From ab686777fc1467d6258b88efb37faf196b021bdb Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 2 Jun 2023 16:17:34 +0300
Subject: Add dataset link that uses RDF

* wqflask/wqflask/templates/dataset.html: New page.
* wqflask/wqflask/templates/show_trait_details.html: Add link to GN2
datasets page.
* wqflask/wqflask/views.py (get_dataset): New endpoint.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 wqflask/wqflask/templates/dataset.html            | 114 ++++++++++++++++++++++
 wqflask/wqflask/templates/show_trait_details.html |   4 +
 wqflask/wqflask/views.py                          |  23 +++++
 3 files changed, 141 insertions(+)
 create mode 100644 wqflask/wqflask/templates/dataset.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/dataset.html b/wqflask/wqflask/templates/dataset.html
new file mode 100644
index 00000000..402e4aa1
--- /dev/null
+++ b/wqflask/wqflask/templates/dataset.html
@@ -0,0 +1,114 @@
+{% extends "base.html" %}
+
+{% block css %}
+<style type="text/css">
+ .page-header {
+     text-underline-offset: 0.9em;
+     padding: 1em;
+ }
+ .panel-about {
+     background: #F8F8F8;
+     max-width: 35em;
+     margin: 10px;
+ }
+ .panel-metadata {
+     display: inline-block;
+     width: fit-content;
+     height: fit-content;
+     padding: 0;
+ }
+
+ .panel-metadata dt {
+     color: green;
+ }
+
+ .panel-metadata dt::after {
+     content: ":";
+ }
+
+</style>
+{% endblock %}
+
+{% block title %}Dataset: {{ name }}{% endblock %}
+
+{% block content %}
+
+<header class="page-header text-justify">
+    <h1><u>
+        {% if metadata.title %}
+        {{ metadata.title }}
+        {% else %}
+        {{ name }}
+        {% endif %}
+    </u></h1>
+</header>
+
+<div class="container">
+    {% if metadata == {} %}
+    <p class="lead">We appreciate your interest, but unfortunately, we don't have any additional information available for: <strong>{{ name }}</strong>. If you have any other questions or need assistance with something else, please feel free to reach out to us.</p>
+    {% else %}
+    <div class="panel-about panel panel-info panel-metadata text-muted{{ float_p }}">
+        <div class="panel-heading"><strong><span class="glyphicon glyphicon-info-sign aria-hidden=true"></span> Details</strong> </div>
+        <div class="panel-body">
+            <dl class="dl-horizontal">
+                {% if metadata.name %} <dt>Name</dt> <dd>{{ metadata.name}}</dd> {% endif %}
+                {% if metadata.specifics %} <dt>Specifics</dt> <dd>{{ metadata.specifics}}</dd> {% endif %}
+                {% if metadata.created %} <dt>Created</dt> <dd>{{ metadata.created }}</dd> {% endif %}
+                {% if metadata.accessionId %} <dt>Accession Id</dt> <dd>{{ metadata.accessionId }}</dd> {% endif %}
+                {% if metadata.geoSeries %} <dt>Geo Series</dt> <dd>{{ metadata.geoSeries }}</dd> {% endif %}
+                {% if metadata.normalization %} <dt>Normalization</dt> <dd>{{ metadata.normalization }}</dd> {% endif %}
+                {% if metadata.datasetGroup %} <dt>Group</dt> <dd>{{ metadata.datasetGroup }}</dd> {% endif %}
+                {% if metadata.investigatorName %}
+                <dt>Investigator</dt>
+                <dd>
+                    <a href="{{ metadata.investigatorWebUrl }}" target="_blank">{{ metadata.investigatorName }}</a>
+                </dd>
+                {% endif %}
+                {% if metadata.contributors %} <dt>Contributors</dt> <dd>{{ metadata.contributors|safe }}</dd> {% endif %}
+                {% if metadata.citation|trim %} <dt>Citation</dt> <dd>{{ metadata.citation|safe}}</dd> {% endif %}
+                {% if metadata.acknowledgment|trim %} <dt>Acknowledgment</dt> <dd>{{ metadata.acknowledgment|safe}}</dd> {% endif %}
+            </dl>
+        </div>
+    </div>
+
+    <div class="container">
+        {% if metadata.summary %}
+        <h3><strong>Summary</strong></h3>
+        <div>{{ metadata.summary|safe }}</div>
+        {% endif %}
+
+        {% if metadata.experimentDesign %}
+        <h3><strong>Experiment Design</strong></h3>
+        <div>{{ metadata.experimentDesign|safe }}</div>
+        {% endif %}
+
+        {% if metadata.aboutCases %}
+        <h3><strong>About Cases</strong></h3>
+        <div>{{ metadata.aboutCases|safe }}</div>
+        {% endif %}
+
+        {% if metadata.aboutTissue %}
+        <h3><strong>About Tissue</strong></h3>
+        <div>{{ metadata.aboutTissue|safe }}</div>
+        {% endif %}
+
+        {% if metadata.aboutPlatform %}
+        <h3><strong>About Platform</strong></h3>
+        <div>{{ metadata.aboutPlatform|safe }}</div>
+        {% endif %}
+
+        {% if metadata.aboutDataProcessing %}
+        <h3><strong>About Data Processing</strong></h3>
+        <div>{{ metadata.aboutDataProcessing|safe }}</div>
+        {% endif %}
+
+        {% if metadata.notes %}
+        <h3><strong>GeneNetwork Notes</strong></h3>
+        <div>{{ metadata.notes|safe }}</div>
+        {% endif %}
+    </div>
+    {% endif %}
+
+</div>
+
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index cd8671bb..c745fce8 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -62,6 +62,10 @@
             <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" target="_blank">
                 {{ dataset.fullname }}
             </a>
+	    <br/>
+	    <a href="{{ url_for('get_dataset', name=dataset.name) }}" target="_blank">
+                GN2 Link: {{ dataset.fullname }}
+            </a>
         </td>
     </tr>
     {% if this_trait.probe_set_specificity %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 243c79b2..895ad0cb 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1095,3 +1095,26 @@ def display_generif_page(symbol):
         symbol=symbol,
         entries=entries
     )
+
+
+@app.route("/dataset/<name>", methods=('GET',))
+def get_dataset(name):
+    metadata = requests.get(
+        urljoin(
+            GN3_LOCAL_URL,
+            f"/api/metadata/dataset/{name}")
+    ).json()
+    float_p = ""
+    if any([metadata.get("summary"),
+            metadata.get("experimentDesign"),
+            metadata.get("aboutCases"),
+            metadata.get("aboutTissue"),
+            metadata.get("aboutPlatform"),
+            metadata.get("aboutDataProcesing"), metadata.get("notes")]):
+        float_p = " pull-right"
+    return render_template(
+        "dataset.html",
+        name=name,
+        metadata=metadata,
+        float_p=float_p
+    )
-- 
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