New website display + some cleanup

.gcloudignore

@@ -11,7 +11,7 @@
 # from your .gitignore file, remove the corresponding line
 # below:
 .git
-.github/
+.github
 .gitignore
 
 # Static directories (GAE uses the ones in /static instead)
@@ -20,27 +20,31 @@
 /curation_tracker/static/
 
 # Curation and release directories (not needed for the website)
-/curation/
-/release/
-/curation_tracker/scripts/
+/curation
+/release
+/curation_tracker/scripts
 
 # Migrations
-**/migrations/
+**/migrations
 
 # Tests
-**/tests/
+**/tests
+**/tests.py
 
 # Python pycache:
-**/__pycache__/
+**/__pycache__
 # Ignored by the build system
 /setup.cfg
 
 # Other
-/rest_api/fixtures/
-/static/CACHE/
+/rest_api/fixtures
+/static/CACHE
 app.yaml_template
 pgs-catalog-cred.json_template
+requirements_local.txt
 LICENSE.md
 README.md
-requirements_local.txt
 **/.DS_Store
+
+## Only for Live Webiste ##
+#/curation_tracker

app.yaml_template

@@ -1,6 +1,6 @@
 # [START django_app]
 
-runtime: python310
+runtime: python311
 
 # For the live site, comment the following line (it uses the default service value 'default')
 service: <service_name>
@@ -38,28 +38,32 @@ env_variables:
     PGS_LIVE_SITE: '<False_or_True>' # Need to be set to True for live website
     PGS_CURATION_SITE: '<False_or_True>' # Line optional: Only used for the curation website
     ALLOWED_HOSTS: '*'
-    # PGS database #
+
+    ## PGS database ##
     DATABASE_NAME: '<db_name>'
     DATABASE_USER: '<db_user>'
     DATABASE_PASSWORD: '<db_password>'
     DATABASE_PORT: '<db_port>'
     DATABASE_PORT_LOCAL: '<db_port_local>'
     DATABASE_HOST: '<db_host>' # e.g.: localhost, IP address, /cloudsql/...
-    # PGS Benchmark database
+
+    ## PGS Benchmark database ##
     DATABASE_NAME_2: '<benchmark_db_name>'
     DATABASE_USER_2: '<db_user>'
     DATABASE_PASSWORD_2: '<db_password>'
     DATABASE_PORT_2: '<db_port>'
     DATABASE_PORT_LOCAL_2: '<db_port_local>'
     DATABASE_HOST_2: '<db_host>' # e.g.: localhost, IP address, /cloudsql/...
-    # Curation Tracker database #
+
+    ## Curation Tracker database ##
     DATABASE_NAME_TRACKER: '<db_name>' # e.g.: pgs_curation_tracker
     DATABASE_USER_TRACKER: '<db_user>'
     DATABASE_PASSWORD_TRACKER: '<db_password>'
     DATABASE_PORT_TRACKER: '<db_port>'
     DATABASE_PORT_LOCAL_TRACKER: '<db_port_local>'
     DATABASE_HOST_TRACKER: '<db_host>' # e.g.: localhost, IP address, /cloudsql/...
-    # Search
+
+    ## Search ##
     ELASTICSEARCH_URL_ROOT: '<url_to_elasticsearch_service>'
 
 # [END django_app]

benchmark/static/benchmark/benchmark.scss

@@ -31,19 +31,6 @@ $chart_font_family:"Verdana", "Arial", "sans-serif";
   }
 }
 
-// .filter_container {
-//   border:1px solid $pgs_darkC;
-//   border-radius:4px;
-//   padding:4px 10px;
-// }
-// .filter_header {
-//   font-weight: 200;
-//   border-bottom:1px solid $pgs_darkC;
-//   color: $pgs_dark0;
-//   padding-bottom:4px;
-//   text-align:center;
-// }
-
 .tooltip {
   font-size: 12px;
 }
@@ -100,7 +87,7 @@ $pgs_benchmark_colours: (
   .pgs_benchmark_anc_#{$label} {
     &:before {
       color: $colour;
-      font-family: "Font Awesome 5 Free";
+      font-family: "Font Awesome 6 Free";
       content: "\f068";
       font-weight:900;
     }
@@ -110,22 +97,19 @@ $pgs_benchmark_colours: (
     &:before {
       padding-right:5px;
       color: $colour;
-      // font-family: "Font Awesome 5 Free";
-      // content: "\f0c8";
-      // font-weight:900;
     }
   }
 }
 
 .pgs_benchmark_shape_circle:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f111";
   font-weight:900;
 }
 .pgs_benchmark_shape_circle_o:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f111";
 }
 
@@ -186,37 +170,37 @@ $pgs_benchmark_colours: (
 
 .pgs_benchmark_shape_square:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f0c8";
   font-weight:900;
 }
 .pgs_benchmark_shape_square_o:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f0c8";
 }
 
 .pgs_benchmark_shape_star:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f005";
   font-weight:900;
 }
 .pgs_benchmark_shape_star_o:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f005";
 }
 
 .pgs_benchmark_shape_cross:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
-  content: "\f067";
+  font-family: "Font Awesome 6 Free";
+  content: "\2b";
   font-weight:900;
 }
 .pgs_benchmark_shape_cross_o:before {
   font-size: 10px;
-  font-family: "Font Awesome 5 Free";
+  font-family: "Font Awesome 6 Free";
   content: "\f0fe";
   font-weight:900;
 }

benchmark/templates/benchmark/benchmark.html

@@ -13,7 +13,7 @@
     </nav>
 
     <h2>
-      <span class="pgs_benchmark_logo pr-2"></span>Trait: <span class="pgs_title">{{ trait.label }}</span>
+      <span class="pgs_benchmark_logo pgs_color_2 pr-2"></span>Trait <small class="fa-solid fa-angle-right pgs_color_2"></small> <span class="pgs_title">{{ trait.label }}</span>
       <span class="ml-4" style="border:2px solid #BE4A81;padding:4px;border-radius:5px;font-size:16px;line-height:37px;vertical-align:middle;color:#BE4A81">
         <span class="fas fa-cogs pr-1 pgs_color_2"></span>Prototype
       </span>

benchmark/views.py

@@ -163,7 +163,7 @@ def add_global_data(data, cohort_name, entry_name, data_type):
 
 def benchmark(request):
     trait_id = 'EFO_0000378'
-    efotrait = BM_EFOTrait.objects.using('benchmark').prefetch_related('phenotype_structured').get(id=trait_id)
+    efotrait = BM_EFOTrait.objects.using(bm_db).prefetch_related('phenotype_structured').get(id=trait_id)
 
     pgs_data, cohort_max_sample = benchmark_data(efotrait)
 
@@ -174,11 +174,10 @@ def benchmark(request):
         for score in pgs_data['pgs_ids'][cohort]:
             scores.add(score)
 
-    score_only_attributes = ['id','name','publication','trait_efo','trait_reported','variants_number','publication__id','publication__date_publication','publication__journal','publication__firstauthor']
-    table_scores = BM_Browse_ScoreTable(Score.objects.only(*score_only_attributes).select_related('publication').filter(id__in=list(scores)).prefetch_related(pgs_prefetch['trait']), order_by="num")
+    score_defer = ['publication__title','publication__PMID','publication__doi','publication__authors','publication__curation_status','publication__curation_notes','publication__date_released','curation_notes']
+    table_scores = BM_Browse_ScoreTable(Score.objects.defer(*score_defer).select_related('publication').filter(id__in=list(scores)).prefetch_related(pgs_prefetch['trait']), order_by="num")
 
-
-    bm_cohorts = BM_Cohort.objects.using('benchmark').filter(name_short__in=cohorts).prefetch_related('cohort_sample').distinct()
+    bm_cohorts = BM_Cohort.objects.using(bm_db).filter(name_short__in=cohorts).prefetch_related('cohort_sample').distinct()
 
     cohort_data = {}
     for bm_cohort in bm_cohorts:

catalog/context_processors.py

@@ -44,6 +44,24 @@ def pgs_search_examples(request):
         'pgs_search_examples': html
     }
 
+def pgs_browse_examples(request):
+    eg_count = 0
+    html = ''
+    # Build the list of search examples
+    for example in constants.BROWSE_EXAMPLES:
+        link = f'<a href="/browse/scores?bq={example}">{example}</a>'
+        eg_count += 1
+        if eg_count > 1:
+            if eg_count == 4:
+                html += '<span class="extra_example">'
+            html += ', '
+        html += link
+    if eg_count > 3:
+        html += '</span>'
+    return {
+        'pgs_browse_examples': html
+    }
+
 def pgs_info(request):
     return {
         'pgs_citation': constants.PGS_CITATION,
@@ -63,11 +81,11 @@ def get_group_index(group_private_index):
             groups_to_print.append(group)
         group_index = groups_to_print.index(group) + 1
         return(f'<a title="{group_name}" style="border-bottom: 0px;">{group_index}</a>')
-    
+
     def html_author(author):
         name = author['name']
         group_sup = ','.join(map(get_group_index,author['group']))
-        
+
         return f'<span>{ name }<sup>{ group_sup }</sup></span>'
 
     html += ', '.join(map(html_author,constants.PGS_CONTRIBUTORS))