replaced dummy examples with real queries from caseologue; updated th…

…e structure of the menu

src/webapp/app.py

@@ -156,59 +156,115 @@ def edam_last_report():
 
     return render_template('edam_last_report.html', output_edamci_list=edamci_output_list, robot_output_list=robot_output_list)
 
+#################################################
+# How to contribute
+#################################################
 @app.route('/high_priority')
 def high_priority():
-
-    return render_template('high_priority.html')
-
-@app.route('/quick_curation')
-def quick_curation():
-
     dir_queries = "./queries"
 
-    ## Get topics without a wikipedia link (WARNING)
-    query = dir_queries + "/no_wikipedia_link_topic.rq"
+    ## Checks that all mandatory properties are filled in.
+    query = dir_queries + "/mandatory_property_missing.rq"
     with open(query, "r") as f:
         query = f.read()
         results = g.query(query)
     f.close()
 
-    no_wikipedia_link_topic = []
+    mandatory_property_missing = []
     for r in results:
-        no_wikipedia_link_topic.append({"term": r["term"], "class": r["concept"]})
+        mandatory_property_missing.append({"term": r["label"], "class": r["entity"]})
 
-    ## Get operations without a wikipedia link (WARNING)
-    query = dir_queries + "/no_wikipedia_link_operation.rq"
+    ## Checks that all IDs have a unique number.
+    query = dir_queries + "/get_uri.rq"
     with open(query, "r") as f:
         query = f.read()
         results = g.query(query)
     f.close()
 
-    no_wikipedia_link_operation = []
+    id_unique = []
     for r in results:
-        no_wikipedia_link_operation.append({"term": r["term"], "class": r["concept"]})
+        id_unique.append({"term": r["label"], "class": r["entity"]})
+
+    return render_template('high_priority.html',
+                            mandatory_property_missing = mandatory_property_missing,
+                            id_unique = id_unique,
+                            random = random)
+
+####################################
+@app.route('/quick_curation')
+def quick_curation():
+
+    dir_queries = "./queries"
 
-    ## Get topics without any broad synonym (OPTIONAL)
-    query = dir_queries + "/no_broad_synonym_topic.rq"
+    ## Checks that all webpage and doi are declared as literal links.
+    query = dir_queries + "/literal_links.rq"
     with open(query, "r") as f:
         query = f.read()
         results = g.query(query)
     f.close()
 
-    no_broad_synonym_topic = []
+    literal_links = []
     for r in results:
-        no_broad_synonym_topic.append({"term": r["term"], "class": r["concept"]})
+        literal_links.append({"term": r["label"], "class": r["entity"]})
+
+    ## Formatting of def and labels 
+    # end_dot_def_missing.rq;end_dot_label.rq;end_space_annotation.rq;eol_in_annotation.rq;start_space_annotation.rq;tab_in_annotation.rq
+    queries = [ dir_queries + "/end_dot_def_missing.rq", dir_queries + "/end_dot_label.rq", dir_queries + "/end_space_annotation.rq", dir_queries + "/eol_in_annotation.rq", 
+               dir_queries + "/start_space_annotation.rq", dir_queries + "/tab_in_annotation.rq"]
+    results = {}
+    for q in queries:
+        with open(q, "r") as f:
+            q = f.read()
+            results.update(g.query(q))
+        f.close()
+
+    formatting = []
+    for r in results:
+        formatting.append({"term": r["label"], "class": r["entity"]})
 
-    ## Get topics without a definition (ERROR)
-    query = dir_queries + "/no_definition_topic.rq"
+    ## Get topics without a wikipedia link (WARNING)
+    query = dir_queries + "/no_wikipedia_link_topic.rq"
     with open(query, "r") as f:
         query = f.read()
         results = g.query(query)
     f.close()
 
-    no_definition_topic = []
+    no_wikipedia_link_topic = []
     for r in results:
-        no_definition_topic.append({"term": r["term"], "class": r["concept"]})
+        no_wikipedia_link_topic.append({"term": r["term"], "class": r["concept"]})
+
+    # ## Get operations without a wikipedia link (WARNING)
+    # query = dir_queries + "/no_wikipedia_link_operation.rq"
+    # with open(query, "r") as f:
+    #     query = f.read()
+    #     results = g.query(query)
+    # f.close()
+
+    # no_wikipedia_link_operation = []
+    # for r in results:
+    #     no_wikipedia_link_operation.append({"term": r["term"], "class": r["concept"]})
+
+    # ## Get topics without any broad synonym (OPTIONAL)
+    # query = dir_queries + "/no_broad_synonym_topic.rq"
+    # with open(query, "r") as f:
+    #     query = f.read()
+    #     results = g.query(query)
+    # f.close()
+
+    # no_broad_synonym_topic = []
+    # for r in results:
+    #     no_broad_synonym_topic.append({"term": r["term"], "class": r["concept"]})
+
+    # ## Get topics without a definition (ERROR)
+    # query = dir_queries + "/no_definition_topic.rq"
+    # with open(query, "r") as f:
+    #     query = f.read()
+    #     results = g.query(query)
+    # f.close()
+
+    # no_definition_topic = []
+    # for r in results:
+    #     no_definition_topic.append({"term": r["term"], "class": r["concept"]})
 
 
     # NO wikipedia
@@ -252,12 +308,11 @@ def quick_curation():
     return render_template('quick_curation.html',
                            #count_no_wikipedia = count_no_wikipedia,
                            no_wikipedia_link_topic = no_wikipedia_link_topic,
-                           no_wikipedia_link_operation = no_wikipedia_link_operation,
-                           no_broad_synonym_topic = no_broad_synonym_topic,
-                           no_definition_topic = no_definition_topic,
-                           #no_regex_identifier = no_regex_identifier,
+                           literal_links = literal_links,
+                           formatting = formatting,
                            random = random)
 
+##############################################
 @app.route('/field_specific')
 def field_specific():
     dir_queries = "./queries"

src/webapp/templates/field_specific.html

@@ -1,4 +1,4 @@
-eee{% extends "layout.html" %}
+{% extends "layout.html" %}
 
 {% block nav %}
 {% include 'nav.html' %}
@@ -9,10 +9,10 @@
 <h1 class="title">Field specific contributions</h1>
 
     <section class="section">
-        <h2 class="subtitle"> <span class="tag is-warning is-medium">{{ no_regex_identifier|length }} </span> EDAM hybrid identifiers with missing regex. </h2>
+        <h2 class="subtitle"> <span class="tag is-info is-medium">{{ no_regex_identifier|length }} </span> EDAM hybrid identifiers with missing regex. </h2>
         <div class="buttons">
             {% for item in random.sample(no_regex_identifier, 8) %}
-                <a href="{{ item.class }}" class="button is-outlined is-warning " target="_blank" >{{ item.term }}</a>
+                <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-info " target="_blank" >{{ item.term }}</a>
             {% endfor %}
         </div>
     </section>

src/webapp/templates/high_priority.html

@@ -7,16 +7,32 @@
 {% block body %}
 
 <h1 class="title">High priority</h1>
+
+<section class="section">
+    <h2 class="subtitle"> <span class="tag is-danger is-medium">{{ mandatory_property_missing|length }} </span> Concepts with missing mandatory properties. </h2>
+    <div class="buttons">
+        {% if mandatory_property_missing|length < 8 %}
+            {% for item in mandatory_property_missing %}
+                <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% else %}
+            {% for item in random.sample(mandatory_property_missing, 8) %}
+                <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% endif %}
+    </div>
+</section>
+
 <section class="section">
-    <h2 class="subtitle"> <span class="tag is-danger is-medium">{{ no_definition_topic|length }} </span> EDAM topics with no definition. </h2>
+    <h2 class="subtitle"> <span class="tag is-danger is-medium">{{ mandatory_property_missing|length }} </span> ID numbers that are no unique. </h2>
     <div class="buttons">
-        {% if no_definition_topic|length < 8 %}
-            {% for item in no_definition_topic %}
-                <a href="{{ item.class }}" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+        {% if id_unique|length < 8 %}
+            {% for item in id_unique %}
+                <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
             {% endfor %}
         {% else %}
-            {% for item in random.sample(no_broad_synonym_topic, 8) %}
-                <a href="{{ item.class }}" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+            {% for item in random.sample(id_unique, 8) %}
+                <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
             {% endfor %}
         {% endif %}
     </div>

src/webapp/templates/nav.html

@@ -1,6 +1,7 @@
 <aside class="menu">
     <a href="{{ url_for('index') }}"><img src="https://github.com/edamontology/edamontology/raw/main/EDAM-logo-square.svg" alt="EDAM logo"></a>
 
+    <p class="menu-label">About EDAM</p>
     <ul class="menu-list">
         <li><a href="{{ url_for('index') }}">Home</a></li>
         <li><a href="{{ url_for('current') }}">Overview</a></li>

src/webapp/templates/quality.html

@@ -9,11 +9,17 @@
 <h1 class="title">Quality reports</h1>
 
 <section class="section">
-    <h2 class="subtitle">To do</h2>
 
+    <h2 class="subtitle">Quality report (temp screen capture)</h2>
 
-</section>
-
+    <nav class="level is-mobile">
 
+                <div class="content">
+                    <figure>
+                        <img src="/static/img/screencap_quality_report_temp.png" alt="Screenshot of the Rmd report from Caseologue tests" width="1000">
+                    </figure>
+                </div>
+    </nav>
+</section>
 
 {% endblock %}

src/webapp/templates/quick_curation.html

@@ -11,69 +11,52 @@ <h1 class="title">Quick and easy tasks</h1>
     <p> . </p>
 
 <section class="section">
-    <h2 class="subtitle"> <span class="tag is-warning is-medium">{{ no_wikipedia_link_topic|length }} </span> EDAM topics with missing wikipedia
+    <h2 class="subtitle"> <span class="tag is-primary is-medium">{{ no_wikipedia_link_topic|length }} </span> EDAM topics with missing wikipedia
         links. </h2>
     <div class="buttons">
-        {% for item in random.sample(no_wikipedia_link_operation, 8) %}
-{#        {% for item in no_wikipedia_link_topic %}#}
-        <a href="{{ item.class }}" class="button is-outlined is-warning " target="_blank" >{{ item.term }}</a>
-        {% endfor %}
+        {% if no_wikipedia_link_topic|length < 8 %}
+            {% for item in no_wikipedia_link_topic %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% else %}
+            {% for item in random.sample(no_wikipedia_link_topic, 8) %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% endif %}
     </div>
 </section>
 
-<section class="section">
-    <h2 class="subtitle"> <span class="tag is-warning is-medium">{{ no_wikipedia_link_operation|length }} </span> EDAM operations with missing wikipedia
-        links. </h2>
-    <div class="buttons">
-        {% for item in random.sample(no_wikipedia_link_operation, 8) %}
-{#        {% for item in no_wikipedia_link_operation %}#}
-        <a href="{{ item.class }}" class="button is-outlined is-warning " target="_blank" >{{ item.term }}</a>
-        {% endfor %}
-    </div>
-
-</section>
 
 <section class="section">
-    <h2 class="subtitle"> <span class="tag is-success is-medium">{{ no_broad_synonym_topic|length }} </span> EDAM topics with no broad synonyms. </h2>
+    <h2 class="subtitle"> <span class="tag is-primary is-medium">{{ literal_links|length }} </span> EDAM concepts have webpage and/or DOI not declared as literal links </h2>
     <div class="buttons">
-        {% for item in random.sample(no_broad_synonym_topic, 8) %}
-{#        {% for item in no_wikipedia_link_operation %}#}
-        <a href="{{ item.class }}" class="button is-outlined is-success " target="_blank" >{{ item.term }}</a>
-        {% endfor %}
+        {% if literal_links|length < 8 %}
+            {% for item in literal_links %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% else %}
+            {% for item in random.sample(literal_links, 8) %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
+            {% endfor %}
+        {% endif %}
     </div>
+
 </section>
 
 <section class="section">
-    <h2 class="subtitle"> <span class="tag is-danger is-medium">{{ no_definition_topic|length }} </span> EDAM topics with no definition. </h2>
+    <h2 class="subtitle"> <span class="tag is-primary is-medium">{{ formatting|length }} </span> Formatting </h2>
+        EDAM concepts that could use some proper formatting: labels and definitions starting with capital letters, definitions ending with a full stop, and no additional spaces at the beginning or end of any field. 
     <div class="buttons">
-        {% if no_definition_topic|length < 8 %}
-            {% for item in no_definition_topic %}
-                <a href="{{ item.class }}" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+        {% if formatting|length < 8 %}
+            {% for item in formatting %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
             {% endfor %}
         {% else %}
-            {% for item in random.sample(no_broad_synonym_topic, 8) %}
-                <a href="{{ item.class }}" class="button is-outlined is-danger " target="_blank" >{{ item.term }}</a>
+            {% for item in random.sample(formatting, 8) %}
+            <a href="https://edamontology.github.io/edam-browser/edit.html?term={{ item.class }}&branch=edam" class="button is-outlined is-primary " target="_blank" >{{ item.term }}</a>
             {% endfor %}
         {% endif %}
     </div>
 </section>
 
-
-{#    <h2 class="subtitle"> <span class="tag">17 </span> EDAM topics with no synonyms. </h2>
-    <div class="buttons">
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:forestgreen;color:forestgreen;background-color: #BBFFCC">Topic A</a>
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:forestgreen;color:forestgreen;background-color: #BBFFCC">Topic B</a>
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:forestgreen;color:forestgreen;background-color: #BBFFCC">Topic C</a>
-    </div>
-
-    <h2 class="subtitle"> <span class="tag">123 </span> EDAM operations with missing input attribute(s). </h2>
-    <div class="content">
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:indianred;color:indianred;background-color: #FFCCDD">Operation X</a>
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:indianred;color:indianred;background-color: #FFCCDD">Operation Y</a>
-        <a href="{{ url_for('quick_curation') }}" class="button" target="_blank" style="border-color:indianred;color:indianred;background-color: #FFCCDD">Operation Z</a>
-
-    </div>#}
-
-
-
 {% endblock %}