From 7df45fb25bd760959120123d92fed1345f44e7d0 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 14 Apr 2023 18:35:52 +0300
Subject: Add genewiki page

* wqflask/wqflask/templates/generif.html: New template.
* wqflask/wqflask/views.py (display_diffs_users): New route.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 wqflask/wqflask/templates/generif.html | 96 ++++++++++++++++++++++++++++++++++
 wqflask/wqflask/views.py               | 16 ++++++
 2 files changed, 112 insertions(+)
 create mode 100644 wqflask/wqflask/templates/generif.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/generif.html b/wqflask/wqflask/templates/generif.html
new file mode 100644
index 00000000..affcbbed
--- /dev/null
+++ b/wqflask/wqflask/templates/generif.html
@@ -0,0 +1,96 @@
+{% extends "base.html" %}
+
+{% block title %}
+GeneWiki Entry for {{ symbol }}
+{% endblock %}
+
+{% block css %}
+<style>
+
+ .badge {
+     vertical-align: top;
+     background-color: #336699;
+ }
+
+ .list-group {
+     counter-reset: gnentries;
+ }
+
+ summary::before {
+     counter-increment: gnentries;
+     content: counter(gnentries) "." " ";
+ }
+
+ summary:hover {
+     cursor: zoom-in;
+ }
+</style>
+
+{% endblock %}
+{% block content %}
+
+
+<div class="container">
+    <h1 class="page-header">GeneWiki For {{ symbol }}</h1>
+    <p class="well"><strong>GeneWiki</strong> enables you to enrich the annotation of genes and transcripts.</p>
+
+    <h3>
+	<strong>GeneNetwork</strong>
+	<span class="badge">
+	    {{ entries.gn_entries|length if entries.gn_entries[0] else 0 }}
+	</span>:
+    </h3>
+    {% if entries.gn_entries[0] %}
+    <ul class="list-group">
+	{% for entry in entries.gn_entries %}
+	<li class="list-group-item">
+	    <details>
+		<summary>{{ entry["entry"]["value"] }}</summary>
+		<dl class="dl-horizontal">
+		    <dt>Author:</dt>
+		    <dd>{{ entry["author"]["value"] }}</dd>
+
+		    {% if entry.get("geneCategory") %}
+		    <dt>Category:</dt>
+		    <dd>{{ entry["geneCategory"]["value"]}}</dd>
+		    {% endif %}
+
+		    <dt>Add Time:</dt>
+		    <dd>{{ entry["created"]["value"]}}</dd>
+		</dl>
+	    </details>
+	</li>
+	{% endfor %}
+    </ul>
+
+    {% else %}
+
+    <p class="well"><u>There are no GeneNetwork entries for <b>{{ symbol }}.</b></u></p>
+
+    {% endif %}
+
+    <h3>
+	<strong>GeneRIF from NCBI</strong>
+	<span class="badge">
+	    {{ entries.ncbi_entries|length if entries.ncbi_entries[0] else 0 }}
+	</span>:
+    </h3>
+    {% if entries.ncbi_entries[0] %}
+	<ol>
+	{% for entry in entries.ncbi_entries %}
+	<li>
+	    {{ entry.entry.value }}
+	    (<a href="{{ entry['generif']['value'] }}" target="_blank">{{ entry["speciesBinomialName"]["value"] }}</a>)
+            {% if entry.PubMedId.value != "" %}
+	    {% set pmids = entry.PubMedId.value.split(",") %}
+	    (PubMed: {% for id in pmids %} <a href="http://rdf.ncbi.nlm.nih.gov/pubmed/{{ id }}" target="_blank">{{ id }}</a>{% endfor %})
+	    <sup><small><em>{{ entry.createdOn.value }}</em></small></sup>
+	    {% endif %}
+	</li>
+	{% endfor %}
+    </ol>
+    {% else %}
+    <p class="well"><u>There are no NCBI entries for <b>{{ symbol }}.</b></u></p>
+    {% endif %}
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 69576cc4..24426539 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1048,3 +1048,19 @@ def display_diffs_users():
                        files)
     return render_template("display_files_user.html",
                            files=files)
+
+
+@app.route("/genewiki/<symbol>")
+def display_generif_page(symbol):
+    """Fetch GeneRIF metadata from GN3 and display it"""
+    entries = requests.get(
+        urljoin(
+            GN3_LOCAL_URL,
+            f"/api/metadata/genewiki/{symbol}"
+        )
+    ).json()
+    return render_template(
+        "generif.html",
+        symbol=symbol,
+        entries=entries
+    )
-- 
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