Display a dataset's metadata in the "Trait Data and Analysis" page

* wqflask/wqflask/static/new/css/show_trait.css: Show a pointer when a
user hovers over summary data.  Add extra styling for the metadata
table.
* wqflask/wqflask/templates/search_result_page.html: Replace
dataset.accession_id with metadata.accession_id.
* wqflask/wqflask/templates/show_metadata_details.html: New template.
file that displays a dataset's metadata in tabular form.
* wqflask/wqflask/templates/show_trait.html: Sub-template
'show_metadata_details' conditionally.
* wqflask/wqflask/views.py (show_trait_page): Explicitly pass metadata
as a dictionary to the template.

5 files changed, 229 insertions, 5 deletions

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 3780a8f1..2ce07fec 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -6,6 +6,23 @@ table.dataTable tbody tr.selected {
   background-color: #ffee99;
 }
 
+table.metadata {
+    table-layout: fixed;
+}
+
+table.metadata td:nth-child(1) {
+    width: 10%;
+}
+
+table summary b {
+    cursor: pointer;
+    text-decoration: underline;
+}
+
+table details[open] {
+    width: 80%;
+}
+
 #bar_chart_container {
   overflow-x:scroll;
 }
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 2bcfe92b..3a6f6e91 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -17,7 +17,7 @@
         <div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
         <!-- Need to customize text more for other types of searches -->
 
-        <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if not dataset.accession_id %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+            <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if metadata.accession_id %}GN_AccessionId={{ metadata.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
           <br>
           to find all records
                 {% if go_term is not none %}
@@ -97,8 +97,8 @@
               <input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}">
               <input type="hidden" name="file_name" id="file_name" value="search_results">
               <input type="hidden" name="filter_term" id="filter_term" value="None">
-              {% if dataset.accession_id is defined %}
-              <input type="hidden" name="accession_id" id="accession_id" value="{{ dataset.accession_id }}">
+              {% if metadata.accession_id %}
+              <input type="hidden" name="accession_id" id="accession_id" value="{{ metadata.accession_id }}">
               {% endif %}
               <input type="hidden" name="export_data" id="export_data" value="">
               <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search For...">
diff --git a/wqflask/wqflask/templates/show_metadata_details.html b/wqflask/wqflask/templates/show_metadata_details.html
new file mode 100644
index 00000000..36b0f9b5
--- /dev/null
+++ b/wqflask/wqflask/templates/show_metadata_details.html
@@ -0,0 +1,186 @@
+<table class="table metadata">
+    {% if metadata.accession_id %}
+    <tr>
+        <td><b>Title:</b></td>
+        <td><div>{{ metadata.accession_id }} {% if metadata.title %}: {{ metadata.title }} {% endif %}</div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.geo_series %}
+    <tr>
+        <td><b>Geo Series:</b></td>
+        <td><div>{{ metadata.geo_series|safe }}</div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.dataset_group %}
+    <tr>
+        <td><b>Dataset Group:</b></td>
+        <td><div>{{ metadata.dataset_group }}</div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.species_name %}
+    <tr>
+        <td><b>Species:</b></td>
+        <td><div>{{ metadata.species_name }}</div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.inbred_set_name %}
+    <tr>
+        <td><b>Group:</b></td>
+        <td><div>{{ metadata.inbred_set_name }}</div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.investigators %}
+    <tr>
+        <td><b>Investigator(s):</b></td>
+        <td><div>{{ metadata.investigators.name }}, {{ metadata.investigators.city }}, {{ metadata.investigators.country }} </div></td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.tissue_name %}
+    <tr>
+	<td><b>Tissue:</b></td>
+	<td>
+	    {% if metadata.about_tissue %}
+	    <div></div>
+	    <details>
+		<summary><b title="Click to view tissue information">{{ metadata.tissue_name }}</b></summary>
+		<b>About the tissue used to generate this set of data:</b>
+		<div>{{ metadata.about_tissue|safe }}</div>
+	    </details>
+	    {% else %}
+	    {{ metadata.tissue_name }}
+	    {% endif %}
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.platform_name %}
+    <tr>
+	<td><b>Platforms:</b></td>
+	<td>
+	    {% if metadata.about_platform %}
+	    <details>
+		<summary><b title="Click to view platform information">{{ metadata.platform_name }}</b></summary>
+		<b>About the array platform:</b>
+		{{ metadata.about_platform|safe }}
+	    </details>
+	    {% else %}
+	    {{ metadata.platform_name }}
+	    {% endif %}
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.normalization_name %}
+    <tr>
+	<td><b>Normalization:</b></td>
+	<td>
+	    {{ metadata.normalization_name }}
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.summary %}
+    <tr>
+        <td></td>
+        <td>
+            <details>
+                <summary><b title="Click to view summary">Summary</b></summary>
+                {{ metadata.summary|safe  }}
+            </details>
+        </td>
+    </tr>
+    {% endif %}
+
+
+    {% if metadata.about_cases %}
+    <tr>
+	<td></td>
+	<td>
+	    <details>
+		<summary><b title="Click to view case information">About the cases used to generate this set of data</b></summary>
+		{{ metadata.about_cases|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.about_data_processing %}
+    <tr>
+        <td></td>
+	<td>
+	    <details>
+		<summary><b title="Click to view data values and processing">About Data Values and Data Processing</b></summary>
+		{{ metadata.about_data_processing.value|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.notes %}
+    <tr>
+        <td></td>
+	<td>
+	    <details>
+		<summary><b>Notes</b></summary>
+		{{ metadata.notes|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.experiment_design %}
+    <tr>
+        <td></td>
+	<td>
+	    <details>
+		<summary><b>Experiment Type</b></summary>
+		{{ metadata.experiment_design|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.contributors %}
+    <tr>
+        <td></td>
+	<td>
+	    <details>
+		<summary><b>Contributor(s)</b></summary>
+		{{ metadata.contributors|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.citation  %}
+    <tr>
+        <td>
+            <td>
+		<details>
+		    <summary><b>Citation</b></summary>
+		    {{ metadata.citation|safe }}
+		</details>
+	    </td>
+    </tr>
+    {% endif %}
+
+    {% if metadata.acknowledgment  %}
+    <tr>
+        <td></td>
+        <td>
+	    <details>
+	    <summary><b>Data source acknowledgment</b></summary>
+	    {{ metadata.acknowledgment|safe }}
+	    </details>
+	</td>
+    </tr>
+    {% endif %}
+
+
+</table>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0f93188b..4b92545c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -51,8 +51,20 @@
                         <div class="panel-body">
                             {% include 'show_trait_details.html' %}
                         </div>
+		    </div>
+		    {% if metadata.accession_id %}
+		    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseMeta">
+                        <h3 class="panel-title">
+                            <span class="glyphicon glyphicon-chevron-down"></span> Data Set Group: {{  dataset.fullname }}
+                        </h3>
                     </div>
-                </div>    
+                    <div id="collapseMeta" class="panel-collapse collapse in">
+                        <div class="panel-body">
+			    {% include 'show_metadata_details.html' %}
+                        </div>
+		    </div>
+		    {% endif %}
+                </div>
                 <div class="panel panel-default">
                     <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
                         <h3 class="panel-title">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 211a8f13..8a0bede3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -83,6 +83,7 @@ from utility.helper_functions import get_species_groups
 from utility.redis_tools import get_redis_conn
 
 import utility.hmac as hmac
+from gn3.db.rdf import get_dataset_metadata
 
 
 from base.webqtlConfig import TMPDIR
@@ -487,7 +488,15 @@ def show_trait_page():
         template_vars.js_data = json.dumps(template_vars.js_data,
                                            default=json_default_handler,
                                            indent="   ")
-        return render_template("show_trait.html", **template_vars.__dict__)
+        metadata = (
+            template_vars.dataset.accession_id
+            .bind(
+                lambda idx: get_dataset_metadata(f"GN{idx}")
+            )
+        ).data
+
+        return render_template("show_trait.html",
+                               metadata=metadata, **template_vars.__dict__)
 
 
 @app.route("/heatmap", methods=('POST',))