Merge branch 'dev_thomas' of https://github.com/IFB-ElixirFr/fair-che…

…cker into dev_thomas
IFB-ElixirFr · Jul 9, 2021 · 8c0909f · 8c0909f
2 parents a28a9de + e453583
commit 8c0909f
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Showing 5 changed files with 47 additions and 35 deletions.
diff --git a/app.py b/app.py
@@ -994,21 +994,21 @@ def check_kg(data):
         if util.ask_OLS(c['name']):
             c['tag'].append('OLS')
             emit('done_check', table_content)
-        # if util.ask_LOV(c['name']):
-        #     c['tag'].append('LOV')
-        #     emit('done_check', table_content)
-        if util.ask_BioPortal(c['name']):
+        if util.ask_LOV(c['name']):
+            c['tag'].append('LOV')
+            emit('done_check', table_content)
+        if util.ask_BioPortal(c['name'], "class"):
             c['tag'].append('BioPortal')
             emit('done_check', table_content)
 
     for p in table_content['properties']:
         if util.ask_OLS(p['name']):
             p['tag'].append('OLS')
             emit('done_check', table_content)
-        # if util.ask_LOV(p['name']):
-        #     p['tag'].append('LOV')
-        #     emit('done_check', table_content)
-        if util.ask_BioPortal(p['name']):
+        if util.ask_LOV(p['name']):
+            p['tag'].append('LOV')
+            emit('done_check', table_content)
+        if util.ask_BioPortal(p['name'], "property"):
             p['tag'].append('BioPortal')
             emit('done_check', table_content)
 

diff --git a/metrics/util.py b/metrics/util.py
@@ -154,7 +154,8 @@ def get_DOI(uri):
     match = re.search(regex, uri, re.MULTILINE | re.IGNORECASE)
     return match.group(0)
 
-def ask_BioPortal(uri):
+
+def ask_BioPortal(uri, type):
 
     print(f'Call to the BioPortal REST API for [ {uri} ]')
     # print(app.config)
@@ -164,8 +165,11 @@ def ask_BioPortal(uri):
             'Accept': 'application/json',
             'Authorization': 'apikey token=' + api_key
         }
-    # res = requests.get("https://data.bioontology.org/property_search?q=" + uri, headers=h, verify=True)
-    res = requests.get("https://data.bioontology.org/search?q=" + uri + "&require_exact_match=true", headers=h, verify=True)
+
+    if type == "property":
+        res = requests.get("https://data.bioontology.org/property_search?q=" + uri, headers=h, verify=True)
+    elif type == "class":
+        res = requests.get("https://data.bioontology.org/search?q=" + uri + "&require_exact_match=true", headers=h, verify=True)
     # print(res)
 
 

diff --git a/templates/kg_metrics_2.html b/templates/kg_metrics_2.html
@@ -565,14 +565,18 @@ <h1 class="title">How to enhance metadata quality for my tools, datasets, workfl
         </div>
         <!-- <div class="section"> -->
             {% for k in sample_data.keys() %}
-<!--            <p class="button is-info is-small">{{k}}<i class="fa fa-chevron-down fa-fw"></i></p>-->
-<!--            <br>-->
-<!--            <br>-->
-            <div class="field is-grouped is-grouped-centered">
-                {% for s in sample_data[k] %}
-                <p id="resource_{{k}}_{{loop.index}}"class="control"><a class="button is-small is-text" data-url="{{ s.url }}">{{ s.text }}</a></p>
-                {% endfor %}
-            </div>
+            <p class="button is-info is-small">{{k}}<i class="fa fa-chevron-down fa-fw"></i></p>
+                <!-- <br> -->
+                <!-- <br> -->
+                <div class="panel">
+                  <div class="panel-block is-centered">
+                    <div class="field is-grouped is-grouped-centered">
+                        {% for s in sample_data[k] %}
+                        <p id="resource_{{k}}_{{loop.index}}"class="control"><a class="button is-small is-text" data-url="{{ s.url }}">{{ s.text }}</a></p>
+                        {% endfor %}
+                    </div>
+                  </div>
+                </div>
             {% endfor %}
         <!-- </div> -->
       </div>

diff --git a/templates/metrics_summary.html b/templates/metrics_summary.html
@@ -433,16 +433,20 @@ <h1 class="title">How FAIR is my resource ?</h1>
         </article>
       </div> -->
       <!-- <div class="section"> -->
-        {% for k in sample_data.keys() %}
-        <!-- <p class="button is-info is-small">{{k}}<i class="fa fa-chevron-down fa-fw"></i></p> -->
-        <!-- <br> -->
-        <!-- <br> -->
-        <div class="field is-grouped is-grouped-centered">
-            {% for s in sample_data[k] %}
-            <p id="resource_{{k}}_{{loop.index}}"class="control"><a class="button is-small is-text" data-url="{{ s.url }}">{{ s.text }}</a></p>
-            {% endfor %}
-        </div>
-        {% endfor %}
+      {% for k in sample_data.keys() %}
+      <p class="button is-info is-small">{{k}}<i class="fa fa-chevron-down fa-fw"></i></p>
+          <!-- <br> -->
+          <!-- <br> -->
+          <div class="panel">
+            <div class="panel-block is-centered">
+              <div class="field is-grouped is-grouped-centered">
+                  {% for s in sample_data[k] %}
+                  <p id="resource_{{k}}_{{loop.index}}"class="control"><a class="button is-small is-text" data-url="{{ s.url }}">{{ s.text }}</a></p>
+                  {% endfor %}
+              </div>
+            </div>
+          </div>
+      {% endfor %}
 
       <!-- </div> -->
     </div>

diff --git a/tests/test_vocab.py b/tests/test_vocab.py
@@ -102,19 +102,19 @@ def test_validate_shape_tool(self):
             print(f'{row["prop"]}')
 
         for c in table_content['classes']:
-            print(util.ask_BioPortal(c['name']))
+            print(util.ask_BioPortal(c['name'], "class"))
             if util.ask_OLS(c['name']):
                 c['tag'].append('OLS')
-            # if util.ask_LOV(c['name']):
-            #     c['tag'].append('LOV')
+            if util.ask_LOV(c['name']):
+                c['tag'].append('LOV')
 
         for p in table_content['properties']:
-            print(util.ask_BioPortal(p['name']))
+            print(util.ask_BioPortal(p['name'], "property"))
             # print(util.ask_OLS(p['name']))
             if util.ask_OLS(p['name']):
                 p['tag'].append('OLS')
-            # if util.ask_LOV(p['name']):
-            #     p['tag'].append('LOV')
+            if util.ask_LOV(p['name']):
+                p['tag'].append('LOV')
 
 
 if __name__ == '__main__':