Merge pull request #388 from ImagingDataCommons/idc-prod-sp

v18

Author: s-paquette

cohorts/migrations/0009_alter_filter_operator.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.20 on 2023-11-17 00:18
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('cohorts', '0008_auto_20230531_1711'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='filter',
+            name='operator',
+            field=models.CharField(choices=[('B', '_btw'), ('EB', '_btwe'), ('BE', '_ebtw'), ('EBE', '_ebtwe'), ('GE', '_gte'), ('LE', '_lte'), ('G', '_gt'), ('L', '_lt'), ('A', '_and'), ('O', '_or'), ('E', '_eq')], default='O', max_length=4),
+        ),
+    ]

idc_collections/admin.py

@@ -21,8 +21,9 @@
 
 class Program_Admin(admin.ModelAdmin):
     list_display = (
-        'name',
+        'full_name',
         'short_name',
+        'display_name',
         'description',
         'active',
         'owner',

idc_collections/collex_metadata_utils.py

@@ -468,7 +468,8 @@ def build_explorer_context(is_dicofdic, source, versions, filters, fields, order
                     'projects': {},
                     'val': 0,
                     'prog_attr_id': prog_attr_id,
-                    'collex_attr_id': collex_attr_id
+                    'collex_attr_id': collex_attr_id,
+                    'display_name': collection.program.display_name if collection.program else collection.name.upper()
                 }
             if collection.collection_id in context['collections']:
                 name = collection.program.short_name if collection.program else collection.name
@@ -778,7 +779,7 @@ def get_collex_metadata(filters, fields, record_limit=3000, offset=0, counts_onl
                         collapse_on='PatientID', order_docs=None, sources=None, versions=None, with_derived=True,
                         facets=None, records_only=False, sort=None, uniques=None, record_source=None, totals=None,
                         search_child_records_by=None, filtered_needed=True, custom_facets=None, raw_format=False,
-                        default_facets=True):
+                        default_facets=True, aux_sources=None):
 
     try:
         source_type = sources.first().source_type if sources else DataSource.SOLR
@@ -816,7 +817,7 @@ def get_collex_metadata(filters, fields, record_limit=3000, offset=0, counts_onl
                 filters, fields, sources, counts_only, collapse_on, record_limit, offset, facets, records_only, sort,
                 uniques, record_source, totals, search_child_records_by=search_child_records_by,
                 filtered_needed=filtered_needed, custom_facets=custom_facets, raw_format=raw_format,
-                default_facets=default_facets
+                default_facets=default_facets,aux_sources=aux_sources
             )
         stop = time.time()
         logger.debug("Metadata received: {}".format(stop-start))
@@ -933,7 +934,7 @@ def create_query_set(solr_query, sources, source, all_ui_attrs, image_source, Da
 def get_metadata_solr(filters, fields, sources, counts_only, collapse_on, record_limit, offset=0, attr_facets=None,
                       records_only=False, sort=None, uniques=None, record_source=None, totals=None, cursor=None,
                       search_child_records_by=None, filtered_needed=True, custom_facets=None, sort_field=None,
-                      raw_format=False, default_facets=True):
+                      raw_format=False, default_facets=True, aux_sources=None):
 
     filters = filters or {}
     results = {'docs': None, 'facets': {}}
@@ -950,9 +951,15 @@ def get_metadata_solr(filters, fields, sources, counts_only, collapse_on, record
             cache_as="ui_facet_set" if not sources.contains_inactive_versions() and not attr_facets else None
         )
 
-    all_ui_attrs = fetch_data_source_attr(
-        sources, {'for_ui': True, 'for_faceting': False, 'active_only': True},
-        cache_as="all_ui_attr" if not sources.contains_inactive_versions() else None)
+    all_ui_attrs =[]
+    if aux_sources is None:
+      all_ui_attrs = fetch_data_source_attr(
+          sources, {'for_ui': True, 'for_faceting': False, 'active_only': True},
+          cache_as="all_ui_attr" if not sources.contains_inactive_versions() else None)
+    else:
+        all_ui_attrs = fetch_data_source_attr(
+            aux_sources, {'for_ui': True, 'for_faceting': False, 'active_only': True},
+            cache_as="all_ui_attr" if not sources.contains_inactive_versions() else None)
 
     source_data_types = fetch_data_source_types(sources)
 
@@ -1010,7 +1017,10 @@ def get_metadata_solr(filters, fields, sources, counts_only, collapse_on, record
                         solr_facets_filtered = {}
                     solr_facets_filtered.update(custom_facets)
 
-        query_set = create_query_set(solr_query, sources, source, all_ui_attrs, image_source, DataSetType)
+        if aux_sources is None:
+            query_set = create_query_set(solr_query, sources, source, all_ui_attrs, image_source, DataSetType)
+        else:
+            query_set = create_query_set(solr_query, aux_sources, source, all_ui_attrs, image_source, DataSetType)
 
         stop = time.time()
         logger.debug("[STATUS] Time to build Solr submission: {}s".format(str(stop-start)))
@@ -1477,10 +1487,10 @@ def get_bq_metadata(filters, fields, data_version, sources_and_attrs=None, group
                     break
         order_by = new_order
 
-    # Failures to find grouping tables typically mean:
-    # * the wrong version is being polled for the data sources
-    # * the attribute isn't found in any of these tables
-    # Make sure the right version is being used!
+    # Two main reasons you'll get an exception here:
+    # the wrong version is being used
+    # there are no attributes in the data source
+    # Check those before wasting ANY time debugging
     if group_by:
         new_groups = []
         for grouping in group_by:

idc_collections/migrations/0011_auto_20231116_1627.py

@@ -0,0 +1,23 @@
+# Generated by Django 3.2.20 on 2023-11-17 00:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('idc_collections', '0010_alter_collection_cancer_type'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='program',
+            old_name='name',
+            new_name='full_name',
+        ),
+        migrations.AddField(
+            model_name='program',
+            name='display_name',
+            field=models.CharField(max_length=255, null=True),
+        ),
+    ]

idc_collections/models.py

@@ -49,8 +49,10 @@ class Program(models.Model):
     id = models.AutoField(primary_key=True)
     # Eg. TCGA
     short_name = models.CharField(max_length=15, null=False, blank=False)
+    # Preferred name to display in the UI if not the short name
+    display_name = models.CharField(max_length=255, null=True)
     # Eg. The Cancer Genome Atlas
-    name = models.CharField(max_length=255, null=True)
+    full_name = models.CharField(max_length=255, null=True)
     description = models.TextField(null=True, blank=True)
     active = models.BooleanField(default=True)
     objects = ProgramManager()