Rename module: qc_app --> uploader

21 files changed, 1768 insertions, 0 deletions

diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
new file mode 100644
index 0000000..1b50221
--- /dev/null
+++ b/uploader/templates/rqtl2/create-geno-dataset-success.html
@@ -0,0 +1,55 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="explainer">
+  <p>You successfully created the genotype dataset with the following
+    information.
+    <dl>
+      <dt>ID</dt>
+      <dd>{{geno_dataset.id}}</dd>
+
+      <dt>Name</dt>
+      <dd>{{geno_dataset.name}}</dd>
+
+      <dt>Full Name</dt>
+      <dd>{{geno_dataset.fname}}</dd>
+
+      <dt>Short Name</dt>
+      <dd>{{geno_dataset.sname}}</dd>
+
+      <dt>Created On</dt>
+      <dd>{{geno_dataset.today}}</dd>
+
+      <dt>Public?</dt>
+      <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
+    </dl>
+  </p>
+</div>
+
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">select from existing genotype datasets</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id"
+	   value="{{geno_dataset.id}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
new file mode 100644
index 0000000..790d174
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-dataset-success.html
@@ -0,0 +1,59 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Create ProbeSet Dataset</h2>
+
+<div class="row">
+  <p>You successfully created the ProbeSet dataset with the following
+    information.
+    <dl>
+      <dt>Averaging Method</dt>
+      <dd>{{avgmethod.Name}}</dd>
+
+      <dt>ID</dt>
+      <dd>{{dataset.datasetid}}</dd>
+
+      <dt>Name</dt>
+      <dd>{{dataset.name2}}</dd>
+
+      <dt>Full Name</dt>
+      <dd>{{dataset.fname}}</dd>
+
+      <dt>Short Name</dt>
+      <dd>{{dataset.sname}}</dd>
+
+      <dt>Created On</dt>
+      <dd>{{dataset.today}}</dd>
+
+      <dt>DataScale</dt>
+      <dd>{{dataset.datascale}}</dd>
+    </dl>
+  </p>
+</div>
+
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">Create ProbeSet dataset</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+    <input type="hidden" name="probe-study-id" value="{{study.Id}}" />
+    <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
new file mode 100644
index 0000000..d0ee508
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-study-success.html
@@ -0,0 +1,49 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Create ProbeSet Study</h2>
+
+<div class="row">
+  <p>You successfully created the ProbeSet study with the following
+    information.
+    <dl>
+      <dt>ID</dt>
+      <dd>{{study.id}}</dd>
+
+      <dt>Name</dt>
+      <dd>{{study.name}}</dd>
+
+      <dt>Full Name</dt>
+      <dd>{{study.fname}}</dd>
+
+      <dt>Short Name</dt>
+      <dd>{{study.sname}}</dd>
+
+      <dt>Created On</dt>
+      <dd>{{study.today}}</dd>
+    </dl>
+  </p>
+
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">Create ProbeSet study</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="probe-study-id" value="{{study.studyid}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html
new file mode 100644
index 0000000..5f2c5a0
--- /dev/null
+++ b/uploader/templates/rqtl2/create-tissue-success.html
@@ -0,0 +1,106 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Tissue</h2>
+
+<div class="row">
+  <p>You have successfully added a new tissue, organ or biological material with
+    the following details:</p>
+</div>
+
+<div class="row">
+  {{flash_all_messages()}}
+
+  <form id="frm-create-tissue-display"
+        method="POST"
+        action="#">
+    <legend class="heading">Create Tissue</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+    <div class="form-group">
+      <label>Name</label>
+      <label>{{tissue.TissueName}}</label>
+    </div>
+
+    <div class="form-group">
+      <label>Short Name</label>
+      <label>{{tissue.Short_Name}}</label>
+    </div>
+
+    {%if tissue.BIRN_lex_ID%}
+    <div class="form-group">
+      <label>BIRN Lex ID</label>
+      <label>{{tissue.BIRN_lex_ID}}</label>
+    </div>
+    {%endif%}
+
+    {%if tissue.BIRN_lex_Name%}
+    <div class="form-group">
+      <label>BIRN Lex Name</label>
+      <label>{{tissue.BIRN_lex_Name}}</label>
+    </div>
+    {%endif%}
+  </form>
+
+  <div id="action-buttons"
+       style="width:65ch;display:inline-grid;column-gap:5px;">
+
+    <form id="frm-create-tissue-success-continue"
+          method="POST"
+          action="{{url_for('upload.rqtl2.select_dataset_info',
+	          species_id=species.SpeciesId,
+	          population_id=population.InbredSetId)}}"
+          style="display: inline; width: 100%; grid-column: 1 / 2;
+                 padding-top: 0.5em; text-align: center; border: none;
+                 background-color: inherit;">
+
+      <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+      <input type="hidden" name="population_id"
+	     value="{{population.InbredSetId}}" />
+      <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+      <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+      <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+      <button type="submit" class="btn btn-primary">continue</button>
+    </form>
+  </div>
+</div>
+
+<div class="row">
+  <p style="display:inline;width:100%;grid-column:2/3;text-align:center;
+            color:#336699;font-weight:bold;">
+    OR
+  </p>
+</div>
+
+<div class="row">
+  <form id="frm-create-tissue-success-select-existing"
+        method="POST"
+        action="{{url_for('upload.rqtl2.select_tissue',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        style="display: inline; width: 100%; grid-column: 3 / 4;
+               padding-top: 0.5em; text-align: center; border: none;
+               background-color: inherit;">
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+    <button type="submit" class="btn btn-primary">
+      select from existing tissues</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
new file mode 100644
index 0000000..f3329c2
--- /dev/null
+++ b/uploader/templates/rqtl2/index.html
@@ -0,0 +1,36 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 data upload</h1>
+
+<h2>R/qtl2 Upload</h2>
+
+<form method="POST" action="{{url_for('upload.rqtl2.select_species')}}"
+      id="frm-rqtl2-upload">
+  <legend class="heading">upload R/qtl2 bundle</legend>
+  {{flash_messages("error-rqtl2")}}
+
+  <div class="form-group">
+    <label for="select:species" class="form-label">Species</label>
+    <select id="select:species"
+            name="species_id"
+            required="required"
+            class="form-control">
+      <option value="">Select species</option>
+      {%for spec in species%}
+      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
+      {%endfor%}
+    </select>
+    <small class="form-text text-muted">
+      Data that you upload to the system should belong to a know species.
+      Here you can select the species that you wish to upload data for.
+    </small>
+  </div>
+
+  <button type="submit" class="btn btn-primary" />submit</button>
+</form>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/rqtl2/no-such-job.html
new file mode 100644
index 0000000..b17004f
--- /dev/null
+++ b/uploader/templates/rqtl2/no-such-job.html
@@ -0,0 +1,13 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 job status</h1>
+
+<h2>R/qtl2 Upload: No Such Job</h2>
+
+<p class="alert-danger">No job with ID {{jobid}} was found.</p>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/rqtl2/rqtl2-job-error.html
new file mode 100644
index 0000000..9817518
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-error.html
@@ -0,0 +1,39 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 job status</h1>
+
+<h2>R/qtl2 Upload: Job Status</h2>
+
+<div class="explainer">
+  <p>The processing of the R/qtl2 bundle you uploaded has failed. We have
+    provided some information below to help you figure out what the problem
+    could be.</p>
+  <p>If you find that you cannot figure out what the problem is on your own,
+    please contact the team running the system for assistance, providing the
+    following details:
+    <ul>
+      <li>R/qtl2 bundle you uploaded</li>
+      <li>This URL: <strong>{{request_url()}}</strong></li>
+      <li>(maybe) a screenshot of this page</li>
+    </ul>
+  </p>
+</div>
+
+<h4>stdout</h4>
+{{cli_output(job, "stdout")}}
+
+<h4>stderr</h4>
+{{cli_output(job, "stderr")}}
+
+<h4>Log</h4>
+<div class="cli-output">
+  {%for msg in messages%}
+  {{msg}}<br />
+  {%endfor%}
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/rqtl2/rqtl2-job-results.html
new file mode 100644
index 0000000..4ecd415
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-results.html
@@ -0,0 +1,24 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 job status</h1>
+
+<h2>R/qtl2 Upload: Job Status</h2>
+
+<div class="explainer">
+  <p>The processing of the R/qtl2 bundle you uploaded has completed
+    successfully.</p>
+  <p>You should now be able to use GeneNetwork to run analyses on your data.</p>
+</div>
+
+<h4>Log</h4>
+<div class="cli-output">
+  {%for msg in messages%}
+  {{msg}}<br />
+  {%endfor%}
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/rqtl2/rqtl2-job-status.html
new file mode 100644
index 0000000..e896f88
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-status.html
@@ -0,0 +1,20 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block extrameta%}
+<meta http-equiv="refresh" content="3">
+{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 job status</h1>
+
+<h2>R/qtl2 Upload: Job Status</h2>
+
+<h4>Log</h4>
+<div class="cli-output">
+  <pre>{{"\n".join(messages)}}</pre>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
new file mode 100644
index 0000000..90e8887
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
@@ -0,0 +1,120 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
+
+{%macro errors_table(tableid, errors)%}
+<table id="{{tableid}}" class="table error-table">
+  <caption>{{caption}}</caption>
+  <thead>
+    <tr>
+      <th>Line</th>
+      <th>Column</th>
+      <th>Value</th>
+      <th>Message</th>
+    </tr>
+  </thead>
+  <tbody>
+    {%for error in errors%}
+    <tr>
+      <td>{{error.line}}</td>
+      <td>{{error.column}}</td>
+      <td>{{error.value}}</td>
+      <td>{{error.message}}</td>
+    </tr>
+    {%else%}
+    <tr>
+      <td colspan="4">No errors to display here.</td>
+    </tr>
+    {%endfor%}
+  </tbody>
+</table>
+{%endmacro%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 bundle: QC job Error</h1>
+
+<div class="explainer">
+  <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p>
+  <p>We list below some of the errors that need to be fixed before the data can
+    be uploaded onto GeneNetwork.</p>
+</div>
+
+{%if errorsgeneric | length > 0%}
+<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3>
+<div class="explainer">
+  We found the following generic errors in your R/qtl2 bundle:
+</div>
+
+<h3>Missing Files</h3>
+<div class="explainer">
+  <p>These files are listed in the bundle's control file, but do not actually
+    exist in the bundle</p>
+</div>
+<table id="tbl-errors-missing-files" class="table error-table">
+  <thead>
+    <tr>
+      <th>Control File Key</th>
+      <th>Bundle File Name</th>
+      <th>Message</th>
+    </tr>
+  </thead>
+  <tbody>
+    {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%}
+    <tr>
+      <td>{{error.controlfilekey}}</td>
+      <td>{{error.filename}}</td>
+      <td>{{error.message}}</td>
+    </tr>
+    {%endfor%}
+  </tbody>
+</table>
+
+<h3>Other Generic Errors</h3>
+{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}}
+{%endif%}
+
+{%if errorsgeno | length > 0%}
+<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'geno' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
+{%endif%}
+
+{%if errorspheno | length > 0%}
+<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'pheno' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
+{%endif%}
+
+{%if errorsphenose | length > 0%}
+<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'phenose' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
+{%endif%}
+
+{%if errorsphenocovar | length > 0%}
+<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
+</div>
+{{errorsphenocovar}}
+{%endif%}
+
+<h4>stdout</h4>
+{{cli_output(job, "stdout")}}
+
+<h4>stderr</h4>
+{{cli_output(job, "stderr")}}
+
+<h4>Log</h4>
+<div class="cli-output">
+  <pre>{{"\n".join(messages)}}</pre>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
new file mode 100644
index 0000000..59bc8cd
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
@@ -0,0 +1,66 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC job results{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 bundle: QC job results</h1>
+
+<div class="row">
+  <p>The R/qtl2 bundle you uploaded has passed all automated quality-control
+    checks successfully.</p>
+  <p>You may now continue to load the data into GeneNetwork for the bundle, with
+    the following details:</p>
+</div>
+
+<div class="row">
+  <form id="form-qc-job-results"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.Id)}}"
+        method="POST">
+    <div class="form-group">
+      <legend>Species</legend>
+      <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+
+      <span class="form-label">Name</span>
+      <span class="form-text">{{species.Name | capitalize}}</span>
+
+      <span class="form-label">Scientific</span>
+      <span class="form-text">{{species.FullName | capitalize}}</span>
+    </div>
+
+    <div class="form-group">
+      <legend>population</legend>
+      <input type="hidden" name="population_id" value="{{population.Id}}" />
+
+      <span class="form-label">Name</span>
+      <span class="form-text">{{population.InbredSetName}}</span>
+
+      <span class="form-label">Full Name</span>
+      <span class="form-text">{{population.FullName}}</span>
+
+      <span class="form-label">Genetic Type</span>
+      <span class="form-text">{{population.GeneticType}}</span>
+
+      <span class="form-label">Description</span>
+      <span class="form-text">{{population.Description or "-"}}</span>
+    </div>
+
+    <div class="form-group">
+      <legend>R/qtl2 Bundle File</legend>
+      <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" />
+      <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" />
+
+      <span class="form-label">Original Name</span>
+      <span class="form-text">{{rqtl2bundleorig}}</span>
+
+      <span class="form-label">Internal Name</span>
+      <span class="form-text">{{rqtl2bundle[0:25]}}&hellip;</span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
new file mode 100644
index 0000000..f4a6266
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
@@ -0,0 +1,41 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block extrameta%}
+<meta http-equiv="refresh" content="3">
+{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 bundle: QC job status</h1>
+
+{%if geno_percent%}
+<p>
+  <h2>Checking 'geno' file:</h2>
+  <progress id="prg-geno-checking" value="{{geno_percent}}" max="100">
+    {{geno_percent}}%</progress>
+  {{geno_percent}}%</p>
+{%endif%}
+
+{%if pheno_percent%}
+<p>
+  <h2>Checking 'pheno' file:</h2>
+  <progress id="prg-pheno-checking" value="{{pheno_percent}}" max="100">
+    {{pheno_percent}}%</progress>
+  {{pheno_percent}}%</p>
+{%endif%}
+
+{%if phenose_percent%}
+<p>
+  <h2>Checking 'phenose' file:</h2>
+  <progress id="prg-phenose-checking" value="{{phenose_percent}}" max="100">
+    {{phenose_percent}}%</progress>
+  {{phenose_percent}}%</p>
+{%endif%}
+
+<h4>Log</h4>
+<div class="cli-output">
+  <pre>{{"\n".join(messages)}}</pre>
+</div>
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
new file mode 100644
index 0000000..2861a04
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
@@ -0,0 +1,37 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%}
+
+{%block contents%}
+<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2>
+
+<div class="row">
+  <p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control
+    checks successfully, and is now ready for uploading into the database.</p>
+  <p>Click "Continue" below to proceed.</p>
+</div>
+
+<!--
+    The "action" on this form takes us to the next step, where we can
+    select all the other data necessary to enter the data into the database.
+  -->
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    {{flash_all_messages()}}
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..873f9c3
--- /dev/null
+++ b/uploader/templates/rqtl2/select-geno-dataset.html
@@ -0,0 +1,144 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="row">
+  <p>Your R/qtl2 files bundle contains a "geno" specification. You will
+    therefore need to select from one of the existing Genotype datasets or
+    create a new one.</p>
+  <p>This is the dataset where your data will be organised under.</p>
+</div>
+
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_geno_dataset',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">select from existing genotype datasets</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+
+    {{flash_messages("error-rqtl2-select-geno-dataset")}}
+
+    <div class="form-group">
+      <legend>Datasets</legend>
+      <label for="select:geno-datasets" class="form-label">Dataset</label>
+      <select id="select:geno-datasets"
+	      name="geno-dataset-id"
+	      required="required"
+	      {%if datasets | length == 0%}
+	      disabled="disabled"
+	      {%endif%}
+              class="form-control"
+              aria-describedby="help-geno-dataset-select-dataset">
+        <option value="">Select dataset</option>
+        {%for dset in datasets%}
+        <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
+        {%endfor%}
+      </select>
+      <span id="help-geno-dataset-select-dataset" class="form-text text-muted">
+        Select from the existing genotype datasets for species
+        {{species.SpeciesName}} ({{species.FullName}}).
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">select dataset</button>
+  </form>
+</div>
+
+<div class="row">
+  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+
+<div class="row">
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.create_geno_dataset',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">create a new genotype dataset</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+
+    {{flash_messages("error-rqtl2-create-geno-dataset")}}
+
+    <div class="form-group">
+      <label for="txt:dataset-name" class="form-label">Name</label>
+      <input type="text"
+	     id="txt:dataset-name"
+	     name="dataset-name"
+	     maxlength="100"
+	     required="required"
+             class="form-control"
+             aria-describedby="help-geno-dataset-name" />
+      <span id="help-geno-dataset-name" class="form-text text-muted">
+        Provide the new name for the genotype dataset, e.g. "BXDGeno"
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:dataset-fullname" class="form-label">Full Name</label>
+      <input type="text"
+	     id="txt:dataset-fullname"
+	     name="dataset-fullname"
+	     required="required"
+	     maxlength="100"
+             class="form-control"
+             aria-describedby="help-geno-dataset-fullname" />
+
+      <span id="help-geno-dataset-fullname" class="form-text text-muted">
+        Provide a longer name that better describes the genotype dataset, e.g.
+        "BXD Genotypes"
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:dataset-shortname" class="form-label">Short Name</label>
+      <input type="text"
+	     id="txt:dataset-shortname"
+	     name="dataset-shortname"
+	     maxlength="100"
+             class="form-control"
+             aria-describedby="help-geno-dataset-shortname" />
+
+      <span id="help-geno-dataset-shortname" class="form-text text-muted">
+        Provide a short name for the genotype dataset. This is optional. If not
+        provided, we'll default to the same value as the "Name" above.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <input type="checkbox"
+	     id="chk:dataset-public"
+	     name="dataset-public"
+	     checked="checked"
+             class="form-check"
+             aria-describedby="help-geno-datasent-public" />
+      <label for="chk:dataset-public" class="form-check-label">Public?</label>
+
+      <span id="help-geno-dataset-public" class="form-text text-muted">
+        Specify whether the dataset will be available publicly. Check to make the
+        dataset publicly available and uncheck to limit who can access the dataset.
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">create new dataset</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
new file mode 100644
index 0000000..37731f0
--- /dev/null
+++ b/uploader/templates/rqtl2/select-population.html
@@ -0,0 +1,136 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Select Grouping/Population{%endblock%}
+
+{%block contents%}
+<h1 class="heading">Select grouping/population</h1>
+
+<div class="explainer">
+  <p>The data is organised in a hierarchical form, beginning with
+    <em>species</em> at the very top. Under <em>species</em> the data is
+    organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
+    (In some really old documents/systems, you might see this referred to as
+    <em>InbredSet</em>.)</p>
+  <p>In this section, you get to define what population your data is to be
+    organised by.</p>
+</div>
+
+<form method="POST"
+      action="{{url_for('upload.rqtl2.select_population', species_id=species.SpeciesId)}}">
+  <legend class="heading">select grouping/population</legend>
+  {{flash_messages("error-select-population")}}
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+
+  <div class="form-group">
+    <label for="select:inbredset" class="form-label">population</label>
+    <select id="select:inbredset"
+	    name="inbredset_id"
+	    required="required"
+	    class="form-control">
+      <option value="">Select a grouping/population</option>
+      {%for pop in populations%}
+      <option value="{{pop.InbredSetId}}">
+	{{pop.InbredSetName}} ({{pop.FullName}})</option>
+      {%endfor%}
+    </select>
+    <span class="form-text text-muted">If you are adding data to an already existing
+      population, simply pick the population from this drop-down selector. If
+      you cannot find your population from this list, try the form below to
+      create a new one..</span>
+  </div>
+
+  <button type="submit" class="btn btn-primary" />select population</button>
+</form>
+
+<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+
+<form method="POST"
+      action="{{url_for('upload.rqtl2.create_population', species_id=species.SpeciesId)}}">
+  <legend class="heading">create new grouping/population</legend>
+  {{flash_messages("error-create-population")}}
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+
+  <div class="form-group">
+    <legend class="heading">mandatory</legend>
+
+    <div class="form-group">
+      <label for="txt:inbredset-name" class="form-label">name</label>
+      <input id="txt:inbredset-name"
+	     name="inbredset_name"
+	     type="text"
+	     required="required"
+	     maxlength="30"
+	     placeholder="Enter grouping/population name"
+	     class="form-control" />
+      <span class="form-text text-muted">This is a short name that identifies the
+        population. Useful for menus, and quick scanning.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:" class="form-label">full name</label>
+      <input id="txt:inbredset-fullname"
+	     name="inbredset_fullname"
+	     type="text"
+	     required="required"
+	     maxlength="100"
+	     placeholder="Enter the grouping/population's full name"
+	     class="form-control" />
+      <span class="form-text text-muted">This can be the same as the name above, or can
+        be longer. Useful for documentation, and human communication.</span>
+    </div>
+  </div>
+
+  <div class="form-group">
+    <legend class="heading">optional</legend>
+
+    <div class="form-group">
+      <label for="num:public" class="form-label">public?</label>
+      <select id="num:public"
+	      name="public"
+	      class="form-control">
+        <option value="0">0 - Only accessible to authorised users</option>
+        <option value="1">1 - Publicly accessible to all users</option>
+        <option value="2" selected>
+	  2 - Publicly accessible to all users</option>
+      </select>
+      <span class="form-text text-muted">This determines whether the
+        population/grouping will appear on the menus for users.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:inbredset-family" class="form-label">family</label>
+      <input id="txt:inbredset-family"
+	     name="inbredset_family"
+	     type="text"
+	     placeholder="I am not sure what this is about."
+	     class="form-control" />
+      <span class="form-text text-muted">I do not currently know what this is about.
+        This is a failure on my part to figure out what this is and provide a
+        useful description. Please feel free to remind me.</span>
+    </div>
+
+    <div class="form-group">
+    <label for="txtarea:" class="form-label">Description</label>
+    <textarea id="txtarea:description"
+	      name="description"
+	      rows="5"
+	      placeholder="Enter a description of this grouping/population"
+	      class="form-control"></textarea>
+    <span class="form-text text-muted">
+      A long-form description of what the population consists of. Useful for
+      humans.</span>
+    </div>
+  </div>
+
+  <button type="submit" class="btn btn-primary" />
+  create grouping/population</button>
+</form>
+
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html
new file mode 100644
index 0000000..26f52ed
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-dataset.html
@@ -0,0 +1,191 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
+
+<div class="row">
+  <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+    file(s). This data needs to be organised under a dataset.</p>
+  <p>This page gives you the ability to do that.</p>
+</div>
+
+{%if datasets | length > 0%}
+<div class="row">
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.select_probeset_dataset',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:select-probeset-dataset">
+    <legend class="heading">Select from existing ProbeSet datasets</legend>
+    {{flash_messages("error-rqtl2")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+    <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="select:probe-dataset">Dataset</label>
+      <select id="select:probe-dataset"
+	      name="probe-dataset-id"
+	      required="required"
+	      {%if datasets | length == 0%}disabled="disabled"{%endif%}
+              class="form-control"
+              aria-describedby="help-probe-dataset">
+        <option value="">Select a dataset</option>
+        {%for dataset in datasets%}
+        <option value={{dataset.Id}}>
+	  {{dataset.Name}}
+	  {%if dataset.FullName%}
+	  -- ({{dataset.FullName}})
+	  {%endif%}
+        </option>
+        {%endfor%}
+      </select>
+
+      <span id="help-probe-dataset" class="form-text text-muted">
+        Select from existing ProbeSet datasets.</span>
+    </div>
+
+    <button type="submit" class="btn btn-primary" />select dataset</button>
+</form>
+</div>
+
+<div class="row">
+  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+{%endif%}
+
+<div class="row">
+  <p>Create an entirely new ProbeSet dataset for your data.</p>
+</div>
+
+<div class="row">
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.create_probeset_dataset',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:create-probeset-dataset">
+    <legend class="heading">Create a new ProbeSet dataset</legend>
+    {{flash_messages("error-rqtl2-create-probeset-dataset")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+    <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="select:average">averaging method</label>
+      <select id="select:average"
+	      name="averageid"
+	      required="required"
+              class="form-control"
+              aria-describedby="help-average">
+        <option value="">Select averaging method</option>
+        {%for avgmethod in avgmethods%}
+        <option value="{{avgmethod.Id}}">
+	  {{avgmethod.Name}}
+	  {%if avgmethod.Normalization%}
+	  ({{avgmethod.Normalization}})
+	  {%endif%}
+        </option>
+        {%endfor%}
+      </select>
+
+      <span id="help-average" class="form-text text-muted">
+        Select the averaging method used for your data.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label class="form-label" for="txt:datasetname">Name</label>
+      <input type="text" id="txt:datasetname" name="datasetname"
+	     required="required"
+	     maxlength="40"
+	     title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)"
+             class="form-control"
+             aria-describedby="help-dataset-name" />
+
+      <span id="help-dataset-name" class="form-text text-muted">
+        Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
+        is mandatory <strong>MUST</strong> be provided.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label class="form-label" for="txt:datasetfullname">Full Name</label>
+      <input type="text" id="txt:datasetfullname" name="datasetfullname"
+	     required="required"
+	     maxlength="100"
+	     title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)"
+             class="form-control"
+             aria-describedby="help-dataset-fullname" />
+
+      <span id="help-dataset-fullname" class="form-text text-muted">
+        Provide a longer, more descriptive name for the dataset e.g.
+        "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
+        <strong>MUST</strong> be provided.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label class="form-label" for="txt:datasetshortname">Short Name</label>
+      <input type="text" id="txt:datasetshortname" name="datasetshortname"
+	     maxlength="100"
+	     title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)"
+             class="form-control"
+             aria-describedby="help-dataset-shortname" />
+
+      <span id="help-dataset-shortname" class="form-text text-muted">
+        Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
+        This is optional.
+      </span>
+    </div>
+
+    <div class="form-check">
+      <input type="checkbox" id="chk:public" name="datasetpublic"
+	     checked="checked"
+	     title="Whether or not the dataset is accessible by the general public."
+             class="form-check-input"
+             aria-describedby="help-public" />
+      <label class="form-check-label" for="chk:datasetpublic">Public?</label>
+
+      <span id="help-public" class="form-text text-muted">
+        Check to specify that the dataset will be publicly available. Uncheck to
+        limit access to the dataset.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label class="form-label" for="select:datasetdatascale">Data Scale</label>
+      <select id="select:datasetdatascale"
+	      name="datasetdatascale"
+	      required="required"
+              class="form-control"
+              aria-describedby="help-dataset-datascale">
+        <option value="log2" selected="selected">log2</option>
+        <option value="z_score">z_score</option>
+        <option value="log2_ratio">log2_ratio</option>
+        <option value="linear">linear</option>
+        <option value="linear_positive">linear_positive</option>
+      </select>
+
+      <span id="help-dataset-datascale" class="form-text text-muted">
+        Select from a list of scaling methods.
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">create dataset</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..b9bf52e
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,143 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages %}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Study</h2>
+
+<div class="row">
+  <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+    file(s). This data needs to be organised under a study.</p>
+  <p>In this page, you can either select from a existing dataset:</p>
+
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.select_probeset_study',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:select-probeset-study">
+    <legend class="heading">Select from existing ProbeSet studies</legend>
+    {{flash_messages("error-rqtl2-select-probeset-study")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+    <div>
+      <label for="select:probe-study" class="form-label">Study</label>
+      <select id="select:probe-study"
+	      name="probe-study-id"
+	      required="required"
+              aria-describedby="help-select-probeset-study"
+	      {%if studies | length == 0%}disabled="disabled"{%endif%}
+              class="form-control">
+        <option value="">Select a study</option>
+        {%for study in studies%}
+        <option value={{study.Id}}>
+	  {{study.Name}}
+	  {%if study.FullName%}
+	  -- ({{study.FullName}})
+	  {%endif%}
+        </option>
+        {%endfor%}
+      </select>
+      <small id="help-select-probeset-study" class="form-text text-muted">
+        Select from existing ProbeSet studies.
+      </small>
+    </div>
+
+    <button type="submit" class="btn btn-primary">select study</button>
+  </form>
+</div>
+
+<div class="row">
+  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+
+<div class="row">
+
+  <p>Create a new ProbeSet dataset below:</p>
+
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.create_probeset_study',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:create-probeset-study">
+    <legend class="heading">Create new ProbeSet study</legend>
+
+    {{flash_messages("error-rqtl2-create-probeset-study")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+    <div>
+      <label for="select:platform" class="form-label">Platform</label>
+      <select id="select:platform"
+	      name="platformid"
+	      required="required"
+              aria-describedby="help-select-platform"
+	      {%if platforms | length == 0%}disabled="disabled"{%endif%}
+              class="form-control">
+        <option value="">Select a platform</option>
+        {%for platform in platforms%}
+        <option value="{{platform.GeneChipId}}">
+	  {{platform.GeneChipName}} ({{platform.Name}})
+        </option>
+        {%endfor%}
+      </select>
+      <small id="help-select-platform" class="form-text text-muted">
+        Select from a list of known genomics platforms.
+      </small>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:studyname" class="form-label">Study name</label>
+      <input type="text" id="txt:studyname" name="studyname"
+	     placeholder="Name of the study. (Required)"
+	     required="required"
+	     maxlength="100"
+             class="form-control" />
+      <span class="form-text text-muted" id="help-study-name">
+        Provide a name for the study.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:studyfullname" class="form-label">Full Study Name</label>
+      <input type="text"
+             id="txt:studyfullname"
+             name="studyfullname"
+	     placeholder="Longer name of the study. (Optional)"
+	     maxlength="100"
+             class="form-control" />
+      <span class="form-text text-muted" id="help-study-full-name">
+        Provide a longer, more descriptive name for the study. This is optional
+        and you can leave it blank.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt:studyshortname" class="form-label">Short Study Name</label>
+      <input type="text"
+             id="txt:studyshortname"
+             name="studyshortname"
+	     placeholder="Shorter name of the study. (Optional)"
+	     maxlength="100"
+             class="form-control" />
+      <span class="form-text text-muted" id="help-study-short-name">
+        Provide a shorter name for the study. This is optional and you can leave
+        it blank.
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">create study</button>
+  </form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html
new file mode 100644
index 0000000..34e1758
--- /dev/null
+++ b/uploader/templates/rqtl2/select-tissue.html
@@ -0,0 +1,115 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Tissue</h2>
+
+<div class="row">
+  <p>The data you are uploading concerns a tissue, cell, organ, or other
+    biological material used in an experiment.</p>
+  <p>Select the appropriate biological material below</p>
+</div>
+
+{%if tissues | length > 0%}
+<div class="row">
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.select_tissue',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:select-probeset-dataset">
+    <legend class="heading">Select from existing ProbeSet datasets</legend>
+    {{flash_messages("error-select-tissue")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="select-tissue">Tissue</label>
+      <select id="select-tissue"
+	      name="tissueid"
+	      required="required"
+	      {%if tissues | length == 0%}disabled="disabled"{%endif%}
+              class="form-control"
+              aria-describedby="help-select-tissue">
+        <option value="">Select a tissue</option>
+        {%for tissue in tissues%}
+        <option value={{tissue.Id}}>
+	  {{tissue.Name}}
+	  {%if tissue.Short_Name%}
+	  -- ({{tissue.Short_Name}})
+	  {%endif%}
+        </option>
+        {%endfor%}
+      </select>
+
+      <span id="help-select-tissue" class="form-text text-muted">
+        Select from existing biological material.</span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">use selected</button>
+  </form>
+</div>
+
+<div class="row">
+  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+{%endif%}
+
+<div class="row">
+  <p>If you cannot find the biological material in the drop-down above, add it
+    to the system below.</p>
+
+  <form method="POST"
+        action="{{url_for('upload.rqtl2.create_tissue',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:create-probeset-dataset">
+    <legend class="heading">Add new tissue, organ or biological material</legend>
+    {{flash_messages("error-create-tissue")}}
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="tissue-name">name</label>
+      <input type="text"
+             id="txt-tissuename"
+             name="tissuename"
+             required="required"
+             title = "A name to identify the tissue, organ or biological material."
+             class="form-control"
+             aria-describedby="help-tissue-name" />
+
+      <span class="form-text text-muted" id="help-tissue-name">
+        A name to identify the tissue, organ or biological material.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-shortname" class="form-label">short name</label>
+      <input type="text" id="txt-tissueshortname" name="tissueshortname"
+	     required="required"
+	     maxlength="7"
+	     title="A short name (e.g. 'Mam') for the biological material."
+             class="form-control"
+             aria-describedby="help-tissue-short-name" />
+
+      <span class="form-text text-muted" id="help-tissue-short-name">
+        Provide a short name for the tissue, organ or biological material used in
+        the experiment.
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary" />add new material</button>
+</form>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html
new file mode 100644
index 0000000..1be87fa
--- /dev/null
+++ b/uploader/templates/rqtl2/summary-info.html
@@ -0,0 +1,65 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Summary</h2>
+
+<div class="row">
+  <p>This is the information you have provided to accompany the R/qtl2 bundle
+    you have uploaded. Please verify the information is correct before
+    proceeding.</p>
+</div>
+
+<div class="row">
+  <dl>
+    <dt>Species</dt>
+    <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
+
+    <dt>Population</dt>
+    <dd>{{population.InbredSetName}}</dd>
+
+    {%if geno_dataset%}
+    <dt>Genotype Dataset</dt>
+    <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+    {%endif%}
+
+    {%if tissue%}
+    <dt>Tissue</dt>
+    <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd>
+    {%endif%}
+
+    {%if probe_study%}
+    <dt>ProbeSet Study</dt>
+    <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
+    {%endif%}
+
+    {%if probe_dataset%}
+    <dt>ProbeSet Dataset</dt>
+    <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
+    {%endif%}
+  </dl>
+</div>
+
+<div class="row">
+  <form id="frm:confirm-rqtl2bundle-details"
+        action="{{url_for('upload.rqtl2.confirm_bundle_details',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    <legend class="heading">Create ProbeSet dataset</legend>
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+    <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+{%endblock%}
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
new file mode 100644
index 0000000..07c240f
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -0,0 +1,276 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "upload_progress_indicator.html" import upload_progress_indicator%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+{%macro rqtl2_file_help()%}
+<span class="form-text text-muted">
+  <p>
+    Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle
+    contains exactly one control file and the corresponding files mentioned in
+    the control file.
+  </p>
+  <p>
+    The control file can be either a YAML or JSON file. <em>ALL</em> other data
+    files in the zip bundle should be CSV files.
+  </p>
+  <p>See the
+    <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
+       target="_blank">
+      R/qtl2 file format specifications
+    </a>
+    for more details.
+  </p>
+</span>
+{%endmacro%}
+{{upload_progress_indicator()}}
+
+<div id="resumable-file-display-template"
+     class="panel panel-info"
+     style="display: none">
+  <div class="panel-heading"></div>
+  <div class="panel-body"></div>
+</div>
+
+
+<h2 class="heading">Upload R/qtl2 Bundle</h2>
+
+<div id="resumable-drop-area"
+     style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;">
+  <p>
+    <a id="resumable-browse-button" href="#"
+       class="btn btn-info">Browse</a>
+  </p>
+  <p class="form-text text-muted">
+    You can drag and drop your file here, or click the browse button.
+    Click on the file to remove it.
+  </p>
+  {{rqtl2_file_help()}}
+  <div id="resumable-selected-files"
+       style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div>
+  <div id="resumable-class-buttons" style="text-align: right;">
+    <button id="resumable-upload-button"
+            class="btn btn-primary"
+            style="display: none">start upload</button>
+    <button id="resumable-cancel-upload-button"
+            class="btn btn-danger"
+            style="display: none">cancel upload</button>
+  </div>
+  <div id="resumable-progress-bar" class="progress" style="display: none">
+    <div class="progress-bar"
+         role="progress-bar"
+         aria-valuenow="60"
+         aria-valuemin="0"
+         aria-valuemax="100"
+         style="width: 0%;">
+      Uploading: 60%
+    </div>
+  </div>
+</div>
+
+<form id="frm-upload-rqtl2-bundle"
+      action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
+	      species_id=species.SpeciesId,
+	      population_id=population.InbredSetId)}}"
+      method="POST"
+      enctype="multipart/form-data"
+      data-resumable-target="{{url_for(
+                             'upload.rqtl2.upload_rqtl2_bundle_chunked_post',
+                             species_id=species.SpeciesId,
+                             population_id=population.InbredSetId)}}">
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+
+  {{flash_all_messages()}}
+
+  <div class="form-group">
+    <legend class="heading">file upload</legend>
+    <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label>
+    <input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file"
+	   accept="application/zip, .zip"
+	   required="required"
+           class="form-control" />
+    {{rqtl2_file_help()}}
+  </div>
+
+  <button type="submit"
+          class="btn btn-primary"
+          data-toggle="modal"
+          data-target="#upload-progress-indicator">upload R/qtl2 bundle</button>
+</form>
+
+{%endblock%}
+
+{%block javascript%}
+<script src="{{url_for('base.node_modules',
+             filename='resumablejs/resumable.js')}}"></script>
+<script type="text/javascript" src="/static/js/upload_progress.js"></script>
+<script type="text/javascript">
+  function readBinaryFile(file) {
+      return new Promise((resolve, reject) => {
+          var _reader = new FileReader();
+          _reader.onload = (event) => {resolve(_reader.result);};
+          _reader.readAsArrayBuffer(file);
+      });
+  }
+
+  function computeFileChecksum(file) {
+      return readBinaryFile(file)
+          .then((content) => {
+              return window.crypto.subtle.digest(
+                  "SHA-256", new Uint8Array(content));
+          }).then((digest) => {
+              return Uint8ArrayToHex(new Uint8Array(digest))
+          });
+  }
+
+  function Uint8ArrayToHex(arr) {
+      var toHex = (val) => {
+          _hex = val.toString(16);
+          if(_hex.length < 2) {
+              return "0" + val;
+          }
+          return _hex;
+      };
+      _hexstr = ""
+      arr.forEach((val) => {_hexstr += toHex(val)});
+      return _hexstr
+  }
+
+  var r = Resumable({
+      target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"),
+      fileType: ["zip"],
+      maxFiles: 1,
+      forceChunkSize: true,
+      generateUniqueIdentifier: (file, event) => {
+          return computeFileChecksum(file).then((checksum) => {
+              var _relativePath = (file.webkitRelativePath
+                                   || file.relativePath
+                                   || file.fileName
+                                   || file.name);
+              return checksum + "-" + _relativePath.replace(
+                  /[^a-zA-Z0-9_-]/img, "");
+          });
+      }
+  });
+
+  if(r.support) {
+      //Hide form and display drag&drop UI
+      $("#frm-upload-rqtl2-bundle").css("display", "none");
+      $("#resumable-drop-area").css("display", "block");
+
+      // Define UI elements for browse and drag&drop
+      r.assignDrop(document.getElementById("resumable-drop-area"));
+      r.assignBrowse(document.getElementById("resumable-browse-button"));
+
+      // Event handlers
+
+      function display_files(files) {
+          displayArea = $("#resumable-selected-files")
+          displayArea.empty();
+          files.forEach((file) => {
+              var displayElement = $(
+                  "#resumable-file-display-template").clone();
+              displayElement.removeAttr("id");
+              displayElement.css("display", "");
+              displayElement.find(".panel-heading").text(file.fileName);
+              list = $("<ul></ul>");
+              list.append($("<li><strong>Name</strong>: "
+                            + (file.name
+                               || file.fileName
+                               || file.relativePath
+                               || file.webkitRelativePath)
+                            + "</li>"));
+              list.append($("<li><strong>Size</strong>: "
+                            + (file.size / (1024*1024)).toFixed(2)
+                            + " MB</li>"));
+              list.append($("<li><strong>Unique Identifier</strong>: "
+                            + file.uniqueIdentifier + "</li>"));
+              list.append($("<li><strong>Mime</strong>: "
+                            + file.file.type
+                            + "</li>"));
+              displayElement.find(".panel-body").append(list);
+              displayElement.appendTo("#resumable-selected-files");
+          });
+      }
+
+      r.on("filesAdded", function(files) {
+          display_files(files);
+          $("#resumable-upload-button").css("display", "");
+          $("#resumable-upload-button").on("click", (event) => {
+              r.upload();
+          });
+      });
+
+      r.on("uploadStart", (event) => {
+          $("#resumable-upload-button").css("display", "none");
+          $("#resumable-cancel-upload-button").css("display", "");
+          $("#resumable-cancel-upload-button").on("click", (event) => {
+              r.files.forEach((file) => {
+                  if(file.isUploading()) {
+                      file.abort();
+                  }
+              });
+              $("#resumable-cancel-upload-button").css("display", "none");
+              $("#resumable-upload-button").on("click", (event) => {
+                  r.files.forEach((file) => {file.retry();});
+              });
+              $("#resumable-upload-button").css("display", "");
+          });
+      });
+
+      r.on("progress", () => {
+          var progress = (r.progress() * 100).toFixed(2);
+          var pbar = $("#resumable-progress-bar > .progress-bar");
+          $("#resumable-progress-bar").css("display", "");
+          pbar.css("width", progress+"%");
+          pbar.attr("aria-valuenow", progress);
+          pbar.text("Uploading: " + progress + "%");
+      })
+
+      r.on("fileSuccess", (file, message) => {
+          if(message != "OK") {
+              var uri = (window.location.protocol
+                         + "//"
+                         + window.location.host
+                         + message);
+              window.location.replace(uri);
+          }
+      });
+
+      r.on("error", (message, file) => {
+          filename = (file.webkitRelativePath
+                      || file.relativePath
+                      || file.fileName
+                      || file.name);
+          jsonmsg = JSON.parse(message);
+          alert("There was an error while uploading your file '"
+                + filename
+                + "'. The error message was:\n\n\t"
+                + jsonmsg.error
+                + " ("
+                + jsonmsg.statuscode
+                + "): " + jsonmsg.message);
+      })
+  } else {
+      setup_upload_handlers(
+          "frm-upload-rqtl2-bundle", make_data_uploader(
+	      function (form) {
+	          var formdata = new FormData();
+	          formdata.append(
+		      "species_id",
+		      form.querySelector('input[name="species_id"]').value);
+	          formdata.append(
+		      "population_id",
+		      form.querySelector('input[name="population_id"]').value);
+	          formdata.append(
+		      "rqtl2_bundle_file",
+		      form.querySelector("#file-rqtl2-bundle").files[0]);
+	          return formdata;
+	      }));
+  }
+</script>
+{%endblock%}
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
new file mode 100644
index 0000000..93b1dc9
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -0,0 +1,33 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Upload R/qtl2 Bundle</h2>
+
+<div class="row">
+  <p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p>
+  <p>The next step is to select the various extra information we need to figure
+    out what to do with the data. You will select/create the relevant studies
+    and/or datasets to organise the data in the steps that follow.</p>
+  <p>Click "Continue" below to proceed.</p>
+
+  <form id="frm-upload-rqtl2-bundle"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        method="POST"
+        enctype="multipart/form-data">
+    {{flash_all_messages()}}
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file"
+	   value="{{rqtl2_bundle_file}}" />
+
+    <button type="submit" class="btn btn-primary">continue</button>
+  </form>
+</div>
+
+{%endblock%}