Index variantcallingactivity entities (#4617)

DataBiosphere · Dec 7, 2022 · b018e05 · b018e05
1 parent f0e3c70
commit b018e05
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Showing 2 changed files with 23 additions and 1 deletion.
diff --git a/src/azul/plugins/metadata/anvil/indexer/transform.py b/src/azul/plugins/metadata/anvil/indexer/transform.py
@@ -360,7 +360,8 @@ def _only_dataset(self) -> MutableJSON:
         'activity',
         'alignmentactivity',
         'assayactivity',
-        'sequencingactivity'
+        'sequencingactivity',
+        'variantcallingactivity'
     }
 
 

diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py
@@ -329,6 +329,15 @@ def _upstream_from_files(self,
                   FROM file AS f
                   JOIN {backtick(self._full_table_name(source, 'sequencingactivity'))} AS sqa
                     ON f.file_id IN UNNEST(sqa.generated_file_id)
+                UNION ALL SELECT
+                    f.file_id,
+                    'variantcallingactivity',
+                    vca.variantcallingactivity_id,
+                    vca.used_file_id,
+                    []
+                  FROM file AS f
+                  JOIN {backtick(self._full_table_name(source, 'variantcallingactivity'))} AS vca
+                    ON f.file_id IN UNNEST(vca.generated_file_id)
                 UNION ALL SELECT
                     f.file_id,
                     'activity',
@@ -419,6 +428,12 @@ def _downstream_from_files(self,
                         ala.used_file_id,
                         ala.generated_file_id
                     FROM {backtick(self._full_table_name(source, 'alignmentactivity'))} AS ala
+                    UNION ALL SELECT
+                        vca.variantcallingactivity_id,
+                        'variantcallingactivity',
+                        vca.used_file_id,
+                        vca.generated_file_id
+                    FROM {backtick(self._full_table_name(source, 'variantcallingactivity'))} AS vca
                     UNION ALL SELECT
                         a.activity_id,
                         'activity',
@@ -555,6 +570,12 @@ def convert_column(value):
             'activity_type',
             'assay_type',
             'data_modality',
+        },
+        'variantcallingactivity': {
+            'variatncallingactivity_id',
+            'activity_type',
+            'reference_assembly',
+            'data_modality'
         }
     }