From b35b48b3ad1af9088ab3f63897bc224a4444abb3 Mon Sep 17 00:00:00 2001 From: Eric Vergnaud Date: Tue, 9 Jul 2024 20:03:52 +0200 Subject: [PATCH] whitelist hail (#2053) ## Changes whitelist hail ### Linked issues Progresses #1901 ### Functionality None ### Tests - [x] manually tested --------- Co-authored-by: Eric Vergnaud --- .../labs/ucx/source_code/known.json | 310 ++++++++++++++++++ 1 file changed, 310 insertions(+) diff --git a/src/databricks/labs/ucx/source_code/known.json b/src/databricks/labs/ucx/source_code/known.json index 1e05a3cd3a..8215e6ff6a 100644 --- a/src/databricks/labs/ucx/source_code/known.json +++ b/src/databricks/labs/ucx/source_code/known.json @@ -4010,6 +4010,316 @@ "h5py": { "h5py": [] }, + "hail": { + "hail": [], + "hail.backend": [], + "hail.backend.backend": [], + "hail.backend.local_backend": [], + "hail.backend.py4j_backend": [ + { + "code": "jvm-access-in-shared-clusters", + "message": "Cannot access Spark Driver JVM on UC Shared Clusters" + } + ], + "hail.backend.service_backend": [], + "hail.backend.spark_backend": [ + { + "code": "jvm-access-in-shared-clusters", + "message": "Cannot access Spark Driver JVM on UC Shared Clusters" + }, + { + "code": "legacy-context-in-shared-clusters", + "message": "sc is not supported on UC Shared Clusters. Rewrite it using spark" + } + ], + "hail.builtin_references": [], + "hail.conftest": [], + "hail.context": [], + "hail.experimental": [], + "hail.experimental.datasets": [], + "hail.experimental.datasets_metadata": [], + "hail.experimental.db": [], + "hail.experimental.export_entries_by_col": [], + "hail.experimental.expressions": [], + "hail.experimental.filtering_allele_frequency": [], + "hail.experimental.full_outer_join_mt": [], + "hail.experimental.function": [], + "hail.experimental.haplotype_freq_em": [], + "hail.experimental.import_gtf": [], + "hail.experimental.interact": [], + "hail.experimental.ld_score_regression": [], + "hail.experimental.ldscore": [], + "hail.experimental.ldscsim": [], + "hail.experimental.lens": [], + "hail.experimental.loop": [], + "hail.experimental.pca": [], + "hail.experimental.phase_by_transmission": [], + "hail.experimental.plots": [], + "hail.experimental.sparse_mt": [], + "hail.experimental.sparse_mt.densify": [], + "hail.experimental.sparse_mt.sparse_split_multi": [], + "hail.experimental.table_ndarray_utils": [], + "hail.experimental.tidyr": [], + "hail.experimental.time": [], + "hail.experimental.write_multiple": [], + "hail.expr": [], + "hail.expr.aggregators": [], + "hail.expr.aggregators.aggregators": [], + "hail.expr.blockmatrix_type": [], + "hail.expr.builders": [], + "hail.expr.expressions": [], + "hail.expr.expressions.base_expression": [], + "hail.expr.expressions.expression_typecheck": [], + "hail.expr.expressions.expression_utils": [], + "hail.expr.expressions.indices": [], + "hail.expr.expressions.typed_expressions": [], + "hail.expr.functions": [], + "hail.expr.matrix_type": [], + "hail.expr.nat": [], + "hail.expr.table_type": [], + "hail.expr.type_parsing": [], + "hail.expr.types": [], + "hail.fs": [], + "hail.fs.hadoop_fs": [], + "hail.genetics": [], + "hail.genetics.allele_type": [], + "hail.genetics.call": [], + "hail.genetics.locus": [], + "hail.genetics.pedigree": [], + "hail.genetics.reference_genome": [], + "hail.ggplot": [], + "hail.ggplot.aes": [], + "hail.ggplot.coord_cartesian": [], + "hail.ggplot.facets": [], + "hail.ggplot.geoms": [], + "hail.ggplot.ggplot": [], + "hail.ggplot.labels": [], + "hail.ggplot.scale": [], + "hail.ggplot.stats": [], + "hail.ggplot.utils": [], + "hail.hail_logging": [], + "hail.ir": [], + "hail.ir.base_ir": [], + "hail.ir.blockmatrix_ir": [], + "hail.ir.blockmatrix_reader": [], + "hail.ir.blockmatrix_writer": [], + "hail.ir.export_type": [], + "hail.ir.ir": [], + "hail.ir.matrix_ir": [], + "hail.ir.matrix_reader": [], + "hail.ir.matrix_writer": [], + "hail.ir.register_aggregators": [], + "hail.ir.register_functions": [], + "hail.ir.renderer": [], + "hail.ir.table_ir": [], + "hail.ir.table_reader": [], + "hail.ir.table_writer": [], + "hail.ir.utils": [], + "hail.linalg": [], + "hail.linalg.blockmatrix": [], + "hail.linalg.utils": [], + "hail.linalg.utils.misc": [], + "hail.matrixtable": [], + "hail.methods": [], + "hail.methods.family_methods": [], + "hail.methods.impex": [ + { + "code": "jvm-access-in-shared-clusters", + "message": "Cannot access Spark Driver JVM on UC Shared Clusters" + } + ], + "hail.methods.import_lines_helpers": [], + "hail.methods.misc": [], + "hail.methods.pca": [], + "hail.methods.qc": [], + "hail.methods.relatedness": [], + "hail.methods.relatedness.identity_by_descent": [], + "hail.methods.relatedness.king": [], + "hail.methods.relatedness.mating_simulation": [], + "hail.methods.relatedness.pc_relate": [], + "hail.methods.statgen": [], + "hail.nd": [], + "hail.nd.nd": [], + "hail.plot": [], + "hail.plot.plots": [], + "hail.stats": [], + "hail.stats.linear_mixed_model": [], + "hail.table": [], + "hail.typecheck": [], + "hail.typecheck.check": [], + "hail.utils": [], + "hail.utils.byte_reader": [], + "hail.utils.deduplicate": [], + "hail.utils.frozendict": [], + "hail.utils.genomic_range_table": [], + "hail.utils.hadoop_utils": [], + "hail.utils.interval": [], + "hail.utils.java": [], + "hail.utils.jsonx": [], + "hail.utils.linkedlist": [], + "hail.utils.misc": [], + "hail.utils.placement_tree": [], + "hail.utils.struct": [], + "hail.utils.tutorial": [], + "hail.vds": [], + "hail.vds.combiner": [], + "hail.vds.combiner.combine": [], + "hail.vds.combiner.variant_dataset_combiner": [], + "hail.vds.functions": [], + "hail.vds.methods": [], + "hail.vds.sample_qc": [], + "hail.vds.variant_dataset": [], + "hailtop": [], + "hailtop.aiocloud": [], + "hailtop.aiocloud.aioaws": [], + "hailtop.aiocloud.aioaws.fs": [], + "hailtop.aiocloud.aioazure": [], + "hailtop.aiocloud.aioazure.client": [], + "hailtop.aiocloud.aioazure.client.arm_client": [], + "hailtop.aiocloud.aioazure.client.base_client": [], + "hailtop.aiocloud.aioazure.client.compute_client": [], + "hailtop.aiocloud.aioazure.client.graph_client": [], + "hailtop.aiocloud.aioazure.client.network_client": [], + "hailtop.aiocloud.aioazure.client.pricing_client": [], + "hailtop.aiocloud.aioazure.client.resources_client": [], + "hailtop.aiocloud.aioazure.credentials": [], + "hailtop.aiocloud.aioazure.fs": [], + "hailtop.aiocloud.aiogoogle": [], + "hailtop.aiocloud.aiogoogle.client": [], + "hailtop.aiocloud.aiogoogle.client.base_client": [], + "hailtop.aiocloud.aiogoogle.client.bigquery_client": [], + "hailtop.aiocloud.aiogoogle.client.billing_client": [], + "hailtop.aiocloud.aiogoogle.client.compute_client": [], + "hailtop.aiocloud.aiogoogle.client.container_client": [], + "hailtop.aiocloud.aiogoogle.client.iam_client": [], + "hailtop.aiocloud.aiogoogle.client.logging_client": [], + "hailtop.aiocloud.aiogoogle.client.metadata_server_client": [], + "hailtop.aiocloud.aiogoogle.client.storage_client": [], + "hailtop.aiocloud.aiogoogle.credentials": [], + "hailtop.aiocloud.aiogoogle.user_config": [], + "hailtop.aiocloud.aioterra": [], + "hailtop.aiocloud.aioterra.azure": [], + "hailtop.aiocloud.aioterra.azure.client": [], + "hailtop.aiocloud.aioterra.azure.client.terra_client": [], + "hailtop.aiocloud.aioterra.azure.fs": [], + "hailtop.aiocloud.common": [], + "hailtop.aiocloud.common.base_client": [], + "hailtop.aiocloud.common.credentials": [], + "hailtop.aiocloud.common.session": [], + "hailtop.aiogoogle": [], + "hailtop.aiotools": [], + "hailtop.aiotools.aio_contextlib": [], + "hailtop.aiotools.copy": [], + "hailtop.aiotools.delete": [], + "hailtop.aiotools.diff": [], + "hailtop.aiotools.fs": [], + "hailtop.aiotools.fs.copier": [], + "hailtop.aiotools.fs.exceptions": [], + "hailtop.aiotools.fs.fs": [], + "hailtop.aiotools.fs.stream": [], + "hailtop.aiotools.local_fs": [], + "hailtop.aiotools.router_fs": [], + "hailtop.aiotools.tasks": [], + "hailtop.aiotools.utils": [], + "hailtop.aiotools.validators": [], + "hailtop.aiotools.weighted_semaphore": [], + "hailtop.auth": [], + "hailtop.auth.auth": [], + "hailtop.auth.flow": [], + "hailtop.auth.sql_config": [], + "hailtop.auth.tokens": [], + "hailtop.batch": [], + "hailtop.batch.backend": [], + "hailtop.batch.batch": [], + "hailtop.batch.batch_pool_executor": [], + "hailtop.batch.conftest": [], + "hailtop.batch.docker": [], + "hailtop.batch.exceptions": [], + "hailtop.batch.globals": [], + "hailtop.batch.hail_genetics_images": [], + "hailtop.batch.job": [], + "hailtop.batch.resource": [], + "hailtop.batch.utils": [], + "hailtop.batch_client": [], + "hailtop.batch_client.aioclient": [], + "hailtop.batch_client.client": [], + "hailtop.batch_client.globals": [], + "hailtop.batch_client.parse": [], + "hailtop.batch_client.types": [], + "hailtop.cleanup_gcr": [], + "hailtop.config": [], + "hailtop.config.deploy_config": [], + "hailtop.config.user_config": [], + "hailtop.config.variables": [], + "hailtop.dictfix": [], + "hailtop.frozendict": [], + "hailtop.fs": [], + "hailtop.fs.fs": [], + "hailtop.fs.fs_utils": [], + "hailtop.fs.router_fs": [], + "hailtop.fs.stat_result": [], + "hailtop.hail_decorator": [], + "hailtop.hail_event_loop": [], + "hailtop.hail_frozenlist": [], + "hailtop.hail_logging": [], + "hailtop.hailctl": [], + "hailtop.hailctl.auth": [], + "hailtop.hailctl.auth.cli": [], + "hailtop.hailctl.auth.create_user": [], + "hailtop.hailctl.auth.delete_user": [], + "hailtop.hailctl.auth.login": [], + "hailtop.hailctl.batch": [], + "hailtop.hailctl.batch.batch_cli_utils": [], + "hailtop.hailctl.batch.billing": [], + "hailtop.hailctl.batch.billing.cli": [], + "hailtop.hailctl.batch.cli": [], + "hailtop.hailctl.batch.initialize": [], + "hailtop.hailctl.batch.list_batches": [], + "hailtop.hailctl.batch.submit": [], + "hailtop.hailctl.batch.utils": [], + "hailtop.hailctl.config": [], + "hailtop.hailctl.config.cli": [], + "hailtop.hailctl.config.config_variables": [], + "hailtop.hailctl.dataproc": [], + "hailtop.hailctl.dataproc.cli": [], + "hailtop.hailctl.dataproc.cluster_config": [], + "hailtop.hailctl.dataproc.connect": [], + "hailtop.hailctl.dataproc.deploy_metadata": [], + "hailtop.hailctl.dataproc.diagnose": [], + "hailtop.hailctl.dataproc.gcloud": [], + "hailtop.hailctl.dataproc.modify": [], + "hailtop.hailctl.dataproc.start": [], + "hailtop.hailctl.dataproc.submit": [], + "hailtop.hailctl.dataproc.utils": [], + "hailtop.hailctl.describe": [], + "hailtop.hailctl.dev": [], + "hailtop.hailctl.dev.ci_client": [], + "hailtop.hailctl.dev.cli": [], + "hailtop.hailctl.dev.config": [], + "hailtop.hailctl.hdinsight": [], + "hailtop.hailctl.hdinsight.cli": [], + "hailtop.hailctl.hdinsight.start": [], + "hailtop.hailctl.hdinsight.submit": [], + "hailtop.httpx": [], + "hailtop.humanizex": [], + "hailtop.test_utils": [], + "hailtop.timex": [], + "hailtop.tls": [], + "hailtop.utils": [], + "hailtop.utils.filesize": [], + "hailtop.utils.gcs_requester_pays": [], + "hailtop.utils.process": [], + "hailtop.utils.rate_limiter": [], + "hailtop.utils.rates": [], + "hailtop.utils.rich_progress_bar": [], + "hailtop.utils.serialization": [], + "hailtop.utils.time": [], + "hailtop.utils.utils": [], + "hailtop.utils.validate": [], + "hailtop.utils.validate.validate": [], + "hailtop.uvloopx": [], + "hailtop.yamlx": [] + }, "html5lib": { "html5lib": [] },