finding a few more locs

Author: bpblanken

v03_pipeline/lib/tasks/__init__.py

@@ -1,6 +1,6 @@
 from v03_pipeline.lib.tasks.update_project_table import UpdateProjectTableTask
-from v03_pipeline.lib.tasks.update_sample_lookup_table import (
-    UpdateSampleLookupTableTask,
+from v03_pipeline.lib.tasks.update_lookup_table import (
+    UpdateLookupTableTask,
 )
 from v03_pipeline.lib.tasks.update_variant_annotations_table_with_new_samples import (
     UpdateVariantAnnotationsTableWithNewSamplesTask,
@@ -12,7 +12,7 @@
 
 __all__ = [
     'UpdateProjectTableTask',
-    'UpdateSampleLookupTableTask',
+    'UpdateLookupTableTask',
     'UpdateVariantAnnotationsTableWithNewSamplesTask',
     'WriteMetadataForRunTask',
     'WriteProjectFamilyTablesTask',

v03_pipeline/lib/tasks/update_lookup_table_test.py

@@ -2,8 +2,8 @@
 import luigi.worker
 
 from v03_pipeline.lib.model import DatasetType, ReferenceGenome, SampleType
-from v03_pipeline.lib.tasks.update_sample_lookup_table import (
-    UpdateSampleLookupTableTask,
+from v03_pipeline.lib.tasks.update_lookup_table import (
+    UpdateLookupTableTask,
 )
 from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
 
@@ -15,7 +15,7 @@
 class UpdateSampleLookupTableTest(MockedDatarootTestCase):
     def test_update_sample_lookup_table_task(self) -> None:
         worker = luigi.worker.Worker()
-        uslt_task = UpdateSampleLookupTableTask(
+        uslt_task = UpdateLookupTableTask(
             reference_genome=ReferenceGenome.GRCh38,
             dataset_type=DatasetType.SNV_INDEL,
             sample_type=SampleType.WGS,
@@ -30,6 +30,7 @@ def test_update_sample_lookup_table_task(self) -> None:
         self.assertTrue(uslt_task.output().exists())
         self.assertTrue(uslt_task.complete())
         ht = hl.read_table(uslt_task.output().path)
+        print(ht.globals.collect())
         self.assertEqual(
             ht.globals.collect(),
             [

v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples.py

@@ -19,8 +19,8 @@
 from v03_pipeline.lib.tasks.reference_data.update_variant_annotations_table_with_updated_reference_dataset import (
     UpdateVariantAnnotationsTableWithUpdatedReferenceDataset,
 )
-from v03_pipeline.lib.tasks.update_sample_lookup_table import (
-    UpdateSampleLookupTableTask,
+from v03_pipeline.lib.tasks.update_lookup_table import (
+    UpdateLookupTableTask,
 )
 from v03_pipeline.lib.tasks.write_remapped_and_subsetted_callset import (
     WriteRemappedAndSubsettedCallsetTask,
@@ -85,11 +85,11 @@ def requires(self) -> list[luigi.Task]:
             ]
         else:
             upstream_table_tasks: list[luigi.Task] = []
-        if self.dataset_type.has_sample_lookup_table:
-            # NB: the sample lookup table task has remapped and subsetted callset tasks as dependencies.
+        if self.dataset_type.has_lookup_table:
+            # NB: the lookup table task has remapped and subsetted callset tasks as dependencies.
             upstream_table_tasks.extend(
                 [
-                    UpdateSampleLookupTableTask(
+                    UpdateLookupTableTask(
                         self.reference_genome,
                         self.dataset_type,
                         self.sample_type,
@@ -241,13 +241,13 @@ def update_table(self, ht: hl.Table) -> hl.Table:
             new_variants_ht = new_variants_ht.join(rdc_ht, 'left')
 
         # 4) Union with the existing variant annotations table
-        # and annotate with the sample lookup table.
+        # and annotate with the lookup table.
         ht = ht.union(new_variants_ht, unify=True)
-        if self.dataset_type.has_sample_lookup_table:
+        if self.dataset_type.has_lookup_table:
             ht = ht.annotate(
                 **get_fields(
                     ht,
-                    self.dataset_type.sample_lookup_table_annotation_fns,
+                    self.dataset_type.lookup_table_annotation_fns,
                     **self.rdc_annotation_dependencies,
                     **self.other_annotation_dependencies,
                     **self.param_kwargs,