[pull] master from PGScatalog:master

catalog/migrations/0003_release_efotrait_count.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.10 on 2024-03-25 15:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0002_alter_metric_name'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='release',
+            name='efotrait_count',
+            field=models.IntegerField(default=0, verbose_name='Number of new EFO traits released'),
+        ),
+    ]

catalog/models.py

@@ -1138,6 +1138,7 @@ class Release(models.Model):
     score_count = models.IntegerField('Number of new PGS scores released', default=0)
     performance_count = models.IntegerField('Number of new PGS Performance metrics released', default=0)
     publication_count = models.IntegerField('Number of new PGS Publication released', default=0)
+    efotrait_count = models.IntegerField('Number of new EFO traits released', default=0)
     notes = models.TextField(verbose_name='Release notes', max_length=600, blank=True)
     updated_score_count = models.IntegerField('Number of PGS scores updated', default=0)
     updated_performance_count = models.IntegerField('Number of PGS Performance metrics updated', default=0)
@@ -1160,3 +1161,9 @@ def released_publication_ids(self):
     def released_performance_ids(self):
         performances = Performance.objects.values_list('id', flat=True).filter(date_released__exact=self.date).order_by('id')
         return list(performances)
+
+    @property
+    def released_new_trait_ids(self):
+        previous_traits = Score.objects.values_list('trait_efo__id', flat=True).filter(date_released__lt=self.date).distinct()
+        new_traits = Score.objects.values_list('trait_efo__id', flat=True).filter(date_released__exact=self.date).distinct()
+        return list(new_traits.difference(previous_traits))

catalog/static/catalog/pgs_bar_charts.js

@@ -1,15 +1,17 @@
-var rest_url = 'https://www.pgscatalog.org/rest/release/'
+var rest_url = '/rest/release/'
 
 bg_colours = {
   'score': '#007C82',
   'publication': '#BE4A81',
   'performance': 'DodgerBlue',
+  'trait': '#c03b23',
   'new_entry': '#FFC200'
 };
 bg_hover_colours = {
   'score': '#00adb5',
   'publication': '#e83e8c',
   'performance': '#51a9ff',
+  'trait': '#f67d51',
   'new_entry': '#FFD700'
 };
 
@@ -41,6 +43,15 @@ $('.get_pgs_ids').click(function() {
         html_pub += '</ul>';
         $(list_pub_id).html(html_pub);
         $('#list_'+id).show();
+
+        list_trait_id = '#list_'+id.replace(type,'trait');
+        html_trait = "<ul>";
+        $.each(result.released_new_trait_ids, function(index, trait_id) {
+          html_trait += '<li><a href="/trait/'+trait_id+'/">'+trait_id+'</a></li>';
+        });
+        html_trait += '</ul>';
+        $(list_trait_id).html(html_trait);
+        $('#list_'+id).show();
     })
     .fail(function (xhRequest, ErrorText, thrownError) {
       console.log(xhRequest);

catalog/templates/catalog/releases.html

@@ -20,6 +20,7 @@ <h3 style="font-weight:200"><i class="far fa-calendar-check pgs_color_1 pr-3"></
               <th>Score(s)</th>
               <th>Publication(s)</th>
               <th>Performance(s)</th>
+              <th>Trait(s)</th>
               <th>Notes</th>
             </tr>
           </thead>
@@ -32,7 +33,7 @@ <h3 style="font-weight:200"><i class="far fa-calendar-check pgs_color_1 pr-3"></
                   {% if latest_release.score_count > 0 %}
                     <span class="badge badge-pill badge-pgs-2">{{ latest_release.score_count }}</span>
                     <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_score_{{ latest_release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of PGS Score IDs"></a>
-                    <div class="toggle_list mt-2" id="list_release_score_{{ latest_release.date|date:'Y-m-d' }}"></div>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_score_{{ latest_release.date|date:'Y-m-d' }}"></div>
                   {% else %}
                     -
                   {% endif %}
@@ -41,7 +42,7 @@ <h3 style="font-weight:200"><i class="far fa-calendar-check pgs_color_1 pr-3"></
                   {% if latest_release.publication_count > 0 %}
                     <span class="badge badge-pill badge-pgs-2">{{ latest_release.publication_count }}</span>
                     <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_pub_{{ latest_release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of PGS Publication IDs"></a>
-                    <div class="toggle_list mt-2" id="list_release_pub_{{ latest_release.date|date:'Y-m-d' }}"></div>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_pub_{{ latest_release.date|date:'Y-m-d' }}"></div>
                   {% else %}
                     -
                   {% endif %}
@@ -53,6 +54,15 @@ <h3 style="font-weight:200"><i class="far fa-calendar-check pgs_color_1 pr-3"></
                     -
                   {% endif %}
                 </td>
+                <td>
+                  {% if latest_release.efotrait_count > 0 %}
+                    <span class="badge badge-pill badge-pgs-2">{{ latest_release.efotrait_count }}</span>
+                    <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_trait_{{ latest_release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of Trait IDs"></a>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_trait_{{ latest_release.date|date:'Y-m-d' }}"></div>
+                  {% else %}
+                    -
+                  {% endif %}
+                </td>
                 <td style="text-align:left">{{ latest_release.notes }}</td>
               </tr>
           </tbody>
@@ -70,6 +80,7 @@ <h3 class="pt-4" style="font-weight:200;border-top:2px dashed #CCC"><i class="fa
               <th>Score(s)</th>
               <th>Publication(s)</th>
               <th>Performance(s)</th>
+              <th>Trait(s)</th>
               <th>Notes</th>
             </tr>
           </thead>
@@ -88,7 +99,7 @@ <h3 class="pt-4" style="font-weight:200;border-top:2px dashed #CCC"><i class="fa
                   {% if release.score_count > 0 %}
                     <span class="badge badge-pill badge-pgs-2">{{ release.score_count }}</span>
                     <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_score_{{ release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of PGS Score IDs"></a>
-                    <div class="toggle_list mt-2" id="list_release_score_{{ release.date|date:'Y-m-d' }}"></div>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_score_{{ release.date|date:'Y-m-d' }}"></div>
                   {% else %}
                     -
                   {% endif %}
@@ -97,7 +108,7 @@ <h3 class="pt-4" style="font-weight:200;border-top:2px dashed #CCC"><i class="fa
                   {% if release.publication_count > 0 %}
                     <span class="badge badge-pill badge-pgs-2">{{ release.publication_count }}</span>
                     <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_pub_{{ release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of PGS Publication IDs"></a>
-                    <div class="toggle_list mt-2" id="list_release_pub_{{ release.date|date:'Y-m-d' }}"></div>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_pub_{{ release.date|date:'Y-m-d' }}"></div>
                   {% else %}
                     -
                   {% endif %}
@@ -109,6 +120,15 @@ <h3 class="pt-4" style="font-weight:200;border-top:2px dashed #CCC"><i class="fa
                     -
                   {% endif %}
                 </td>
+                <td>
+                  {% if release.efotrait_count > 0 %}
+                    <span class="badge badge-pill badge-pgs-2">{{ release.efotrait_count }}</span>
+                    <a class="toggle_btn pgs_btn_plus get_pgs_ids pgs_no_icon_link ml-1" id="release_trait_{{ release.date|date:'Y-m-d' }}" data-toggle="tooltip" title="Click to display the list of Trait IDs"></a>
+                    <div class="toggle_list mt-2" style="text-align:left" id="list_release_trait_{{ release.date|date:'Y-m-d' }}"></div>
+                  {% else %}
+                    -
+                  {% endif %}
+                </td>
                 <td style="text-align:left">{{ release.notes }}</td>
               </tr>
           {% endfor %}
@@ -130,6 +150,7 @@ <h3 class="pt-4" style="font-weight:200;border-top:2px dashed #CCC"><i class="fa
         draw_js_barchart(data_chart, 'release_score', 'score');
         draw_js_barchart(data_chart, 'release_publication', 'publication');
         draw_js_barchart(data_chart, 'release_perf', 'performance');
+        draw_js_barchart(data_chart, 'release_trait', 'trait');
         draw_js_barchart_with_label(pub_year_chart.all, 'pub_per_year_all', 'Publications per year (All)', 'publication');
         if (pub_year_chart.nr) {
           draw_js_barchart_with_label(pub_year_chart.r, 'pub_per_year_r', 'Publications per year (Released)', 'publication');
@@ -148,7 +169,7 @@ <h3 class="mt-5 pt-4 mb-4" style="font-weight:200;border-top:2px dashed #CCC"><i
       </div>
     </div>
 
-    <h3 style="font-weight:200"><i class="fa-solid fa-chart-column pgs_color_1 pr-3"></i>Scores, Publications and Performance Metrics per release</h3>
+    <h3 style="font-weight:200"><i class="fa-solid fa-chart-column pgs_color_1 pr-3"></i>Scores, Publications, Performance Metrics and Traits per release</h3>
     <div class="clearfix mb-2">
       <div class="mb-4 mr-4" style="float:left;width:425px;height:300px">
         <canvas id="release_score" width="425" height="300"></canvas>
@@ -159,6 +180,9 @@ <h3 style="font-weight:200"><i class="fa-solid fa-chart-column pgs_color_1 pr-3"
       <div class="mb-4" style="float:left;width:425px;height:300px">
         <canvas id="release_perf" width="425" height="300"></canvas>
       </div>
+      <div class="mb-4" style="float:left;width:425px;height:300px">
+        <canvas id="release_trait" width="425" height="300"></canvas>
+      </div>
     </div>
 
     <h3 style="font-weight:200"><i class="fa-solid fa-chart-column pgs_color_2 pr-3"></i>Distribution of publications per year</h3>

catalog/views.py

@@ -689,6 +689,7 @@ def releases(request):
     total_score = 0
     total_perf = 0
     total_publi = 0
+    total_trait = 0
     max_score = 0
     max_publi = 0
     max_perf = 0
@@ -756,20 +757,24 @@ def releases(request):
         score = release.score_count
         perf  = release.performance_count
         publi = release.publication_count
+        trait = release.efotrait_count
         date  = release.date
 
         release_item = {
                         'date': date.strftime('%d/%m/%y'),
                         'score_count': score,
                         'performance_count': perf,
                         'publication_count': publi,
+                        'trait_count': trait,
                         'total_score_count': total_score,
                         'total_performance_count': total_perf,
-                        'total_publication_count': total_publi
+                        'total_publication_count': total_publi,
+                        'total_trait_count': total_trait
                        }
         total_score += score
         total_perf += perf
         total_publi += publi
+        total_trait += trait
 
         release_data.append(release_item)
 

release/scripts/CreateRelease.py

@@ -11,6 +11,7 @@ class CreateRelease:
 
     new_scores = {}
     new_performances = {}
+    new_traits = set()
 
     def __init__(self, release_tomorrow=None):
         self.release_tomorrow = release_tomorrow
@@ -30,6 +31,7 @@ def update_data_to_release(self):
         by adding a date in the 'date_released' columns
         """
         self.get_release_date()
+        previous_traits = set(Score.objects.values_list('trait_efo__id', flat=True).exclude(date_released__isnull=True).distinct())
         #### Add release date for each publications and dependent models ####
         for publication in self.new_publications:
             publication.date_released = self.new_release_date
@@ -42,6 +44,9 @@ def update_data_to_release(self):
                 # Update date_release
                 score.date_released = self.new_release_date
                 score.save()
+                # Get new traits
+                score_traits = {efotrait.id for efotrait in score.trait_efo.all()}
+                self.new_traits.update(score_traits.difference(previous_traits))
 
             # Performances
             performances_list = Performance.objects.filter(date_released__isnull=True, publication=publication)
@@ -55,12 +60,13 @@ def update_data_to_release(self):
     def create_new_release(self):
         """ Create new release instance and save it in the database """
         #### Create new release instance ####
-        release_notes = 'This release contains {} new Score(s), {} new Publication(s) and {} new Performance metric(s)'.format(len(self.new_scores.keys()), len(self.new_publications), len(self.new_performances.keys()))
+        release_notes = 'This release contains {} new Score(s), {} new Publication(s), {} new Performance metric(s) and {} new Trait(s)'.format(len(self.new_scores.keys()), len(self.new_publications), len(self.new_performances.keys()), len(self.new_traits))
         release = Release.objects.create(
                 date=self.new_release_date,
                 performance_count=len(self.new_performances.keys()),
                 publication_count=len(self.new_publications),
                 score_count=len(self.new_scores.keys()),
+                efotrait_count=len(self.new_traits),
                 notes=release_notes
               )
         return release
@@ -123,6 +129,7 @@ def run():
     print(', '.join(release.new_scores.keys()))
     print("Number of new Publications: "+str(new_release.publication_count))
     print("Number of new Performances: "+str(new_release.performance_count))
+    print("Number of new Traits: " + str(new_release.efotrait_count))
 
     # Scores
     scores_direct = Score.objects.filter(date_released__isnull=True)

release/scripts/run_release_script.py

@@ -181,6 +181,7 @@ def call_create_release():
     output_report(', '.join(release.new_scores.keys()))
     output_report("Number of new Publications: "+str(new_release.publication_count))
     output_report("Number of new Performances: "+str(new_release.performance_count))
+    output_report("Number of new Traits: " + str(new_release.efotrait_count))
 
     if new_release.score_count == 0 or new_release.publication_count == 0 or new_release.performance_count == 0:
         error_report("at least one of the main components (Score, Publication or Performance Metrics) hasn't a new entry this release")

rest_api/serializers.py

@@ -196,8 +196,8 @@ class ReleaseSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Release
-        meta_fields = ('date', 'score_count', 'performance_count', 'publication_count', 'notes',
-                    'released_score_ids', 'released_publication_ids', 'released_performance_ids')
+        meta_fields = ('date', 'score_count', 'performance_count', 'publication_count', 'efotrait_count', 'notes',
+                    'released_score_ids', 'released_publication_ids', 'released_performance_ids', 'released_new_trait_ids')
         fields = meta_fields
         read_only_fields = meta_fields