Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

5 files changed, 627 insertions, 0 deletions

diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_error.html b/gn2/wqflask/templates/partial_correlations/pcorrs_error.html
new file mode 100644
index 00000000..8d6c4bbe
--- /dev/null
+++ b/gn2/wqflask/templates/partial_correlations/pcorrs_error.html
@@ -0,0 +1,65 @@
+{% extends "base.html" %}
+{% block title %}Error: {{message}}{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+<div class="container">
+  <div class="col-md-8">
+    <div class="form-group has-error">
+      <div class="control-label" for="inputError1">
+
+	<img src="/static/gif/error/{{ error_image }}">
+
+	<h1>ERROR</h1>
+
+	<p>
+	  This error is not what we wanted to see. Unfortunately errors
+	  are part of all software systems and we need to resolve this
+	  together.
+	</p>
+	<p>
+	  <b>It is important to report this ERROR so we can fix it for everyone</b>.
+	</p>
+
+	<p>
+	  Report to the GeneNetwork team by recording the steps you take
+	  to reproduce this ERROR. Next to those steps, copy-paste below
+	  stack trace, either as
+	  a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new
+	    issue</a> or E-mail this full page to one of the developers
+	  directly.
+	</p>
+      </div>
+
+      <p>
+	GeneNetwork error:<br />
+	{{message}}
+      </p>
+
+      {%if command_id %}
+      <p>
+	Please provide the following information to help with
+	troubleshooting:<br />
+	<strong>Command ID</strong>: <em>{{command_id}}</em>
+      </p>
+      {%endif%}
+
+      <p>
+	To check if this already a known issue, search the
+	<a href="https://github.com/genenetwork/genenetwork2/issues">issue
+	  tracker</a>.
+      </p>
+
+      <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
+      <div id="Stack" class="collapse">
+	<pre>
+	  GeneNetwork {{ version }} {% for line in stack %} {{ line }}
+	  {% endfor %}
+	</pre>
+      </div>
+    </div>
+  </div>
+</div>
+
+
+{% endblock %}
diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html b/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html
new file mode 100644
index 00000000..38577c32
--- /dev/null
+++ b/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html
@@ -0,0 +1,19 @@
+{%extends "base.html"%}
+
+{%block title%}Partial Correlations:{%endblock%}
+
+{%block css%}
+<meta http-equiv="refresh"
+      content="5;URL=/partial_correlations/{{command_id}}">
+{%endblock%}
+
+{%block content%}
+
+<div class="container">
+  <center>
+    <h1>Computing partial correlations...</h1>
+    <img src="/static/gif/waitAnima2.gif"
+	 alt="Image indicating computation of partial correlations is ongoing" />
+    </center>
+</div>
+{%endblock%}
diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html
new file mode 100644
index 00000000..dac02397
--- /dev/null
+++ b/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html
@@ -0,0 +1,261 @@
+{%extends "base.html"%}
+
+{%block title%}Partial Correlations:{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css" href="/static/new/css/partial_correlations.css" />
+<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{%endblock%}
+
+{%block content%}
+<div class="container">
+  <p>
+    <strong>Primary Trait</strong><br /><br />
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=primary['trait_name'],
+	     dataset=primary['dataset_name'])}}"
+       title="Link to trait data for trait {{primary['trait_name']}}">
+      {{primary["dataset_type"]}}/{{primary["trait_name"]}}
+      [{{primary["symbol"] }} on Chr {{primary["chr"]}} @ {{primary["mb"]}}]:
+      {{primary["description"]}}
+    </a> --- FROM: {{primary["dataset_name"]}}
+  </p>
+  <p><strong>Control Traits</strong><br /><br />
+    {%for trait in controls:%}
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=trait['trait_name'],
+	     dataset=trait['dataset_name'])}}"
+       title="Link to trait data for trait {{trait['trait_name']}}">
+      {{trait["dataset_type"]}}/{{trait["trait_name"]}}
+      [{{trait["symbol"] }} on Chr {{trait["chr"]}} @ {{trait["mb"]}}]:
+      {{trait["description"]}}
+    </a> --- FROM: {{trait["dataset_name"]}}<br />
+    {%endfor%}
+  </p>
+
+  <div id="partial-correlation-results">
+    {%if dataset_type == "Publish":%}
+    <table id="part-corr-results-publish"
+	   class="table-hover table-striped cell-border dataTable"
+	   style="float: left;">
+      <thead>
+	<tr>
+	  <th>
+	  </th>
+	  <th>Index</th>
+	  <th>Record</th>
+	  <th>Phenotype</th>
+	  <th>Authors</th>
+	  <th>Year</th>
+	  <th>N</th>
+	  <th>Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>{%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	</tr>
+      </thead>
+
+      <tbody>
+	{%for idx, trait in enumerate(correlations, start=1):%}
+	<tr class="results-row">
+	  <td>
+	    <input type="checkbox" name="chk_{{trait['trait_name']}}"
+		   value="{{trait['trait_fullname']}}" />
+	  </td>
+	  <td data-column-heading="Index">{{idx}}</td>
+	  <td data-column-heading="Record">
+	    <a href="{{url_for(
+		     'show_trait_page',
+		     trait_id=trait['trait_name'],
+		     dataset=trait['dataset_name'])}}"
+	       title="Link to trait data for trait {{trait['trait_name']}}">
+	      {{trait["trait_name"]}}
+	    </a>
+	  </td>
+	  <td data-column-heading="Phenotype">
+	    {{trait["post_publication_description"]}}</td>
+	  <td data-column-heading="Authors">{{trait["authors"]}}</td>
+	  <td data-column-heading="Year">{{trait["year"]}}</td>
+	  <td data-column-heading="N">{{trait["noverlap"]}}</td>
+	  <td data-column-heading="Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("partial_corr"))}}
+	  </td>
+	  <td data-column-heading="p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("partial_corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="{%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("corr"))}}
+	  </td>
+	  <td data-column-heading="p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("delta"))}}
+	  </td>
+	</tr>
+	{%endfor%}
+      </tbody>
+    </table>
+    {%endif%}
+
+    {%if dataset_type == "Geno":%}
+    <table id="part-corr-results-geno"
+	   class="table-hover table-striped cell-border dataTable"
+	   style="float: left;">
+      <thead>
+	<tr>
+	  <th></th>
+	  <th>Index</th>
+	  <th>Locus</th>
+	  <th>Chr</th>
+	  <th>Megabase</th>
+	  <th>N</th>
+	  <th>Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>{%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	</tr>
+      </thead>
+
+      <tbody>
+	{%for idx, trait in enumerate(correlations, start=1):%}
+	<tr class="results-row">
+	  <td>
+	    <input type="checkbox" name="chk_{{trait['trait_name']}}"
+		   value="{{trait['trait_fullname']}}" />
+	  </td>
+	  <td data-column-heading="Index">{{idx}}</td>
+	  <td data-column-heading="Locus">
+	    <a href="{{url_for(
+		     'show_trait_page',
+		     trait_id=trait['trait_name'],
+		     dataset=trait['dataset_name'])}}"
+	       title="Link to trait data for trait {{trait['trait_name']}}">
+	      {{trait["trait_name"]}}
+	    </a>
+	  </td>
+	  <td data-column-heading="Chr">{{trait["chr"]}}</td>
+	  <td data-column-heading="Megabase">{{trait["mb"]}}</td>
+	  <td data-column-heading="N">{{trait["noverlap"]}}</td>
+	  <td data-column-heading="Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("partial_corr"))}}
+	  </td>
+	  <td data-column-heading="p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("partial_corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="{%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("corr"))}}
+	  </td>
+	  <td data-column-heading="p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("delta"))}}
+	  </td>
+	</tr>
+	{%endfor%}
+      </tbody>
+    </table>
+    {%endif%}
+
+    {%if dataset_type == "ProbeSet":%}
+    <table id="part-corr-results-probeset"
+	   class="table-hover table-striped cell-border dataTable"
+	   style="float: left;">
+      <thead>
+	<tr>
+	  <th></th>
+	  <th>Index</th>
+	  <th>Record</th>
+	  <th>Gene ID</th>
+	  <th>Homologene ID</th>
+	  <th>Symbol</th>
+	  <th>Description</th>
+	  <th>Chr</th>
+	  <th>Megabase</th>
+	  <th>Mean Expr</th>
+	  <th>N</th>
+	  <th>Sample Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>Sample p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>Sample {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>Sample p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	  <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>Lit Corr</th>
+	  <th>Tissue {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th>
+	  <th>Tissue p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th>
+	</tr>
+      </thead>
+
+      <tbody>
+	{%for idx, trait in enumerate(correlations, start=1):%}
+	<tr class="results-row">
+	  <td>
+	    <input type="checkbox" name="chk_{{trait['trait_name']}}"
+		   value="{{trait['trait_fullname']}}" />
+	  </td>
+	  <td data-column-heading="Index">{{idx}}</td>
+	  <td data-column-heading="Record">
+	    <a href="{{url_for(
+		     'show_trait_page',
+		     trait_id=trait['trait_name'],
+		     dataset=trait['dataset_name'])}}"
+	       title="Link to trait data for trait {{trait['trait_name']}}">
+	      {{trait["trait_name"]}}
+	    </a>
+	  </td>
+	  <td data-column-heading="Gene ID">{{trait["geneid"]}}</td>
+	  <td data-column-heading="Homologene ID">{{trait["homologeneid"]}}</td>
+	  <td data-column-heading="Symbol">{{trait["symbol"]}}</td>
+	  <td data-column-heading="Description">{{trait["description"]}}</td>
+	  <td data-column-heading="Chr">{{trait["chr"]}}</td>
+	  <td data-column-heading="Megabase">{{trait["mb"]}}</td>
+	  <td data-column-heading="Mean Expr">{{trait["mean_expr"]}}</td>
+	  <td data-column-heading="N">{{trait["noverlap"]}}</td>
+	  <td data-column-heading="Sample Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("partial_corr"))}}
+	  </td>
+	  <td data-column-heading="Sample p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("partial_corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="Sample {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("corr"))}}
+	  </td>
+	  <td data-column-heading="Sample p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("corr_p_value"))}}
+	  </td>
+	  <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("delta"))}}
+	  </td>
+	  <td data-column-heading="Lit Corr">
+	    {{format_number(trait.get("l_corr"))}}
+	  </td>
+	  <td data-column-heading="Tissue {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}">
+	    {{format_number(trait.get("tissue_corr"))}}
+	  </td>
+	  <td data-column-heading="Tissue p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})">
+	    {{format_number(trait.get("tissue_p_value"))}}
+	  </td>
+	</tr>
+	{%endfor%}
+      </tbody>
+    </table>
+    {%endif%}
+
+  </div>
+</div>
+{%endblock%}
+
+{%block js%}
+{%if step == "select-corr-method":%}
+<script type="text/javascript"
+	src="/static/new/javascript/partial_correlations.js"></script>
+<script language="javascript" type="text/javascript"
+	src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+{%endif%}
+{%endblock%}
diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
new file mode 100644
index 00000000..c1ef6001
--- /dev/null
+++ b/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
@@ -0,0 +1,115 @@
+{%extends "base.html"%}
+
+{%block title%}Partial Correlations:{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('css', filename='DataTables/css/jquery.dataTables.css')}}" />
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css')}}">
+<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
+<link rel="stylesheet" type="text/css"
+      href="/static/new/css/partial_correlations.css" />
+{%endblock%}
+
+{%block content%}
+<div class="container">
+  <p>
+    <strong>Primary Trait</strong><br /><br />
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=primary['trait_name'],
+	     dataset=primary['dataset_name'])}}"
+       title="Link to trait data for trait {{primary['trait_name']}}">
+      {{primary["dataset_type"]}}/{{primary["trait_name"]}}
+      [{{primary["symbol"] }} on Chr {{primary["chr"]}} @ {{primary["mb"]}}]:
+      {{primary["description"]}}
+    </a> --- FROM: {{primary["dataset_name"]}}
+  </p>
+  <p><strong>Control Traits</strong><br /><br />
+    {%for trait in controls:%}
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=trait['trait_name'],
+	     dataset=trait['dataset_name'])}}"
+       title="Link to trait data for trait {{trait['trait_name']}}">
+      {{trait["dataset_type"]}}/{{trait["trait_name"]}}
+      [{{trait["symbol"] }} on Chr {{trait["chr"]}} @ {{trait["mb"]}}]:
+      {{trait["description"]}}
+    </a> --- FROM: {{trait["dataset_name"]}}<br />
+    {%endfor%}
+  </p>
+
+  <table id="part-corr-results-publish"
+	 class="table-hover table-striped cell-border dataTable">
+    <thead>
+      <tr>
+	<th>_</th>
+	<th>Index</th>
+	<th>Database</th>
+	<th>Record</th>
+	<th>Symbol</th>
+	<th>Description</th>
+	<th>N</th>
+	{%if method == "spearmans":%}
+	<th>Partial rho</th>
+	<th>p(partial rho)</th>
+	<th>rho</th>
+	<th>p(rho)</th>
+	<th>delta rho</th>
+	{%else:%}
+	<th>Partial r</th>
+	<th>p(partial r)</th>
+	<th>r</th>
+	<th>p(r)</th>
+	<th>delta r</th>
+	{%endif%}
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for idx, trait in enumerate(pcorrs, start=1):%}
+      <tr>
+	<td>
+	  <input type="checkbox" name="chk_{{trait['trait_name']}}"
+		 value="{{trait['trait_fullname']}}">
+	</td>
+	<td>{{idx}}</td>
+	<td>{{trait["dataset_name"]}}</td>
+	<td>
+	  <a href="{{url_for(
+		     'show_trait_page',
+		     trait_id=trait['trait_name'],
+		     dataset=trait['dataset_name'])}}">
+	    {{trait["trait_name"]}}
+	  </a>
+	</td>
+	<td>{{trait["symbol"]}}</td>
+	<td>{{trait["description"]}}</td>
+	<td>{{trait["noverlap"]}}</td>
+	<td>{{format_number(trait["partial_corr"])}}</td>
+	<td>{{format_number(trait["partial_corr_p_value"])}}</td>
+	<td>{{format_number(trait["corr"])}}</td>
+	<td>{{format_number(trait["corr_p_value"])}}</td>
+	<td>{{format_number(trait["delta"])}}</td>
+      </tr>
+      {%else:%}
+      <tr>
+	<td colspan="12">
+	  No correlations were computed
+	</td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+
+</div>
+{%endblock%}
+
+{%block js%}
+<!--
+  <script type="text/javascript"
+	  src="/static/new/javascript/partial_correlations.js"></script>
+-->
+{%endblock%}
diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html b/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html
new file mode 100644
index 00000000..fe7f8cd4
--- /dev/null
+++ b/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html
@@ -0,0 +1,167 @@
+{%extends "base.html"%}
+
+{%block title%}Partial Correlations:{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('css', filename='DataTables/css/jquery.dataTables.css')}}" />
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css')}}">
+<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
+<link rel="stylesheet" type="text/css"
+      href="/static/new/css/partial_correlations.css" />
+{%endblock%}
+
+{%block content%}
+<div class="container">
+  <form id="pcorrs-form"
+	method="POST"
+	action="{{url_for('partial_correlations')}}">
+    {%with messages = get_flashed_messages(with_categories=true)%}
+    {%if messages:%}
+    <ul class=flashes>
+      {%for category, message in messages:%}
+      <li class="{{category}}">{{message}}</li>
+      {%endfor%}
+    </ul>
+    {%endif%}
+    {%endwith%}
+
+    <input type="hidden" value="{{trait_list_str}}" name="trait_list">
+	<h1>Partial Correlation</h1>
+	<div>Please select one primary trait, one to three control traits, and at least one target trait.</div>
+    <br />
+    <table id="pcorrs_traits_table"
+	   class="table-hover table-striped cell-border dataTable"
+	   role="grid">
+      <thead>
+	<tr>
+	  <th>Primary (X)</th>
+	  <th>Controls (Z)</th>
+	  <th>Targets (Y)</th>
+	  <th>Ignored</th>
+	  <th>Dataset</th>
+	  <th>Trait ID</th>
+	  <th>Symbol</th>
+	  <th>Description</th>
+	  <th>Location</th>
+	  <th>Mean</th>
+	  <th>Max LRS</th>
+	  <th>Max LRS Location Chr and Mb</th>
+	</tr>
+      </thead>
+
+      <tbody>
+	{%for trait in traits:%}
+	<tr>
+	  <td>
+	    <input type="radio" name="trait_{{trait['trait_name']}}"
+		   id="trait_{{trait['trait_name']}}"
+		   value="primary_{{trait['trait_name']}}" />
+	  </td>
+	  <td>
+	    <input type="radio" name="trait_{{trait['trait_name']}}"
+		   id="trait_{{trait['trait_name']}}"
+		   value="controls_{{trait['trait_name']}}" />
+	  </td>
+	  <td>
+	    <input type="radio" name="trait_{{trait['trait_name']}}"
+		   id="trait_{{trait['trait_name']}}"
+		   value="targets_{{trait['trait_name']}}" checked="checked" />
+	  </td>
+	  <td>
+	    <input type="radio" name="trait_{{trait['trait_name']}}"
+		   id="trait_{{trait['trait_name']}}"
+		   value="ignored_{{trait['trait_name']}}" />
+	  </td>
+	  <td>{{trait.get("dataset", "_")}}
+	  <td>{{trait.get("trait_name", "_")}}</td>
+	  <td>{{trait.get("symbol", "_")}}</td>
+	  <td>{{trait.get("description", "_")}}</td>
+	  <td>{{trait.get("location", "_")}}</td>
+	  <td>{{trait.get("mean", "_")}}</td>
+	  <td>{{trait.get("lrs", "_")}}</td>
+	  <td>{{trait.get("lrs_location", "_")}}</td>
+	</tr>
+	{%endfor%}
+      </tbody>
+    </table>
+
+    <br />
+    <p>Compute partial correlations for target selected above:</p>
+    <button type="submit" class="btn btn-primary" name="submit"
+	    value="with_target_pearsons">
+      Pearson's r
+    </button>
+    <button type="submit" class="btn btn-primary" name="submit"
+	    value="with_target_spearmans">
+      Spearman's rho
+    </button>
+
+    <hr />
+
+    <p style="color: red; font-weight: bold;">OR</p>
+    <p>Compute partial correlation for each trait in the database below:</p>
+
+    <div class="form-group">
+      <label for="corr-method-input" class="form-label">Compute</label>
+      <select id="corr-method-input" required="required" name="method"
+	      class="form-control">
+	<option value="Pearson's r">Pearson's r</option>
+	<option value="Spearman's rho">Spearman's rho</option>
+      </select>
+    </div>
+
+    <div class="form-group">
+      <label for="target-db-input" class="form-label">Choose Database</label>
+      <select id="target-db-input" required="required" name="target_db"
+	      class="form-control">
+	{%if target_dbs:%}
+	{%for item in target_dbs:%}
+	{%if "description" in item.keys():%}
+	<option value="{{item['value']}}">{{item['description']}}</option>
+	{%else:%}
+	{%for group, opts in item.items()%}
+	{%if opts | length > 0:%}
+	<optgroup label="{{group}} ------">
+	  {%for item2 in opts:%}
+	  <option value="{{item2['value']}}">{{item2['description']}}</option>
+	  {%endfor%}
+	</optgroup>
+	{%endif%}
+	{%endfor%}
+	{%endif%}
+	{%endfor%}
+	{%endif%}
+      </select>
+    </div>
+
+    <div class="form-group">
+      <label for="criteria-input" class="form-label">Return</label>
+      <select id="criteria-input" required="required" name="criteria" size="1"
+	      class="form-control">
+	<option value="100">top 100</option>
+	<option value="200">top 200</option>
+	<option value="500" selected="selected">top 500</option>
+	<option value="1000">top 1000</option>
+	<option value="2000">top 2000</option>
+	<option value="5000">top 5000</option>
+	<option value="10000">top 10000</option>
+	<option value="15000">top 15000</option>
+	<option value="20000">top 20000</option>
+      </select>
+    </div>
+
+    <button type="submit" class="btn btn-primary" name="submit"
+	    value="Run Partial Correlations">
+      Run Partial Correlations
+    </button>
+  </form>
+</div>
+{%endblock%}
+
+{%block js%}
+<script type="text/javascript"
+	src="/static/new/javascript/partial_correlations.js"></script>
+{%endblock%}