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Benb/delete unreleased features (#1147)
* delete hail search migration code * delete delete files
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v03_pipeline/lib/migration/__init__.py

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v03_pipeline/lib/migration/base_migration.py

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v03_pipeline/lib/migration/misc.py

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v03_pipeline/lib/migration/misc_test.py

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v03_pipeline/lib/tasks/__init__.py

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@@ -1,39 +1,14 @@
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from v03_pipeline.lib.tasks.clickhouse_migration.migrate_all_projects_to_clickhouse import (
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MigrateAllProjectsToClickHouseTask,
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)
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from v03_pipeline.lib.tasks.delete_family_table import DeleteFamilyTableTask
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from v03_pipeline.lib.tasks.delete_family_tables import DeleteFamilyTablesTask
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from v03_pipeline.lib.tasks.delete_project_family_tables import (
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DeleteProjectFamilyTablesTask,
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)
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from v03_pipeline.lib.tasks.delete_project_tables import DeleteProjectTablesTask
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from v03_pipeline.lib.tasks.migrate_all_lookup_tables import MigrateAllLookupTablesTask
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from v03_pipeline.lib.tasks.migrate_all_variant_annotations_tables import (
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MigrateAllVariantAnnotationsTablesTask,
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)
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from v03_pipeline.lib.tasks.reference_data.update_variant_annotations_table_with_updated_reference_dataset import (
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UpdateVariantAnnotationsTableWithUpdatedReferenceDataset,
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)
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from v03_pipeline.lib.tasks.run_pipeline import RunPipelineTask
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from v03_pipeline.lib.tasks.update_lookup_table import (
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UpdateLookupTableTask,
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)
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from v03_pipeline.lib.tasks.update_lookup_table_with_deleted_families import (
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UpdateLookupTableWithDeletedFamiliesTask,
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)
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from v03_pipeline.lib.tasks.update_lookup_table_with_deleted_project import (
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UpdateLookupTableWithDeletedProjectTask,
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)
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from v03_pipeline.lib.tasks.update_project_table import UpdateProjectTableTask
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from v03_pipeline.lib.tasks.update_project_tables_with_deleted_families import (
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UpdateProjectTablesWithDeletedFamiliesTask,
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)
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from v03_pipeline.lib.tasks.update_variant_annotations_table_with_deleted_families import (
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UpdateVariantAnnotationsTableWithDeletedFamiliesTask,
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)
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from v03_pipeline.lib.tasks.update_variant_annotations_table_with_deleted_project import (
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UpdateVariantAnnotationsTableWithDeletedProjectTask,
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)
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from v03_pipeline.lib.tasks.update_variant_annotations_table_with_new_samples import (
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UpdateVariantAnnotationsTableWithNewSamplesTask,
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)
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from v03_pipeline.lib.tasks.write_success_file import WriteSuccessFileTask
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__all__ = [
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'DeleteFamilyTableTask',
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'DeleteFamilyTablesTask',
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'DeleteProjectFamilyTablesTask',
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'DeleteProjectTablesTask',
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'MigrateAllLookupTablesTask',
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'MigrateAllProjectsToClickHouseTask',
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'MigrateAllVariantAnnotationsTablesTask',
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'RunPipelineTask',
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'UpdateLookupTableTask',
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'UpdateLookupTableWithDeletedFamiliesTask',
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'UpdateLookupTableWithDeletedProjectTask',
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'UpdateProjectTableTask',
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'UpdateProjectTablesWithDeletedFamiliesTask',
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'UpdateVariantAnnotationsTableWithDeletedFamiliesTask',
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'UpdateVariantAnnotationsTableWithDeletedProjectTask',
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'UpdateVariantAnnotationsTableWithNewSamplesTask',
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'UpdateVariantAnnotationsTableWithUpdatedReferenceDataset',
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'WriteMetadataForRunTask',

v03_pipeline/lib/tasks/base/base_delete_table.py

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v03_pipeline/lib/tasks/base/base_migrate.py

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v03_pipeline/lib/tasks/delete_family_table.py

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v03_pipeline/lib/tasks/delete_family_table_test.py

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v03_pipeline/lib/tasks/delete_family_tables.py

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