Merge branch 'dev' of github.com:broadinstitute/seqr-loading-pipelines into dev

Author: bpblanken

v03_pipeline/lib/tasks/base/base_update_lookup_table.py

@@ -46,5 +46,6 @@ def initialize_table(self) -> hl.Table:
                         remap_pedigree_hash=hl.tint32,
                     ),
                 ),
+                migrations=hl.empty_array(hl.tstr),
             ),
         )

v03_pipeline/lib/tasks/update_lookup_table.py

@@ -115,5 +115,6 @@ def update_table(self, ht: hl.Table) -> hl.Table:
                         ),
                     ),
                 ),
+                migrations=ht.migrations,
             )
         return ht

v03_pipeline/lib/tasks/update_lookup_table_test.py

@@ -51,6 +51,7 @@ def test_skip_update_lookup_table_task(self) -> None:
                             ),
                         ),
                     },
+                    migrations=[],
                 ),
             ],
         )
@@ -89,6 +90,7 @@ def test_update_lookup_table_task(self) -> None:
                             ),
                         ),
                     },
+                    migrations=[],
                 ),
             ],
         )

v03_pipeline/lib/tasks/update_lookup_table_with_deleted_families_test.py

@@ -33,6 +33,7 @@ def test_delete_project_empty_table(
                     project_sample_types=[],
                     project_families={},
                     updates=set(),
+                    migrations=[],
                 ),
             ],
         )
@@ -137,6 +138,7 @@ def test_delete_project(
                         remap_pedigree_hash=123,
                     ),
                 },
+                migrations=hl.empty_array(hl.tstr),
             ),
         )
         worker = luigi.worker.Worker()
@@ -172,6 +174,7 @@ def test_delete_project(
                             remap_pedigree_hash=123,
                         ),
                     },
+                    migrations=[],
                 ),
             ],
         )

v03_pipeline/lib/tasks/update_lookup_table_with_deleted_project_test.py

@@ -32,6 +32,7 @@ def test_delete_project_empty_table(
                     project_sample_types=[],
                     project_families={},
                     updates=set(),
+                    migrations=[],
                 ),
             ],
         )
@@ -136,6 +137,7 @@ def test_delete_project(
                         remap_pedigree_hash=123,
                     ),
                 },
+                migrations=hl.empty_array(hl.tstr),
             ),
         )
         worker = luigi.worker.Worker()
@@ -162,6 +164,7 @@ def test_delete_project(
                             remap_pedigree_hash=123,
                         ),
                     },
+                    migrations=[],
                 ),
             ],
         )

v03_pipeline/lib/tasks/update_variant_annotations_table_with_deleted_project_test.py

@@ -107,6 +107,7 @@ def setUp(self) -> None:
                         remap_pedigree_hash=123,
                     ),
                 },
+                migrations=hl.empty_array(hl.tstr),
             ),
         )
         ht.write(