From b4615fd47790c203b4c119744984b1e42750fef4 Mon Sep 17 00:00:00 2001 From: Szymon Szyszkowski Date: Wed, 31 Jul 2024 10:25:48 +0100 Subject: [PATCH] feat: pipeline setup --- .env | 5 + Makefile | 19 +- .../airflow-dev}/.dockerignore | 0 Dockerfile => docker/airflow-dev/Dockerfile | 0 docker/genetics_etl/.dockerignore | 2 + {images => docker}/genetics_etl/Dockerfile | 0 docker/genetics_etl/README.md | 3 + docs/gwas_catalog_dag.svg | 242 +++++++ images/genetics_etl/README.md | 3 - poetry.lock | 638 +++++++++--------- pyproject.toml | 7 +- src/ot_orchestration/cli/__init__.py | 4 +- src/ot_orchestration/cli/process_in_batch.py | 138 ++-- src/ot_orchestration/dags/branching.py | 80 --- src/ot_orchestration/types.py | 8 +- src/ot_orchestration/utils/__init__.py | 11 +- src/ot_orchestration/utils/gcs_path.py | 179 ----- src/ot_orchestration/utils/manifest.py | 82 ++- src/ot_orchestration/utils/path.py | 343 ++++++++++ src/ot_orchestration/utils/qrcp.py | 14 +- .../gwas_catalog_batch_job/SSF_GCST001.h.tsv | Bin 0 -> 5503 bytes .../data/gwas_catalog_batch_job/manifest.json | 14 + tests/test_gwas_catalog_batch_job.py | 89 +++ 23 files changed, 1199 insertions(+), 682 deletions(-) rename {images/genetics_etl => docker/airflow-dev}/.dockerignore (100%) rename Dockerfile => docker/airflow-dev/Dockerfile (100%) create mode 100644 docker/genetics_etl/.dockerignore rename {images => docker}/genetics_etl/Dockerfile (100%) create mode 100644 docker/genetics_etl/README.md create mode 100644 docs/gwas_catalog_dag.svg delete mode 100644 images/genetics_etl/README.md delete mode 100644 src/ot_orchestration/dags/branching.py delete mode 100644 src/ot_orchestration/utils/gcs_path.py create mode 100644 src/ot_orchestration/utils/path.py create mode 100644 tests/data/gwas_catalog_batch_job/SSF_GCST001.h.tsv create mode 100644 tests/data/gwas_catalog_batch_job/manifest.json create mode 100644 tests/test_gwas_catalog_batch_job.py diff --git a/.env b/.env index 2bcd824..2a209a3 100644 --- a/.env +++ b/.env @@ -4,3 +4,8 @@ GOOGLE_DOCKER_CREDENTIALS_PATH=/.config/gcloud GOOGLE_APPLICATION_CREDENTIALS=/.config/gcloud/service_account_credentials.json AIRFLOW_CONN_GOOGLE_CLOUD_DEFAULT='google-cloud-platform://?extra__google_cloud_platform__key_path=/.config/gcloud/service_account_credentials.json' GCP_PROJECT_ID=open-targets-genetics-dev +AIRFLOW_UID=503 +AIRFLOW__CORE__MAX_MAP_LENGTH=50000 +AIRFLOW__WEBSERVER__EXPOSE_CONFIG=True +AIRFLOW__CORE__PARALLELISM=500 +AIRFLOW__CORE__MAX_ACTIVE_TASKS_PER_DAG=500 diff --git a/Makefile b/Makefile index 52d40ad..a85672a 100644 --- a/Makefile +++ b/Makefile @@ -6,6 +6,7 @@ APP_NAME ?= $$(cat pyproject.toml| grep -m 1 "name" | cut -d" " -f3 | sed 's/"/ VERSION := $$(grep '^version' pyproject.toml | sed 's%version = "\(.*\)"%\1%') BUCKET_NAME=gs://genetics_etl_python_playground/initialisation/${VERSION}/ DOCKER_IMAGE := "Orchestration-Airflow" +TEST_COVERAGE := 40 .PHONY: $(shell sed -n -e '/^$$/ { n ; /^[^ .\#][^ ]*:/ { s/:.*$$// ; p ; } ; }' $(MAKEFILE_LIST)) .DEFAULT_GOAL := help @@ -29,17 +30,18 @@ format: ## run formatting @poetry run python -m ruff check --fix src/$(APP_NAME) tests test: ## run unit tests - @poetry run python -m pytest tests/*.py + @poetry run coverage run -m pytest tests/*.py -s -p no:warnings + @poetry run coverage report --omit="tests/*" --fail-under=$(TEST_COVERAGE) check: format check-types test ## run all checks generate-requirements: ## generate requirements.txt from poetry dependencies to install in the docker image - poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt + poetry export --without-hashes --with dev --format=requirements.txt > docker/airflow-dev/requirements.txt build-airflow-image: generate-requirements ## build local airflow image for the infrastructure - docker build . \ + docker build docker/airflow-dev \ --tag extending_airflow:latest \ - -f Dockerfile \ + -f docker/airflow-dev/Dockerfile \ --no-cache build-whl: ## build ot-orchestration package wheel @@ -53,13 +55,14 @@ build-genetics-etl-image: build-whl ## build local genetics-etl image for the te --build-arg DIST=$(shell find dist -name 'ot_orchestration*') test-gwas-catalog-batch-script: ## test harmonisation task - # mkdir -p test_batch - # gsutil -m rsync -r gs://ot_orchestration/tests/gwas_catalog/basic_test/GCST004600 test_batch + mkdir -p test_batch + gsutil -m rsync -r gs://ot_orchestration/tests/gwas_catalog/basic_test/GCST004600 test_batch docker run \ -v $(HOME)/.config/gcloud:/root/.config/gcloud \ -e MANIFEST_PATH=gs://ot_orchestration/tests/gwas_catalog/basic_test/GCST004600/manifest.json \ -e GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/service_account_credentials.json \ -ti \ --rm \ - genetics_etl:test - # gsutil -m rsync -r test_batch gs://ot_orchestration/tests/gwas_catalog/basic_test/GCST004600 + genetics_etl:test \ + -c "ot gwas-catalog-process-in-batch" + gsutil -m rsync -r test_batch gs://ot_orchestration/tests/gwas_catalog/basic_test/GCST004600 diff --git a/images/genetics_etl/.dockerignore b/docker/airflow-dev/.dockerignore similarity index 100% rename from images/genetics_etl/.dockerignore rename to docker/airflow-dev/.dockerignore diff --git a/Dockerfile b/docker/airflow-dev/Dockerfile similarity index 100% rename from Dockerfile rename to docker/airflow-dev/Dockerfile diff --git a/docker/genetics_etl/.dockerignore b/docker/genetics_etl/.dockerignore new file mode 100644 index 0000000..937932b --- /dev/null +++ b/docker/genetics_etl/.dockerignore @@ -0,0 +1,2 @@ +# Ignore generated credentials from google-github-actions/auth +gha-creds-*.json diff --git a/images/genetics_etl/Dockerfile b/docker/genetics_etl/Dockerfile similarity index 100% rename from images/genetics_etl/Dockerfile rename to docker/genetics_etl/Dockerfile diff --git a/docker/genetics_etl/README.md b/docker/genetics_etl/README.md new file mode 100644 index 0000000..c384ba7 --- /dev/null +++ b/docker/genetics_etl/README.md @@ -0,0 +1,3 @@ +# genetics_etl docker image + +This is the genetics_etl docker image that is currently used by the GWAS_Catalog_dag batch processing. The image is based on gentropy image from [gentropy repository](https://github.com/opentargets/gentropy) diff --git a/docs/gwas_catalog_dag.svg b/docs/gwas_catalog_dag.svg new file mode 100644 index 0000000..8d37c9f --- /dev/null +++ b/docs/gwas_catalog_dag.svg @@ -0,0 +1,242 @@ + + + + + + +GWAS_Catalog_dag + +GWAS_Catalog_dag + +cluster_gwas_catalog_batch_processing + +gwas_catalog_batch_processing + + +cluster_manifest_preparation + +manifest_preparation + + + +gwas_catalog_batch_processing.upstream_join_id + + + + +gwas_catalog_batch_processing.get_manifests_from_preparation + +get_manifests_from_preparation + + + +gwas_catalog_batch_processing.upstream_join_id->gwas_catalog_batch_processing.get_manifests_from_preparation + + + + + +gwas_catalog_batch_processing.batch_job + +batch_job + + + +gwas_catalog_batch_processing.get_manifests_from_preparation->gwas_catalog_batch_processing.batch_job + + + + + +manifest_preparation.downstream_join_id + + + + +manifest_preparation.downstream_join_id->gwas_catalog_batch_processing.upstream_join_id + + + + + +manifest_preparation.amend_curation_metadata + +amend_curation_metadata + + + +manifest_preparation.save_manifests + +save_manifests + + + +manifest_preparation.amend_curation_metadata->manifest_preparation.save_manifests + + +Amending curation metadata to the generated manifests + + + +manifest_preparation.choose_manifest_paths + +choose_manifest_paths + + + +manifest_preparation.save_config + +save_config + + + +manifest_preparation.choose_manifest_paths->manifest_preparation.save_config + + +Dumping configuration to GCS + + + +manifest_preparation.collect_sumstats_and_generate_new_manifests + +collect_sumstats_and_generate_new_manifests + + + +manifest_preparation.collect_sumstats_and_generate_new_manifests->manifest_preparation.amend_curation_metadata + + +Generating manifests + + + +manifest_preparation.exit_when_no_new_sumstats + +exit_when_no_new_sumstats + + + +manifest_preparation.exit_when_no_new_sumstats->manifest_preparation.collect_sumstats_and_generate_new_manifests + + +Getting list of new sumstats + + + +manifest_preparation.get_all_sumstat_paths + +get_all_sumstat_paths + + + +manifest_preparation.get_all_sumstat_paths->manifest_preparation.collect_sumstats_and_generate_new_manifests + + +Getting list of all sumstats + + + +manifest_preparation.get_execution_mode + +get_execution_mode + + + +manifest_preparation.get_execution_mode->manifest_preparation.get_all_sumstat_paths + + +Forcing rerun on all sumstats + + + +manifest_preparation.get_new_sumstat_paths + +get_new_sumstat_paths + + + +manifest_preparation.get_execution_mode->manifest_preparation.get_new_sumstat_paths + + +Running only on new sumstats + + + +manifest_preparation.read_manifests + +read_manifests + + + +manifest_preparation.get_execution_mode->manifest_preparation.read_manifests + + +Resume from existing manifests + + + +manifest_preparation.get_new_sumstat_paths->manifest_preparation.exit_when_no_new_sumstats + + + + + +manifest_preparation.list_existing_manifests + +list_existing_manifests + + + +manifest_preparation.list_existing_manifests->manifest_preparation.get_new_sumstat_paths + + + + + +manifest_preparation.list_existing_manifests->manifest_preparation.read_manifests + + + + + +manifest_preparation.list_raw_harmonised + +list_raw_harmonised + + + +manifest_preparation.list_raw_harmonised->manifest_preparation.get_all_sumstat_paths + + + + + +manifest_preparation.list_raw_harmonised->manifest_preparation.get_new_sumstat_paths + + + + + +manifest_preparation.read_manifests->manifest_preparation.choose_manifest_paths + + +Filtering manifests by curation status + + + +manifest_preparation.save_config->manifest_preparation.downstream_join_id + + + + + +manifest_preparation.save_manifests->manifest_preparation.choose_manifest_paths + + +Dumping manifests to GCS + + + diff --git a/images/genetics_etl/README.md b/images/genetics_etl/README.md deleted file mode 100644 index 1fce809..0000000 --- a/images/genetics_etl/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# genetics_etl docker image - -This is the genetics_etl docker image that is currently used by the Harmonisation DAG. The base gentropy image from diff --git a/poetry.lock b/poetry.lock index 5f8dfb0..aa1f4b6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1623,13 +1623,13 @@ dev = ["polib"] [[package]] name = "croniter" -version = "2.0.7" +version = "3.0.3" description = "croniter provides iteration for datetime object with cron like format" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.6" files = [ - {file = "croniter-2.0.7-py2.py3-none-any.whl", hash = "sha256:f15e80828d23920c4bb7f4d9340b932c9dcabecafc7775703c8b36d1253ed526"}, - {file = "croniter-2.0.7.tar.gz", hash = "sha256:1041b912b4b1e03751a0993531becf77851ae6e8b334c9c76ffeffb8f055f53f"}, + {file = "croniter-3.0.3-py2.py3-none-any.whl", hash = "sha256:b3bd11f270dc54ccd1f2397b813436015a86d30ffc5a7a9438eec1ed916f2101"}, + {file = "croniter-3.0.3.tar.gz", hash = "sha256:34117ec1741f10a7bd0ec3ad7d8f0eb8fa457a2feb9be32e6a2250e158957668"}, ] [package.dependencies] @@ -2525,13 +2525,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] [[package]] name = "google-api-python-client" -version = "2.137.0" +version = "2.138.0" description = "Google API Client Library for Python" optional = false python-versions = ">=3.7" files = [ - {file = "google_api_python_client-2.137.0-py2.py3-none-any.whl", hash = "sha256:a8b5c5724885e5be9f5368739aa0ccf416627da4ebd914b410a090c18f84d692"}, - {file = "google_api_python_client-2.137.0.tar.gz", hash = "sha256:e739cb74aac8258b1886cb853b0722d47c81fe07ad649d7f2206f06530513c04"}, + {file = "google_api_python_client-2.138.0-py2.py3-none-any.whl", hash = "sha256:1dd279124e4e77cbda4769ffb4abe7e7c32528ef1e18739320fef2a07b750764"}, + {file = "google_api_python_client-2.138.0.tar.gz", hash = "sha256:31080fbf0e64687876135cc23d1bec1ca3b80d7702177dd17b04131ea889eb70"}, ] [package.dependencies] @@ -2599,13 +2599,13 @@ tool = ["click (>=6.0.0)"] [[package]] name = "google-cloud-aiplatform" -version = "1.59.0" +version = "1.60.0" description = "Vertex AI API client library" optional = false python-versions = ">=3.8" files = [ - {file = "google-cloud-aiplatform-1.59.0.tar.gz", hash = "sha256:2bebb59c0ba3e3b4b568305418ca1b021977988adbee8691a5bed09b037e7e63"}, - {file = "google_cloud_aiplatform-1.59.0-py2.py3-none-any.whl", hash = "sha256:549e6eb1844b0f853043309138ebe2db00de4bbd8197b3bde26804ac163ef52a"}, + {file = "google-cloud-aiplatform-1.60.0.tar.gz", hash = "sha256:782c7f1ec0e77a7c7daabef3b65bfd506ed2b4b1dc2186753c43cd6faf8dd04e"}, + {file = "google_cloud_aiplatform-1.60.0-py2.py3-none-any.whl", hash = "sha256:5f14159c9575f4b46335027e3ceb8fa57bd5eaa76a07f858105b8c6c034ec0d6"}, ] [package.dependencies] @@ -2627,8 +2627,8 @@ cloud-profiler = ["tensorboard-plugin-profile (>=2.4.0,<3.0.0dev)", "tensorflow datasets = ["pyarrow (>=10.0.1)", "pyarrow (>=14.0.0)", "pyarrow (>=3.0.0,<8.0dev)"] endpoint = ["requests (>=2.28.1)"] full = ["cloudpickle (<3.0)", "docker (>=5.0.3)", "explainable-ai-sdk (>=1.0.0)", "fastapi (>=0.71.0,<=0.109.1)", "google-cloud-bigquery", "google-cloud-bigquery-storage", "google-cloud-logging (<4.0)", "google-vizier (>=0.1.6)", "httpx (>=0.23.0,<0.25.0)", "immutabledict", "lit-nlp (==0.4.0)", "mlflow (>=1.27.0,<=2.1.1)", "numpy (>=1.15.0)", "pandas (>=1.0.0)", "pandas (>=1.0.0,<2.2.0)", "pyarrow (>=10.0.1)", "pyarrow (>=14.0.0)", "pyarrow (>=3.0.0,<8.0dev)", "pyarrow (>=6.0.1)", "pydantic (<2)", "pyyaml (>=5.3.1,<7)", "ray[default] (>=2.4,<2.5.dev0 || >2.9.0,!=2.9.1,!=2.9.2,<=2.9.3)", "ray[default] (>=2.5,<=2.9.3)", "requests (>=2.28.1)", "setuptools (<70.0.0)", "starlette (>=0.17.1)", "tensorboard-plugin-profile (>=2.4.0,<3.0.0dev)", "tensorflow (>=2.3.0,<3.0.0dev)", "tensorflow (>=2.3.0,<3.0.0dev)", "tensorflow (>=2.4.0,<3.0.0dev)", "tqdm (>=4.23.0)", "urllib3 (>=1.21.1,<1.27)", "uvicorn[standard] (>=0.16.0)", "werkzeug (>=2.0.0,<2.1.0dev)"] -langchain = ["langchain (>=0.1.16,<0.3)", "langchain-core (<0.2)", "langchain-google-vertexai (<2)", "openinference-instrumentation-langchain (>=0.1.19,<0.2)", "tenacity (<=8.3)"] -langchain-testing = ["absl-py", "cloudpickle (>=3.0,<4.0)", "langchain (>=0.1.16,<0.3)", "langchain-core (<0.2)", "langchain-google-vertexai (<2)", "openinference-instrumentation-langchain (>=0.1.19,<0.2)", "opentelemetry-exporter-gcp-trace (<2)", "opentelemetry-sdk (<2)", "pydantic (>=2.6.3,<3)", "pytest-xdist", "tenacity (<=8.3)"] +langchain = ["langchain (>=0.1.16,<0.3)", "langchain-core (<0.3)", "langchain-google-vertexai (<2)", "openinference-instrumentation-langchain (>=0.1.19,<0.2)", "tenacity (<=8.3)"] +langchain-testing = ["absl-py", "cloudpickle (>=3.0,<4.0)", "google-cloud-trace (<2)", "langchain (>=0.1.16,<0.3)", "langchain-core (<0.3)", "langchain-google-vertexai (<2)", "openinference-instrumentation-langchain (>=0.1.19,<0.2)", "opentelemetry-exporter-gcp-trace (<2)", "opentelemetry-sdk (<2)", "pydantic (>=2.6.3,<3)", "pytest-xdist", "tenacity (<=8.3)"] lit = ["explainable-ai-sdk (>=1.0.0)", "lit-nlp (==0.4.0)", "pandas (>=1.0.0)", "tensorflow (>=2.3.0,<3.0.0dev)"] metadata = ["numpy (>=1.15.0)", "pandas (>=1.0.0)"] pipelines = ["pyyaml (>=5.3.1,<7)"] @@ -2638,7 +2638,7 @@ private-endpoints = ["requests (>=2.28.1)", "urllib3 (>=1.21.1,<1.27)"] rapid-evaluation = ["pandas (>=1.0.0,<2.2.0)", "tqdm (>=4.23.0)"] ray = ["google-cloud-bigquery", "google-cloud-bigquery-storage", "immutabledict", "pandas (>=1.0.0,<2.2.0)", "pyarrow (>=6.0.1)", "pydantic (<2)", "ray[default] (>=2.4,<2.5.dev0 || >2.9.0,!=2.9.1,!=2.9.2,<=2.9.3)", "ray[default] (>=2.5,<=2.9.3)", "setuptools (<70.0.0)"] ray-testing = ["google-cloud-bigquery", "google-cloud-bigquery-storage", "immutabledict", "pandas (>=1.0.0,<2.2.0)", "pyarrow (>=6.0.1)", "pydantic (<2)", "pytest-xdist", "ray[default] (>=2.4,<2.5.dev0 || >2.9.0,!=2.9.1,!=2.9.2,<=2.9.3)", "ray[default] (>=2.5,<=2.9.3)", "ray[train] (==2.9.3)", "scikit-learn", "setuptools (<70.0.0)", "tensorflow", "torch (>=2.0.0,<2.1.0)", "xgboost", "xgboost-ray"] -reasoningengine = ["cloudpickle (>=3.0,<4.0)", "opentelemetry-exporter-gcp-trace (<2)", "opentelemetry-sdk (<2)", "pydantic (>=2.6.3,<3)"] +reasoningengine = ["cloudpickle (>=3.0,<4.0)", "google-cloud-trace (<2)", "opentelemetry-exporter-gcp-trace (<2)", "opentelemetry-sdk (<2)", "pydantic (>=2.6.3,<3)"] tensorboard = ["tensorboard-plugin-profile (>=2.4.0,<3.0.0dev)", "tensorflow (>=2.3.0,<3.0.0dev)", "tensorflow (>=2.4.0,<3.0.0dev)", "werkzeug (>=2.0.0,<2.1.0dev)"] testing = ["bigframes", "cloudpickle (<3.0)", "docker (>=5.0.3)", "explainable-ai-sdk (>=1.0.0)", "fastapi (>=0.71.0,<=0.109.1)", "google-api-core (>=2.11,<3.0.0)", "google-cloud-bigquery", "google-cloud-bigquery-storage", "google-cloud-logging (<4.0)", "google-vizier (>=0.1.6)", "grpcio-testing", "httpx (>=0.23.0,<0.25.0)", "immutabledict", "ipython", "kfp (>=2.6.0,<3.0.0)", "lit-nlp (==0.4.0)", "mlflow (>=1.27.0,<=2.1.1)", "nltk", "numpy (>=1.15.0)", "pandas (>=1.0.0)", "pandas (>=1.0.0,<2.2.0)", "pyarrow (>=10.0.1)", "pyarrow (>=14.0.0)", "pyarrow 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Logging API client library" optional = false python-versions = ">=3.7" files = [ - {file = "google-cloud-logging-3.10.0.tar.gz", hash = "sha256:d93d347351240ddb14cfe201987a2d32cf9d7f478b8b2fabed3015b425b3274f"}, - {file = "google_cloud_logging-3.10.0-py2.py3-none-any.whl", hash = "sha256:132192beb45731130a2ffbcd4b2b5cbd87370e7dcfa7397ae4002154f542bd20"}, + {file = "google_cloud_logging-3.11.0-py2.py3-none-any.whl", hash = "sha256:ec79ed3ea04e794d590a41eb35bd0d875fb6733048aeeac8323701733f6d45f5"}, + {file = "google_cloud_logging-3.11.0.tar.gz", hash = "sha256:e53205510652df5794f04176ea395c6cc1862a8e8d2bd0678370a2defeb74bff"}, ] [package.dependencies] @@ -3033,6 +3033,7 @@ google-cloud-appengine-logging = ">=0.1.0,<2.0.0dev" google-cloud-audit-log = ">=0.1.0,<1.0.0dev" google-cloud-core = ">=2.0.0,<3.0.0dev" grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev" +opentelemetry-api = ">=1.0.0" proto-plus = ">=1.22.0,<2.0.0dev" protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || 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(>=1.0.1,!=1.1.2)"] mssql = ["pyodbc"] -mssql-pymssql = ["pymssql"] -mssql-pyodbc = ["pyodbc"] +mssql-pymssql = ["pymssql", "pymssql"] +mssql-pyodbc = ["pyodbc", "pyodbc"] mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"] mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"] -mysql-connector = ["mysql-connector-python"] +mysql-connector = ["mysql-connector-python", "mysql-connector-python"] oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] postgresql = ["psycopg2 (>=2.7)"] -postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] -postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"] +postgresql-asyncpg = ["asyncpg", "asyncpg", "greenlet (!=0.4.17)", "greenlet (!=0.4.17)"] +postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)", "pg8000 (>=1.16.6,!=1.29.0)"] postgresql-psycopg2binary = ["psycopg2-binary"] postgresql-psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] @@ -6924,13 +6928,13 @@ widechars = ["wcwidth"] [[package]] name = "tenacity" -version = "8.5.0" +version = "9.0.0" description = "Retry code until it succeeds" optional = false python-versions = ">=3.8" files = [ - {file = "tenacity-8.5.0-py3-none-any.whl", hash = "sha256:b594c2a5945830c267ce6b79a166228323ed52718f30302c1359836112346687"}, - {file = "tenacity-8.5.0.tar.gz", hash = "sha256:8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78"}, + {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"}, + {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"}, ] [package.extras] diff --git a/pyproject.toml b/pyproject.toml index dd4c841..abbc70e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,9 +27,9 @@ pyyaml = "^6.0.1" google = "^3.0.0" pendulum = "^3.0.0" apache-airflow-providers-apache-beam = "^5.7.1" -pandas = "<2.2" typing-extensions = "^4.12.2" requests = "^2.32.3" +pandas = "<2.2" [tool.poetry.group.dev.dependencies] ruff = "^0.4.9" @@ -95,13 +95,14 @@ ignore = [ ] - [tool.ruff.lint.flake8-quotes] docstring-quotes = "double" [tool.ruff.lint.pydocstyle] convention = "google" - [tool.pytest] pytonpath = "src/" + +[tool.pytest.ini_options] +markers = ["integration_test"] diff --git a/src/ot_orchestration/cli/__init__.py b/src/ot_orchestration/cli/__init__.py index eec4859..d37acad 100644 --- a/src/ot_orchestration/cli/__init__.py +++ b/src/ot_orchestration/cli/__init__.py @@ -4,7 +4,7 @@ import logging from ot_orchestration.cli.fetch_raw_sumstat_paths import fetch_raw_sumstat_paths from ot_orchestration.cli.generate_dotenv import generate_dotenv -from ot_orchestration.cli.process_in_batch import gwas_catalog_process_in_batch +from ot_orchestration.cli.process_in_batch import gwas_catalog_pipeline logging.basicConfig(level=logging.INFO) asci_art = """ @@ -24,7 +24,7 @@ def cli(): cli.add_command(fetch_raw_sumstat_paths) cli.add_command(generate_dotenv) -cli.add_command(gwas_catalog_process_in_batch) +cli.add_command(gwas_catalog_pipeline) __all__ = ["cli"] diff --git a/src/ot_orchestration/cli/process_in_batch.py b/src/ot_orchestration/cli/process_in_batch.py index a66ff93..14f8883 100644 --- a/src/ot_orchestration/cli/process_in_batch.py +++ b/src/ot_orchestration/cli/process_in_batch.py @@ -1,21 +1,27 @@ """Process GWAS Catalog summary statistics in batch job.""" -import os -from ot_orchestration.utils import GCSIOManager -from ot_orchestration.types import Manifest_Object +from ot_orchestration.utils import IOManager, GWASCatalogPipelineManifest import logging import subprocess import click +import os +import sys +MANIFEST_PATH_ENV_VAR = "MANIFEST_PATH" -def harmonise(manifest: Manifest_Object) -> Manifest_Object: + +def harmonise_step( + manifest: GWASCatalogPipelineManifest, +) -> GWASCatalogPipelineManifest: """Run Harmonisation.""" raw_path = manifest["rawPath"] harmonised_path = manifest["harmonisedPath"] study_id = manifest["studyId"] + manifest_path = manifest["manifestPath"] + pass_harmonisation = manifest["passHarmonisation"] + logging.info("Running %s for %s", "harmonisation", study_id) + command = [ - "poetry", - "run", "gentropy", "step=gwas_catalog_sumstat_preprocess", f'step.raw_sumstats_path="{raw_path}"', @@ -26,34 +32,38 @@ def harmonise(manifest: Manifest_Object) -> Manifest_Object: "+step.session.extended_spark_conf={spark.kryoserializer.buffer.max:'500m'}", "+step.session.extended_spark_conf={spark.driver.maxResultSize:'5g'}", ] - if GCSIOManager().exists(harmonised_path): - logging.info("Harmonisation result exists for %s. Skipping", study_id) - manifest["passHarmonisation"] = True + if IOManager().resolve(harmonised_path).exists(): + if not pass_harmonisation: + logging.info("Harmonisation result exists for %s. Skipping", study_id) + manifest["passHarmonisation"] = True return manifest + logging.info("Running command %s", " ".join(command)) + command = ["echo", "RUNNING!"] result = subprocess.run(args=command, capture_output=True) + logging.info(result) if result.returncode != 0: logging.error("Harmonisation for study %s failed!", study_id) error_msg = result.stderr.decode() logging.error(error_msg) manifest["passHarmonisation"] = False - logging.info("Dumping manifest to %s", manifest["manifestPath"]) - GCSIOManager().dump(manifest["manifestPath"], manifest) - exit(1) + logging.info("Dumping manifest to %s", manifest_path) + IOManager().resolve(manifest_path).dump(manifest) + sys.exit(1) logging.info("Harmonisation for study %s succeded!", study_id) manifest["passHarmonisation"] = True return manifest -def qc(manifest: Manifest_Object) -> Manifest_Object: +def qc_step(manifest: GWASCatalogPipelineManifest) -> GWASCatalogPipelineManifest: """Run QC.""" harmonised_path = manifest["harmonisedPath"] qc_path = manifest["qcPath"] study_id = manifest["studyId"] + manifest_path = manifest["manifestPath"] + command = [ - "poetry", - "run", "gentropy", "step=summary_statistics_qc", f'step.gwas_path="{harmonised_path}"', @@ -65,9 +75,8 @@ def qc(manifest: Manifest_Object) -> Manifest_Object: "+step.session.extended_spark_conf={spark.kryoserializer.buffer.max:'500m'}", "+step.session.extended_spark_conf={spark.driver.maxResultSize:'5g'}", ] - result_exists = GCSIOManager().exists(qc_path) - logging.info("Result exists: %s", result_exists) - if GCSIOManager().exists(qc_path): + result_exists = IOManager().resolve(qc_path).exists() + if result_exists: logging.info("QC result exists for %s. Skipping", study_id) manifest["passQC"] = True return manifest @@ -78,8 +87,8 @@ def qc(manifest: Manifest_Object) -> Manifest_Object: error_msg = result.stderr.decode() logging.error(error_msg) manifest["passQC"] = False - logging.info("Dumping manifest to %s", manifest["manifestPath"]) - GCSIOManager().dump(manifest["manifestPath"], manifest) + logging.info("Dumping manifest to %s", manifest_path) + IOManager().resolve(manifest_path).dump(manifest) exit(1) logging.info("QC for study %s succeded!", study_id) @@ -87,67 +96,42 @@ def qc(manifest: Manifest_Object) -> Manifest_Object: return manifest -def qc_consolidation(manifest: Manifest_Object) -> Manifest_Object: - pass +def qc_consolidation_step( + manifest: GWASCatalogPipelineManifest, +) -> GWASCatalogPipelineManifest: + """Check if sumstats pass qc thresholds.""" + return manifest -def clumping(manifest: Manifest_Object) -> Manifest_Object: +def clump_step(manifest: GWASCatalogPipelineManifest) -> GWASCatalogPipelineManifest: """Run Clumping.""" - harmonised_path = manifest["harmonisedPath"] - clumping_path = manifest["clumpingPath"] - study_id = manifest["studyId"] - command = [ - "poetry", - "run", - "gentropy", - "step=clumping", - f'step.gwas_path="{harmonised_path}"', - f'step.output_path="{clumping_path}"', - f'step.study_id="{study_id}"', - "+step.session.extended_spark_conf={spark.jars:'https://storage.googleapis.com/hadoop-lib/gcs/gcs-connector-hadoop3-latest.jar'}", - "+step.session.extended_spark_conf={spark.dynamicAllocation.enabled:'false'}", - "+step.session.extended_spark_conf={spark.driver.memory:'30g'}", - "+step.session.extended_spark_conf={spark.kryoserializer.buffer.max:'500m'}", - "+step.session.extended_spark_conf={spark.driver.maxResultSize:'5g'}", - ] - if GCSIOManager().exists(clumping_path): - logging.info("Clumping result exists for %s. Skipping", study_id) - manifest["passClumping"] = True - return manifest - - result = subprocess.run(args=command, capture_output=True) - if result.returncode != 0: - logging.error("Clumping for study %s failed!", study_id) - error_msg = result.stderr.decode() - logging.error(error_msg) - manifest["passClumping"] = False - logging.info("Dumping manifest to %s", manifest["manifestPath"]) - GCSIOManager().dump(manifest["manifestPath"], manifest) - exit(1) return manifest @click.command() -def gwas_catalog_process_in_batch(): - """Run gwas catalog processing of summary statistics in batch. This includes harmonisation, QC and clumping.""" - PROCESSING_ORDER = ["harmonisation"] - MANIFEST_PATH = os.environ.get("MANIFEST_PATH") - if MANIFEST_PATH is None: - logging.error("MANIFEST_PATH not set!") - exit(1) - - manifest = GCSIOManager().load(MANIFEST_PATH) - study = manifest["studyId"] - PROCESSING_STEPS = {"harmonisation": harmonise, "qc": qc, "clumping": clumping} - for step in PROCESSING_ORDER: - if manifest[f"pass{step.capitalize()}"]: - logging.info("Skipping %s", step) - continue - logging.info("Running %s for %s", step, study) - manifest = PROCESSING_STEPS[step](manifest) - logging.info("Finished %s for %s", step, study) - - GCSIOManager().dump(MANIFEST_PATH, manifest) - - -__all__ = ["gwas_catalog_process_in_batch"] +def gwas_catalog_pipeline(): + """Run gwas catalog processing of summary statistics in batch. + + This includes harmonisation, QC and clumping. + This command requires setting the `MANIFEST_PATH` in the + environment. The variable should be the reference to the path with the + manifest file. + """ + logging.debug("Reading MANIFEST_PATH env variable") + manifest_path = os.getenv(MANIFEST_PATH_ENV_VAR) + if not manifest_path: + logging.error("MANIFEST_PATH environment variable is missing") + sys.exit(1) + logging.debug("MANIFEST_PATH: %s", manifest_path) + manifest = GWASCatalogPipelineManifest.from_file(manifest_path) + logging.debug("MANIFEST: %s", manifest) + # for now dummy implementatin of the pipeline processing order + manifest = harmonise_step(manifest) + manifest = qc_step(manifest) + manifest = qc_consolidation_step(manifest) + manifest = clump_step(manifest) + + IOManager().resolve(manifest_path).dump(manifest) + + +__all__ = ["gwas_catalog_pipeline"] diff --git a/src/ot_orchestration/dags/branching.py b/src/ot_orchestration/dags/branching.py deleted file mode 100644 index 4918461..0000000 --- a/src/ot_orchestration/dags/branching.py +++ /dev/null @@ -1,80 +0,0 @@ -# -# Licensed to the Apache Software Foundation (ASF) under one -# or more contributor license agreements. See the NOTICE file -# distributed with this work for additional information -# regarding copyright ownership. The ASF licenses this file -# to you under the Apache License, Version 2.0 (the -# "License"); you may not use this file except in compliance -# with the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, -# software distributed under the License is distributed on an -# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY -# KIND, either express or implied. See the License for the -# specific language governing permissions and limitations -# under the License. - -"""Example DAG demonstrating the usage of the BranchPythonOperator.""" - -import random -from datetime import datetime - -from airflow import DAG -from airflow.decorators import task -from airflow.operators.empty import EmptyOperator -from airflow.utils.edgemodifier import Label -from airflow.utils.trigger_rule import TriggerRule - -with DAG( - dag_id="example_branch_python_operator_decorator", - start_date=datetime(2021, 1, 1), - catchup=False, - schedule_interval="@daily", - tags=["example", "example2"], -) as dag: - run_this_first = EmptyOperator( - task_id="run_this_first", - ) - - options = ["branch_a", "branch_b", "branch_c", "branch_d"] - - @task.branch(task_id="branching") - def random_choice(): - return random.choice(options) - - random_choice_instance = random_choice() - - run_this_first >> random_choice_instance - - join = EmptyOperator( - task_id="join", - trigger_rule=TriggerRule.NONE_FAILED_MIN_ONE_SUCCESS, - ) - - for option in options: - if option == "branch_a": - empty_follow_3 = EmptyOperator( - task_id="follow_" + option, - ) - random_choice_instance >> Label(option) >> empty_follow_3 >> join - if option == "branch_b": - empty_follow_2 = EmptyOperator( - task_id="follow_" + option, - ) - random_choice_instance >> Label(option) >> empty_follow_2 >> join - if option == "branch_c": - random_choice_instance >> Label(option) >> join - - if option == "branch_d": - t = EmptyOperator( - task_id=option, - ) - - empty_follow = EmptyOperator( - task_id="follow_" + option, - ) - - # Label is optional here, but it can help identify more complex branches - random_choice_instance >> Label(option) >> t >> empty_follow diff --git a/src/ot_orchestration/types.py b/src/ot_orchestration/types.py index 1f74a12..cd895ff 100644 --- a/src/ot_orchestration/types.py +++ b/src/ot_orchestration/types.py @@ -26,8 +26,8 @@ "manifestPath": Required[str], "studyType": str | None, "analysisFlag": str | None, - "isCurated": str | None, - "pubmetId": str | None, + "isCurated": bool | None, + "pubmedId": str | None, }, ) @@ -54,8 +54,6 @@ GCS_Mount_Object = TypedDict( "GCS_Mount_Object", {"remote_path": Required[str], "mount_point": Required[str]} ) -GCS_Bucket_Name = str -GCS_Path_Suffix = str Provider_Name = Literal["googlebatch", "dataproc"] Step_Name = Literal["harmonisation"] @@ -133,8 +131,6 @@ "Provider_Name", "Step_Name", "DagConfigNotFound", - "GCS_Bucket_Name", - "GCS_Path_Suffix", "Log_Level", "Manifest_Preparation_Params", "Spark_Options", diff --git a/src/ot_orchestration/utils/__init__.py b/src/ot_orchestration/utils/__init__.py index 6ae91bb..304d1dd 100644 --- a/src/ot_orchestration/utils/__init__.py +++ b/src/ot_orchestration/utils/__init__.py @@ -12,12 +12,17 @@ time_to_seconds, ) from ot_orchestration.utils.batch import create_task_spec, create_batch_job -from ot_orchestration.utils.gcs_path import GCSPath, GCSIOManager +from ot_orchestration.utils.path import GCSPath, IOManager, NativePath +from ot_orchestration.utils.manifest import ( + GWASCatalogPipelineManifest, + extract_study_id_from_path, +) __all__ = [ "QRCP", - "GCSIOManager", + "IOManager", "GCSPath", + "NativePath", "ConfigModel", "check_gcp_folder_exists", "read_yaml_config", @@ -26,4 +31,6 @@ "create_batch_job", "get_step_params", "get_full_config", + "extract_study_id_from_path", + "GWASCatalogPipelineManifest", ] diff --git a/src/ot_orchestration/utils/gcs_path.py b/src/ot_orchestration/utils/gcs_path.py deleted file mode 100644 index 732b44e..0000000 --- a/src/ot_orchestration/utils/gcs_path.py +++ /dev/null @@ -1,179 +0,0 @@ -"""Module for Google Cloud Path naive parsers.""" - -import re -import concurrent.futures -from google.cloud.storage.blob import Blob -from google.cloud.storage.client import Client -from google.cloud.storage.bucket import Bucket -from requests.adapters import HTTPAdapter -from ot_orchestration.types import GCS_Bucket_Name, GCS_Path_Suffix -import json -from ot_orchestration.types import Manifest_Object -import yaml -from pathlib import Path - - -class GCSPath: - """Google Cloud Storage Path.""" - - def __init__(self, gcs_path: str): - self.gcs_path = gcs_path - path_pattern = re.compile("^(gs://)?(?P[(\\w)-]+)") - self._match = path_pattern.match(gcs_path) - if self._match is None: - raise ValueError("Invalid GCS path %s", gcs_path) - - @property - def bucket(self) -> GCS_Bucket_Name: - """Return Bucket Name.""" - return self._match.group("bucket_name") - - @property - def path(self) -> GCS_Path_Suffix: - """Return Path segment after Bucket Name.""" - # +1 to remove "/" afer bucket name - return self.gcs_path[self._match.end() + 1 :] - - def split(self) -> tuple[GCS_Bucket_Name, GCS_Path_Suffix]: - """Return both, bucket and path.""" - return self.bucket, self.path - - def __repr__(self) -> str: - """Reprint object.""" - return f"gcs_path={self.gcs_path}, bucket={self.bucket}, path={self.path}" - - -class GCSIOManager: - """Input Output manager class.""" - - def __init__(self): - self.client = Client() - adapter = HTTPAdapter(pool_connections=128, pool_maxsize=1024, max_retries=3) - self.client._http.mount("https://", adapter) - self.client._http._auth_request.session.mount("https://", adapter) - - def exists(self, gcs_path: str) -> bool: - """Check if file exists in Google Cloud Storage.""" - gcs_path = GCSPath(gcs_path) - bucket_name, file_name = gcs_path.split() - bucket = Bucket(client=self.client, name=bucket_name) - blob = Blob(name=file_name, bucket=bucket) - return blob.exists() - - def dump(self, gcs_path: str, data: dict) -> None: - """Write data to Google Cloud Storage.""" - gcs_path = GCSPath(gcs_path) - bucket_name, file_name = gcs_path.split() - bucket = Bucket(client=self.client, name=bucket_name) - blob = Blob(name=file_name, bucket=bucket) - with blob.open("w") as fp: - match Path(file_name).suffix: - case ".json": - return json.dump(data, fp) - case ".yaml" | ".yml": - return yaml.safe_dump(data, fp) - case _: - return fp.write(data) - - def load(self, gcs_path: str) -> dict: - """Read data from Google Cloud Storage.""" - gcs_path = GCSPath(gcs_path) - bucket_name, file_name = gcs_path.split() - bucket = Bucket(client=self.client, name=bucket_name) - blob = Blob(name=file_name, bucket=bucket) - - with blob.open("r") as fp: - match Path(file_name).suffix: - case ".json": - return json.load(fp) - case ".yaml" | ".yml": - return yaml.safe_load(fp) - case _: - return {"data": fp.read()} - - def load_many(self, gcs_paths: list[str]) -> list[Manifest_Object]: - """Load many json objects from google cloud by concurrent operations. - - Args: - gcs_paths (list[str]): Google Cloud Storage Paths. - - Returns: - list[Manifest_Object]: Manifest objects - """ - if not gcs_paths: - return [] - n_threads = len(gcs_paths) - print(f"LOADING {len(gcs_paths)} MANIFESTS.") - with concurrent.futures.ThreadPoolExecutor(max_workers=n_threads) as executor: - futures: list[concurrent.futures.Future] = [] - for gcs_path in gcs_paths: - gcs_path = GCSPath(gcs_path) - bucket_name, file_name = gcs_path.split() - bucket = Bucket(name=bucket_name, client=self.client) - blob = Blob(name=file_name, bucket=bucket) - - def load_manifest(blob: Blob) -> Manifest_Object: - """Load manifest with blob.""" - with blob.open("r") as fp: - manifest: Manifest_Object = json.load(fp) - return manifest - - method = lambda: load_manifest(blob) - futures.append(executor.submit(method)) - results: list[Manifest_Object] = [] - concurrent.futures.wait(futures) - for future in futures: - exe = future.exception() - if exe: - continue - results.append(future.result()) - return results - - def dump_many( - self, manifest_objects: list[Manifest_Object], gcs_paths: list[str] - ) -> None: - """Dump many manifest objects to corresponding Google Cloud Storage paths. - - Args: - manifest_objects (list[Manifest_Object]): Manifest objects - gcs_paths (list[str]): Google Cloud Storage paths. - - Raises: - ValueError: When number of manifest objects does not match gcs paths. - - """ - if len(gcs_paths) != len(manifest_objects): - raise ValueError("Empty gcs_paths or unequal number of file_blobs") - if not gcs_paths: - return None - print(f"DUMPING {len(gcs_paths)} MANIFESTS.") - n_threads = len(gcs_paths) - chunk_size = 1024 * 256 - with concurrent.futures.ThreadPoolExecutor(max_workers=n_threads) as executor: - futures: list[concurrent.futures.Future] = [] - for gcs_path, manifest_object in zip( - gcs_paths, manifest_objects, strict=True - ): - gcs_path = GCSPath(gcs_path) - bucket_name, file_name = gcs_path.split() - bucket = Bucket(client=self.client, name=bucket_name) - blob = Blob(name=file_name, bucket=bucket, chunk_size=chunk_size) - - def dump_manifest(blob: Blob, manifest: Manifest_Object) -> None: - """Dump manifest to blob.""" - with blob.open("w") as fp: - json.dump(manifest, fp, indent=2) - - method = lambda: dump_manifest(blob, manifest_object) - futures.append(executor.submit(method)) - results = [] - concurrent.futures.wait(futures) - for future in futures: - exe = future.exception() - if exe: - continue - results.append(future.result()) - return results - - -__all__ = ["GCSPath", "GCSIOManager"] diff --git a/src/ot_orchestration/utils/manifest.py b/src/ot_orchestration/utils/manifest.py index e8d456f..e276b3d 100644 --- a/src/ot_orchestration/utils/manifest.py +++ b/src/ot_orchestration/utils/manifest.py @@ -1,15 +1,91 @@ """Utility functions to handle manifests.""" +from __future__ import annotations import re +from ot_orchestration.types import Manifest_Object +from ot_orchestration.utils import IOManager +import logging def extract_study_id_from_path(path: str) -> str: - """Extract study id from path.""" - pattern = re.compile("\/(GCST\d+)\/") + """Extract study id from path. + + Args: + path: str: path to extract study id from. + + Returns: + str: study id. + """ + pattern = r"\/(GCST\d+)\/" + pattern = re.compile(pattern) result = pattern.search(path) if not result: raise ValueError("Gwas Catalog identifier was not found in %s", path) return result.group(1) -__all__ = ["extract_study_id_from_path"] +class GWASCatalogPipelineManifest: + """Create Manifest object for gwas catalog study. + + Args: + manifest_object (Manifest_Object): manifest object. + """ + + def __init__(self, manifest_object: Manifest_Object): + self._mo = manifest_object + + def __getitem__(self, key: str) -> str: + """Get one of manifest keys. + + Args: + key (str): key to get. + + Returns: + str: value of the key. + """ + return self._mo[key] + + def __setitem__(self, key: str, val: str | bool) -> None: + """Set one of the manifest keys. + + Args: + key (str): key to set. + val (str | bool): value to set. + """ + self._mo[key] = val + + @classmethod + def from_file(cls, mp: str) -> GWASCatalogPipelineManifest: + """Constructor from a file. + + File can be either google cloud storage or local file. + + Args: + mp (str): path to the manifest file. + + Returns: + GWASCatalogPipelineManifest: manifest object. + """ + if not mp.endswith(".json"): + raise IOError("Manifest needs to be a json file") + path = IOManager().resolve(mp) + manifest: Manifest_Object = path.load() + return cls(manifest) + + def write(self) -> None: + """Write manifest object to the path derived from manifestPath.""" + mp = self._mo["manifestPath"] + logging.info("WRITING MANIFEST OBJECT TO %s", mp) + path = IOManager().resolve(mp) + path.dump(self._mo) + + def __repr__(self) -> str: + """Representation of the manifest object. + + Returns: + str: inlined dict representation. + """ + return str(self._mo) + + +__all__ = ["extract_study_id_from_path", "GWASCatalogPipelineManifest"] diff --git a/src/ot_orchestration/utils/path.py b/src/ot_orchestration/utils/path.py new file mode 100644 index 0000000..8155f56 --- /dev/null +++ b/src/ot_orchestration/utils/path.py @@ -0,0 +1,343 @@ +"""Module for Google Cloud Path naive parsers.""" + +import re +import concurrent.futures +from google.cloud.storage.blob import Blob, TextIOWrapper +from google.cloud.storage.client import Client +from google.cloud.storage.bucket import Bucket +from requests.adapters import HTTPAdapter +import json +import yaml +from pathlib import Path +from typing import Any +import logging +from typing import Protocol +from abc import abstractmethod + + +class ProtoPath(Protocol): + @abstractmethod + def dump(self, data: Any) -> None: + """Dump data to storage. + + Args: + data (Any): Data to dump. + + Raises: + NotImplementedError: this method is required for classes to follow the protocol. + """ + raise NotImplementedError + + @abstractmethod + def load(self) -> Any: + """Load data from storage. + + Raises: + NotImplementedError: this method is required for classes to follow the protocol. + + Returns: + Any: Loaded data. + """ + raise NotImplementedError + + @abstractmethod + def exists(self) -> bool: + """Check if path exists. + + Raises: + NotImplementedError: this method is required for classes to follow the protocol. + + Returns: + bool: True if path exists. + """ + raise NotImplementedError + + +class NativePath(ProtoPath): + """Create Native Path object. + + This represents a local file path. + + Args: + path (str): Local file path. + """ + + def __init__(self, path: str): + self.native_path = Path(path) + + def dump(self, data: Any) -> None: + """Write data to Native storage. + + Args: + data (Any): Data to write. + """ + with open(self.native_path, "w") as fp: + match self.native_path.suffix: + case ".json": + json.dump(data, fp) + case ".yaml" | ".yml": + yaml.safe_dump(data, fp) + case _: + fp.write(data) + + def load(self) -> Any: + """Read data from Native storage. + + Returns: + Any: Loaded data. + """ + with open(self.native_path, "r") as fp: + match self.native_path.suffix: + case ".json": + return json.load(fp) + case ".yaml" | ".yml": + return yaml.safe_load(fp) + case _: + return fp.read() + + def exists(self) -> bool: + """Check if path exists preserved for the interface of ProtoPath implementation. + + Returns: + bool: True if path exists. + """ + return self.native_path.exists() + + +class GCSPath(ProtoPath): + """Create GCS Path object. + + Args: + gcs_path (str): Google Cloud Storage path. + chunk_size (int, optional): Chunk size for reading and writing. Defaults to 1024*256. + """ + + def __init__(self, gcs_path: str, chunk_size: int = 1024 * 256): + self.gcs_path = gcs_path + self.path_pattern = re.compile("^(gs://)?(?P[(\\w)-]+)") + self.chunk_size = chunk_size + + @property + def _match(self) -> re.Match: + """Match the path with the pattern. + + Raises: + ValueError: When path does not match the pattern. + + Returns: + re.Match: Match object. + """ + _match = self.path_pattern.match(self.gcs_path) + if _match is None: + raise ValueError("Invalid GCS path %s", self.gcs_path) + return _match + + def __post_init__(self): + """Create a client object. + + This is a post init method that allows to expand the number of concurrent tasks that can be run. + """ + self.client = Client() + adapter = HTTPAdapter(pool_connections=128, pool_maxsize=1024, max_retries=3) + self.client._http.mount("https://", adapter) + self.client._http._auth_request.session.mount("https://", adapter) + + @property + def bucket(self) -> str: + """Return Bucket Name. + + Returns: + str: Bucket name. + + """ + return self._match.group("bucket_name") + + @property + def path(self) -> str: + """Get path segment after the bucket name. + + Returns: + str: Path segment after Bucket Name. + """ + # +1 to remove "/" afer bucket name + return self.gcs_path[self._match.end() + 1 :] + + def exists(self) -> bool: + """Check if file exists in Google Cloud Storage. + + Returns: + bool: True if file exists. + """ + bucket = Bucket(client=self.client, name=self.bucket) + blob = Blob(name=self.path, bucket=bucket, chunk_size=self.chunk_size) + return blob.exists() + + def split(self) -> tuple[str, str]: + """Return both, bucket and path after split. + + Returns: + tuple[str, str]: Bucket name and path. + """ + return self.bucket, self.path + + def __repr__(self) -> str: + """Path representation.""" + return self.gcs_path + + def dump(self, data: Any) -> None: + """Write data to Google Cloud Storage. + + Args: + data (Any): Data to write. + """ + bucket = Bucket(client=self.client, name=self.bucket) + blob = Blob(name=self.path, bucket=bucket) + with blob.open("w") as fp: + assert isinstance(fp, TextIOWrapper) + match Path(self.path).suffix: + case ".json": + json.dump(data, fp) + case ".yaml" | ".yml": + yaml.safe_dump(data, fp, indent=2) + case _: + fp.write(data) + + def load(self) -> Any: + """Read data from Google Cloud Storage. + + Returns: + Any: Loaded data. + """ + bucket = Bucket(client=self.client, name=self.bucket) + blob = Blob(name=self.path, bucket=bucket) + + with blob.open("r") as fp: + match Path(self.path).suffix: + case ".json": + return json.load(fp) + case ".yaml" | ".yml": + return yaml.safe_load(fp) + case _: + return fp.read() + + +class IOManager: + """Input Output manager class.""" + + def resolve(self, path: str) -> ProtoPath: + """Resolve path by its protocol. + + Depending on the protocol the following are defined + + - gs:// for Google Cloud Storage + - file:// for local file system + - no protocol for local file system + - s3:// (currently not implemented) + - s3a:// (currently not implemented) + - http:// (currently not implemented) + - https:// (currently not implemented) + - ftp:// (currently not implemented) + + Based on registred protocols, the path is resolved to the appropriate Path object + + Args: + path (str): Path to resolve. + + Returns: + ProtoPath: Path object instance following ProtoPath protocol. + """ + match path.split("://"): + case ["gs", _]: + return GCSPath(path) + case [_] | ["file", _]: + return NativePath(path) + case [protocol, _]: + raise NotImplementedError( + "IOManager.resolve does not implement %s protocol resolution", + protocol, + ) + case _: + raise NotImplementedError( + "IOManager.resolve is not implemented for path=%s", path + ) + + def resolve_paths(self, paths: list[str]) -> list[ProtoPath]: + """Resolve multiple paths by the protocols. + + Args: + paths (list[str]): Paths to resolve. + + Returns: + list[ProtoPath]: List of path objects following ProtoPath protocol. + """ + return [self.resolve(p) for p in paths] + + def load_many(self, paths: list[str], n_threads=100) -> list[Any]: + """Load many objects by concurrent operations. + + Args: + paths (list[str]): Paths to read from. + n_threads (int): number of concurrent threads to use. + + Returns: + list[Any]: Objects that were read. + """ + if not paths: + logging.warning("Nothing to load.") + return [] + + resolved_paths = self.resolve_paths(paths) + + logging.info(f"LOADING {len(paths)} OBJECTS.") + with concurrent.futures.ThreadPoolExecutor(max_workers=n_threads) as executor: + futures: list[concurrent.futures.Future] = [] + for path in resolved_paths: + method = lambda: path.load() + futures.append(executor.submit(method)) + results = [] + + concurrent.futures.wait(futures) + for idx, future in enumerate(futures): + exe = future.exception() + if exe: + logging.error(exe) + else: + logging.info(f"Successfully loaded {idx + 1}/{len(futures)} objects.") + results.append(future.result()) + return results + + def dump_many(self, objects: list[Any], paths: list[str], n_threads=100) -> None: + """Dump many objects by concurrent operations. + + Args: + objects (list[Any]): Objects to write. + paths (list[str]): Paths to write the objects to. + n_threads (int): number of concurrent threads to use. + + Raises: + ValueError: When number of objects does not match paths. + """ + if len(paths) != len(objects): + raise ValueError("Empty paths or unequal number of objects") + if not paths: + logging.warning("Nothing to dump.") + return None + + resolved_paths = self.resolve_paths(paths) + logging.info(f"DUMPING {len(paths)} OBJECTS.") + with concurrent.futures.ThreadPoolExecutor(max_workers=n_threads) as executor: + futures: list[concurrent.futures.Future] = [] + for path, ob in zip(resolved_paths, objects, strict=True): + method = lambda: path.dump(ob) + futures.append(executor.submit(method)) + + concurrent.futures.wait(futures) + for idx, future in enumerate(futures): + exe = future.exception() + if exe: + logging.error(exe) + else: + logging.info(f"Successfully dumped {idx + 1}/{len(futures)} objects.") + + +__all__ = ["GCSPath", "IOManager", "NativePath"] diff --git a/src/ot_orchestration/utils/qrcp.py b/src/ot_orchestration/utils/qrcp.py index 62774b3..2803e41 100644 --- a/src/ot_orchestration/utils/qrcp.py +++ b/src/ot_orchestration/utils/qrcp.py @@ -74,7 +74,15 @@ def default_config_parser( class QRCP: - """Initialize Quick and Robust Configuration Parser.""" + """Initialize QRCP object. + + Args: + conf (Any): Configuration object. + parser (Config_Parser, optional): configuration parser. Defaults to default_config_parser. + + Raises: + TypeError: _description_ + """ @classmethod def from_file(cls, path: Path | str, **kwargs: Any) -> QRCP: @@ -145,7 +153,7 @@ def to_file(self, path: Path | str) -> None: def get_full_config() -> QRCP: """Get full configuration.""" - return QRCP(get_current_context()["params"]) + return QRCP(get_current_context().get("params")) def get_step_params(step: str) -> dict[str, Base_Type]: @@ -157,6 +165,8 @@ def get_step_params(step: str) -> dict[str, Base_Type]: return params case Failure(msg): raise TypeError(msg) + case _: + raise NotImplementedError __all__ = ["QRCP", "ConfigModel", "get_step_params", "get_full_config"] diff --git a/tests/data/gwas_catalog_batch_job/SSF_GCST001.h.tsv b/tests/data/gwas_catalog_batch_job/SSF_GCST001.h.tsv new file mode 100644 index 0000000000000000000000000000000000000000..861257a1dd91ed1644601a0a585f6dec4049d33e GIT binary patch literal 5503 zcmV-_6@cm=iwFqt&!1)h17>M#Wil>wb9Ml&TupNwxo%zG{FPK*@f+aVskHDeEALf$ zV@<|Y_IM)uC6#}lgAcNsyizNR$S(7$DIKEGAaDSp{m1vG|9XD?`uyjwr>|dbe|&#> z{b}QGf4u(qE+78-@l%E$zy5f6eR}@(?d98xeE;(M?=QdoI$ik3%dcns!7pEaKD|Ew z`uam*zCL~X@!v16{`sGO{biq*Uw``j_2obR`SRy)|D!+l%w?)2HxaV)bp1yzm^T+G$%hy+2mmgPYfBt&@^UL$=m#3H4 zSIqteRebyB%kBHOAO8`_CQUt)NQrPlKF@bu~S`m;8UoI1r@ z3^$#)J={Ls!rww>DmBsV-yi%ht_6HAKNtSqLg^o1{Cb7V|9XbP$5I+M>iC$s%1~mi zArEjL#+oiI)u+!-kGfLhT2iRK64l%1+vDxutk##59Nwi{lnI^`Irnp+`k7xuN9Jxckl2AO(Y<&9;^%i#lzll?jr zKDGdDW|6Z;(`JV867zufVUf26DA=B5i;Rt0n=U2Sr#Xbs@yO4=E1SBt*iT1JwfDHj1Kq_C4 z19bJMc9l95xotpLZB>b5NFP8P3Li+KaQqmnVNi@}Fooewc!2w`N}Ef@QV;rU6NeaL zwxuwErOXB?_VaI=uZ+V!@N_@GINP&hi9=@UL(m}V<(lH~YblOllb6c$$nZ==$)6@B zbnl2xV!*~qo4k3-o8t!_gRgjKwyZ;`^{ljOX(7Xf6XDAKN=tlSF22j}K-O zaJumPWl?hL^`vBaA0`{j*-;EQ^Ao)Ur4)$Su}R=7)iqva$e=8{)TPZm(+Zwx^k<5R zq34u@+Pv$RBUE>dads01rG7akP#<*@Y77#0*l*=Mx77~7I46T2Faj17d zsea)CNvwdHT5ODn))cSwiwGYlpJfD}=zLZt^hrV|sWHRDZyad42t43$jd9ZNz>=pA z7h%e58WiE$sMT`Ch+9;5|6ueRY%8;QBbmTLDjGZ!Lg%Jk1f}ZI)_e_dD0d(UTWC3u zIskaUri2ZVWrQ6&TF<;H?>7 zY+FbsrtMbbGiM9MtqR{qoB{9>%*1?tYWQj8If0ei(-Mj|* zf0ekkS*wv`RZ?7A3?z0C;FN0u*Sm|wLt+Z`8sseT02AR6TdEpyBb8W;x=_6e#tbs# zo7>Yx+b(kbDEWZ=#lGZk5|%vUEZFiM-0mSHww;NjBPoxBl<&9CXE`h z#wu*j!E;;OYsrOOYciq9txDTuH^g<*A(xr@<(VPBgL2mIL=%uEL{~$GZ8p%2&@}1S z1$t+OVh$DD zvh{Rj4jpa}yTyn~sU5kZuY?I$o-$ut2cO+{+>FOHYCd#o{5=>$ilu{pAHx)7WLI|6P)YuRd3CtW@700)0=3Iz&l&9f|?E2o>(nH z>3Yu`s+#nuS#3pDc=?!zi z54ar=oxEGjq;Oy}`5I(lMGj_00|OH6r=)VW(lxzzd>>Yc!5BxfQ;^Lv9C+?z%AEn zjEyZTmT-HxouWlcuBOojKUqg6?f0l5uAQ{m3+)PY(%2d-uC=^7Vn+PJhxm`%APLd?bjfSybiX=D^5~eMXbe* z_dS6N%c0O`wLAiWC919*%wVa{z6u_1|~D zSipx>Xqb@`8>EJ@r|kL>^ZGRX8jDL@IR`SgHxFwV4#3M;_lTc2(lLO|s6q6UG=n

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