Merge pull request PGScatalog#284 from ens-lgil/feature/updates_oct23

Feature/updates oct23

catalog/tables.py

@@ -453,40 +453,40 @@ class Meta:
         template_name = 'catalog/pgs_catalog_django_table.html'
 
 
-class Browse_SampleSetTable(tables.Table):
-    '''Table to browse SampleSets (PSS; used in PGS evaluations) in the PGS Catalog'''
-    sample_merged = Column_sample_merged(accessor='display_samples_for_table', verbose_name='Sample Numbers', orderable=False)
-    sample_ancestry = Column_ancestry(accessor='display_ancestry', verbose_name='Sample Ancestry', orderable=False)
-    sampleset = tables.Column(accessor='display_sampleset', verbose_name=format_html('PGS Sample Set ID<br /><span>(PSS)</span>'), orderable=False)
-    phenotyping_free = Column_shorten_text_content(accessor='phenotyping_free', verbose_name='Phenotype Definitions and Methods')
-    cohorts = Column_cohorts(accessor='cohorts', verbose_name='Cohort(s)')
-
-    class Meta:
-        model = Sample
-        attrs = {
-            "id": "sampleset_table",
-            "data-show-columns" : "true",
-            "data-page-size" : page_size,
-            "data-export-options" : '{"fileName": "pgs_samplesets_data"}'
-        }
-        fields = [
-            'sampleset',
-            'phenotyping_free',
-            'sample_merged',
-            'sample_ancestry','ancestry_additional',
-            'cohorts', 'cohorts_additional',
-        ]
-
-        template_name = 'catalog/pgs_catalog_django_table.html'
-
-    def render_sampleset(self, value):
-        sampleset = f'<a href="/sampleset/{value.id}">{value.id}</a>'
-        if is_pgs_on_curation_site == 'True' and value.name:
-            sampleset += f' <div class="small">({value.name})</div>'
-        return format_html(sampleset)
-
-    def render_cohorts_additional(self, value):
-        return format_html('<span class="more">{}</span>', value)
+# class Browse_SampleSetTable(tables.Table):
+#     '''Table to browse SampleSets (PSS; used in PGS evaluations) in the PGS Catalog'''
+#     sample_merged = Column_sample_merged(accessor='display_samples_for_table', verbose_name='Sample Numbers', orderable=False)
+#     sample_ancestry = Column_ancestry(accessor='display_ancestry', verbose_name='Sample Ancestry', orderable=False)
+#     sampleset = tables.Column(accessor='display_sampleset', verbose_name=format_html('PGS Sample Set ID<br /><span>(PSS)</span>'), orderable=False)
+#     phenotyping_free = Column_shorten_text_content(accessor='phenotyping_free', verbose_name='Phenotype Definitions and Methods')
+#     cohorts = Column_cohorts(accessor='cohorts', verbose_name='Cohort(s)')
+#
+#     class Meta:
+#         model = Sample
+#         attrs = {
+#             "id": "sampleset_table",
+#             "data-show-columns" : "true",
+#             "data-page-size" : page_size,
+#             "data-export-options" : '{"fileName": "pgs_samplesets_data"}'
+#         }
+#         fields = [
+#             'sampleset',
+#             'phenotyping_free',
+#             'sample_merged',
+#             'sample_ancestry','ancestry_additional',
+#             'cohorts', 'cohorts_additional',
+#         ]
+#
+#         template_name = 'catalog/pgs_catalog_django_table.html'
+#
+#     def render_sampleset(self, value):
+#         sampleset = f'<a href="/sampleset/{value.id}">{value.id}</a>'
+#         if is_pgs_on_curation_site == 'True' and value.name:
+#             sampleset += f' <div class="small">({value.name})</div>'
+#         return format_html(sampleset)
+#
+#     def render_cohorts_additional(self, value):
+#         return format_html('<span class="more">{}</span>', value)
 
 
 class SampleTable_variants(tables.Table):

catalog/templates/catalog/includes/footer.html

@@ -33,7 +33,7 @@
     <!-- Copyright -->
   </footer>
 
-  {% if is_pgs_live_site %}
+  {% if is_pgs_live_site == 'True' %}
     <!-- Google Analytics details... -->
     <script type="text/javascript">!function(e,a,n,t,i,o,c){e.GoogleAnalyticsObject=i,e[i]=e[i]||function(){(e[i].q=e[i].q||[]).push(arguments)},e[i].l=1*new Date,o=a.createElement(n),c=a.getElementsByTagName(n)[0],o.async=1,o.src="//www.google-analytics.com/analytics.js",c.parentNode.insertBefore(o,c)}(window,document,"script",0,"ga"),ga("create","UA-145149243-1",{cookieDomain:"auto"}),ga("require","linkid","linkid.js"),ga("set","anonymizeIp",!0),ga("send","pageview");</script>
     <!-- Global site tag (gtag.js) - Google Analytics -->

catalog/tests/test_urls.py

@@ -11,13 +11,14 @@ def test_urls(self):
             '/browse/scores/',
             '/browse/traits/',
             '/browse/studies/',
-            '/browse/sample_set/',
+            # '/browse/sample_set/',
             '/docs/',
             '/docs/ancestry/',
             '/downloads/',
             '/latest_release/',
             '/rest/',
-            '/robots.txt'
+            '/robots.txt',
+            '/search/'
         ]
         self.url_response(urls, 200)
 

catalog/views.py

@@ -268,10 +268,10 @@ def browseby(request, view_selection):
             'view_name': 'Pending Publications',
             'table': table
         }
-    elif view_selection == 'sample_set':
-        context['view_name'] = 'Sample Sets'
-        table = Browse_SampleSetTable(Sample.objects.defer(*pgs_defer['sample']).filter(sampleset__isnull=False).prefetch_related('sampleset', pgs_prefetch['cohorts']).order_by('sampleset__num'))
-        context['table'] = table
+    # elif view_selection == 'sample_set':
+    #     context['view_name'] = 'Sample Sets'
+    #     table = Browse_SampleSetTable(Sample.objects.defer(*pgs_defer['sample']).filter(sampleset__isnull=False).prefetch_related('sampleset', pgs_prefetch['cohorts']).order_by('sampleset__num'))
+    #     context['table'] = table
     elif view_selection == 'scores' :
         score_only_attributes = ['id','name','trait_efo','trait_reported','variants_number','ancestries','license','publication__id','publication__date_publication','publication__journal','publication__firstauthor']
         table = Browse_ScoreTable(Score.objects.only(*score_only_attributes).select_related('publication').all().order_by('num').prefetch_related(pgs_prefetch['trait']))
@@ -537,7 +537,7 @@ def efo(request, efo_id):
             exclude_children = True
 
     try:
-        ontology_trait = EFOTrait_Ontology.objects.prefetch_related('scores_direct_associations','scores_child_associations','child_traits').get(id__exact=efo_id)
+        ontology_trait = EFOTrait_Ontology.objects.prefetch_related('scores_direct_associations','scores_child_associations','child_traits','traitcategory').get(id__exact=efo_id)
     except EFOTrait_Ontology.DoesNotExist:
         raise Http404("Trait: \"{}\" does not exist".format(efo_id))
 
@@ -547,7 +547,9 @@ def efo(request, efo_id):
     if exclude_children:
         related_scores = related_direct_scores
     else:
-        related_scores = list(related_direct_scores) + list(related_child_scores)
+        merged_related_scores = list(related_direct_scores) + list(related_child_scores)
+        # Remove potential duplicates (e.g. one of the trait is also a child of the second trait)
+        related_scores = list(set(merged_related_scores))
         related_scores.sort(key=lambda x: x.id)
 
     context = {

pgs_web/urls.py

@@ -23,6 +23,6 @@
     re_path(r'^search/', search_views.search, name="PGS Catalog Search"),
     re_path(r'^autocomplete/', search_views.autocomplete, name="PGS Catalog Autocomplete")
 ]
-if settings.PGS_ON_CURATION_SITE == 'True':
+if settings.PGS_ON_CURATION_SITE == True:
     from django.contrib import admin
     urlpatterns.append(path('admin/', admin.site.urls))

release/scripts/shell/copy2ftp_and_update_write_access.sh

@@ -19,15 +19,15 @@ else
       # Update write access on FTP
       echo "# Update write access on FTP"
       cd ${ftp_dir}
-      find pgs_scores_list.txt -type f -exec chmod 664 {} +
+      find pgs_scores_list.txt -type f -exec chmod -f 664 {} +
       echo "  > pgs_scores_list.txt file - done"
-      find scores/ -type d -exec chmod 775 {} +
+      find scores/ -type d -exec chmod -f 775 {} +
       echo "  > scores directories - done"
-      find scores/ -type f -exec chmod 664 {} +
+      find scores/ -type f -exec chmod -f 664 {} +
       echo "  > scores files - done"
-      find metadata/ -type d -exec chmod 775 {} +
+      find metadata/ -type d -exec chmod -f 775 {} +
       echo "  > metadata directories - done"
-      find metadata/ -type f -exec chmod 664 {} +
+      find metadata/ -type f -exec chmod -f 664 {} +
       echo "  > metadata files - done"
     else
       echo "Directory '${local_data_dir}' can't be found"

requirements.txt

@@ -1,5 +1,5 @@
 #### Django library
-Django==4.1.10
+Django==4.1.11
 #### Compress SCSS/SASS files in CSS
 django-compressor==4.3
 #### Library to build the HTML tables
@@ -10,6 +10,6 @@ psycopg2-binary==2.9.6
 djangorestframework==3.14.0
 django-cors-headers==3.13.0
 #### Python & Django Elasticsearch libraries
-elasticsearch==7.17.8
-elasticsearch-dsl==7.4.0
-django-elasticsearch-dsl==7.2.2
+elasticsearch==7.17.9
+elasticsearch-dsl==7.4.1
+django-elasticsearch-dsl==7.3

requirements_local.txt

@@ -23,4 +23,4 @@ google-cloud-storage==2.4.0
 pandas==1.5.3
 
 #### For webpage testing ####
-django-debug-toolbar==3.8.1
+django-debug-toolbar==4.2.0