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-rw-r--r--uploader/genotypes/models.py100
-rw-r--r--uploader/genotypes/views.py104
-rw-r--r--uploader/phenotypes/views.py79
-rw-r--r--uploader/static/css/layout-large.css1
-rw-r--r--uploader/static/css/layout-medium.css1
-rw-r--r--uploader/static/css/layout-small.css1
-rw-r--r--uploader/static/js/files.js215
-rw-r--r--uploader/templates/genotypes/add-genotypes-records-base.html39
-rw-r--r--uploader/templates/genotypes/add-genotypes-records-csv.html146
-rw-r--r--uploader/templates/genotypes/base.html7
-rw-r--r--uploader/templates/genotypes/create-dataset.html4
-rw-r--r--uploader/templates/genotypes/index.html200
-rw-r--r--uploader/templates/genotypes/list-genotypes.html226
-rw-r--r--uploader/templates/genotypes/macro-display-dataset-card.html24
-rw-r--r--uploader/templates/macro-csv-fields.html102
-rw-r--r--uploader/templates/phenotypes/view-dataset.html26
-rw-r--r--uploader/templates/populations/view-population.html35
17 files changed, 976 insertions, 334 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 34d2cfe..41270da 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -1,13 +1,17 @@
 """Functions for handling genotypes."""
+import logging
 from typing import Optional
+from functools import reduce
 from datetime import datetime
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
-from flask import current_app as app
 
 from gn_libs.mysqldb import debug_query
 
+logger = logging.getLogger(__name__)
+
+
 def genocode_by_population(
         conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
     """Get the allele/genotype codes."""
@@ -29,30 +33,102 @@ def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
 def genotype_markers(
         conn: mdb.Connection,
         species_id: int,
+        population_id: int,
         offset: int = 0,
-        limit: Optional[int] = None
+        limit: int = -1# no limit if negative, zero returns empty list.
 ) -> tuple[tuple[dict, ...], int]:
-    """Retrieve markers from the database."""
+    """Retrieve markers from the database.
+
+    Return: A tuple of:
+            - Listing of the markers,
+            - The total number of markers found in the system.
+    """
     _query_template = (
-        "SELECT %%COLS%% FROM Geno AS gno "
-        "WHERE gno.SpeciesId=%s "
+        "SELECT %%COLS%% "
+        "FROM Species AS spc "
+        "INNER JOIN InbredSet AS iset "
+        "ON spc.Id = iset.SpeciesId "
+        "INNER JOIN GenoFreeze AS gfr "
+        "ON iset.Id = gfr.InbredSetId "
+        "INNER JOIN GenoXRef AS gxr "
+        "ON gfr.Id = gxr.GenoFreezeId "
+        "INNER JOIN Geno AS gno "
+        "ON gxr.GenoId = gno.Id "
+        "WHERE spc.Id=%s "
+        "AND iset.Id=%s "
         "%%LIMIT%%")
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             _query_template.replace("%%LIMIT%%", "").replace(
                 "%%COLS%%", "COUNT(gno.Id) AS total_records"),
-            (species_id,))
+            (species_id, population_id))
         _total_records = cursor.fetchone()["total_records"]
         cursor.execute(
-            _query_template.replace("%%COLS%%", "gno.*").replace(
+            _query_template.replace("%%COLS%%", "gno.*, gxr.cM").replace(
                 "%%LIMIT%%",
                 (f"LIMIT {int(limit)} OFFSET {int(offset)}"
-                 if bool(limit) and limit > 0
+                 if bool(limit) and limit >= 0
                  else "")),
-            (species_id,))
-        debug_query(cursor, app.logger)
-        return tuple(dict(row) for row in cursor.fetchall()), _total_records
+            (species_id, population_id))
+        debug_query(cursor, logger)
+        _records = tuple(dict(row) for row in cursor.fetchall())
+        return _records, _total_records
+
+
+def genotype_records(
+        conn: mdb.Connection,
+        species_id: int,
+        population_id: int,
+        offset: int = 0,
+        limit: int = -1# no limit if negative, zero returns empty list.
+) -> tuple[tuple[dict, ...], int]:
+    """Retrieve the actual genotype records from the database.
+
+    Returns: A tuple of:
+             - the listing of the genotype data,
+             - the total number of genotype records for this population.
+    """
+    def __organise_geno_records__(acc, row):
+        _current_row = acc.get(row["GenoId"], {
+            "GenoId": row["GenoId"],
+            "data": {}
+        })
+        _current_row["data"][row["StrainName"]] = row["value"]
+        return {
+            **acc,
+            _current_row["GenoId"]: _current_row
+        }
+
+    _query_template = (
+        "SELECT gxr.GenoId, gxr.DataId, gdt.value, strn.Name AS StrainName "
+        "FROM GenoXRef AS gxr "
+        "INNER JOIN GenoData AS gdt ON gxr.DataId = gdt.Id "
+        "INNER JOIN Strain AS strn ON gdt.StrainId = strn.Id "
+        "WHERE gxr.GenoId IN (%%PARAMS_STR%%)")
+
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        _markers, _num_records = genotype_markers(
+            conn, species_id, population_id, offset, limit)
+        if len(_markers) == 0:
+            return (tuple(), 0)
+
+        _genoids = tuple(_marker["Id"] for _marker in _markers)
+        cursor.execute(
+            _query_template.replace(
+                "%%PARAMS_STR%%", ",".join(["%s"] * len(_genoids))),
+            _genoids)
+        debug_query(cursor, logger)
+        _records: dict[str, dict] = reduce(
+            __organise_geno_records__, cursor.fetchall(), {})
+        return (
+            tuple({
+                **_marker,
+                "data": _records.get(
+                    _marker["Id"], {}
+                ).get("data", {})
+            } for _marker in _markers),
+            _num_records)
 
 
 def genotype_dataset(
@@ -77,7 +153,7 @@ def genotype_dataset(
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, _params)
-        debug_query(cursor, app.logger)
+        debug_query(cursor, logger)
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index f27671c..648b38e 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -3,12 +3,15 @@ import logging
 
 from MySQLdb.cursors import DictCursor
 from pymonad.either import Left, Right, Either
+from gn_libs.requests import request_json
 from gn_libs.mysqldb import database_connection
+from werkzeug.exceptions import UnsupportedMediaType
 from flask import (flash,
                    request,
                    jsonify,
                    redirect,
                    Blueprint,
+                   make_response,
                    render_template,
                    current_app as app)
 
@@ -16,17 +19,16 @@ from uploader.flask_extensions import url_for
 from uploader.ui import make_template_renderer
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
-from uploader.route_utils import generic_select_population
-from uploader.datautils import safe_int, enumerate_sequence
-from uploader.species.models import all_species, species_by_id
+from uploader.species.models import species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.population.models import population_by_species_and_id
-from uploader.request_checks import with_species, with_dataset, with_population
+from uploader.request_checks import with_dataset, with_population
+
 
 from .models import (genotype_markers,
+                     genotype_records,
                      genotype_dataset,
                      save_new_dataset,
-                     genotype_markers_count,
                      genocode_by_population)
 
 logger = logging.getLogger(__name__)
@@ -36,32 +38,65 @@ render_template = make_template_renderer("genotypes")
 
 @genotypesbp.route(
     "/<int:species_id>/populations/<int:population_id>/genotypes",
-    methods=["GET"])
+    methods=["GET", "POST"])
 @require_login
 @with_population(species_redirect_uri="species.list_species",
                  redirect_uri="species.populations.list_species_populations")
-def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
-    """List genotype details for species and population."""
+def index(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
+    """Entry-point to the genotypes management section."""
     with database_connection(app.config["SQL_URI"]) as conn:
-        return render_template("genotypes/list-genotypes.html",
-                               species=species,
-                               population=population,
-                               genocode=genocode_by_population(
-                                   conn, population["Id"]),
-                               total_markers=genotype_markers_count(
-                                   conn, species["SpeciesId"]),
-                               dataset=genotype_dataset(conn,
-                                                        species["SpeciesId"],
-                                                        population["Id"]),
-                               activelink="list-genotypes")
+        form = request_json()
+        offset = int(form.get("start", "0"))
+        number_of_records = int(form.get("length", "10"))
+        _markers, _total_markers, = genotype_markers(
+            conn, species["SpeciesId"], population["Id"])
+        _genotype_records, _count = genotype_records(
+            conn,
+            species["SpeciesId"],
+            population["Id"],
+            offset,
+            number_of_records)
+        _genotype_records = tuple(
+            {**_record, "index": _idx}
+            for _idx, _record
+            in enumerate(_genotype_records, start=offset+1))
+
+        ## Order these correctly
+        _samples = (tuple() if len(_genotype_records) == 0
+                    else tuple(_genotype_records[0]["data"].keys()))
+
+        if "application/json" in request.headers["Accept"]:
+            return make_response(
+                jsonify({
+                    "genotype_records": _genotype_records,
+                    "total_genotype_records": _count,
+                    "fetched_genotype_records": len(_genotype_records),
+                    "samples_order": _samples,
+                    "draw": int(request.args.get("draw", "0"))
+                }), 200)
+
+        if "text/html" in request.headers["Accept"]:
+            return render_template(
+                "genotypes/index.html",
+                species=species,
+                population=population,
+                genocode=genocode_by_population(conn, population["Id"]),
+                dataset=genotype_dataset(
+                    conn, species["SpeciesId"], population["Id"]),
+                genotype_records=_genotype_records,
+                samples=_samples,
+                activelink="list-genotypes")
+
+        raise UnsupportedMediaType("This endpoint can only server HTML or JSON")
 
 
 @genotypesbp.route(
     "/<int:species_id>/populations/<int:population_id>/genotypes/<int:dataset_id>/list-markers",
     methods=["GET"])
 @require_login
-@with_species(redirect_uri="species.populations.genotypes.list_genotypes")
-def list_markers(species: dict, **_kwargs):
+@with_population(species_redirect_uri="species.list_species",
+                 redirect_uri="species.populations.index")
+def list_markers(species: dict, population: dict, **_kwargs):
     """List the markers that exist for this species."""
     args = request.args
     offset = int(args.get("start") or 0)
@@ -69,11 +104,12 @@ def list_markers(species: dict, **_kwargs):
         markers, total_records = genotype_markers(
             conn,
             species["SpeciesId"],
+            population["Id"],
             offset=offset,
             limit=int(args.get("length") or 0))
         return jsonify({
-            **({"draw": int(args.get("draw"))}
-               if bool(args.get("draw") or False)
+            **({"draw": int(args.get("draw", "0"))}
+               if bool(args.get("draw"))
                else {}),
             "recordsTotal": total_records,
             "recordsFiltered": len(markers),
@@ -146,7 +182,7 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
                     form["geno-dataset-name"],
                     form["geno-dataset-fullname"],
                     form["geno-dataset-shortname"]))
-            except Exception:
+            except Exception:# pylint: disable=[broad-exception-caught]
                 msg = "Error adding new Genotype dataset to database."
                 logger.error(msg, exc_info=True)
                 return Left(Exception(msg))
@@ -176,3 +212,23 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
             make_either_error_handler(
                 "There was an error creating the genotype dataset."),
             __success__)
+
+
+@genotypesbp.route(
+    "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
+    "<int:dataset_id>/add-records",
+    methods=["GET", "POST"])
+@require_login
+@with_population(species_redirect_uri="species.list_species",
+                 redirect_uri="species.populations.list_species_populations")
+@with_dataset(species_redirect_uri="species.list_species",
+              population_redirect_uri="species.populations.list_species_populations",
+              redirect_uri="species.populations.genotypes.index",
+              dataset_by_id=genotype_dataset)
+def add_genotype_records(species: dict, population: dict, dataset: dict, **kwargs):
+    """Add new Genotype records to the dataset."""
+    return render_template("genotypes/add-genotypes-records-csv.html",
+                           species=species,
+                           population=population,
+                           dataset=dataset,
+                           activelink="add-genotypes-records")
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index c03f3f5..85d6357 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -8,7 +8,7 @@ import logging
 from typing import Any
 from pathlib import Path
 from zipfile import ZipFile
-from functools import wraps, reduce
+from functools import reduce
 from urllib.parse import urljoin, urlparse, ParseResult, urlunparse, urlencode
 
 import datetime
@@ -51,7 +51,7 @@ from uploader.datautils import safe_int, enumerate_sequence
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.publications.models import fetch_publication_by_id
-from uploader.request_checks import with_species, with_population
+from uploader.request_checks import with_species, with_dataset, with_population
 from uploader.input_validation import (encode_errors,
                                        decode_errors,
                                        is_valid_representative_name)
@@ -136,45 +136,6 @@ def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[
                                activelink="list-datasets")
 
 
-def with_dataset(
-        species_redirect_uri: str,
-        population_redirect_uri: str,
-        redirect_uri: str
-):
-    """Ensure the dataset actually exists."""
-    def __decorator__(func):
-        @wraps(func)
-        @with_population(species_redirect_uri, population_redirect_uri)
-        def __with_dataset__(**kwargs):
-            try:
-                _spcid = int(kwargs["species_id"])
-                _popid = int(kwargs["population_id"])
-                _dsetid = int(kwargs.get("dataset_id"))
-                select_dataset_uri = redirect(url_for(
-                    redirect_uri, species_id=_spcid, population_id=_popid))
-                if not bool(_dsetid):
-                    flash("You need to select a valid 'dataset_id' value.",
-                          "alert-danger")
-                    return select_dataset_uri
-                with database_connection(app.config["SQL_URI"]) as conn:
-                    dataset = dataset_by_id(conn, _spcid, _popid, _dsetid)
-                    if not bool(dataset):
-                        flash("You must select a valid dataset.",
-                              "alert-danger")
-                        return select_dataset_uri
-            except ValueError as _verr:
-                app.logger.debug(
-                    "Exception converting 'dataset_id' to integer: %s",
-                    kwargs.get("dataset_id"),
-                    exc_info=True)
-                flash("Expected 'dataset_id' value to be an integer."
-                      "alert-danger")
-                return select_dataset_uri
-            return func(dataset=dataset, **kwargs)
-        return __with_dataset__
-    return __decorator__
-
-
 @phenotypesbp.route(
     "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
     "/<int:dataset_id>/view",
@@ -183,7 +144,8 @@ def with_dataset(
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def view_dataset(# pylint: disable=[unused-argument]
         species: dict, population: dict, dataset: dict, **kwargs):
     """View a specific dataset"""
@@ -223,7 +185,8 @@ def view_dataset(# pylint: disable=[unused-argument]
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def view_phenotype(# pylint: disable=[unused-argument]
         species: dict,
         population: dict,
@@ -412,7 +375,8 @@ def process_phenotypes_individual_files(error_uri):
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# pylint: disable=[unused-argument, too-many-locals]
     """Add one or more phenotypes to the dataset."""
     use_bundle = request.args.get("use_bundle", "").lower() == "true"
@@ -501,7 +465,8 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def job_status(
         species: dict,
         population: dict,
@@ -537,7 +502,8 @@ def job_status(
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def download_errors(
         species: dict,
         population: dict,
@@ -596,7 +562,8 @@ def download_errors(
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def review_job_data(
         species: dict,
         population: dict,
@@ -696,7 +663,8 @@ def proceed_to_job_status(job):
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def load_data_to_database(
         species: dict,
         population: dict,
@@ -909,7 +877,8 @@ def update_phenotype_data(conn, data: dict):
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def edit_phenotype_data(# pylint: disable=[unused-argument]
         species: dict,
         population: dict,
@@ -1029,7 +998,8 @@ def edit_phenotype_data(# pylint: disable=[unused-argument]
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def load_data_success(
         species: dict,
         population: dict,
@@ -1095,7 +1065,8 @@ def load_data_success(
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def recompute_means(# pylint: disable=[unused-argument]
         species: dict,
         population: dict,
@@ -1171,7 +1142,8 @@ def recompute_phenotype_means_success_handler(job):
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def rerun_qtlreaper(# pylint: disable=[unused-argument]
         species: dict,
         population: dict,
@@ -1249,7 +1221,8 @@ def delete_phenotypes_success_handler(job):
 @with_dataset(
     species_redirect_uri="species.populations.phenotypes.index",
     population_redirect_uri="species.populations.phenotypes.select_population",
-    redirect_uri="species.populations.phenotypes.list_datasets")
+    redirect_uri="species.populations.phenotypes.list_datasets",
+    dataset_by_id=dataset_by_id)
 def delete_phenotypes(# pylint: disable=[unused-argument, too-many-locals]
         species: dict,
         population: dict,
diff --git a/uploader/static/css/layout-large.css b/uploader/static/css/layout-large.css
index 2d53627..c1950b1 100644
--- a/uploader/static/css/layout-large.css
+++ b/uploader/static/css/layout-large.css
@@ -52,6 +52,7 @@
 
         grid-column-start: 1;
         grid-column-end: 2;
+        overflow-x: auto;
     }
 
     #main #sidebar-content {
diff --git a/uploader/static/css/layout-medium.css b/uploader/static/css/layout-medium.css
index 50ceeb4..a29411d 100644
--- a/uploader/static/css/layout-medium.css
+++ b/uploader/static/css/layout-medium.css
@@ -52,6 +52,7 @@
 
         /* Define layout for the children elements */
         max-width: 100%;
+        overflow-x: auto;
     }
 
     #main #sidebar-content {
diff --git a/uploader/static/css/layout-small.css b/uploader/static/css/layout-small.css
index 2e47217..87dd910 100644
--- a/uploader/static/css/layout-small.css
+++ b/uploader/static/css/layout-small.css
@@ -56,6 +56,7 @@
     #main #main-content {
         grid-row-start: 2;
         grid-row-end: 3;
+        overflow-x: auto;
     }
 
     #main #sidebar-content {
diff --git a/uploader/static/js/files.js b/uploader/static/js/files.js
index 0bde6f7..7cb3d0e 100644
--- a/uploader/static/js/files.js
+++ b/uploader/static/js/files.js
@@ -116,3 +116,218 @@ var makeResumableElement = (targeturi, fileinput, droparea, uploadbutton, filety
 
     return resumable;
 };
+
+
+var CSVFilesMetadata = () => {
+    return {
+        "separator": $("#txt-file-separator").val(),
+        "comment_char": $(
+            "#txt-file-comment-character").val(),
+        "na_strings": $("#txt-file-na").val()
+    }
+};
+
+
+var updatePreview = (table, filedata, formdata, numrows) => {
+    table.find("thead tr").remove()
+    table.find(".data-row").remove();
+    var linenum = 0;
+    var tableheader = table.find("thead");
+    var tablebody = table.find("tbody");
+    var numheadings = 0;
+    var comment_chars = formdata
+        .comment_char
+        .split(" ")
+        .map((v) => {return v.trim();})
+        .filter((v) => {return Boolean(v);});
+    var navalues = formdata
+        .na_strings
+        .split(" ")
+        .map((v) => {return v.trim();})
+        .filter((v) => {return Boolean(v);});
+    filedata.forEach((line) => {
+        if(comment_chars.includes(line[0]) || linenum >= numrows) {
+            return false;
+        }
+        var row = $("<tr></tr>");
+        line.split(formdata.separator)
+            .map((field) => {
+                var value = field.trim();
+                if(navalues.includes(value)) {
+                    return "[NO-VALUE]";
+                }
+                return value;
+            })
+            .filter((field) => {
+                return (field !== "" && field != undefined && field != null);
+            })
+            .forEach((field) => {
+                if(linenum == 0) {
+                    numheadings += 1;
+                    var tablefield = $("<th></th>");
+                    tablefield.text(field);
+                    row.append(tablefield);
+                } else {
+                    add_class(row, "data-row");
+                    var tablefield = $("<td></td>");
+                    tablefield.text(field);
+                    row.append(tablefield);
+                }
+            });
+
+        if(linenum == 0) {
+            tableheader.append(row);
+        } else {
+            tablebody.append(row);
+        }
+        linenum += 1;
+    });
+
+    if(table.find("tbody tr.data-row").length > 0) {
+        add_class(table.find(".data-row-template"), "visually-hidden");
+    } else {
+        remove_class(table.find(".data-row-template"), "visually-hidden");
+    }
+};
+
+
+var makePreviewUpdater = (preview_table, preview_rows) => {
+    return (data) => {
+        updatePreview(
+            preview_table,
+            data,
+            CSVFilesMetadata(),
+            preview_rows);
+    };
+};
+
+
+var resumableDisplayFiles = (display_area, files) => {
+    files.forEach((file) => {
+        display_area.find(".file-display").remove();
+        var display_element = display_area
+            .find(".file-display-template")
+            .clone();
+        remove_class(display_element, "visually-hidden");
+        remove_class(display_element, "file-display-template");
+        add_class(display_element, "file-display");
+        display_element.find(".filename").text(file.name
+                                               || file.fileName
+                                               || file.relativePath
+                                               || file.webkitRelativePath);
+        display_element.find(".filesize").text(
+            (file.size / (1024*1024)).toFixed(2) + "MB");
+        display_element.find(".fileuniqueid").text(file.uniqueIdentifier);
+        display_element.find(".filemimetype").text(file.file.type);
+        display_area.append(display_element);
+    });
+};
+
+
+var indicateProgress = (resumable, progress_bar) => {
+    return () => {/*Has no event!*/
+        var progress = (resumable.progress() * 100).toFixed(2);
+        var pbar = progress_bar.find(".progress-bar");
+        remove_class(progress_bar, "visually-hidden");
+        pbar.css("width", progress+"%");
+        pbar.attr("aria-valuenow", progress);
+        pbar.text("Uploading: " + progress + "%");
+    };
+};
+
+
+var retryUpload = (retry_button, cancel_button) => {
+    retry_button.on("click", (event) => {
+        resumable.files.forEach((file) => {file.retry();});
+        add_class(retry_button, "visually-hidden");
+        remove_class(cancel_button, "visually-hidden");
+        add_class(browse_button, "visually-hidden");
+    });
+};
+
+
+var cancelUpload = (cancel_button, retry_button) => {
+    cancel_button.on("click", (event) => {
+        resumable.files.forEach((file) => {
+            if(file.isUploading()) {
+                file.abort();
+            }
+        });
+        add_class(cancel_button, "visually-hidden");
+        remove_class(retry_button, "visually-hidden");
+        remove_class(browse_button, "visually-hidden");
+    });
+};
+
+
+var startUpload = (browse_button, retry_button, cancel_button) => {
+    return (event) => {
+        remove_class(cancel_button, "visually-hidden");
+        add_class(retry_button, "visually-hidden");
+        add_class(browse_button, "visually-hidden");
+    };
+};
+
+
+var uploadSuccess = (file_input_name) => {
+    return (file, message) => {
+        submitForm({...JSON.parse(message), "file-input-name": file_input_name});
+    };
+};
+
+
+var uploadError = () => {
+    return (message, file) => {
+        $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled");
+        console.log("THE FILE:", file);
+        console.log("THE ERROR MESSAGE:", message);
+    };
+};
+
+var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id, filetypes=["csv", "tsv", "txt"], preview_rows=5) => {
+    var the_form = $("#" + form_id);
+    var file_input = $("#" + file_input_id);
+    var submit_button = the_form.find("input[type=submit]");
+    if(file_input.length != 1) {
+        return false;
+    }
+    var r = errorHandler(
+        fileSuccessHandler(
+            uploadStartHandler(
+                filesAddedHandler(
+                    markResumableDragAndDropElement(
+                        makeResumableElement(
+                            the_form.attr("data-resumable-target"),
+                            file_input.parent(),
+                            $("#" + resumable_element_id),
+                            submit_button,
+                            filetypes),
+                        file_input.parent(),
+                        $("#" + resumable_element_id),
+                        $("#" + resumable_element_id + "-browse-button")),
+                    (files) => {
+                        // TODO: Also trigger preview!
+                        resumableDisplayFiles(
+                            $("#" + resumable_element_id + "-selected-files"), files);
+                        files.forEach((file) => {
+                            readFirstNLines(
+                                file.file,
+                                100,
+                                [makePreviewUpdater(
+                                    $("#" + preview_table_id),
+                                    preview_rows)])
+                        });
+                    }),
+                startUpload($("#" + resumable_element_id + "-browse-button"),
+                            $("#" + resumable_element_id + "-retry-button"),
+                            $("#" + resumable_element_id + "-cancel-button"))),
+            uploadSuccess(file_input.attr("name"))),
+        uploadError());
+
+    /** Setup progress indicator **/
+    progressHandler(
+        r,
+        indicateProgress(r, $("#" + resumable_element_id + "-progress-bar")));
+
+    return r;
+};
diff --git a/uploader/templates/genotypes/add-genotypes-records-base.html b/uploader/templates/genotypes/add-genotypes-records-base.html
new file mode 100644
index 0000000..bf3812f
--- /dev/null
+++ b/uploader/templates/genotypes/add-genotypes-records-base.html
@@ -0,0 +1,39 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Genotypes{%endblock%}
+
+{%block pagetitle%}Genotypes{%endblock%}
+
+{%block contents%}
+
+<div class="row">
+  <form id="frm-add-genotypes-records"
+        method="POST"
+        enctype="multipart/form-data"
+        action="{{url_for(
+                'species.populations.genotypes.add_genotype_records',
+                species_id=species.SpeciesId, population_id=population.Id,
+                dataset_id=dataset.Id)}}"
+        data-resumable-target="{{url_for('files.resumable_upload_post')}}">
+    <legend>Add New Genotype Records</legend>
+
+    {%block frm_add_genotypes_records_elements%}{%endblock%}
+
+    <div class="form-group">
+      <input type="submit"
+             value="upload genotypes"
+             class="btn btn-primary" />
+    </div>
+  </form>
+</div>
+
+<div class="row">
+  <h2 class="heading" id="page-documentation">Help</h2>
+  {%block page_documentation%}{%endblock%}
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/genotypes/add-genotypes-records-csv.html b/uploader/templates/genotypes/add-genotypes-records-csv.html
new file mode 100644
index 0000000..58dbe81
--- /dev/null
+++ b/uploader/templates/genotypes/add-genotypes-records-csv.html
@@ -0,0 +1,146 @@
+{%extends "genotypes/add-genotypes-records-base.html"%}
+{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%}
+{%from "macro-csv-fields.html" import display_csv_fields, display_csv_fields_documentation%}
+{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%}
+
+{%block frm_add_genotypes_records_elements%}
+<div class="form-text help-block">
+  <p>You can add new genotype records here.</p>
+</div>
+
+{{display_csv_fields()}}
+
+<div class="form-group">
+  <div class="non-resumable-elements">
+    <label for="finput-genotypes-records-file" class="form-label">
+      genotypes records</label>
+    <input id="finput-genotypes-records-file"
+           name="genotypes-records-file"
+           class="form-control"
+           type="file"
+           data-preview-table="tbl-preview-geno-records"
+           required="required"  />
+    <span class="form-text text-muted">
+      Provide a file that contains only the genotypes records,
+      <a href="#docs-file-genotypes-records-csv"
+         title="Documentation of the genotypes records file format.">
+        the documentation for the expected format of the file</a>.</span>
+  </div>
+  {{display_resumable_elements(
+  "resumable-genotypes-records-file",
+  "Genotypes records",
+  '<p>Drag and drop the CSV file here, that contains the genotype records you
+    want to add.</p>
+
+  <p>Please see the
+    <a href="#docs-file-genotypes-records"
+       title="Documentation of the genotypes records data file format.">
+      "Genotypes records" documentation</a> section below for more
+    information on the expected format of the file provided here.</p>')}}
+  {{display_preview_table("tbl-preview-geno-records", "genotypes records")}}
+</div>
+
+<div class="">
+  <h4 class="subheading">Genotype Encoding</h4>
+  <div class="form-text help-block">
+    <p>The symbols in your genotype file need to be mapped to known values to
+      enable mapping.</p>
+  </div>
+
+  <div class="form-group">
+    <div class="row mb-3">
+      <label for="txt-geno-encoding-mat"
+             class="col-form-label col-sm-2">Maternal</label>
+      <div class="col-sm-10">
+        <div class="input-group">
+        <input type="text"
+               maxlength="3"
+               id="txt-geno-encoding-mat"
+               name="geno_encoding_mat"
+               class="form-control" />
+        <div class="input-group-append">
+          <span class="input-group-text">Value = -1</span>
+        </div>
+        </div>
+      </div>
+      <span class="form-text text-muted col-sm-12">
+        Enter the symbol in your file that represents the allele inherited from
+        the mother. This allele will be mapped to the value -1.</span>
+    </div>
+  </div>
+
+  <div class="form-group">
+    <div class="row mb-3">
+      <label for="txt-geno-encoding-pat"
+             class="col-form-label col-sm-2">Paternal</label>
+      <div class="col-sm-10">
+        <div class="input-group">
+          <input type="text"
+                 maxlength="3"
+                 id="txt-geno-encoding-pat"
+                 name="geno_encoding_pat"
+                 class="form-control" />
+          <div class="input-group-append">
+            <span class="input-group-text">Value = 1</span>
+          </div>
+        </div>
+      </div>
+      <span class="form-text text-muted">
+        Enter the symbol in your file that represents the allele inherited from
+        the father. This allele will be mapped to the value 1.</span>
+    </div>
+  </div>
+
+  <div class="form-group">
+    <div class="row mb-3">
+      <label for="txt-geno-encoding-het"
+             class="col-form-label col-sm-2">Heterozygous (value = 0)</label>
+      <div class="col-sm-10">
+        <div class="input-group">
+          <input type="text"
+                 maxlength="3"
+                 id="txt-geno-encoding-het"
+                 name="geno_encoding_het"
+                 class="form-control" />
+          <div class="input-group-append">
+            <span class="input-group-text">Value = 0</span>
+          </div>
+        </div>
+      </div>
+      <span class="form-text text-muted">
+        Enter the symbol in your file that represents the allele inherited from
+        both parents. This allele will be mapped to the value 0.</span>
+    </div>
+  </div>
+</div>
+{%endblock%}
+
+{%block page_documentation%}
+{{super()}}
+
+<h3 class="sub-heading">CSV file metadata</h3>
+{{display_csv_fields_documentation()}}
+{%endblock%}
+
+{%block javascript%}
+{{super()}}
+<script src="{{url_for('base.node_modules',
+             filename='resumablejs/resumable.js')}}"></script>
+<script src="/static/js/files.js"></script>
+
+<script type="text/javascript">
+  $(function(evt) {
+      
+      var preview_tables_to_elements_map = {
+          "#tbl-preview-geno-records": "#finput-genotypes-records-file",
+      };
+
+      makeResumableObject(
+          form_id="frm-add-genotypes-records",
+          file_input_id="finput-genotypes-records-file",
+          resumable_element_id="resumable-genotypes-records-file",
+          preview_table_id="tbl-preview-geno-records",
+          filetypes=["csv", "tsv", "txt", "geno"]);
+  });
+</script>
+{%endblock%}
diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html
index 8d1b951..c2abc63 100644
--- a/uploader/templates/genotypes/base.html
+++ b/uploader/templates/genotypes/base.html
@@ -1,10 +1,11 @@
 {%extends "populations/base.html"%}
 {%from "populations/macro-display-population-card.html" import display_sui_population_card%}
+{%from "genotypes/macro-display-dataset-card.html" import display_dataset_card%}
 
 {%block breadcrumbs%}
 {{super()}}
 <li class="breadcrumb-item">
-  <a href="{{url_for('species.populations.genotypes.list_genotypes',
+  <a href="{{url_for('species.populations.genotypes.index',
            species_id=species['SpeciesId'],
            population_id=population['Id'])}}">
     genotype
@@ -14,5 +15,9 @@
 
 
 {%block sidebarcontents%}
+{%if dataset is defined and dataset is not none%}
+{{display_dataset_card(species, population, dataset)}}
+{%else%}
 {{display_sui_population_card(species, population)}}
+{%endif%}
 {%endblock%}
diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html
index ff174fb..7f435a1 100644
--- a/uploader/templates/genotypes/create-dataset.html
+++ b/uploader/templates/genotypes/create-dataset.html
@@ -40,9 +40,7 @@
              readonly="readonly" />
       <small class="form-text text-muted">
         <p>This is a short representative, but constrained name for the genotype
-          dataset.<br />
-          It is used internally by the Genenetwork system. Do not change this
-          value.</p>
+          dataset. It is used internally by GeneNetwork.</p>
       </small>
     </div>
 
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
new file mode 100644
index 0000000..1c3483d
--- /dev/null
+++ b/uploader/templates/genotypes/index.html
@@ -0,0 +1,200 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Genotypes{%endblock%}
+
+{%block pagetitle%}Genotypes{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+
+{%if dataset is defined and dataset is not none%}
+
+<div class="row">
+  <h2>Genotype Data</h2>
+
+  <div class="row">
+    <div class="col">
+      <p>
+        <a href="{{url_for(
+                 'species.populations.genotypes.add_genotype_records',
+                 species_id=species.SpeciesId, population_id=population.Id,
+                 dataset_id=dataset.Id)}}"
+           class="btn btn-primary">
+          Add genotype records
+        </a>
+      </p>
+    </div>
+  </div>
+
+  <div class="table-responsive">
+    <table id="tbl-genotype-records" class="table compact stripe cell-border">
+      <thead>
+        <tr>
+          <th title="">#</th>
+          <th title="">Index</th>
+          <th title="Locus of marker on the chromosome">Locus</th>
+          <th title="Chromosome">Chr</th>
+          <th title="Physical location of marker in centimorgans">cM</th>
+          <th title="Physical location of marker in megabasepairs">Mb</th>
+          {%for sample in samples%}
+          <th title="Data for sample {{sample}}">{{sample}}</th>
+          {%endfor%}
+        </tr>
+      </thead>
+
+      <tbody>
+        {%for record in genotype_records%}
+        <tr>
+          <td>
+            <input type="checkbox"
+                   id="chk-geno-record-{{record.Id}}"
+                   name="geno_record_id"
+                   value="{{record.Id}}" />
+          </td>
+          <td>{{record.index}}</td>
+          <td>{{record.Name}}</td>
+          <td>{{record.Chr}}</td>
+          <td>{{record.cM}}</td>
+          <td>{{record.Mb}}</td>
+          {%for sample in samples%}
+          <td>{{record.data[sample]}}</td>
+          {%endfor%}
+        </tr>
+        {%else%}
+        <tr>
+          <td colspan="6" class="text-info">
+            There are no records
+          </td>
+        </tr>
+        {%endfor%}
+      </tbody>
+    </table>
+  </div>
+</div>
+
+<div class="row">
+  <h2>Genotype Encoding</h2>
+  <p>The numerical values in the table above are mapped from the following allele symbols:</p>
+
+  <table class="table">
+    <thead>
+      <tr>
+        <th>Allele Type</th>
+        <th>Allele Symbol</th>
+        <th>Mapped To</th>
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for row in genocode%}
+      <tr>
+        <td {%if row.AlleleType == 'mat'%}
+            title="Maternal allele"
+            {%elif row.AlleleType == "pat"%}
+            title="Paternal allele"
+            {%elif row.AlleleType == "het"%}
+            title="Heterozygous allele"
+            {%else%}
+            title="Unknown allele"
+            {%endif%}>
+          {{row.AlleleType}}</td>
+        <td>{{row.AlleleSymbol}}</td>
+        <td>{{row.DatabaseValue if row.DatabaseValue is not none}}</td>
+      </tr>
+      {%else%}
+      <tr>
+        <td colspan="3" class="text-info">
+          There is no genotype encoding defined for this data.
+        </td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+</div>
+
+{%else%}
+
+<div class="row">
+  <p>We need to create a dataset to hold the genotype information for this
+    species/population, before we can proceed to upload the genotype data.</p>
+  <p>Please click the button below to create the dataset.</p>
+
+  <div class="col">
+  <a href="{{url_for('species.populations.genotypes.create_dataset', species_id=species.SpeciesId, population_id=population.Id)}}"
+     class="btn btn-primary">create genotype dataset</a>
+  </div>
+</div>
+
+{%endif%}
+
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+  $(function() {
+      var genoRecordsUrl = "{{url_for('species.populations.genotypes.index', species_id=species.SpeciesId, population_id=population.Id)}}";
+
+      var dtGenotypeRecords = false;
+      fetch(genoRecordsUrl, {
+          method: "POST",
+          headers: {
+              "Accept": "application/json",
+              "Content-Type": "application/json"
+          },
+          body: JSON.stringify({})
+      })
+          .then(response => response.json())
+          .then(recordsData => {
+              var records = recordsData.genotype_records;
+              var samples = recordsData.samples_order;
+              var columns = [
+                  {
+                      data: function(record) {
+                          return `<input type="checkbox"`
+                              + `id="chk-geno-record-` + record.Id + `"`
+                              + `name="geno_record_id"`
+                              + `value="` + record.Id + `"`
+                              + ` />`;
+                      }
+                  },
+                  {data: "index"},
+                  {data: "Name"},
+                  {data: "Chr"},
+                  {data: "cM"},
+                  {data: "Mb"}
+              ].concat(samples.map((sample) => {
+                  return {data: (record) => record.data[sample]};
+              }));
+
+              dtGenotypeRecords = buildDataTable(
+                  "#tbl-genotype-records",
+                  [],
+                  columns,
+                  {
+                      serverSide: true,
+                      ajax: {
+                          url: genoRecordsUrl,
+                          dataSrc: "genotype_records",
+                          recordsTotal: "total_genotype_records",
+                          recordsFiltered: "fetched_genotype_records"
+                      },
+                      paging: true,
+                      scroller: true,
+                      scrollY: "50vh",
+                      scrollCollapse: false,
+                      layout: {
+                          top: "info",
+                          topStart: null,
+                          topEnd: null,
+                          bottom: null,
+                          bottomStart: null,
+                          bottomEnd: null
+                      }
+                  });
+          });
+  });
+</script>
+{%endblock%}
diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html
deleted file mode 100644
index 131576f..0000000
--- a/uploader/templates/genotypes/list-genotypes.html
+++ /dev/null
@@ -1,226 +0,0 @@
-{%extends "genotypes/base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Genotypes{%endblock%}
-
-{%block pagetitle%}Genotypes{%endblock%}
-
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <h2>Genotype Encoding</h2>
-  <p>
-    The genotype encoding used for the "{{population.FullName}}" population from
-    the "{{species.FullName}}" species is as shown in the table below.
-  </p>
-  <table class="table">
-
-    <thead>
-      <tr>
-        <th>Allele Type</th>
-        <th>Allele Symbol</th>
-        <th>Allele Value</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      {%for row in genocode%}
-      <tr>
-        <td>{{row.AlleleType}}</td>
-        <td>{{row.AlleleSymbol}}</td>
-        <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td>
-      </tr>
-      {%else%}
-      <tr>
-        <td colspan="7" class="text-info">
-          <span class="glyphicon glyphicon-exclamation-sign"></span>
-          There is no explicit genotype encoding defined for this population.
-        </td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-
-  {%if genocode | length < 1%}
-  <div class="col">
-    <a href="#add-genotype-encoding"
-       title="Add a genotype encoding system for this population"
-       class="btn btn-primary not-implemented">
-      define genotype encoding
-    </a>
-  </div>
-  {%endif%}
-</div>
-
-<div class="row">
-  <h2>Genotype Dataset</h2>
-</div>
-
-{%if dataset is not none%}
-
-<div class="row">
-  <h3>Dataset Details</h3>
-  <table class="table">
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Full Name</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      <tr>
-        <td>{{dataset.Name}}</td>
-        <td><a href="{{url_for('species.populations.genotypes.view_dataset',
-                     species_id=species.SpeciesId,
-                     population_id=population.Id,
-                     dataset_id=dataset.Id)}}"
-               title="View details regarding and manage dataset '{{dataset.FullName}}'"
-               target="_blank">
-            {{dataset.FullName}}</a></td>
-      </tr>
-    </tbody>
-  </table>
-
-  <p>
-    To see more information regarding this dataset (e.g. which markers have
-    sample allele data, the allele data itself, etc) click on the "Full Name"
-    link above.</p>
-</div>
-
-<div class="row">
-  <h3>Genotype Markers</h3>
-
-  <div class="row">
-    <p>
-      The table below lists all of the markers that exist for species
-      {{species.SpeciesName}} ({{species.FullName}}), regardless of whether
-      (or not) we have corresponding sample allele data for a particular marker.
-    </p>
-  <table id="tbl-genetic-markers" class="table compact stripe cell-border">
-    <thead>
-      <tr>
-        <th title="">#</th>
-        <th title="">Index</th>
-        <th title="">Marker Name</th>
-        <th title="Chromosome">Chr</th>
-        <th title="Physical location of the marker in megabasepairs">
-          Location (Mb)</th>
-        <th title="">Source</th>
-        <th title="">Source2</th>
-    </thead>
-
-    <tbody>
-      {%for marker in markers%}
-      <tr>
-        <td></td>
-        <td></td>
-        <td></td>
-        <td></td>
-        <td></td>
-        <td></td>
-        <td></td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-</div>
-
-{%else%}
-
-<div class="row">
-  <p>
-    Your genotype data will need to be under a dataset. Unfortunately there is
-    currently no dataset defined for this population.
-  </p>
-
-  <p class="text-warning">
-    <span class="glyphicon glyphicon-exclamation-sign"></span>
-    Click the button below to define the genotype dataset for this population.
-  </p>
-  <p>
-    <a href="{{url_for('species.populations.genotypes.create_dataset',
-             species_id=species.SpeciesId,
-             population_id=population.Id)}}"
-       title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species."
-       class="btn btn-primary">
-      create new genotype dataset</a></p>
-</div>
-
-{%endif%}
-
-<div class="row">
-  <h2>Notes</h2>
-  <div class="row text-danger">
-    <h3>Genetic Markers: Some Important Concepts to Consider/Remember</h3>
-    <ul>
-      <li>Reference vs. Non-reference alleles</li>
-      <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li>
-    </ul>
-    <h3>Possible references</h3>
-    <ul>
-      <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li>
-      <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li>
-    </ul>
-  </div>
-
-  <div class="row text-warning">
-    <h3>Genotype Dataset</h3>
-    <p>
-      <span class="glyphicon glyphicon-exclamation-sign"></span>
-      <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a
-      single genotype dataset per population. If there is more than one, the
-      system apparently fails in unpredictable ways.
-    </p>
-  </div>
-</div>
-
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript">
-
-  $(function() {
-      var dtGeneticMarkers = buildDataTable(
-          "#tbl-genetic-markers",
-          [],
-          [
-              {
-                  data: function(marker) {
-                      return `<input type="checkbox" name="selected-markers" ` +
-                          `id="chk-selected-markers-${marker.Id}-${marker.GenoFreezeId}" ` +
-                          `value="${marker.Id}_${marker.GenoFreezeId}" ` +
-                          `class="chk-row-select" />`;
-                  }
-              },
-              {data: 'index'},
-              {data: "Name", searchable: true},
-              {data: "Chr", searchable: true},
-              {data: "Mb", searchable: true},
-              {data: "Source", searchable: true},
-              {data: "Source2", searchable: true}
-          ],
-          {
-              ajax: {
-                  url: "{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id)}}",
-                  dataSrc: "markers"
-              },
-              paging: true,
-              scroller: true,
-              scrollY: "50vh",
-              scrollCollapse: true,
-              layout: {
-                  top: "info",
-                  topStart: null,
-                  topEnd: null,
-                  bottom: null,
-                  bottomStart: null,
-                  bottomEnd: null
-              }
-          });
-  });
-
-</script>
-{%endblock%}
diff --git a/uploader/templates/genotypes/macro-display-dataset-card.html b/uploader/templates/genotypes/macro-display-dataset-card.html
new file mode 100644
index 0000000..2b197d4
--- /dev/null
+++ b/uploader/templates/genotypes/macro-display-dataset-card.html
@@ -0,0 +1,24 @@
+{%from "populations/macro-display-population-card.html" import display_sui_population_card%}
+
+{%macro display_dataset_card(species, population, dataset)%}
+{{display_sui_population_card(species, population)}}
+<div class="row">
+  <table class="table">
+    <caption>Current genotype dataset</caption>
+    <tbody>
+      <tr>
+        <th>Name</th>
+        <td>{{dataset.Name}}</td>
+      </tr>
+      <tr>
+        <th>Full Name</th>
+        <td>{{dataset.FullName}}</td>
+      </tr>
+      <tr>
+        <th>Short Name</th>
+        <td>{{dataset.ShortName}}</td>
+      </tr>
+    </tbody>
+  </table>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/macro-csv-fields.html b/uploader/templates/macro-csv-fields.html
new file mode 100644
index 0000000..d4b0f57
--- /dev/null
+++ b/uploader/templates/macro-csv-fields.html
@@ -0,0 +1,102 @@
+{%macro display_csv_fields()%}
+<div class="form-group">
+  <label for="txt-file-separator" class="form-label">File Separator</label>
+  <div class="input-group">
+    <input id="txt-file-separator"
+           name="file-separator"
+           type="text"
+           value="&#9;"
+           class="form-control"
+           maxlength="1" />
+    <span class="input-group-btn">
+      <button id="btn-reset-file-separator" class="btn btn-info">Reset Default</button>
+    </span>
+  </div>
+  <span class="form-text text-muted">
+    Provide the character that separates the fields in your file(s). It should
+    be the same character for all files (if more than one is provided).<br />
+    A tab character will be assumed if you leave this field blank. See
+    <a href="#docs-file-separator"
+       title="Documentation for file-separator characters">
+      documentation for more information</a>.
+  </span>
+</div>
+
+<div class="form-group">
+  <label for="txt-file-comment-character" class="form-label">File Comment-Characters</label>
+  <div class="input-group">
+    <input id="txt-file-comment-character"
+           name="file-comment-character"
+           type="text"
+           value="#"
+           class="form-control" />
+    <span class="input-group-btn">
+      <button id="btn-reset-file-comment-character" class="btn btn-info">
+        Reset Default</button>
+    </span>
+  </div>
+  <span class="form-text text-muted">
+    This specifies that lines that begin with the character(s) provided will be
+    considered comment lines and ignored in their entirety. See
+    <a href="#docs-file-comment-character"
+       title="Documentation for comment characters">
+      documentation for more information</a>.
+  </span>
+</div>
+
+<div class="form-group">
+  <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label>
+  <div class="input-group">
+    <input id="txt-file-na"
+           name="file-na"
+           type="text"
+           value="- NA N/A"
+           class="form-control" />
+    <span class="input-group-btn">
+      <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button>
+    </span>
+  </div>
+  <span class="form-text text-muted">
+    This specifies strings in your file indicate that there is no value for a
+    particular cell (a cell is where a column and row intersect). Provide a
+    space-separated list of strings if you have more than one way of
+    indicating no values. See
+    <a href="#docs-file-na" title="Documentation for no-value fields">
+      documentation for more information</a>.</span>
+</div>
+{%endmacro%}
+
+
+{%macro display_csv_fields_documentation()%}
+<dl>
+  <dt id="docs-file-separator">File separator</dt>
+  <dd>The files you provide should be character-separated value (CSV) files.
+    We need to know what character you used to separate the values in your
+    file. Some common ones are the Tab character, the comma, etc.<br />
+    Providing that information makes it possible for the system to parse and
+    process your files correctly.<br>
+    <strong>NOTE:</strong> All the files you upload MUST use the same
+    separator.</dd>
+
+  <dt id="docs-file-comment-character">Comment characters</dt>
+  <dd>We support use of comment lines in your files. We only support one type
+    of comment style, the <em>line comment</em>.<br />
+    This mean the comment begins at the start of the line, and the end of that
+    line indicates the end of that comment. If you have a really long comment,
+    then you need to break it across multiple lines, marking each line a
+    comment line.<br />
+    The "comment character" is the character at the start of the line that
+    indicates that the line is a line comment.<br />
+    You can provide more than one comment character, separated by spaces.</dd>
+
+  <dt id="docs-file-na">No-Value indicator(s)</dt>
+  <dd>Data in the real world is messy, and in some cases, entirely absent. You
+    need to indicate, in your files, that a particular field did not have a
+    value, and once you do that, you then need to let the system know how you
+    mark such fields. Common ways of indicating "empty values" are, leaving
+    the field blank, using a character such as '-', or using strings like
+    "NA", "N/A", "NULL", etc.<br />
+    Providing this information will help with parsing and processing such
+    no-value fields the correct way.</dd>
+</dl>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 3bb2586..fc84757 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -148,14 +148,36 @@
                       return `<a href="${url.toString()}" target="_blank">` +
                           `${pheno.InbredSetCode}_${pheno.xref_id}` +
                           `</a>`;
-                  }
+                  },
+                  title: "Record",
+                  visible: true,
+                  searchable: true
               },
               {
                   data: function(pheno) {
                       return (pheno.Post_publication_description ||
                               pheno.Original_description ||
                               pheno.Pre_publication_description);
-                  }
+                  },
+                  title: "Description",
+                  visible: true,
+                  searchable: true
+              },
+              {
+                  data: function(pheno) {
+                      return pheno.publication.Title;
+                  },
+                  title: "Publication Title",
+                  visible: false,
+                  searchable: true
+              },
+              {
+                  data: function(pheno) {
+                      return pheno.publication.Authors;
+                  },
+                  title: "Authors",
+                  visible: false,
+                  searchable: true
               }
           ],
           {
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 29add29..6da4cd7 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -4,7 +4,7 @@
 
 {%block contents%}
 <div class="row">
-  <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2>
+  <h2 class="heading">Population: {{population.FullName}} ({{population.Name}})</h2>
 </div>
 
 <div class="row">
@@ -58,14 +58,18 @@
          aria-labelledby="samples-content-tab">
       <p>Think of a <strong>"sample"</strong> as say a single case or individual
         in the experiment. It could even be a single strain (where applicable).
+        These are, effectively, identifiers for the organisms (plants, animals,
+        etc) that your data is collected from, and is about.
       </p>
-      <p>This is a convenience feature for when you want to upload phenotypes to
-        the system, but do not have the genotypes data ready yet.</p>
+
+      <p>The samples should be uploaded before any of the other types of data
+        (genotype, phenotype, expression, etc.), or be bundled together with
+        them, since they all need references to the samples.</p>
       <a href="{{url_for('species.populations.samples.list_samples',
                species_id=species.SpeciesId,
                population_id=population.Id)}}"
          title="View and upload samples for population '{{population['Name']}}'"
-         class="btn btn-primary">Manage Samples</a>
+         class="btn btn-primary">manage samples</a>
     </div>
 
     <div class="tab-pane fade show active"
@@ -74,9 +78,11 @@
          aria-labelledby="phenotypes-content-tab">
 
       <div class="row" style="margin-top: 1em;">
-        <h3> Phenotypes in  Population "{{population.FullName}} ({{population.Name}})"</h3>
-
-        <p>To view existing phenotype traits, or upload new ones, click the button below:</p>
+        <p>Phenotype data measures the actual observable traits or
+          characteristics of an organism e.g. physical appearance, biochemical
+          properties, development, behaviour and/or disease states.</p>
+        <p>This section enables you to view existing and/or upload new phenotype
+          data.</p>
 
         <div class="row">
           <div class="col">
@@ -85,7 +91,7 @@
                      species_id=species.SpeciesId,
                      population_id=population.Id)}}"
                title="View and upload phenotype traits"
-               class="btn btn-primary">Phenotypes</a>
+               class="btn btn-primary">manage phenotypes</a>
           </div>
         </div>
       </div>
@@ -95,17 +101,20 @@
          id="genotypes-content"
          role="tabpanel"
          aria-labelledby="genotypes-content-tab">
-      <p>Click the button to view and manage genetic data for individuals in
-        this population.</p>
-      <a href="{{url_for('species.populations.genotypes.list_genotypes',
+      <p>Genotype data records specific genetic variations (e.g. single
+        nucleotide polymorphisms (SNPs)) present at particular locations in an
+        individual's (see "Samples" section) DNA.</p>
+      <p>Click the button below to view existing and/or upload new genotype data
+        for this population.</p>
+      <a href="{{url_for('species.populations.genotypes.index',
                species_id=species.SpeciesId,
                population_id=population.Id)}}"
          title="Upload genotype information for the '{{population.FullName}}' population of the '{{species.FullName}}' species."
          class="btn btn-primary">manage genotypes</a>
     </div>
     <div class="tab-pane fade" id="expression-data-content" role="tabpanel" aria-labelledby="expression-data-content-tab">
-      <p>Upload expression data (mRNA data) for this population.</p>
-      <a href="#" title="" class="btn btn-primary">upload genotypes</a>
+      <p>Expression data is data measuring how much genes are turned on or active.</p>
+      <a href="#" title="" class="btn btn-primary">manage expression data</a>
     </div>
   </div>
 </div>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-09-15 10:19:06 +0000