Move R/qtl2 upload code under the populations package.

24 files changed, 180 insertions, 479 deletions

diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html
index d6fe154..d6fe154 100644
--- a/uploader/templates/rqtl2/create-tissue-success.html
+++ b/uploader/templates/populations/rqtl2/create-tissue-success.html
diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html
new file mode 100644
index 0000000..ec6ffb8
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/index.html
@@ -0,0 +1,54 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 data upload</h1>
+
+<h2>R/qtl2 Upload</h2>
+
+<div class="row">
+  <form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}"
+        id="frm-rqtl2-upload">
+    <legend class="heading">upload R/qtl2 bundle</legend>
+    {{flash_messages("error-rqtl2")}}
+
+    <div class="form-group">
+      <label for="select:species" class="form-label">Species</label>
+      <select id="select:species"
+              name="species_id"
+              required="required"
+              class="form-control">
+        <option value="">Select species</option>
+        {%for spec in species%}
+        <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
+        {%endfor%}
+      </select>
+      <small class="form-text text-muted">
+        Data that you upload to the system should belong to a know species.
+        Here you can select the species that you wish to upload data for.
+      </small>
+    </div>
+
+    <input type="submit" class="btn btn-primary" value="submit" />
+  </form>
+</div>
+
+<div class="row">
+  <h2 class="heading">R/qtl2 Bundles</h2>
+
+  <div class="explainer">
+    <p>This feature combines and extends the two upload methods below. Instead of
+      uploading one item at a time, the R/qtl2 bundle you upload can contain both
+      the genotypes data (samples/individuals/cases and their data) and the
+      expression data.</p>
+    <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
+      of the methods below can handle.</p>
+
+    <a href="{{url_for('expression-data.rqtl2.select_species')}}"
+       title="Upload a zip bundle of R/qtl2 files">
+      <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
+  </div>
+</div>
+{%endblock%}
diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html
index b17004f..b17004f 100644
--- a/uploader/templates/rqtl2/no-such-job.html
+++ b/uploader/templates/populations/rqtl2/no-such-job.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html
index 9817518..9817518 100644
--- a/uploader/templates/rqtl2/rqtl2-job-error.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-error.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html
index 4ecd415..4ecd415 100644
--- a/uploader/templates/rqtl2/rqtl2-job-results.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-results.html
diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html
index e896f88..e896f88 100644
--- a/uploader/templates/rqtl2/rqtl2-job-status.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-job-status.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html
index 90e8887..90e8887 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html
index b3c3a8f..b3c3a8f 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html
index f4a6266..f4a6266 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-status.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html
index f126835..f126835 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html
+++ b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html
diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..3233abc
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html
@@ -0,0 +1,69 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="row">
+  <p>Your R/qtl2 files bundle could contain a "geno" specification. You will
+    therefore need to select from one of the existing Genotype datasets or
+    create a new one.</p>
+  <p>This is the dataset where your data will be organised under.</p>
+</div>
+
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('expression-data.rqtl2.select_geno_dataset',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">select from existing genotype datasets</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+
+    {{flash_messages("error-rqtl2-select-geno-dataset")}}
+
+    <div class="form-group">
+      <legend>Datasets</legend>
+      <label for="select:geno-datasets" class="form-label">Dataset</label>
+      <select id="select:geno-datasets"
+	      name="geno-dataset-id"
+	      required="required"
+	      {%if datasets | length == 0%}
+	      disabled="disabled"
+	      {%endif%}
+              class="form-control"
+              aria-describedby="help-geno-dataset-select-dataset">
+        <option value="">Select dataset</option>
+        {%for dset in datasets%}
+        <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
+        {%endfor%}
+      </select>
+      <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
+        Select from the existing genotype datasets for species
+        {{species.SpeciesName}} ({{species.FullName}}).
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">select dataset</button>
+  </form>
+</div>
+
+<div class="row">
+  <p>If the genotype dataset you need does not currently exist for your dataset,
+    go the <a href="{{url_for(
+                    'species.populations.genotypes.create_dataset',
+                    species_id=species.SpeciesId,
+                    population_id=population.Id)}}"
+              title="Create a new genotypes dataset for {{species.FullName}}">
+      genotypes page to create the genotype dataset</a></p>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html
new file mode 100644
index 0000000..ded425f
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/select-population.html
@@ -0,0 +1,57 @@
+{%extends "expression-data/index.html"%}
+{%from "flash_messages.html" import flash_messages%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
+
+{%block title%}Select Grouping/Population{%endblock%}
+
+{%block contents%}
+<h1 class="heading">Select grouping/population</h1>
+
+<div class="row">
+  <p>The data is organised in a hierarchical form, beginning with
+    <em>species</em> at the very top. Under <em>species</em> the data is
+    organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
+    (In some really old documents/systems, you might see this referred to as
+    <em>InbredSet</em>.)</p>
+  <p>In this section, you get to define what population your data is to be
+    organised by.</p>
+</div>
+
+<div class="row">
+  <form method="POST"
+        action="{{url_for('expression-data.rqtl2.select_population',
+                species_id=species.SpeciesId)}}">
+    <legend class="heading">select grouping/population</legend>
+    {{flash_messages("error-select-population")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+
+    <div class="form-group">
+      <label for="select:inbredset" class="form-label">population</label>
+      <select id="select:inbredset"
+	      name="inbredset_id"
+	      required="required"
+	      class="form-control">
+        <option value="">Select a grouping/population</option>
+        {%for pop in populations%}
+        <option value="{{pop.InbredSetId}}">
+	  {{pop.InbredSetName}} ({{pop.FullName}})</option>
+        {%endfor%}
+      </select>
+      <span class="form-text text-muted">Select the population for your data from
+        the list below.</span>
+    </div>
+
+    <button type="submit" class="btn btn-primary" />select population</button>
+</form>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html
index 74f8f69..74f8f69 100644
--- a/uploader/templates/rqtl2/select-probeset-dataset.html
+++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html
diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
index e3fd9cc..e3fd9cc 100644
--- a/uploader/templates/rqtl2/select-probeset-study-id.html
+++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html
index fe3080a..fe3080a 100644
--- a/uploader/templates/rqtl2/select-tissue.html
+++ b/uploader/templates/populations/rqtl2/select-tissue.html
diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html
index 0adba2e..0adba2e 100644
--- a/uploader/templates/rqtl2/summary-info.html
+++ b/uploader/templates/populations/rqtl2/summary-info.html
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html
index 9d45c5f..9d45c5f 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html
index 8210ed0..8210ed0 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html
diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
deleted file mode 100644
index bb6d63d..0000000
--- a/uploader/templates/rqtl2/create-geno-dataset-success.html
+++ /dev/null
@@ -1,55 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="explainer">
-  <p>You successfully created the genotype dataset with the following
-    information.
-    <dl>
-      <dt>ID</dt>
-      <dd>{{geno_dataset.id}}</dd>
-
-      <dt>Name</dt>
-      <dd>{{geno_dataset.name}}</dd>
-
-      <dt>Full Name</dt>
-      <dd>{{geno_dataset.fname}}</dd>
-
-      <dt>Short Name</dt>
-      <dd>{{geno_dataset.sname}}</dd>
-
-      <dt>Created On</dt>
-      <dd>{{geno_dataset.today}}</dd>
-
-      <dt>Public?</dt>
-      <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
-    </dl>
-  </p>
-</div>
-
-<div class="row">
-  <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('expression-data.rqtl2.select_dataset_info',
-	        species_id=species.SpeciesId,
-	        population_id=population.InbredSetId)}}"
-        method="POST"
-        enctype="multipart/form-data">
-    <legend class="heading">select from existing genotype datasets</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id"
-	   value="{{population.InbredSetId}}" />
-    <input type="hidden" name="rqtl2_bundle_file"
-	   value="{{rqtl2_bundle_file}}" />
-    <input type="hidden" name="geno-dataset-id"
-	   value="{{geno_dataset.id}}" />
-
-    <button type="submit" class="btn btn-primary">continue</button>
-  </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
deleted file mode 100644
index 03b75c7..0000000
--- a/uploader/templates/rqtl2/create-probe-dataset-success.html
+++ /dev/null
@@ -1,59 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Dataset</h2>
-
-<div class="row">
-  <p>You successfully created the ProbeSet dataset with the following
-    information.
-    <dl>
-      <dt>Averaging Method</dt>
-      <dd>{{avgmethod.Name}}</dd>
-
-      <dt>ID</dt>
-      <dd>{{dataset.datasetid}}</dd>
-
-      <dt>Name</dt>
-      <dd>{{dataset.name2}}</dd>
-
-      <dt>Full Name</dt>
-      <dd>{{dataset.fname}}</dd>
-
-      <dt>Short Name</dt>
-      <dd>{{dataset.sname}}</dd>
-
-      <dt>Created On</dt>
-      <dd>{{dataset.today}}</dd>
-
-      <dt>DataScale</dt>
-      <dd>{{dataset.datascale}}</dd>
-    </dl>
-  </p>
-</div>
-
-<div class="row">
-  <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('expression-data.rqtl2.select_dataset_info',
-	        species_id=species.SpeciesId,
-	        population_id=population.InbredSetId)}}"
-        method="POST"
-        enctype="multipart/form-data">
-    <legend class="heading">Create ProbeSet dataset</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id"
-	   value="{{population.InbredSetId}}" />
-    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
-    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
-    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
-    <input type="hidden" name="probe-study-id" value="{{study.Id}}" />
-    <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
-
-    <button type="submit" class="btn btn-primary">continue</button>
-  </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
deleted file mode 100644
index e293f6f..0000000
--- a/uploader/templates/rqtl2/create-probe-study-success.html
+++ /dev/null
@@ -1,49 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Study</h2>
-
-<div class="row">
-  <p>You successfully created the ProbeSet study with the following
-    information.
-    <dl>
-      <dt>ID</dt>
-      <dd>{{study.id}}</dd>
-
-      <dt>Name</dt>
-      <dd>{{study.name}}</dd>
-
-      <dt>Full Name</dt>
-      <dd>{{study.fname}}</dd>
-
-      <dt>Short Name</dt>
-      <dd>{{study.sname}}</dd>
-
-      <dt>Created On</dt>
-      <dd>{{study.today}}</dd>
-    </dl>
-  </p>
-
-  <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('expression-data.rqtl2.select_dataset_info',
-	        species_id=species.SpeciesId,
-	        population_id=population.InbredSetId)}}"
-        method="POST"
-        enctype="multipart/form-data">
-    <legend class="heading">Create ProbeSet study</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id"
-	   value="{{population.InbredSetId}}" />
-    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
-    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
-    <input type="hidden" name="probe-study-id" value="{{study.studyid}}" />
-
-    <button type="submit" class="btn btn-primary">continue</button>
-  </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
deleted file mode 100644
index 8ce13bf..0000000
--- a/uploader/templates/rqtl2/index.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 data upload</h1>
-
-<h2>R/qtl2 Upload</h2>
-
-<form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}"
-      id="frm-rqtl2-upload">
-  <legend class="heading">upload R/qtl2 bundle</legend>
-  {{flash_messages("error-rqtl2")}}
-
-  <div class="form-group">
-    <label for="select:species" class="form-label">Species</label>
-    <select id="select:species"
-            name="species_id"
-            required="required"
-            class="form-control">
-      <option value="">Select species</option>
-      {%for spec in species%}
-      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
-      {%endfor%}
-    </select>
-    <small class="form-text text-muted">
-      Data that you upload to the system should belong to a know species.
-      Here you can select the species that you wish to upload data for.
-    </small>
-  </div>
-
-  <button type="submit" class="btn btn-primary" />submit</button>
-</form>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
deleted file mode 100644
index 1db51e0..0000000
--- a/uploader/templates/rqtl2/select-geno-dataset.html
+++ /dev/null
@@ -1,144 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="row">
-  <p>Your R/qtl2 files bundle contains a "geno" specification. You will
-    therefore need to select from one of the existing Genotype datasets or
-    create a new one.</p>
-  <p>This is the dataset where your data will be organised under.</p>
-</div>
-
-<div class="row">
-  <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('expression-data.rqtl2.select_geno_dataset',
-	        species_id=species.SpeciesId,
-	        population_id=population.InbredSetId)}}"
-        method="POST"
-        enctype="multipart/form-data">
-    <legend class="heading">select from existing genotype datasets</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id"
-	   value="{{population.InbredSetId}}" />
-    <input type="hidden" name="rqtl2_bundle_file"
-	   value="{{rqtl2_bundle_file}}" />
-
-    {{flash_messages("error-rqtl2-select-geno-dataset")}}
-
-    <div class="form-group">
-      <legend>Datasets</legend>
-      <label for="select:geno-datasets" class="form-label">Dataset</label>
-      <select id="select:geno-datasets"
-	      name="geno-dataset-id"
-	      required="required"
-	      {%if datasets | length == 0%}
-	      disabled="disabled"
-	      {%endif%}
-              class="form-control"
-              aria-describedby="help-geno-dataset-select-dataset">
-        <option value="">Select dataset</option>
-        {%for dset in datasets%}
-        <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
-        {%endfor%}
-      </select>
-      <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
-        Select from the existing genotype datasets for species
-        {{species.SpeciesName}} ({{species.FullName}}).
-      </span>
-    </div>
-
-    <button type="submit" class="btn btn-primary">select dataset</button>
-  </form>
-</div>
-
-<div class="row">
-  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-
-<div class="row">
-  <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('expression-data.rqtl2.create_geno_dataset',
-	        species_id=species.SpeciesId,
-	        population_id=population.InbredSetId)}}"
-        method="POST"
-        enctype="multipart/form-data">
-    <legend class="heading">create a new genotype dataset</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id"
-	   value="{{population.InbredSetId}}" />
-    <input type="hidden" name="rqtl2_bundle_file"
-	   value="{{rqtl2_bundle_file}}" />
-
-    {{flash_messages("error-rqtl2-create-geno-dataset")}}
-
-    <div class="form-group">
-      <label for="txt:dataset-name" class="form-label">Name</label>
-      <input type="text"
-	     id="txt:dataset-name"
-	     name="dataset-name"
-	     maxlength="100"
-	     required="required"
-             class="form-control"
-             aria-describedby="help-geno-dataset-name" />
-      <span id="help-geno-dataset-name" class="form-text text-muted">
-        Provide the new name for the genotype dataset, e.g. "BXDGeno"
-      </span>
-    </div>
-
-    <div class="form-group">
-      <label for="txt:dataset-fullname" class="form-label">Full Name</label>
-      <input type="text"
-	     id="txt:dataset-fullname"
-	     name="dataset-fullname"
-	     required="required"
-	     maxlength="100"
-             class="form-control"
-             aria-describedby="help-geno-dataset-fullname" />
-
-      <span id="help-geno-dataset-fullname" class="form-text text-muted">
-        Provide a longer name that better describes the genotype dataset, e.g.
-        "BXD Genotypes"
-      </span>
-    </div>
-
-    <div class="form-group">
-      <label for="txt:dataset-shortname" class="form-label">Short Name</label>
-      <input type="text"
-	     id="txt:dataset-shortname"
-	     name="dataset-shortname"
-	     maxlength="100"
-             class="form-control"
-             aria-describedby="help-geno-dataset-shortname" />
-
-      <span id="help-geno-dataset-shortname" class="form-text text-muted">
-        Provide a short name for the genotype dataset. This is optional. If not
-        provided, we'll default to the same value as the "Name" above.
-      </span>
-    </div>
-
-    <div class="form-group">
-      <input type="checkbox"
-	     id="chk:dataset-public"
-	     name="dataset-public"
-	     checked="checked"
-             class="form-check"
-             aria-describedby="help-geno-datasent-public" />
-      <label for="chk:dataset-public" class="form-check-label">Public?</label>
-
-      <span id="help-geno-dataset-public" class="form-text text-muted">
-        Specify whether the dataset will be available publicly. Check to make the
-        dataset publicly available and uncheck to limit who can access the dataset.
-      </span>
-    </div>
-
-    <button type="submit" class="btn btn-primary">create new dataset</button>
-  </form>
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
deleted file mode 100644
index 7d27303..0000000
--- a/uploader/templates/rqtl2/select-population.html
+++ /dev/null
@@ -1,136 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div class="explainer">
-  <p>The data is organised in a hierarchical form, beginning with
-    <em>species</em> at the very top. Under <em>species</em> the data is
-    organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
-    (In some really old documents/systems, you might see this referred to as
-    <em>InbredSet</em>.)</p>
-  <p>In this section, you get to define what population your data is to be
-    organised by.</p>
-</div>
-
-<form method="POST"
-      action="{{url_for('expression-data.rqtl2.select_population', species_id=species.SpeciesId)}}">
-  <legend class="heading">select grouping/population</legend>
-  {{flash_messages("error-select-population")}}
-
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
-  <div class="form-group">
-    <label for="select:inbredset" class="form-label">population</label>
-    <select id="select:inbredset"
-	    name="inbredset_id"
-	    required="required"
-	    class="form-control">
-      <option value="">Select a grouping/population</option>
-      {%for pop in populations%}
-      <option value="{{pop.InbredSetId}}">
-	{{pop.InbredSetName}} ({{pop.FullName}})</option>
-      {%endfor%}
-    </select>
-    <span class="form-text text-muted">If you are adding data to an already existing
-      population, simply pick the population from this drop-down selector. If
-      you cannot find your population from this list, try the form below to
-      create a new one..</span>
-  </div>
-
-  <button type="submit" class="btn btn-primary" />select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST"
-      action="{{url_for('expression-data.rqtl2.create_population', species_id=species.SpeciesId)}}">
-  <legend class="heading">create new grouping/population</legend>
-  {{flash_messages("error-create-population")}}
-
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
-  <div class="form-group">
-    <legend class="heading">mandatory</legend>
-
-    <div class="form-group">
-      <label for="txt:inbredset-name" class="form-label">name</label>
-      <input id="txt:inbredset-name"
-	     name="inbredset_name"
-	     type="text"
-	     required="required"
-	     maxlength="30"
-	     placeholder="Enter grouping/population name"
-	     class="form-control" />
-      <span class="form-text text-muted">This is a short name that identifies the
-        population. Useful for menus, and quick scanning.</span>
-    </div>
-
-    <div class="form-group">
-      <label for="txt:" class="form-label">full name</label>
-      <input id="txt:inbredset-fullname"
-	     name="inbredset_fullname"
-	     type="text"
-	     required="required"
-	     maxlength="100"
-	     placeholder="Enter the grouping/population's full name"
-	     class="form-control" />
-      <span class="form-text text-muted">This can be the same as the name above, or can
-        be longer. Useful for documentation, and human communication.</span>
-    </div>
-  </div>
-
-  <div class="form-group">
-    <legend class="heading">optional</legend>
-
-    <div class="form-group">
-      <label for="num:public" class="form-label">public?</label>
-      <select id="num:public"
-	      name="public"
-	      class="form-control">
-        <option value="0">0 - Only accessible to authorised users</option>
-        <option value="1">1 - Publicly accessible to all users</option>
-        <option value="2" selected>
-	  2 - Publicly accessible to all users</option>
-      </select>
-      <span class="form-text text-muted">This determines whether the
-        population/grouping will appear on the menus for users.</span>
-    </div>
-
-    <div class="form-group">
-      <label for="txt:inbredset-family" class="form-label">family</label>
-      <input id="txt:inbredset-family"
-	     name="inbredset_family"
-	     type="text"
-	     placeholder="I am not sure what this is about."
-	     class="form-control" />
-      <span class="form-text text-muted">I do not currently know what this is about.
-        This is a failure on my part to figure out what this is and provide a
-        useful description. Please feel free to remind me.</span>
-    </div>
-
-    <div class="form-group">
-    <label for="txtarea:" class="form-label">Description</label>
-    <textarea id="txtarea:description"
-	      name="description"
-	      rows="5"
-	      placeholder="Enter a description of this grouping/population"
-	      class="form-control"></textarea>
-    <span class="form-text text-muted">
-      A long-form description of what the population consists of. Useful for
-      humans.</span>
-    </div>
-  </div>
-
-  <button type="submit" class="btn btn-primary" />
-  create grouping/population</button>
-</form>
-
-{%endblock%}
-
-
-{%block javascript%}
-{%endblock%}