Phenotypes: Move feature to new UI templates.

18 files changed, 43 insertions, 1835 deletions

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 42f2e34..c4c6170 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -31,9 +31,6 @@ from flask import (flash,
 from r_qtl import r_qtl2_qc as rqc
 from r_qtl import exceptions as rqe
 
-
-from uploader.sui import sui_template
-
 from uploader import jobs
 from uploader import session
 from uploader.files import save_file
@@ -197,7 +194,7 @@ def view_dataset(# pylint: disable=[unused-argument]
 
         start_at = max(safe_int(request.args.get("start_at") or 0), 0)
         count = int(request.args.get("count") or 20)
-        return render_template(sui_template("phenotypes/view-dataset.html"),
+        return render_template("phenotypes/view-dataset.html",
                                species=species,
                                population=population,
                                dataset=dataset,
@@ -420,9 +417,9 @@ def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs):# p
         if request.method == "GET":
             today = datetime.date.today()
             return render_template(
-                sui_template("phenotypes/add-phenotypes-with-rqtl2-bundle.html"
-                             if use_bundle
-                             else "phenotypes/add-phenotypes-raw-files.html"),
+                ("phenotypes/add-phenotypes-with-rqtl2-bundle.html"
+                 if use_bundle
+                 else "phenotypes/add-phenotypes-raw-files.html"),
                 species=species,
                 population=population,
                 dataset=dataset,
@@ -509,7 +506,7 @@ def job_status(
         except jobs.JobNotFound as _jnf:
             job = None
 
-        return render_template(sui_template("phenotypes/job-status.html"),
+        return render_template("phenotypes/job-status.html",
                                species=species,
                                population=population,
                                dataset=dataset,
@@ -589,7 +586,7 @@ def review_job_data(
             for filetype,meta in metadata.items()
         }
         _job_metadata = json.loads(job["job-metadata"])
-        return render_template(sui_template("phenotypes/review-job-data.html"),
+        return render_template("phenotypes/review-job-data.html",
                                species=species,
                                population=population,
                                dataset=dataset,
@@ -980,7 +977,7 @@ def load_data_success(
                               (_publication["Title"] or ""))
                              if item != "")
             return render_template(
-                sui_template("phenotypes/load-phenotypes-success.html"),
+                "phenotypes/load-phenotypes-success.html",
                 species=species,
                 population=population,
                 dataset=dataset,
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html
index 9909c20..690c7e1 100644
--- a/uploader/templates/phenotypes/add-phenotypes-base.html
+++ b/uploader/templates/phenotypes/add-phenotypes-base.html
@@ -1,26 +1,13 @@
 {%extends "phenotypes/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
 
 {%block title%}Phenotypes{%endblock%}
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="add-phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">Add Phenotypes</a>
-</li>
-{%endblock%}
-
 {%block contents%}
+{{super()}}
 {{flash_all_messages()}}
 
 <div class="row">
@@ -83,6 +70,8 @@
 {%endblock%}
 
 
+
+
 {%block javascript%}
 <script type="text/javascript">
   $(function() {
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index 67b56e3..a02fae7 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -1,7 +1,6 @@
 {%extends "phenotypes/add-phenotypes-base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
 {%from "phenotypes/macro-display-preview-table.html" import display_preview_table%}
 {%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%}
 
@@ -9,19 +8,6 @@
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="add-phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">Add Phenotypes</a>
-</li>
-{%endblock%}
-
 {%block frm_add_phenotypes_documentation%}
 <p>This page will allow you to upload all the separate files that make up your
   phenotypes. Here, you will have to upload each separate file individually. If
@@ -447,10 +433,6 @@
 
 {%endblock%}
 
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
-
 
 {%block more_javascript%}
 <script src="{{url_for('base.node_modules',
diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
index 898fc0c..4afd6ab 100644
--- a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
+++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html
@@ -1,25 +1,11 @@
 {%extends "phenotypes/add-phenotypes-base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
 
 {%block title%}Phenotypes{%endblock%}
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="add-phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">Add Phenotypes</a>
-</li>
-{%endblock%}
-
 {%block frm_add_phenotypes_documentation%}
 <p>Select the zip file bundle containing information on the phenotypes you
   wish to upload, then click the "Upload Phenotypes" button below to
@@ -201,7 +187,3 @@
     <em>phenotypes × individuals</em>.</p>
 </div>
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html
index adbc012..fe7ccd3 100644
--- a/uploader/templates/phenotypes/base.html
+++ b/uploader/templates/phenotypes/base.html
@@ -1,19 +1,25 @@
 {%extends "populations/base.html"%}
+{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%}
 
-{%block lvl3_breadcrumbs%}
-<li {%if activelink=="phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  {%if dataset is mapping%}
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
   <a href="{{url_for('species.populations.phenotypes.view_dataset',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">{{dataset.Name}}</a>
-  {%else%}
-  <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a>
-  {%endif%}
+           species_id=species['SpeciesId'],
+           population_id=population['Id'],
+           dataset_id=dataset['Id'])}}">
+    {{dataset["Name"]}}
+  </a>
 </li>
-{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+  <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2>
+</div>
+{%endblock%}
+
+
+{%block sidebarcontents%}
+{{display_sui_pheno_dataset_card(species, population, dataset)}}
 {%endblock%}
diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html
index 257f726..0bbe8e0 100644
--- a/uploader/templates/phenotypes/job-status.html
+++ b/uploader/templates/phenotypes/job-status.html
@@ -2,7 +2,6 @@
 {%from "cli-output.html" import cli_output%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
 
 {%block extrameta%}
 {%if job and job.status not in ("success", "completed:success", "error", "completed:error")%}
@@ -14,23 +13,13 @@
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="add-phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">View Datasets</a>
-</li>
-{%endblock%}
-
 {%block contents%}
 
 {%if job%}
-<h4 class="subheading">Progress</h4>
+<div class="row">
+  <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2>
+  <h3 class="subheading">upload progress</h3>
+</div>
 <div class="row" style="overflow:scroll;">
   <p><strong>Process Status:</strong> {{job.status}}</p>
   {%if metadata%}
@@ -80,7 +69,7 @@
   {%endif%}
 </div>
 
-<h4 class="subheading">Errors</h4>
+<h3 class="subheading">upload errors</h3>
 <div class="row" style="max-height: 20em; overflow: scroll;">
   {%if errors | length == 0 %}
   <p class="text-info">
@@ -149,7 +138,3 @@
 </div>
 {%endif%}
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html
index 645be16..1fb0e61 100644
--- a/uploader/templates/phenotypes/load-phenotypes-success.html
+++ b/uploader/templates/phenotypes/load-phenotypes-success.html
@@ -1,26 +1,14 @@
 {%extends "phenotypes/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
 
 {%block title%}Phenotypes{%endblock%}
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="load-phenotypes-success"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">Add Phenotypes</a>
-</li>
-{%endblock%}
-
 {%block contents%}
+{{super()}}
+
 <div class="row">
   <p>You have successfully loaded
     <!-- maybe indicate the number of phenotypes here? -->your
@@ -34,9 +22,5 @@
 </div>
 {%endblock%}
 
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
-
 
 {%block more_javascript%}{%endblock%}
diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html
index 859df74..c8355b2 100644
--- a/uploader/templates/phenotypes/review-job-data.html
+++ b/uploader/templates/phenotypes/review-job-data.html
@@ -104,10 +104,6 @@
 {%endif%}
 {%endblock%}
 
-{%block sidebarcontents%}
-{{display_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
-
 
 {%block javascript%}
 <script type="text/javascript">
diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-base.html b/uploader/templates/phenotypes/sui-add-phenotypes-base.html
deleted file mode 100644
index 1e71267..0000000
--- a/uploader/templates/phenotypes/sui-add-phenotypes-base.html
+++ /dev/null
@@ -1,155 +0,0 @@
-{%extends "phenotypes/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block contents%}
-{{super()}}
-{{flash_all_messages()}}
-
-<div class="row">
-  <form id="frm-add-phenotypes"
-        method="POST"
-        enctype="multipart/form-data"
-        action="{{url_for('species.populations.phenotypes.add_phenotypes',
-                species_id=species.SpeciesId,
-                population_id=population.Id,
-                dataset_id=dataset.Id,
-                use_bundle=use_bundle)}}"
-        data-resumable-target="{{url_for('files.resumable_upload_post')}}">
-    <legend>Add New Phenotypes</legend>
-
-    <div class="form-text help-block">
-      {%block frm_add_phenotypes_documentation%}{%endblock%}
-      <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p>
-    </div>
-
-    {%block frm_add_phenotypes_elements%}{%endblock%}
-
-    <fieldset id="fldset-publication-info">
-      <legend>Publication Information</legend>
-      <input type="hidden" name="publication-id" id="txt-publication-id" />
-      <span class="form-text text-muted">
-        Select a publication for your data. <br />
-        Can't find a publication you can use? Go ahead and
-        <a href="{{url_for(
-                 'publications.create_publication',
-                 return_to='species.populations.phenotypes.add_phenotypes',
-                 species_id=species.SpeciesId,
-                 population_id=population.Id,
-                 dataset_id=dataset.Id)}}">create a new publication</a>.</span>
-      <table id="tbl-select-publication" class="table compact stripe">
-        <thead>
-          <tr>
-            <th>#</th>
-            <th>PubMed ID</th>
-            <th>Title</th>
-            <th>Authors</th>
-          </tr>
-        </thead>
-
-        <tbody></tbody>
-      </table>
-    </fieldset>
-
-    <div class="form-group">
-      <input type="submit"
-             value="upload phenotypes"
-             class="btn btn-primary" />
-    </div>
-  </form>
-</div>
-
-<div class="row">
-  {%block page_documentation%}{%endblock%}
-</div>
-
-{%endblock%}
-
-
-
-
-{%block javascript%}
-<script type="text/javascript">
-  $(function() {
-      var publicationsDataTable = buildDataTable(
-          "#tbl-select-publication",
-          [],
-          [
-              {data: "index"},
-              {
-                  searchable: true,
-                  data: (pub) => {
-                      if(pub.PubMed_ID) {
-                          return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
-                              `${pub.PubMed_ID}/" target="_blank" ` +
-                              `title="Link to publication on NCBI.">` +
-                              `${pub.PubMed_ID}</a>`;
-                      }
-                      return "";
-                  }
-              },
-              {
-                  searchable: true,
-                  data: (pub) => {
-                      var title = "⸻";
-                      if(pub.Title) {
-                          title = pub.Title
-                      }
-                      return `<a href="/publications/view/${pub.Id}" ` +
-                          `target="_blank" ` +
-                          `title="Link to view publication details">` +
-                          `${title}</a>`;
-                  }
-              },
-              {
-                  searchable: true,
-                  data: (pub) => {
-                      authors = pub.Authors.split(",").map(
-                          (item) => {return item.trim();});
-                      if(authors.length > 1) {
-                          return authors[0] + ", et. al.";
-                      }
-                      return authors[0];
-                  }
-              }
-          ],
-          {
-              serverSide: true,
-              ajax: {
-                  url: "/publications/list",
-                  dataSrc: "publications"
-              },
-              select: "single",
-              paging: true,
-              scrollY: 700,
-              deferRender: true,
-              scroller: true,
-              scrollCollapse: true,
-              layout: {
-                  topStart: "info",
-                  topEnd: "search"
-              }
-          });
-      publicationsDataTable.on("select", (event, datatable, type, indexes) => {
-          indexes.forEach((element, index, thearray) => {
-              let row = datatable.row(element).node();
-              console.debug(datatable.row(element).data());
-              $("#frm-add-phenotypes #txt-publication-id").val(
-                  datatable.row(element).data().Id);
-          });
-      });
-      publicationsDataTable.on("deselect", (event, datatable, type, indexes) => {
-          indexes.forEach((element, index, thearray) => {
-              let row = datatable.row(element).node();
-              $("#frm-add-phenotypes #txt-publication-id").val(null);
-          });
-      });
-  });
-</script>
-
-{%block more_javascript%}{%endblock%}
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html b/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html
deleted file mode 100644
index 6038617..0000000
--- a/uploader/templates/phenotypes/sui-add-phenotypes-raw-files.html
+++ /dev/null
@@ -1,829 +0,0 @@
-{%extends "phenotypes/sui-add-phenotypes-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-preview-table.html" import display_preview_table%}
-{%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block frm_add_phenotypes_documentation%}
-<p>This page will allow you to upload all the separate files that make up your
-  phenotypes. Here, you will have to upload each separate file individually. If
-  you want instead to upload all your files as a single ZIP file,
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id,
-           use_bundle=true)}}"
-     title="">click here</a>.</p>
-{%endblock%}
-
-{%block frm_add_phenotypes_elements%}
-<fieldset id="fldset-file-metadata">
-  <legend>File(s) Metadata</legend>
-  <div class="form-group">
-    <label for="txt-file-separator" class="form-label">File Separator</label>
-    <div class="input-group">
-      <input id="txt-file-separator"
-             name="file-separator"
-             type="text"
-             value="&#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-Character</label>
-    <div class="input-group">
-      <input id="txt-file-comment-character"
-             name="file-comment-character"
-             type="text"
-             value="#"
-             class="form-control"
-             maxlength="1" />
-      <span class="input-group-btn">
-        <button id="btn-reset-file-comment-character" class="btn btn-info">
-          Reset Default</button>
-      </span>
-    </div>
-    <span class="form-text text-muted">
-      This specifies that lines that begin with the character provided will be
-      considered comment lines and ignored in their entirety. See
-      <a href="#docs-file-comment-character"
-         title="Documentation for comment characters">
-        documentation for more information</a>.
-    </span>
-  </div>
-
-  <div class="form-group">
-    <label for="txt-file-na" class="form-label">File "No-Value" Indicators</label>
-    <div class="input-group">
-      <input id="txt-file-na"
-             name="file-na"
-             type="text"
-             value="- NA N/A"
-             class="form-control" />
-      <span class="input-group-btn">
-        <button id="btn-reset-file-na" class="btn btn-info">Reset Default</button>
-      </span>
-    </div>
-    <span class="form-text text-muted">
-      This specifies strings in your file indicate that there is no value for a
-      particular cell (a cell is where a column and row intersect). Provide a
-      space-separated list of strings if you have more than one way of
-      indicating no values. See
-      <a href="#docs-file-na" title="Documentation for no-value fields">
-        documentation for more information</a>.</span>
-  </div>
-</fieldset>
-
-<fieldset id="fldset-files">
-  <legend>Data File(s)</legend>
-
-  <fieldset id="fldset-descriptions-file">
-    <div class="form-group">
-      <div class="form-check">
-        <input id="chk-phenotype-descriptions-transposed"
-               name="phenotype-descriptions-transposed"
-               type="checkbox"
-               class="form-check-input"
-               style="border: solid #8EABF0" />
-        <label for="chk-phenotype-descriptions-transposed"
-               class="form-check-label">
-          Description file transposed?</label>
-      </div>
-
-      <div class="non-resumable-elements">
-        <label for="finput-phenotype-descriptions" class="form-label">
-          Phenotype Descriptions</label>
-        <input id="finput-phenotype-descriptions"
-               name="phenotype-descriptions"
-               class="form-control"
-               type="file"
-               data-preview-table="tbl-preview-pheno-desc"
-               required="required"  />
-        <span class="form-text text-muted">
-          Provide a file that contains only the phenotype descriptions,
-          <a href="#docs-file-phenotype-description"
-             title="Documentation of the phenotype data file format.">
-            the documentation for the expected format of the file</a>.</span>
-      </div>
-      {{display_resumable_elements(
-      "resumable-phenotype-descriptions",
-      "phenotype descriptions",
-      '<p>Drag and drop the CSV file that contains the descriptions of your
-        phenotypes here.</p>
-
-      <p>The CSV file should be a matrix of
-        <strong>phenotypes × descriptions</strong> i.e. The first column
-        contains the phenotype names/identifiers whereas the first row is a list
-        of metadata fields like, "description", "units", etc.</p>
-
-      <p>If the format is transposed (i.e.
-        <strong>descriptions × phenotypes</strong>) select the checkbox above.
-      </p>
-
-      <p>Please see the
-        <a href="#docs-file-phenotype-description"
-           title="Documentation of the phenotype data file format.">
-          "Phenotypes Descriptions" documentation</a> section below for more
-        information on the expected format of the file provided here.</p>')}}
-      {{display_preview_table(
-      "tbl-preview-pheno-desc", "phenotype descriptions")}}
-    </div>
-  </fieldset>
-
-
-  <fieldset id="fldset-data-file">
-    <div class="form-group">
-      <div class="form-check">
-        <input id="chk-phenotype-data-transposed"
-               name="phenotype-data-transposed"
-               type="checkbox"
-               class="form-check-input"
-               style="border: solid #8EABF0" />
-        <label for="chk-phenotype-data-transposed" class="form-check-label">
-          Data file transposed?</label>
-      </div>
-
-      <div class="non-resumable-elements">
-        <label for="finput-phenotype-data" class="form-label">Phenotype Data</label>
-        <input id="finput-phenotype-data"
-               name="phenotype-data"
-               class="form-control"
-               type="file"
-               data-preview-table="tbl-preview-pheno-data"
-               required="required"  />
-        <span class="form-text text-muted">
-          Provide a file that contains only the phenotype data. See
-          <a href="#docs-file-phenotype-data"
-             title="Documentation of the phenotype data file format.">
-            the documentation for the expected format of the file</a>.</span>
-      </div>
-
-      {{display_resumable_elements(
-      "resumable-phenotype-data",
-      "phenotype data",
-      '<p>Drag and drop a CSV file that contains the phenotypes numerical data
-        here. You can click the "Browse" button (below and to the right) to
-        select the file from your computer.</p>
-
-      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
-        i.e. The first column contains the samples identifiers while the first
-        row is the list of phenotypes identifiers occurring in the phenotypes
-        descriptions file.</p>
-
-      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
-        select the checkbox above.</p>
-      <p>Please see the
-        <a href="#docs-file-phenotype-data"
-           title="Documentation of the phenotype data file format.">
-          "Phenotypes Data" documentation</a> section below for more information
-        on the expected format for the file provided here.</p>')}}
-      {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}}
-    </div>
-  </fieldset>
-
-  
-  {%if population.Family in families_with_se_and_n%}
-  <fieldset id="fldset-se-file">
-    <div class="form-group">
-      <div class="form-check">
-        <input id="chk-phenotype-se-transposed"
-               name="phenotype-se-transposed"
-               type="checkbox"
-               class="form-check-input"
-               style="border: solid #8EABF0" />
-        <label for="chk-phenotype-se-transposed" class="form-check-label">
-          Standard-Errors file transposed?</label>
-      </div>
-      <div class="group non-resumable-elements">
-        <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
-        <input id="finput-phenotype-se"
-               name="phenotype-se"
-               class="form-control"
-               type="file"
-               data-preview-table="tbl-preview-pheno-se"
-               required="required"  />
-        <span class="form-text text-muted">
-          Provide a file that contains only the standard errors for the phenotypes,
-          computed from the data above.</span>
-      </div>
-
-      {{display_resumable_elements(
-      "resumable-phenotype-se",
-      "standard errors",
-      '<p>Drag and drop a CSV file that contains the phenotypes standard-errors
-        data here. You can click the "Browse" button (below and to the right) to
-        select the file from your computer.</p>
-
-      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
-        i.e. The first column contains the samples identifiers while the first
-        row is the list of phenotypes identifiers occurring in the phenotypes
-        descriptions file.</p>
-
-      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
-        select the checkbox above.</p>
-
-      <p>Please see the
-        <a href="#docs-file-phenotype-se"
-           title="Documentation of the phenotype data file format.">
-          "Phenotypes Data" documentation</a> section below for more information
-        on the expected format of the file provided here.</p>')}}
-
-      {{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
-    </div>
-  </fieldset>
-
-
-  <fieldset id="fldset-n-file">
-    <div class="form-group">
-      <div class="form-check">
-        <input id="chk-phenotype-n-transposed"
-               name="phenotype-n-transposed"
-               type="checkbox"
-               class="form-check-input"
-               style="border: solid #8EABF0" />
-        <label for="chk-phenotype-n-transposed" class="form-check-label">
-          Counts file transposed?</label>
-      </div>
-      <div class="non-resumable-elements">
-        <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
-        <input id="finput-phenotype-n"
-               name="phenotype-n"
-               class="form-control"
-               type="file"
-               data-preview-table="tbl-preview-pheno-n"
-               required="required"  />
-        <span class="form-text text-muted">
-          Provide a file that contains only the number of samples/individuals used in
-          the computation of the standard errors above.</span>
-      </div>
-
-      {{display_resumable_elements(
-      "resumable-phenotype-n",
-      "number of samples/individuals",
-      '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts
-        data here. You can click the "Browse" button (below and to the right) to
-        select the file from your computer.</p>
-
-      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
-        i.e. The first column contains the samples identifiers while the first
-        row is the list of phenotypes identifiers occurring in the phenotypes
-        descriptions file.</p>
-
-      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
-        select the checkbox above.</p>
-
-      <p>Please see the
-        <a href="#docs-file-phenotype-se"
-           title="Documentation of the phenotype data file format.">
-          "Phenotypes Data" documentation</a> section below for more information
-        on the expected format of the file provided here.</p>')}}
-
-      {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}}
-    </div>
-  </fieldset>
-</fieldset>
-{%endif%}
-{%endblock%}
-
-
-{%block page_documentation%}
-<div class="row">
-  <h2 class="heading" id="docs-help">Help</h2>
-  <h3 class="subheading">Common Features</h3>
-  <p>The following are the common expectations for <strong>ALL</strong> the
-    files provided in the form above:
-    <ul>
-      <li>The file <strong>MUST</strong> be character-separated values (CSV)
-        text file</li>
-      <li>The first row in the file <strong>MUST</strong> be a heading row, and
-        will be composed of the list identifiers for all of
-        samples/individuals/cases involved in your study.</li>
-      <li>The first column of data in the file <strong>MUST</strong> be the
-        identifiers for all of the phenotypes you wish to upload.</li>
-    </ul>
-  </p>
-
-  <p>If you do not specify the separator character, then we will assume a
-    <strong>TAB</strong> character was used as your separator.</p>
-
-  <p>We also assume you might include comments lines in your files. In that
-    case, if you do not specify what character denotes that a line in your files
-    is a comment line, we will assume the <strong>#</strong> character.<br />
-    A comment <strong>MUST ALWAYS</strong> begin at the start of the line marked
-    with the comment character specified.</p>
-
-  <h3 class="subheading" id="docs-file-metadata">File Metadata</h3>
-  <p>We request some details about your files to help us parse and process the
-    files correctly. The details we collect are:</p>
-  <dl>
-    <dt id="docs-file-separator">File separator</dt>
-    <dd>The files you provide should be character-separated value (CSV) files.
-      We need to know what character you used to separate the values in your
-      file. Some common ones are the Tab character, the comma, etc.<br />
-      Providing that information makes it possible for the system to parse and
-      process your files correctly.<br>
-      <strong>NOTE:</strong> All the files you upload MUST use the same
-      separator.</dd>
-
-    <dt id="docs-file-comment-character">Comment character</dt>
-    <dd>We support use of comment lines in your files. We only support one type
-      of comment style, the <em>line comment</em>.<br />
-      This mean the comment begins at the start of the line, and the end of that
-      line indicates the end of that comment. If you have a really long comment,
-      then you need to break it across multiple lines, marking each line a
-      comment line.<br />
-      The "comment character" is the character at the start of the line that
-      indicates that the line is a line comment.</dd>
-
-    <dt id="docs-file-na">No-Value indicator(s)</dt>
-    <dd>Data in the real world is messy, and in some cases, entirely absent. You
-      need to indicate, in your files, that a particular field did not have a
-      value, and once you do that, you then need to let the system know how you
-      mark such fields. Common ways of indicating "empty values" are, leaving
-      the field blank, using a character such as '-', or using strings like
-      "NA", "N/A", "NULL", etc.<br />
-      Providing this information will help with parsing and processing such
-      no-value fields the correct way.</dd>
-  </dl>
-
-  <h3 class="subheading" id="docs-file-phenotype-description">
-    file: Phenotypes Descriptions</h3>
-  <p>The data in this file is a matrix of <em>phenotypes × metadata-fields</em>.
-    Please note we use the term "metadata-fields" above loosely, due to lack of
-    a good word for this.</p>
-  <p>The file <strong>MUST</strong> have columns in this order:
-    <dl>
-      <dt>Phenotype Identifiers</dt>
-      <dd>These are the names/identifiers for your phenotypes. These
-        names/identifiers are the same ones you will have in all the other files you are
-        uploading.</dd>
-
-      <dt>Descriptions</dt>
-      <dd>Each phenotype will need a description. Good description are necessary
-        to inform other people of what the data is about. Good description are
-        hard to construct, so we provide
-        <a href="https://info.genenetwork.org/faq.php#q-22"
-           title="How to write phenotype descriptions">
-          advice on describing your phenotypes.</a></dd>
-
-      <dt>Units</dt>
-      <dd>Each phenotype will need units for the measurements taken. If there are
-        none, then indicate the field is a no-value field.</dd>
-  </dl></p>
-  <p>You can add more columns after those three if you want to, but these 3
-    <strong>MUST</strong> be present.</p>
-  <p>The file would, for example, look like the following:</p>
-  <code>id,description,units,…<br />
-    pheno10001|Central nervous system, behavior, cognition; …|mg|…<br />
-    pheno10002|Aging, metabolism, central nervous system: …|mg|…<br />
-    ⋮<br /></code>
-
-  <p><strong>Note 01</strong>: The first usable row is the heading row.</p>
-  <p><strong>Note 02: </strong>This example demonstrates a subtle issue that
-    could make your CSV file invalid &mdash; the choice of your field separator
-    character.<br >
-    In the example above, we use the pipe character (<code>|</code>) as our
-    field separator. This is because, if we follow the advice on how to write
-    good descriptions, then we cannot use the comma as our separator &ndash; if
-    we did, then our CSV file would be invalid because the system would have no
-    way to tell the difference between the comma as a field separator, and the
-    comma as a way to separate the "general category and ontology terms".</p>
-
-  <h3 class="subheading">file: Phenotype Data, Standard Errors and/or Sample Counts</h3>
-  <span id="docs-file-phenotype-data"></span>
-  <span id="docs-file-phenotype-se"></span>
-  <span id="docs-file-phenotype-n"></span>
-  <p>The data is a matrix of <em>samples(or individuals) × phenotypes</em>, e.g.</p>
-  <code>
-    # num-cases: 2549
-    # num-phenos: 13
-    id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br />
-    IND001,61.400002,49,62.5,55.099998,…<br />
-    IND002,54.099998,50.099998,53.299999,55.099998,…<br />
-    IND003,483,403,501,403,…<br />
-    IND004,49.799999,45.5,62.900002,NA,…<br />
-    ⋮<br /></code>
-
-  <p>where <code>IND001,IND002,IND003,IND004,…</code> are the
-    samples/individuals/cases in your study, and
-    <code>pheno10001,pheno10002,pheno10004,pheno10004,…</code> are the
-    identifiers for your phenotypes.</p>
-  <p>The lines beginning with the "<em>#</em>" symbol (i.e.
-    <code># num-cases: 2549</code> and <code># num-phenos: 13</code> are comment
-    lines and will be ignored</p>
-  <p>In this example, the comma (,) is used as the file separator.</p>
-</div>
-
-{%endblock%}
-
-
-{%block more_javascript%}
-<script src="{{url_for('base.node_modules',
-             filename='resumablejs/resumable.js')}}"></script>
-<script type="text/javascript" src="/static/js/files.js"></script>
-
-<script type="text/javascript">
-  $("#btn-reset-file-separator").on("click", (event) => {
-      event.preventDefault();
-      $("#txt-file-separator").val("\t");
-      $("#txt-file-separator").trigger("change");
-  });
-  $("#btn-reset-file-comment-character").on("click", (event) => {
-      event.preventDefault();
-      $("#txt-file-comment-character").val("#");
-      $("#txt-file-comment-character").trigger("change");
-  });
-  $("#btn-reset-file-na").on("click", (event) => {
-      event.preventDefault();
-      $("#txt-file-na").val("- NA N/A");
-      $("#txt-file-na").trigger("change");
-  });
-
-  var update_preview = (table, filedata, formdata, numrows) => {
-      table.find("thead tr").remove()
-      table.find(".data-row").remove();
-      var linenum = 0;
-      var tableheader = table.find("thead");
-      var tablebody = table.find("tbody");
-      var numheadings = 0;
-      var navalues = formdata
-          .na_strings
-          .split(" ")
-          .map((v) => {return v.trim();})
-          .filter((v) => {return Boolean(v);});
-      filedata.forEach((line) => {
-          if(line.startsWith(formdata.comment_char) || linenum >= numrows) {
-              return false;
-          }
-          var row = $("<tr></tr>");
-          line.split(formdata.separator)
-              .map((field) => {
-                  var value = field.trim();
-                  if(navalues.includes(value)) {
-                      return "⋘NUL⋙";
-                  }
-                  return value;
-              })
-              .filter((field) => {
-                  return (field !== "" && field != undefined && field != null);
-              })
-              .forEach((field) => {
-                  if(linenum == 0) {
-                      numheadings += 1;
-                      var tablefield = $("<th></th>");
-                      tablefield.text(field);
-                      row.append(tablefield);
-                  } else {
-                      add_class(row, "data-row");
-                      var tablefield = $("<td></td>");
-                      tablefield.text(field);
-                      row.append(tablefield);
-                  }
-              });
-
-          if(linenum == 0) {
-              tableheader.append(row);
-          } else {
-              tablebody.append(row);
-          }
-          linenum += 1;
-      });
-
-      if(table.find("tbody tr.data-row").length > 0) {
-          add_class(table.find(".data-row-template"), "visually-hidden");
-      } else {
-          remove_class(table.find(".data-row-template"), "visually-hidden");
-      }
-  };
-
-  var makePreviewUpdater = (preview_table) => {
-      return (data) => {
-          update_preview(
-              preview_table,
-              data,
-              filesMetadata(),
-              PREVIEW_ROWS);
-      };
-  };
-
-  var preview_tables_to_elements_map = {
-      "#tbl-preview-pheno-desc": "#finput-phenotype-descriptions",
-      "#tbl-preview-pheno-data": "#finput-phenotype-data",
-      "#tbl-preview-pheno-se": "#finput-phenotype-se",
-      "#tbl-preview-pheno-n": "#finput-phenotype-n"
-  };
-
-  var filesMetadata = () => {
-      return {
-          "separator": $("#txt-file-separator").val(),
-          "comment_char": $(
-              "#txt-file-comment-character").val(),
-          "na_strings": $("#txt-file-na").val()
-      }
-  };
-
-  var PREVIEW_ROWS = 5;
-
-  var handler_update_previews = (event) => {
-      Object.entries(preview_tables_to_elements_map).forEach((mapentry) => {
-          var preview_table = $(mapentry[0]);
-          var file_input = $(mapentry[1]);
-          if(file_input[0].files.length > 0) {
-              readFirstNLines(
-                  file_input[0].files[0],
-                  10,
-                  [makePreviewUpdater(preview_table)]);
-          }
-      });
-
-      if(typeof(resumables) !== "undefined") {
-          resumables.forEach((resumable) => {
-              if(resumable.files.length > 0) {
-                  readFirstNLines(
-                      resumable.files[0].file,
-                      10,
-                      [makePreviewUpdater(resumable.preview_table)]);
-              }
-          });
-      }
-  };
-
-  [
-      "#txt-file-separator",
-      "#txt-file-comment-character",
-      "#txt-file-na"
-  ].forEach((elementid) => {
-      $(elementid).on("change", handler_update_previews);
-  });
-
-  [
-      "#finput-phenotype-descriptions",
-      "#finput-phenotype-data",
-      "#finput-phenotype-se",
-      "#finput-phenotype-n"
-  ].forEach((elementid) => {
-      $(elementid).on("change", (event) => {
-          readFirstNLines(
-              event.target.files[0],
-              10,
-              [makePreviewUpdater(
-                  $("#" + event.target.getAttribute("data-preview-table")))]);
-      });
-  });
-
-
-  var resumableDisplayFiles = (display_area, files) => {
-      files.forEach((file) => {
-          display_area.find(".file-display").remove();
-          var display_element = display_area
-              .find(".file-display-template")
-              .clone();
-          remove_class(display_element, "visually-hidden");
-          remove_class(display_element, "file-display-template");
-          add_class(display_element, "file-display");
-          display_element.find(".filename").text(file.name
-                                                || file.fileName
-                                                || file.relativePath
-                                                || file.webkitRelativePath);
-          display_element.find(".filesize").text(
-              (file.size / (1024*1024)).toFixed(2) + "MB");
-          display_element.find(".fileuniqueid").text(file.uniqueIdentifier);
-          display_element.find(".filemimetype").text(file.file.type);
-          display_area.append(display_element);
-      });
-  };
-
-
-  var indicateProgress = (resumable, progress_bar) => {
-      return () => {/*Has no event!*/
-          var progress = (resumable.progress() * 100).toFixed(2);
-          var pbar = progress_bar.find(".progress-bar");
-          remove_class(progress_bar, "visually-hidden");
-          pbar.css("width", progress+"%");
-          pbar.attr("aria-valuenow", progress);
-          pbar.text("Uploading: " + progress + "%");
-      };
-  };
-
-  var retryUpload = (retry_button, cancel_button) => {
-      retry_button.on("click", (event) => {
-          resumable.files.forEach((file) => {file.retry();});
-          add_class(retry_button, "visually-hidden");
-          remove_class(cancel_button, "visually-hidden");
-          add_class(browse_button, "visually-hidden");
-      });
-  };
-
-  var cancelUpload = (cancel_button, retry_button) => {
-      cancel_button.on("click", (event) => {
-          resumable.files.forEach((file) => {
-              if(file.isUploading()) {
-                  file.abort();
-              }
-          });
-          add_class(cancel_button, "visually-hidden");
-          remove_class(retry_button, "visually-hidden");
-          remove_class(browse_button, "visually-hidden");
-      });
-  };
-
-
-  var startUpload = (browse_button, retry_button, cancel_button) => {
-      return (event) => {
-          remove_class(cancel_button, "visually-hidden");
-          add_class(retry_button, "visually-hidden");
-          add_class(browse_button, "visually-hidden");
-      };
-  };
-
-  var processForm = (form) => {
-      var formdata = new FormData(form);
-      uploaded_files.forEach((msg) => {
-          formdata.delete(msg["file-input-name"]);
-          formdata.append(msg["file-input-name"], JSON.stringify({
-              "uploaded-file": msg["uploaded-file"],
-              "original-name": msg["original-name"]
-          }));
-      });
-      formdata.append("resumable-upload", "true");
-      formdata.append("publication-id", $("#txt-publication-id").val());
-      return formdata;
-  }
-
-  var uploaded_files = new Set();
-  var submitForm = (new_file) => {
-      uploaded_files.add(new_file);
-      if(uploaded_files.size === resumables.length) {
-          var form = $("#frm-add-phenotypes");
-          if(form.length !== 1) {
-              // TODO: Handle error somehow?
-              alert("Could not find form!!!");
-              return false;
-          }
-
-          $.ajax({
-              "url": form.attr("action"),
-              "type": "POST",
-              "data": processForm(form[0]),
-              "processData": false,
-              "contentType": false,
-              "success": (data, textstatus, jqxhr) => {
-                  // TODO: Redirect to endpoint that should come as part of the
-                  //       success/error message.
-                  console.log("SUCCESS DATA: ", data);
-                  console.log("SUCCESS STATUS: ", textstatus);
-                  console.log("SUCCESS jqXHR: ", jqxhr);
-                  window.location.assign(window.location.origin + data["redirect-to"]);
-              },
-          });
-          return false;
-      }
-      return false;
-  };
-
-  var uploadSuccess = (file_input_name) => {
-      return (file, message) => {
-          submitForm({...JSON.parse(message), "file-input-name": file_input_name});
-      };
-  };
-
-
-  var uploadError = () => {
-      return (message, file) => {
-          $("#frm-add-phenotypes input[type=submit]").removeAttr("disabled");
-          console.log("THE FILE:", file);
-          console.log("THE ERROR MESSAGE:", message);
-      };
-  };
-
-
-
-  var makeResumableObject = (form_id, file_input_id, resumable_element_id, preview_table_id) => {
-      var the_form = $("#" + form_id);
-      var file_input = $("#" + file_input_id);
-      var submit_button = the_form.find("input[type=submit]");
-      if(file_input.length != 1) {
-          return false;
-      }
-      var r = errorHandler(
-          fileSuccessHandler(
-              uploadStartHandler(
-                  filesAddedHandler(
-                      markResumableDragAndDropElement(
-                          makeResumableElement(
-                              the_form.attr("data-resumable-target"),
-                              file_input.parent(),
-                              $("#" + resumable_element_id),
-                              submit_button,
-                              ["csv", "tsv", "txt"]),
-                          file_input.parent(),
-                          $("#" + resumable_element_id),
-                          $("#" + resumable_element_id + "-browse-button")),
-                      (files) => {
-                          // TODO: Also trigger preview!
-                          resumableDisplayFiles(
-                              $("#" + resumable_element_id + "-selected-files"), files);
-                          files.forEach((file) => {
-                              readFirstNLines(
-                                  file.file,
-                                  10,
-                                  [makePreviewUpdater(
-                                      $("#" + preview_table_id))])
-                          });
-                      }),
-                  startUpload($("#" + resumable_element_id + "-browse-button"),
-                              $("#" + resumable_element_id + "-retry-button"),
-                              $("#" + resumable_element_id + "-cancel-button"))),
-              uploadSuccess(file_input.attr("name"))),
-          uploadError());
-
-      /** Setup progress indicator **/
-      progressHandler(
-          r,
-          indicateProgress(r, $("#" + resumable_element_id + "-progress-bar")));
-
-      return r;
-  };
-
-  var resumables = [
-      ["frm-add-phenotypes", "finput-phenotype-descriptions", "resumable-phenotype-descriptions", "tbl-preview-pheno-desc"],
-      ["frm-add-phenotypes", "finput-phenotype-data", "resumable-phenotype-data", "tbl-preview-pheno-data"],
-      ["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"],
-      ["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"],
-  ].map((row) => {
-      r = makeResumableObject(row[0], row[1], row[2], row[3]);
-      r.preview_table = $("#" + row[3]);
-      return r;
-  }).filter((val) => {
-      return Boolean(val);
-  });
-
-  $("#frm-add-phenotypes input[type=submit]").on("click", (event) => {
-      event.preventDefault();
-      console.debug();
-      if ($("#txt-publication-id").val() == "") {
-          alert("You MUST provide a publication for the phenotypes.");
-          return false;
-      }
-      // TODO: Check all the relevant files exist
-      // TODO: Verify that files are not duplicated
-      var filenames = [];
-      var nondupfiles = [];
-      resumables.forEach((r) => {
-          var fname = r.files[0].file.name;
-          filenames.push(fname);
-          if(!nondupfiles.includes(fname)) {
-              nondupfiles.push(fname);
-          }
-      });
-
-      // Check that all files were provided
-      if(resumables.length !== filenames.length) {
-          window.alert("You MUST provide all the files requested.");
-          event.target.removeAttribute("disabled");
-          return false;
-      }
-
-      // Check that there are no duplicate files
-      var duplicates = Object.entries(filenames.reduce(
-          (acc, curr, idx, arr) => {
-              acc[curr] = (acc[curr] || 0) + 1;
-              return acc;
-          },
-          {})).filter((entry) => {return entry[1] !== 1;});
-      if(duplicates.length > 0) {
-          var msg = "The file(s):\r\n";
-          msg = msg + duplicates.reduce(
-              (msgstr, afile) => {
-                  return msgstr + "  • " + afile[0] + "\r\n";
-              },
-              "");
-          msg = msg + "is(are) duplicated. Please fix and try again.";
-          window.alert(msg);
-          event.target.removeAttribute("disabled");
-          return false;
-      }
-      // TODO: Check all fields
-      // Start the uploads.
-      event.target.setAttribute("disabled", "disabled");
-      resumables.forEach((r) => {r.upload();});
-  });
-</script>
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html
deleted file mode 100644
index 29a8dea..0000000
--- a/uploader/templates/phenotypes/sui-add-phenotypes-with-rqtl2-bundle.html
+++ /dev/null
@@ -1,189 +0,0 @@
-{%extends "phenotypes/sui-add-phenotypes-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block frm_add_phenotypes_documentation%}
-<p>Select the zip file bundle containing information on the phenotypes you
-  wish to upload, then click the "Upload Phenotypes" button below to
-  upload the data.</p>
-<p>If you wish to upload the files individually instead,
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}"
-     title="">click here</a>.</p>
-<p>See the <a href="#section-file-formats">File Formats</a> section below
-  to get an understanding of what is expected of the bundle files you
-  upload.</p>
-{%endblock%}
-
-{%block frm_add_phenotypes_elements%}
-<div class="form-group">
-  <label for="finput-phenotypes-bundle" class="form-label">
-    Phenotypes Bundle</label>
-  <input type="file"
-         id="finput-phenotypes-bundle"
-         name="phenotypes-bundle"
-         accept="application/zip, .zip"
-	 required="required"
-         class="form-control" />
-</div>
-{%endblock%}
-
-{%block page_documentation%}
-<div class="row">
-  <h2 class="heading" id="section-file-formats">File Formats</h2>
-  <p>We accept an extended form of the
-    <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files"
-       title="R/qtl2 software input file format documentation">
-      input files' format used with the R/qtl2 software</a> as a single ZIP
-    file</p>
-  <p>The files that are used for this feature are:
-    <ul>
-      <li>the <em>control</em> file</li>
-      <li><em>pheno</em> file(s)</li>
-      <li><em>phenocovar</em> file(s)</li>
-      <li><em>phenose</em> files(s)</li>
-    </ul>
-  </p>
-  <p>Other files within the bundle will be ignored, for this feature.</p>
-  <p>The following section will detail the expectations for each of the
-    different file types within the uploaded ZIP file bundle for phenotypes:</p>
-
-  <h3 class="subheading">Control File</h3>
-  <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts
-    as the control file. This file can be:
-    <ul>
-      <li>a <em>JSON</em> file, or</li>
-      <li>a <em>YAML</em> file.</li>
-    </ul>
-  </p>
-
-  <p>The control file is useful for defining things about the bundle such as:</p>
-  <ul>
-    <li>The field separator value (default: <code>sep: ','</code>). There can
-      only ever be one field separator and it <strong>MUST</strong> be the same
-      one for <strong>ALL</strong> files in the bundle.</li>
-    <li>The comment character (default: <code>comment.char: '#'</code>). Any
-      line that starts with this character will be considered a comment line and
-      be ignored in its entirety.</li>
-    <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You
-      can specify more than one code to indicate missing values, e.g.
-      <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li>
-  </ul>
-
-  <h3 class="subheading"><em>pheno</em> File(s)</h3>
-  <p>These files are the main data files. You must have at least one of these
-    files in your bundle for it to be valid for this step.</p>
-  <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as
-    below:<br />
-    <code>
-      id,10001,10002,10003,10004,…<br />
-      BXD1,61.400002,54.099998,483,49.799999,…<br />
-      BXD2,49,50.099998,403,45.5,…<br />
-      BXD5,62.5,53.299999,501,62.900002,…<br />
-      BXD6,53.099998,55.099998,403,NA,…<br />
-      ⋮<br /></code>
-  </p>
-  <p>If the <code>pheno_transposed</code> value is set to <code>True</code>,
-    then the data will be a <em>phenotypes × individuals</em> matrix as in the
-    example below:<br />
-    <code>
-      id,BXD1,BXD2,BXD5,BXD6,…<br />
-      10001,61.400002,49,62.5,53.099998,…<br />
-      10002,54.099998,50.099998,53.299999,55.099998,…<br />
-      10003,483,403,501,403,…<br />
-      10004,49.799999,45.5,62.900002,NA,…<br />
-      ⋮
-    </code>
-  </p>
-
-
-  <h3 class="subheading"><em>phenocovar</em> File(s)</h3>
-  <p>At least one phenotypes metadata file with the metadata values such as
-    descriptions, PubMed Identifier, publication titles (if present), etc.</p>
-  <p>The data in this/these file(s) is a matrix of
-    <em>phenotypes × phenotypes-covariates</em>. The first column is always the
-    phenotype names/identifiers — same as in the R/qtl2 format.</p>
-  <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p>
-  <p>This file <strong>MUST</strong> be present in the bundle, and have data for
-    the bundle to be considered valid by our system for this step.<br />
-    In addition to that, the following are the fields that <strong>must be
-      present</strong>, and
-    have values, in the file before the file is considered valid:
-    <ul>
-      <li><em>description</em>: A description for each phenotype. Useful
-        for users to know what the phenotype is about.</li>
-      <li><em>units</em>: The units of measurement for the phenotype,
-        e.g. milligrams for brain weight, centimetres/millimetres for
-        tail-length, etc.</li>
-  </ul></p>
-
-  <p>The following <em>optional</em> fields can also be provided:
-    <ul>
-      <li><em>pubmedid</em>: A PubMed Identifier for the publication where
-        the phenotype is published. If this field is not provided, the system will
-        assume your phenotype is not published.</li>
-    </ul>
-  </p>
-  <p>These files will be marked up in the control file with the
-    <code>phenocovar</code> key, as in the examples below:
-    <ol>
-      <li>JSON: single file<br />
-        <code>{<br />
-          &nbsp;&nbsp;⋮,<br />
-          &nbsp;&nbsp;"phenocovar": "your_covariates_file.csv",<br />
-          &nbsp;&nbsp;⋮<br />
-          }
-        </code>
-      </li>
-      <li>JSON: multiple files<br />
-        <code>{<br />
-          &nbsp;&nbsp;⋮,<br />
-          &nbsp;&nbsp;"phenocovar": [<br />
-          &nbsp;&nbsp;&nbsp;&nbsp;"covariates_file_01.csv",<br />
-          &nbsp;&nbsp;&nbsp;&nbsp;"covariates_file_01.csv",<br />
-          &nbsp;&nbsp;&nbsp;&nbsp;⋮<br />
-          &nbsp;&nbsp;],<br />
-          &nbsp;&nbsp;⋮<br />
-          }
-        </code>
-      </li>
-      <li>YAML: single file or<br />
-        <code>
-          ⋮<br />
-          phenocovar: your_covariates_file.csv<br />
-          ⋮
-        </code>
-      </li>
-      <li>YAML: multiple files<br />
-        <code>
-          ⋮<br />
-          phenocovar:<br />
-          - covariates_file_01.csv<br />
-          - covariates_file_02.csv<br />
-          - covariates_file_03.csv<br />
-          …<br />
-          ⋮
-        </code>
-      </li>
-    </ol>
-  </p>
-
-  <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3>
-  <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are
-    not supported by the original R/qtl2 file format</p>
-  <p>We use these files to upload the standard errors (<em>phenose</em>) when
-    the data file (<em>pheno</em>) is average data. In that case, the
-    <em>phenonum</em> file(s) contains the number of individuals that were
-    involved when computing the averages.</p>
-  <p>Both types of files are matrices of <em>individuals × phenotypes</em> by
-    default. Like the related <em>pheno</em> files, if
-    <code>pheno_transposed: True</code>, then the file will be a matrix of
-    <em>phenotypes × individuals</em>.</p>
-</div>
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-base.html b/uploader/templates/phenotypes/sui-base.html
deleted file mode 100644
index d7d980f..0000000
--- a/uploader/templates/phenotypes/sui-base.html
+++ /dev/null
@@ -1,25 +0,0 @@
-{%extends "populations/sui-base.html"%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_sui_pheno_dataset_card%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.populations.phenotypes.view_dataset',
-           species_id=species['SpeciesId'],
-           population_id=population['Id'],
-           dataset_id=dataset['Id'])}}">
-    {{dataset["Name"]}}
-  </a>
-</li>
-{%endblock%}
-
-{%block contents%}
-<div class="row">
-  <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2>
-</div>
-{%endblock%}
-
-
-{%block sidebarcontents%}
-{{display_sui_pheno_dataset_card(species, population, dataset)}}
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-job-status.html b/uploader/templates/phenotypes/sui-job-status.html
deleted file mode 100644
index bca87d5..0000000
--- a/uploader/templates/phenotypes/sui-job-status.html
+++ /dev/null
@@ -1,140 +0,0 @@
-{%extends "phenotypes/sui-base.html"%}
-{%from "cli-output.html" import cli_output%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-
-{%block extrameta%}
-{%if job and job.status not in ("success", "completed:success", "error", "completed:error")%}
-<meta http-equiv="refresh" content="5" />
-{%endif%}
-{%endblock%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block contents%}
-
-{%if job%}
-<div class="row">
-  <h2 class="heading">{{dataset.FullName}} ({{dataset.Name}})</h2>
-  <h3 class="subheading">upload progress</h3>
-</div>
-<div class="row" style="overflow:scroll;">
-  <p><strong>Process Status:</strong> {{job.status}}</p>
-  {%if metadata%}
-  <table class="table table-responsive">
-    <thead>
-      <tr>
-        <th>File</th>
-        <th>Status</th>
-        <th>Lines Processed</th>
-        <th>Total Errors</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      {%for file,meta in metadata.items()%}
-      <tr>
-        <td>{{file}}</td>
-        <td>{{meta.status}}</td>
-        <td>{{meta.linecount}}</td>
-        <td>{{meta["total-errors"]}}</td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-  {%endif%}
-</div>
-
-<div class="row">
-  {%if  job.status in ("completed:success", "success")%}
-  <p>
-    {%if errors | length == 0%}
-    <a href="{{url_for('species.populations.phenotypes.review_job_data',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id,
-           job_id=job_id)}}"
-       class="btn btn-primary"
-       title="Continue to process data">Continue</a>
-    {%else%}
-    <span class="text-muted"
-          disabled="disabled"
-          style="border: solid 2px;border-radius: 5px;padding: 0.3em;">
-      Cannot continue due to errors. Please fix the errors first.
-    </span>
-    {%endif%}
-  </p>
-  {%endif%}
-</div>
-
-<h3 class="subheading">upload errors</h3>
-<div class="row" style="max-height: 20em; overflow: scroll;">
-  {%if errors | length == 0 %}
-  <p class="text-info">
-    <span class="glyphicon glyphicon-info-sign"></span>
-    No errors found so far
-  </p>
-  {%else%}
-  <table class="table table-responsive">
-    <thead style="position: sticky; top: 0; background: white;">
-      <tr>
-        <th>File</th>
-        <th>Row</th>
-        <th>Column</th>
-        <th>Value</th>
-        <th>Message</th>
-      </tr>
-    </thead>
-
-    <tbody style="font-size: 0.9em;">
-      {%for error in errors%}
-      <tr>
-        <td>{{error.filename}}</td>
-        <td>{{error.rowtitle}}</td>
-        <td>{{error.coltitle}}</td>
-        <td>{%if error.cellvalue is not none and error.cellvalue | length > 25%}
-          {{error.cellvalue[0:24]}}&hellip;
-          {%else%}
-          {{error.cellvalue}}
-          {%endif%}
-        </td>
-        <td>
-          {%if error.message | length > 250 %}
-          {{error.message[0:249]}}&hellip;
-          {%else%}
-          {{error.message}}
-          {%endif%}
-        </td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-  {%endif%}
-</div>
-
-<div class="row">
-  {{cli_output(job, "stdout")}}
-</div>
-
-<div class="row">
-  {{cli_output(job, "stderr")}}
-</div>
-
-{%else%}
-<div class="row">
-  <h3 class="text-danger">No Such Job</h3>
-  <p>Could not find a job with the ID: {{job_id}}</p>
-  <p>
-    Please go back to
-    <a href="{{url_for('species.populations.phenotypes.view_dataset',
-             species_id=species.SpeciesId,
-             population_id=population.Id,
-             dataset_id=dataset.Id)}}"
-       title="'{{dataset.Name}}' dataset page">
-      the '{{dataset.Name}}' dataset page</a>
-    to upload new phenotypes or edit existing ones.</p>
-</div>
-{%endif%}
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-load-phenotypes-success.html b/uploader/templates/phenotypes/sui-load-phenotypes-success.html
deleted file mode 100644
index dff0682..0000000
--- a/uploader/templates/phenotypes/sui-load-phenotypes-success.html
+++ /dev/null
@@ -1,26 +0,0 @@
-{%extends "phenotypes/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block contents%}
-{{super()}}
-
-<div class="row">
-  <p>You have successfully loaded
-    <!-- maybe indicate the number of phenotypes here? -->your
-    new phenotypes into the database.</p>
-  <!-- TODO: Maybe notify user that they have sole access. -->
-  <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. -->
-  <p>View your data
-    <a href="{{search_page_uri}}"
-       target="_blank">on GeneNetwork2</a>.
-    You might need to login to GeneNetwork2 to view specific traits.</p>
-</div>
-{%endblock%}
-
-
-{%block more_javascript%}{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-review-job-data.html b/uploader/templates/phenotypes/sui-review-job-data.html
deleted file mode 100644
index ea4183d..0000000
--- a/uploader/templates/phenotypes/sui-review-job-data.html
+++ /dev/null
@@ -1,121 +0,0 @@
-{%extends "phenotypes/sui-base.html"%}
-{%from "cli-output.html" import cli_output%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
-
-{%block extrameta%}
-{%if not job%}
-<meta http-equiv="refresh"
-      content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId,
-               population_id=population.Id,
-               dataset_id=dataset.Id)}}" />
-{%endif%}
-{%endblock%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="add-phenotypes"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">View Datasets</a>
-</li>
-{%endblock%}
-
-{%block contents%}
-
-{%if job%}
-<div class="row">
-  <h3 class="heading">Data Review</h3>
-  <p class="text-info"><strong>
-      The data has <em>NOT</em> been added/saved yet. Review the details below
-      and click "Continue" to save the data.</strong></p>
-  <p>The &#x201C;<strong>{{dataset.FullName}}</strong>&#x201D; dataset from the
-    &#x201C;<strong>{{population.FullName}}</strong>&#x201D; population of the
-    species &#x201C;<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>&#x201D;
-    will be updated as follows:</p>
-
-  <ul>
-    {%if publication%}
-    <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes
-      are linked to the following publication:
-      <ul>
-        <li><strong>Publication Title:</strong>
-          {{publication.Title or "—"}}</li>
-        <li><strong>Author(s):</strong>
-          {{publication.Authors or "—"}}</li>
-      </ul>
-    </li>
-    {%endif%}
-  {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%}
-  {%if summary.get(ftype, False)%}
-    <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed
-      adding {%if ftype == "phenocovar"%}(possibly){%endif%}
-      {{summary[ftype]["total-data-rows"]}} new
-      {%if ftype == "phenocovar"%}
-      phenotypes
-      {%else%}
-      {{summary[ftype]["description"]}} rows
-      {%endif%}
-      to the database.
-    </li>
-  {%endif%}
-  {%endfor%}
-  </ul>
-
-  <form id="frm-review-phenotype-data"
-        method="POST"
-        action="{{url_for('species.populations.phenotypes.load_data_to_database',
-                species_id=species.SpeciesId,
-                population_id=population.Id,
-                dataset_id=dataset.Id)}}">
-    <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" />
-    <input type="submit"
-           value="continue"
-           class="btn btn-primary" />
-  </form>
-</div>
-{%else%}
-<div class="row">
-  <h4 class="subheading">Invalid Job</h3>
-  <p class="text-danger">
-    Could not find a job with the ID: <strong>{{job_id}}.</p>
-  <p>You will be redirected in
-    <span id="countdown-element" class="text-info">20</span> second(s)</p>
-  <p class="text-muted">
-    <small>
-      If you are not redirected, please
-      <a href="{{url_for(
-               'species.populations.phenotypes.view_dataset',
-               species_id=species.SpeciesId,
-               population_id=population.Id,
-               dataset_id=dataset.Id)}}">click here</a> to continue
-    </small>
-  </p>
-</div>
-{%endif%}
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript">
-  $(document).ready(function() {
-      var countdown = 20;
-      var countdown_element = $("#countdown-element");
-      if(countdown_element.length === 1) {
-          intv = window.setInterval(function() {
-              countdown = countdown - 1;
-              countdown_element.html(countdown);
-          }, 1000);
-      }
-  });
-</script>
-{%endblock%}
diff --git a/uploader/templates/phenotypes/sui-view-dataset.html b/uploader/templates/phenotypes/sui-view-dataset.html
deleted file mode 100644
index f858c4e..0000000
--- a/uploader/templates/phenotypes/sui-view-dataset.html
+++ /dev/null
@@ -1,207 +0,0 @@
-{%extends "phenotypes/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-table-pagination.html" import table_pagination%}
-
-{%block title%}Phenotypes{%endblock%}
-
-{%block pagetitle%}Phenotypes{%endblock%}
-
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="view-dataset"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.view_dataset',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id)}}">View</a>
-</li>
-{%endblock%}
-
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <p>The basic dataset details are:</p>
-
-  <table class="table">
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Full Name</th>
-        <th>Short Name</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      <tr>
-        <td>{{dataset.Name}}</td>
-        <td>{{dataset.FullName}}</td>
-        <td>{{dataset.ShortName}}</td>
-      </tr>
-    </tbody>
-  </table>
-</div>
-
-<div class="row">
-  <div class="col">
-    <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
-             species_id=species.SpeciesId,
-             population_id=population.Id,
-             dataset_id=dataset.Id)}}"
-       title="Add a bunch of phenotypes"
-       class="btn btn-primary">Add phenotypes</a>
-  </div>
-
-  <div class="col">
-    <form id="frm-recompute-phenotype-means"
-          method="POST"
-          action="{{url_for(
-                  'species.populations.phenotypes.recompute_means',
-                  species_id=species['SpeciesId'],
-                  population_id=population['Id'],
-                  dataset_id=dataset['Id'])}}"
-          class="d-flex flex-row align-items-center flex-wrap"
-          style="display: inline;">
-      <input type="submit"
-             title="Compute/Recompute the means for all phenotypes."
-             class="btn btn-info"
-             value="(rec/c)ompute means"
-             id="submit-frm-recompute-phenotype-means" />
-    </form>
-  </div>
-
-  <div class="col">
-    <form id="frm-run-qtlreaper"
-          method="POST"
-          action="{{url_for(
-                  'species.populations.phenotypes.rerun_qtlreaper',
-                  species_id=species['SpeciesId'],
-                  population_id=population['Id'],
-                  dataset_id=dataset['Id'])}}"
-          class="d-flex flex-row align-items-center flex-wrap"
-          style="display: inline;">
-      <input type="submit"
-             title="Run/Rerun QTLReaper."
-             class="btn btn-info"
-             value="(re)run QTLReaper"
-             id="submit-frm-rerun-qtlreaper" />
-    </form>
-  </div>
-</div>
-
-<div class="row">
-  <h2>Phenotype Data</h2>
-
-  <p>Click on any of the phenotypes in the table below to view and edit that
-    phenotype's data.</p>
-  <p>Use the search to filter through all the phenotypes and find specific
-    phenotypes of interest.</p>
-</div>
-
-
-<div class="row">
-
-  <table id="tbl-phenotypes-list" class="table compact stripe cell-border">
-    <thead>
-      <tr>
-        <th></th>
-        <th>Index</th>
-        <th>Record</th>
-        <th>Description</th>
-      </tr>
-    </thead>
-
-    <tbody></tbody>
-  </table>
-</div>
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript" src="/static/js/urls.js"></script>
-
-<script type="text/javascript">
-  $(function() {
-      var species_id = {{species.SpeciesId}};
-      var population_id = {{population.Id}};
-      var dataset_id = {{dataset.Id}};
-      var dataset_name = "{{dataset.Name}}";
-      var data = {{phenotypes | tojson}};
-
-      var dtPhenotypesList = buildDataTable(
-          "#tbl-phenotypes-list",
-          data,
-          [
-              {
-                  data: function(pheno) {
-                      return `<input type="checkbox" name="selected-phenotypes" `
-                          + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" `
-                          + `value="${pheno.InbredSetCode}_${pheno.xref_id}" `
-                          + `class="chk-row-select" />`
-                  }
-              },
-              {data: "sequence_number"},
-              {
-                  data: function(pheno, type, set, meta) {
-                      var spcs_id = {{species.SpeciesId}};
-                      var pop_id = {{population.Id}};
-                      var dtst_id = {{dataset.Id}};
-                      var url = buildURLFromCurrentURL(
-                          (`/species/${spcs_id}` +
-                          `/populations/${pop_id}` +
-                          `/phenotypes/datasets/${dtst_id}` +
-                           `/phenotype/${pheno.xref_id}`));
-                      return `<a href="${url.toString()}" target="_blank">` +
-                          `${pheno.InbredSetCode}_${pheno.xref_id}` +
-                          `</a>`;
-                  }
-              },
-              {
-                  data: function(pheno) {
-                      return (pheno.Post_publication_description ||
-                              pheno.Original_description ||
-                              pheno.Pre_publication_description);
-                  }
-              }
-          ],
-          {
-              select: "multi+shift",
-              layout: {
-                  top1Start: {
-                      pageLength: {
-                          text: "Show _MENU_ of _TOTAL_"
-                      }
-                  },
-                  topStart: "info",
-                  top1End: null
-              },
-              rowId: function(pheno) {
-                  return `${pheno.InbredSetCode}_${pheno.xref_id}`;
-              }
-          });
-
-
-      $("#submit-frm-rerun-qtlreaper").on(
-          "click",
-          function(event) {
-              // (Re)run the QTLReaper script for selected phenotypes.
-              event.preventDefault();
-              var form = $("#frm-run-qtlreaper");
-              form.find(".dynamically-added-element").remove();
-              dtPhenotypesList.rows({selected: true}).nodes().each((node, index) => {
-                  _cloned = $(node).find(".chk-row-select").clone();
-                  _cloned.removeAttr("id");
-                  _cloned.removeAttr("class");
-                  _cloned.attr("style", "display: none;");
-                  _cloned.attr("data-type", "dynamically-added-element");
-                  _cloned.attr("class", "dynamically-added-element checkbox");
-                  _cloned.prop("checked", true);
-                  form.append(_cloned);
-              });
-              form.submit();
-          });
-  });
-</script>
-{%endblock%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index c634a48..1fd15b2 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -1,7 +1,6 @@
 {%extends "phenotypes/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "macro-table-pagination.html" import table_pagination%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Phenotypes{%endblock%}
 
@@ -119,12 +118,10 @@
 </div>
 {%endblock%}
 
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}
-
 
 {%block javascript%}
+<script type="text/javascript" src="/static/js/urls.js"></script>
+
 <script type="text/javascript">
   $(function() {
       var species_id = {{species.SpeciesId}};
@@ -151,11 +148,12 @@
                       var spcs_id = {{species.SpeciesId}};
                       var pop_id = {{population.Id}};
                       var dtst_id = {{dataset.Id}};
-                      return `<a href="/species/${spcs_id}` +
+                      var url = buildURLFromCurrentURL(
+                          (`/species/${spcs_id}` +
                           `/populations/${pop_id}` +
                           `/phenotypes/datasets/${dtst_id}` +
-                          `/phenotype/${pheno.xref_id}` +
-                          `" target="_blank">` +
+                           `/phenotype/${pheno.xref_id}`));
+                      return `<a href="${url.toString()}" target="_blank">` +
                           `${pheno.InbredSetCode}_${pheno.xref_id}` +
                           `</a>`;
                   }
diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html
index 75e3c1e..a69b024 100644
--- a/uploader/templates/phenotypes/view-phenotype.html
+++ b/uploader/templates/phenotypes/view-phenotype.html
@@ -1,25 +1,10 @@
 {%extends "phenotypes/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Phenotypes{%endblock%}
 
 {%block pagetitle%}Phenotypes{%endblock%}
 
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="view-phenotype"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.phenotypes.view_phenotype',
-           species_id=species.SpeciesId,
-           population_id=population.Id,
-           dataset_id=dataset.Id,
-           xref_id=xref_id)}}">View Phenotype</a>
-</li>
-{%endblock%}
-
 {%block contents%}
 {{flash_all_messages()}}
 
@@ -153,7 +138,3 @@ or "group:resource:delete-resource" in privileges%}
 </div>
 
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}