Rename module: qc_app --> uploader

84 files changed, 6623 insertions, 0 deletions

diff --git a/uploader/__init__.py b/uploader/__init__.py
new file mode 100644
index 0000000..3ee8aa0
--- /dev/null
+++ b/uploader/__init__.py
@@ -0,0 +1,48 @@
+"""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/uploader/base_routes.py b/uploader/base_routes.py
new file mode 100644
index 0000000..9daf439
--- /dev/null
+++ b/uploader/base_routes.py
@@ -0,0 +1,29 @@
+"""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/uploader/check_connections.py b/uploader/check_connections.py
new file mode 100644
index 0000000..2561e55
--- /dev/null
+++ b/uploader/check_connections.py
@@ -0,0 +1,28 @@
+"""Check the various connection used in the application"""
+import sys
+import traceback
+
+import redis
+import MySQLdb
+
+from uploader.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/uploader/db/__init__.py b/uploader/db/__init__.py
new file mode 100644
index 0000000..36e93e8
--- /dev/null
+++ b/uploader/db/__init__.py
@@ -0,0 +1,8 @@
+"""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/uploader/db/averaging.py b/uploader/db/averaging.py
new file mode 100644
index 0000000..62bbe67
--- /dev/null
+++ b/uploader/db/averaging.py
@@ -0,0 +1,23 @@
+"""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/uploader/db/datasets.py b/uploader/db/datasets.py
new file mode 100644
index 0000000..767ec41
--- /dev/null
+++ b/uploader/db/datasets.py
@@ -0,0 +1,133 @@
+"""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/uploader/db/platforms.py b/uploader/db/platforms.py
new file mode 100644
index 0000000..cb527a7
--- /dev/null
+++ b/uploader/db/platforms.py
@@ -0,0 +1,25 @@
+"""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/uploader/db/populations.py b/uploader/db/populations.py
new file mode 100644
index 0000000..4485e52
--- /dev/null
+++ b/uploader/db/populations.py
@@ -0,0 +1,54 @@
+"""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/uploader/db/species.py b/uploader/db/species.py
new file mode 100644
index 0000000..653e59b
--- /dev/null
+++ b/uploader/db/species.py
@@ -0,0 +1,22 @@
+"""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/uploader/db/tissues.py b/uploader/db/tissues.py
new file mode 100644
index 0000000..9fe7bab
--- /dev/null
+++ b/uploader/db/tissues.py
@@ -0,0 +1,50 @@
+"""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/uploader/db_utils.py b/uploader/db_utils.py
new file mode 100644
index 0000000..ef26398
--- /dev/null
+++ b/uploader/db_utils.py
@@ -0,0 +1,46 @@
+"""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/uploader/dbinsert.py b/uploader/dbinsert.py
new file mode 100644
index 0000000..88d16ef
--- /dev/null
+++ b/uploader/dbinsert.py
@@ -0,0 +1,397 @@
+"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 uploader.db_utils import with_db_connection, database_connection
+from uploader.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/uploader/default_settings.py b/uploader/default_settings.py
new file mode 100644
index 0000000..7a9da0f
--- /dev/null
+++ b/uploader/default_settings.py
@@ -0,0 +1,14 @@
+"""
+The default configuration file. The values here should be overridden in the
+actual configuration file used for the production and staging systems.
+"""
+
+import os
+
+LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING")
+SECRET_KEY = b"<Please! Please! Please! Change This!>"
+UPLOAD_FOLDER = "/tmp/qc_app_files"
+REDIS_URL = "redis://"
+JOBS_TTL_SECONDS = 1209600 # 14 days
+GNQC_REDIS_PREFIX="GNQC"
+SQL_URI = ""
diff --git a/uploader/entry.py b/uploader/entry.py
new file mode 100644
index 0000000..4a02f1e
--- /dev/null
+++ b/uploader/entry.py
@@ -0,0 +1,127 @@
+"""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 uploader.db import species
+from uploader.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/uploader/errors.py b/uploader/errors.py
new file mode 100644
index 0000000..3e7c893
--- /dev/null
+++ b/uploader/errors.py
@@ -0,0 +1,29 @@
+"""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/uploader/files.py b/uploader/files.py
new file mode 100644
index 0000000..b163612
--- /dev/null
+++ b/uploader/files.py
@@ -0,0 +1,26 @@
+"""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/uploader/input_validation.py b/uploader/input_validation.py
new file mode 100644
index 0000000..9abe742
--- /dev/null
+++ b/uploader/input_validation.py
@@ -0,0 +1,27 @@
+"""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/uploader/jobs.py b/uploader/jobs.py
new file mode 100644
index 0000000..21889da
--- /dev/null
+++ b/uploader/jobs.py
@@ -0,0 +1,130 @@
+"""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/uploader/parse.py b/uploader/parse.py
new file mode 100644
index 0000000..865dae2
--- /dev/null
+++ b/uploader/parse.py
@@ -0,0 +1,175 @@
+"""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 uploader import jobs
+from uploader.dbinsert import species_by_id
+from uploader.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/uploader/samples.py b/uploader/samples.py
new file mode 100644
index 0000000..9c95770
--- /dev/null
+++ b/uploader/samples.py
@@ -0,0 +1,354 @@
+"""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 uploader import jobs
+from uploader.files import save_file
+from uploader.input_validation import is_integer_input
+from uploader.db_utils import (
+    with_db_connection,
+    database_connection,
+    with_redis_connection)
+from uploader.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/uploader/static/css/custom-bootstrap.css b/uploader/static/css/custom-bootstrap.css
new file mode 100644
index 0000000..67f1199
--- /dev/null
+++ b/uploader/static/css/custom-bootstrap.css
@@ -0,0 +1,23 @@
+/** 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/uploader/static/css/styles.css b/uploader/static/css/styles.css
new file mode 100644
index 0000000..a88c229
--- /dev/null
+++ b/uploader/static/css/styles.css
@@ -0,0 +1,7 @@
+.heading {
+    text-transform: capitalize;
+}
+
+label {
+    text-transform: capitalize;
+}
diff --git a/uploader/static/css/two-column-with-separator.css b/uploader/static/css/two-column-with-separator.css
new file mode 100644
index 0000000..b6efd46
--- /dev/null
+++ b/uploader/static/css/two-column-with-separator.css
@@ -0,0 +1,27 @@
+.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/uploader/static/images/CITGLogo.png b/uploader/static/images/CITGLogo.png
new file mode 100644
index 0000000..ae99fed
--- /dev/null
+++ b/uploader/static/images/CITGLogo.png
diff --git a/uploader/static/js/select_platform.js b/uploader/static/js/select_platform.js
new file mode 100644
index 0000000..4fdd865
--- /dev/null
+++ b/uploader/static/js/select_platform.js
@@ -0,0 +1,70 @@
+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/uploader/static/js/upload_progress.js b/uploader/static/js/upload_progress.js
new file mode 100644
index 0000000..9638b36
--- /dev/null
+++ b/uploader/static/js/upload_progress.js
@@ -0,0 +1,97 @@
+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/uploader/static/js/upload_samples.js b/uploader/static/js/upload_samples.js
new file mode 100644
index 0000000..aed536f
--- /dev/null
+++ b/uploader/static/js/upload_samples.js
@@ -0,0 +1,132 @@
+/*
+ * 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/uploader/static/js/utils.js b/uploader/static/js/utils.js
new file mode 100644
index 0000000..045dd47
--- /dev/null
+++ b/uploader/static/js/utils.js
@@ -0,0 +1,10 @@
+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/uploader/templates/base.html b/uploader/templates/base.html
new file mode 100644
index 0000000..eb5e6b7
--- /dev/null
+++ b/uploader/templates/base.html
@@ -0,0 +1,51 @@
+<!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/uploader/templates/cli-output.html b/uploader/templates/cli-output.html
new file mode 100644
index 0000000..33fb73b
--- /dev/null
+++ b/uploader/templates/cli-output.html
@@ -0,0 +1,8 @@
+{%macro cli_output(job, stream)%}
+
+<h4>{{stream | upper}} Output</h4>
+<div class="cli-output">
+  <pre>{{job.get(stream, "")}}</pre>
+</div>
+
+{%endmacro%}
diff --git a/uploader/templates/continue_from_create_dataset.html b/uploader/templates/continue_from_create_dataset.html
new file mode 100644
index 0000000..03bb49c
--- /dev/null
+++ b/uploader/templates/continue_from_create_dataset.html
@@ -0,0 +1,52 @@
+{%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/uploader/templates/continue_from_create_study.html b/uploader/templates/continue_from_create_study.html
new file mode 100644
index 0000000..34e6e5e
--- /dev/null
+++ b/uploader/templates/continue_from_create_study.html
@@ -0,0 +1,52 @@
+{%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/uploader/templates/data_review.html b/uploader/templates/data_review.html
new file mode 100644
index 0000000..b7528fd
--- /dev/null
+++ b/uploader/templates/data_review.html
@@ -0,0 +1,85 @@
+{%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/uploader/templates/dbupdate_error.html b/uploader/templates/dbupdate_error.html
new file mode 100644
index 0000000..e1359d2
--- /dev/null
+++ b/uploader/templates/dbupdate_error.html
@@ -0,0 +1,12 @@
+{%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/uploader/templates/dbupdate_hidden_fields.html b/uploader/templates/dbupdate_hidden_fields.html
new file mode 100644
index 0000000..ccbc299
--- /dev/null
+++ b/uploader/templates/dbupdate_hidden_fields.html
@@ -0,0 +1,29 @@
+{%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/uploader/templates/errors_display.html b/uploader/templates/errors_display.html
new file mode 100644
index 0000000..715cfcf
--- /dev/null
+++ b/uploader/templates/errors_display.html
@@ -0,0 +1,47 @@
+{%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/uploader/templates/final_confirmation.html b/uploader/templates/final_confirmation.html
new file mode 100644
index 0000000..0727fc8
--- /dev/null
+++ b/uploader/templates/final_confirmation.html
@@ -0,0 +1,47 @@
+{%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/uploader/templates/flash_messages.html b/uploader/templates/flash_messages.html
new file mode 100644
index 0000000..b7af178
--- /dev/null
+++ b/uploader/templates/flash_messages.html
@@ -0,0 +1,25 @@
+{%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/uploader/templates/http-error.html b/uploader/templates/http-error.html
new file mode 100644
index 0000000..374fb86
--- /dev/null
+++ b/uploader/templates/http-error.html
@@ -0,0 +1,18 @@
+{%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/uploader/templates/index.html b/uploader/templates/index.html
new file mode 100644
index 0000000..89d2ae9
--- /dev/null
+++ b/uploader/templates/index.html
@@ -0,0 +1,81 @@
+{%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/uploader/templates/insert_error.html b/uploader/templates/insert_error.html
new file mode 100644
index 0000000..5301288
--- /dev/null
+++ b/uploader/templates/insert_error.html
@@ -0,0 +1,32 @@
+{%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/uploader/templates/insert_progress.html b/uploader/templates/insert_progress.html
new file mode 100644
index 0000000..52177d6
--- /dev/null
+++ b/uploader/templates/insert_progress.html
@@ -0,0 +1,46 @@
+{%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/uploader/templates/insert_success.html b/uploader/templates/insert_success.html
new file mode 100644
index 0000000..7e1fa8d
--- /dev/null
+++ b/uploader/templates/insert_success.html
@@ -0,0 +1,19 @@
+{%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/uploader/templates/job_progress.html b/uploader/templates/job_progress.html
new file mode 100644
index 0000000..1af0763
--- /dev/null
+++ b/uploader/templates/job_progress.html
@@ -0,0 +1,40 @@
+{%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/uploader/templates/no_such_job.html b/uploader/templates/no_such_job.html
new file mode 100644
index 0000000..42a2d48
--- /dev/null
+++ b/uploader/templates/no_such_job.html
@@ -0,0 +1,14 @@
+{%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/uploader/templates/parse_failure.html b/uploader/templates/parse_failure.html
new file mode 100644
index 0000000..31f6be8
--- /dev/null
+++ b/uploader/templates/parse_failure.html
@@ -0,0 +1,26 @@
+{%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/uploader/templates/parse_results.html b/uploader/templates/parse_results.html
new file mode 100644
index 0000000..e2bf7f0
--- /dev/null
+++ b/uploader/templates/parse_results.html
@@ -0,0 +1,30 @@
+{%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/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
new file mode 100644
index 0000000..1b50221
--- /dev/null
+++ b/uploader/templates/rqtl2/create-geno-dataset-success.html
@@ -0,0 +1,55 @@
+{%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/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
new file mode 100644
index 0000000..790d174
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-dataset-success.html
@@ -0,0 +1,59 @@
+{%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/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
new file mode 100644
index 0000000..d0ee508
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-study-success.html
@@ -0,0 +1,49 @@
+{%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/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html
new file mode 100644
index 0000000..5f2c5a0
--- /dev/null
+++ b/uploader/templates/rqtl2/create-tissue-success.html
@@ -0,0 +1,106 @@
+{%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/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
new file mode 100644
index 0000000..f3329c2
--- /dev/null
+++ b/uploader/templates/rqtl2/index.html
@@ -0,0 +1,36 @@
+{%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/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/rqtl2/no-such-job.html
new file mode 100644
index 0000000..b17004f
--- /dev/null
+++ b/uploader/templates/rqtl2/no-such-job.html
@@ -0,0 +1,13 @@
+{%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/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/rqtl2/rqtl2-job-error.html
new file mode 100644
index 0000000..9817518
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-error.html
@@ -0,0 +1,39 @@
+{%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/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/rqtl2/rqtl2-job-results.html
new file mode 100644
index 0000000..4ecd415
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-results.html
@@ -0,0 +1,24 @@
+{%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/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/rqtl2/rqtl2-job-status.html
new file mode 100644
index 0000000..e896f88
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-status.html
@@ -0,0 +1,20 @@
+{%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/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
new file mode 100644
index 0000000..90e8887
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
@@ -0,0 +1,120 @@
+{%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/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
new file mode 100644
index 0000000..59bc8cd
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
@@ -0,0 +1,66 @@
+{%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/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
new file mode 100644
index 0000000..f4a6266
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
@@ -0,0 +1,41 @@
+{%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/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
new file mode 100644
index 0000000..2861a04
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
@@ -0,0 +1,37 @@
+{%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/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..873f9c3
--- /dev/null
+++ b/uploader/templates/rqtl2/select-geno-dataset.html
@@ -0,0 +1,144 @@
+{%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/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
new file mode 100644
index 0000000..37731f0
--- /dev/null
+++ b/uploader/templates/rqtl2/select-population.html
@@ -0,0 +1,136 @@
+{%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/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html
new file mode 100644
index 0000000..26f52ed
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-dataset.html
@@ -0,0 +1,191 @@
+{%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/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..b9bf52e
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,143 @@
+{%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/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html
new file mode 100644
index 0000000..34e1758
--- /dev/null
+++ b/uploader/templates/rqtl2/select-tissue.html
@@ -0,0 +1,115 @@
+{%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/uploader/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html
new file mode 100644
index 0000000..1be87fa
--- /dev/null
+++ b/uploader/templates/rqtl2/summary-info.html
@@ -0,0 +1,65 @@
+{%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/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
new file mode 100644
index 0000000..07c240f
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -0,0 +1,276 @@
+{%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/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
new file mode 100644
index 0000000..93b1dc9
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -0,0 +1,33 @@
+{%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/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
new file mode 100644
index 0000000..da19ddc
--- /dev/null
+++ b/uploader/templates/samples/select-population.html
@@ -0,0 +1,99 @@
+{%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/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html
new file mode 100644
index 0000000..edadc61
--- /dev/null
+++ b/uploader/templates/samples/select-species.html
@@ -0,0 +1,30 @@
+{%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/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html
new file mode 100644
index 0000000..09e2ecf
--- /dev/null
+++ b/uploader/templates/samples/upload-failure.html
@@ -0,0 +1,27 @@
+{%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/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html
new file mode 100644
index 0000000..7bb02be
--- /dev/null
+++ b/uploader/templates/samples/upload-progress.html
@@ -0,0 +1,22 @@
+{%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/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
new file mode 100644
index 0000000..e62de57
--- /dev/null
+++ b/uploader/templates/samples/upload-samples.html
@@ -0,0 +1,139 @@
+{%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/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html
new file mode 100644
index 0000000..cb745c3
--- /dev/null
+++ b/uploader/templates/samples/upload-success.html
@@ -0,0 +1,18 @@
+{%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/uploader/templates/select_dataset.html b/uploader/templates/select_dataset.html
new file mode 100644
index 0000000..2f07de8
--- /dev/null
+++ b/uploader/templates/select_dataset.html
@@ -0,0 +1,161 @@
+{%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/uploader/templates/select_platform.html b/uploader/templates/select_platform.html
new file mode 100644
index 0000000..d9bc68f
--- /dev/null
+++ b/uploader/templates/select_platform.html
@@ -0,0 +1,82 @@
+{%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/uploader/templates/select_species.html b/uploader/templates/select_species.html
new file mode 100644
index 0000000..3b1a8a9
--- /dev/null
+++ b/uploader/templates/select_species.html
@@ -0,0 +1,92 @@
+{%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/uploader/templates/select_study.html b/uploader/templates/select_study.html
new file mode 100644
index 0000000..648ad4c
--- /dev/null
+++ b/uploader/templates/select_study.html
@@ -0,0 +1,108 @@
+{%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/uploader/templates/stdout_output.html b/uploader/templates/stdout_output.html
new file mode 100644
index 0000000..85345a9
--- /dev/null
+++ b/uploader/templates/stdout_output.html
@@ -0,0 +1,8 @@
+{%macro stdout_output(job)%}
+
+<h4>STDOUT Output</h4>
+<div class="cli-output">
+  <pre>{{job.get("stdout", "")}}</pre>
+</div>
+
+{%endmacro%}
diff --git a/uploader/templates/unhandled_exception.html b/uploader/templates/unhandled_exception.html
new file mode 100644
index 0000000..6e6a051
--- /dev/null
+++ b/uploader/templates/unhandled_exception.html
@@ -0,0 +1,21 @@
+{%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/uploader/templates/upload_progress_indicator.html b/uploader/templates/upload_progress_indicator.html
new file mode 100644
index 0000000..e274e83
--- /dev/null
+++ b/uploader/templates/upload_progress_indicator.html
@@ -0,0 +1,35 @@
+{%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/uploader/templates/worker_failure.html b/uploader/templates/worker_failure.html
new file mode 100644
index 0000000..b65b140
--- /dev/null
+++ b/uploader/templates/worker_failure.html
@@ -0,0 +1,24 @@
+{%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/uploader/upload/__init__.py b/uploader/upload/__init__.py
new file mode 100644
index 0000000..5f120d4
--- /dev/null
+++ b/uploader/upload/__init__.py
@@ -0,0 +1,7 @@
+"""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/uploader/upload/rqtl2.py b/uploader/upload/rqtl2.py
new file mode 100644
index 0000000..6aed1f7
--- /dev/null
+++ b/uploader/upload/rqtl2.py
@@ -0,0 +1,1157 @@
+"""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.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.db import (
+    species_by_id,
+    save_population,
+    populations_by_species,
+    population_by_species_and_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"])
+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)