From a9068a80201a743595eeb94b08de2dfd8e1c2138 Mon Sep 17 00:00:00 2001
From: Alban Gaignard <alban.gaignard@univ-nantes.fr>
Date: Mon, 29 Jan 2024 16:51:00 +0100
Subject: [PATCH] many fixes in the dashboard (stats, etc.)

---
 src/webapp/app.py                        | 34 +++++++++----
 src/webapp/templates/index.html          | 63 +++++++++++++++++++++++-
 src/webapp/templates/layout.html         |  3 ++
 src/webapp/templates/nav.html            |  9 ++--
 src/webapp/templates/quick_curation.html |  4 +-
 src/webapp/templates/stats.html          |  2 +-
 6 files changed, 97 insertions(+), 18 deletions(-)

diff --git a/src/webapp/app.py b/src/webapp/app.py
index e256d39..c4f82ad 100644
--- a/src/webapp/app.py
+++ b/src/webapp/app.py
@@ -13,12 +13,12 @@
       }
 
 g = ConjunctiveGraph()
-g.load('https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl', format='xml')
+g.parse('https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl', format='xml')
 g.bind('edam', Namespace('http://edamontology.org/'))
 print(str(len(g)) + ' triples in the EDAM triple store')
 
 g_last_stable = ConjunctiveGraph()
-g_last_stable.load('http://edamontology.org/EDAM.owl', format='xml')
+g_last_stable.parse('http://edamontology.org/EDAM.owl', format='xml')
 
 ## Build an index to retrieve term labels 
 idx_label = {}
@@ -37,11 +37,25 @@
 
 @app.route('/')
 def index():
-    return render_template('index.html')
+    res = get_edam_numbers(g)
+    res_last = get_edam_numbers(g_last_stable)
+
+    return render_template('index.html',
+                           topics=res['nb_topics'],
+                           operations=res['nb_operations'],
+                           data=res['nb_data'],
+                           formats=res['nb_formats'],
+                           new_topics=res['nb_topics'] - res_last['nb_topics'],
+                           new_operations=res['nb_operations'] - res_last['nb_operations'],
+                           new_data=res['nb_data'] - res_last['nb_data'],
+                           new_formats=res['nb_formats'] - res_last['nb_formats']
+                           )
 
 @app.route('/expert_curation')
 def expert_curation():
-    return render_template('index.html')
+    # 1. select a topic
+    # 2. select topic-specific curation actions (subclasses of the identified topic)
+    return render_template('expert_curation.html')
 
 def get_edam_numbers(g):
     query_op = """
@@ -90,13 +104,13 @@ def edam_stats():
 
     return render_template('stats.html', 
         topics = res['nb_topics'], 
-        operations = res['nb_topics'], 
-        data = res['nb_topics'], 
-        format = res['nb_topics'], 
+        operations = res['nb_operations'],
+        data = res['nb_data'],
+        formats = res['nb_formats'],
         new_topics = res['nb_topics'] - res_last['nb_topics'], 
         new_operations = res['nb_operations'] - res_last['nb_operations'], 
         new_data = res['nb_data'] - res_last['nb_data'], 
-        new_formats = res['nb_formats'] - res_last['nb_formats'], 
+        new_formats = res['nb_formats'] - res_last['nb_formats']
         )
     
 @app.route('/edam_validation')
@@ -147,7 +161,7 @@ def quick_curation():
         count_no_wikipedia = str(r["nb_no_wikipedia"])
 
     #########
-    q_no_publication_entries = """
+    q_no_wikipedia_all = """
         SELECT ?c ?term WHERE {
             ?c rdfs:subClassOf+ edam:topic_0003 ; 
                 rdfs:label ?term .
@@ -158,7 +172,7 @@ def quick_curation():
             } .
         }
         """
-    results = g.query(q_no_publication_entries, initNs=ns)
+    results = g.query(q_no_wikipedia_all, initNs=ns)
     no_wikipedia = []
     for r in results:
         no_wikipedia.append({"term": r["term"], "class": r["c"]})
diff --git a/src/webapp/templates/index.html b/src/webapp/templates/index.html
index 133287a..4d67451 100644
--- a/src/webapp/templates/index.html
+++ b/src/webapp/templates/index.html
@@ -6,7 +6,68 @@
 
 {% block body %}
 
-<h1 class="title">EDAM ontology development dashboard</h1>
+<h1 class="title">Welcome to the EDAM ontology dashboard</h1>
 
+<section class="section">
+    <h2 class="subtitle">EDAM concepts</h2>
+
+    <nav class="level is-mobile">
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">Topics</p>
+                <p class="title">{{ topics }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">Operations</p>
+                <p class="title">{{ operations }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">Data</p>
+                <p class="title">{{ data }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">Format</p>
+                <p class="title">{{ formats }}</p>
+            </div>
+        </div>
+    </nav>
+</section>
+
+<section class="section">
+    <h2 class="subtitle">From the last stable release</h2>
+
+    <nav class="level is-mobile">
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">New topics</p>
+                <p class="title">{{ new_topics }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">New operations</p>
+                <p class="title">{{ new_operations }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">New data</p>
+                <p class="title">{{ new_data }}</p>
+            </div>
+        </div>
+        <div class="level-item has-text-centered">
+            <div>
+                <p class="heading">New format</p>
+                <p class="title">{{ new_formats }}</p>
+            </div>
+        </div>
+    </nav>
+</section>
 
 {% endblock %}
\ No newline at end of file
diff --git a/src/webapp/templates/layout.html b/src/webapp/templates/layout.html
index 227ac67..009e389 100644
--- a/src/webapp/templates/layout.html
+++ b/src/webapp/templates/layout.html
@@ -6,6 +6,9 @@
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <link rel="stylesheet" type="text/css" href="{{ url_for('static',filename='css/bulma.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="{{ url_for('static',filename='css/app.css')}}">
+    <script type="application/ld+json">
+        {"@context": {"sc": "https://schema.org/", "dct": "http://purl.org/dc/terms/", "prov": "http://www.w3.org/ns/prov#"}, "@type": ["sc:SoftwareApplication", "prov:Entity"], "@id": "https://github.com/IFB-ElixirFr/EDAM-dashboard", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/1.0-RELEASE", "sc:name": "EDAM-dashboard", "sc:applicationCategory": "Bioinformatics", "sc:applicationSubCategory": "Ontology development"}
+    </script>
 </head>
 
 <body>
diff --git a/src/webapp/templates/nav.html b/src/webapp/templates/nav.html
index 0e9cc88..e585ed7 100644
--- a/src/webapp/templates/nav.html
+++ b/src/webapp/templates/nav.html
@@ -1,16 +1,17 @@
 <aside class="menu">
     <ul class="menu-list">
         <li><a href="{{ url_for('index') }}">Home</a></li>
+        <li><a href="{{ url_for('index') }}">Visualizations</a></li>
     </ul>
-    <p class="menu-label">Contributors</p>
+    <p class="menu-label">I'm a contributor</p>
     <ul class="menu-list">
         <li><a href="{{ url_for('quick_curation') }}">Quick curation</a></li>
         <li><a href="{{ url_for('expert_curation') }}">In my field</a></li>
     </ul>
-    <p class="menu-label">Developers</p>
+    <p class="menu-label">I'm a developers</p>
     <ul class="menu-list">
-        <li><a href="{{ url_for('edam_stats') }}">Statistics</a></li>
-        <li><a href="{{ url_for('edam_validation') }}">Online validation</a></li>
+<!--        <li><a href="{{ url_for('edam_stats') }}">Statistics</a></li>-->
+<!--        <li><a href="{{ url_for('edam_validation') }}">Online validation</a></li>-->
         <li><a href="{{ url_for('edam_last_report') }}">Last validation report</a></li>
     </ul>
 </aside>
\ No newline at end of file
diff --git a/src/webapp/templates/quick_curation.html b/src/webapp/templates/quick_curation.html
index 5ca50fd..5ed8c91 100644
--- a/src/webapp/templates/quick_curation.html
+++ b/src/webapp/templates/quick_curation.html
@@ -10,11 +10,11 @@ <h1 class="title">Finding top priority curation needs</h1>
 <p>In this demo, we randomly pick 5 classes from the EDAM ontology that need to be curated.</p>
 
 <section class="section">
-    <h2 class="subtitle"> <span class="tag is-light">{{ count_no_wikipedia }} </span> EDAM topics with missing wikipedia
+    <h2 class="subtitle"> <span class="tag is-black">{{ count_no_wikipedia }} </span> EDAM topics with missing wikipedia
         links. </h2>
     <div class="buttons">
         {% for item in missing_wikipedia %}
-        <a href="{{ item.class }}" class="button is-danger is-rounded">{{ item.term }}</a>
+        <a href="{{ item.class }}" class="button is-danger is-rounded" target="_blank" >{{ item.term }}</a>
         {% endfor %}
     </div>
 </section>
diff --git a/src/webapp/templates/stats.html b/src/webapp/templates/stats.html
index f5dd693..c8ac48e 100644
--- a/src/webapp/templates/stats.html
+++ b/src/webapp/templates/stats.html
@@ -34,7 +34,7 @@ <h2 class="subtitle">EDAM concepts</h2>
         <div class="level-item has-text-centered">
             <div>
                 <p class="heading">Format</p>
-                <p class="title">{{ format }}</p>
+                <p class="title">{{ formats }}</p>
             </div>
         </div>
     </nav>