data to an already existing
- population, simply pick the population from this drop-down selector. If
- you cannot find your population from this list, try the form below to
- create a new one..</span>
- </div>
-
- <button type="submit" class="btn btn-primary" />select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST"
- action="{{url_for('expression-data.rqtl2.create_population', species_id=species.SpeciesId)}}">
- <legend class="heading">create new grouping/population</legend>
- {{flash_messages("error-create-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <legend class="heading">mandatory</legend>
-
- <div class="form-group">
- <label for="txt:inbredset-name" class="form-label">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- maxlength="30"
- placeholder="Enter grouping/population name"
- class="form-control" />
- <span class="form-text text-muted">This is a short name that identifies the
- population. Useful for menus, and quick scanning.</span>
- </div>
-
- <div class="form-group">
- <label for="txt:" class="form-label">full name</label>
- <input id="txt:inbredset-fullname"
- name="inbredset_fullname"
- type="text"
- required="required"
- maxlength="100"
- placeholder="Enter the grouping/population's full name"
- class="form-control" />
- <span class="form-text text-muted">This can be the same as the name above, or can
- be longer. Useful for documentation, and human communication.</span>
- </div>
- </div>
-
- <div class="form-group">
- <legend class="heading">optional</legend>
-
- <div class="form-group">
- <label for="num:public" class="form-label">public?</label>
- <select id="num:public"
- name="public"
- class="form-control">
- <option value="0">0 - Only accessible to authorised users</option>
- <option value="1">1 - Publicly accessible to all users</option>
- <option value="2" selected>
- 2 - Publicly accessible to all users</option>
- </select>
- <span class="form-text text-muted">This determines whether the
- population/grouping will appear on the menus for users.</span>
- </div>
-
- <div class="form-group">
- <label for="txt:inbredset-family" class="form-label">family</label>
- <input id="txt:inbredset-family"
- name="inbredset_family"
- type="text"
- placeholder="I am not sure what this is about."
- class="form-control" />
- <span class="form-text text-muted">I do not currently know what this is about.
- This is a failure on my part to figure out what this is and provide a
- useful description. Please feel free to remind me.</span>
- </div>
-
- <div class="form-group">
- <label for="txtarea:" class="form-label">Description</label>
- <textarea id="txtarea:description"
- name="description"
- rows="5"
- placeholder="Enter a description of this grouping/population"
- class="form-control"></textarea>
- <span class="form-text text-muted">
- A long-form description of what the population consists of. Useful for
- humans.</span>
- </div>
- </div>
-
- <button type="submit" class="btn btn-primary" />
- create grouping/population</button>
-</form>
-
-{%endblock%}
-
-
-{%block javascript%}
-{%endblock%}