Merge branch 'dev' into yt_sumstat_qc

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
   skip: [poetry-lock]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.2
+    rev: v0.3.3
     hooks:
       - id: ruff
         args:
@@ -104,7 +104,7 @@ repos:
       - id: pydoclint
 
   - repo: https://github.com/python-poetry/poetry
-    rev: "1.8.2"
+    rev: "1.8.0"
     hooks:
       - id: poetry-check
       - id: poetry-lock

config/datasets/ot_gcp.yaml

@@ -1,10 +1,10 @@
 # Release specific configuration:
-release_version: "24.01"
+release_version: "24.03"
 dev_version: XX.XX
 release_folder: gs://genetics_etl_python_playground/releases/${datasets.release_version}
 
 inputs: gs://genetics_etl_python_playground/input
-static_assets: gs://genetics_etl_python_playground/static_assetss
+static_assets: gs://genetics_etl_python_playground/static_assets
 outputs: gs://genetics_etl_python_playground/output/python_etl/parquet/${datasets.dev_version}
 
 ## Datasets:
@@ -36,9 +36,9 @@ anderson: ${datasets.static_assets}/andersson2014/enhancer_tss_associations.bed
 javierre: ${datasets.static_assets}/javierre_2016_preprocessed
 jung: ${datasets.static_assets}/jung2019_pchic_tableS3.csv
 thurman: ${datasets.static_assets}/thurman2012/genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8.gz
-target_index: ${datasets.release_folder}/targets # OTP 23.12 data
+target_index: ${datasets.static_assets}/targets # OTP 23.12 data
+gene_interactions: ${datasets.static_assets}/interaction # OTP 23.12 data
 
-gene_interactions: ${datasets.release_folder}/interaction # OTP 23.12 data
 finngen_finemapping_results_path: ${datasets.inputs}/Finngen_susie_finemapping_r10/full
 finngen_finemapping_summaries_path: ${datasets.inputs}/Finngen_susie_finemapping_r10/Finngen_susie_credset_summary_r10.tsv
 

docs/src_snippets/howto/python_api/c_applying_methods.py

@@ -23,7 +23,7 @@ def apply_class_method_clumping(summary_stats: SummaryStatistics) -> StudyLocus:
     from gentropy.method.window_based_clumping import WindowBasedClumping
 
     clumped_summary_statistics = WindowBasedClumping.clump(
-        summary_stats, window_length=500_000
+        summary_stats, distance=250_000
     )
     # --8<-- [end:apply_class_method_clumping]
     return clumped_summary_statistics

pyproject.toml

@@ -74,7 +74,7 @@ apache-airflow = "^2.8.0"
 apache-airflow-providers-google = "^10.13.1"
 pydoclint = ">=0.3.8,<0.5.0"
 prettier = "^0.0.7"
-deptry = "^0.12.0"
+deptry = ">=0.12,<0.15"
 python-semantic-release = ">=8.7,<10.0"
 yamllint = "^1.33.0"
 

src/airflow/dags/common_airflow.py

@@ -13,7 +13,7 @@
     DataprocSubmitJobOperator,
 )
 from airflow.utils.trigger_rule import TriggerRule
-from google.cloud import dataproc_v1
+from google.cloud import dataproc_v1, storage
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -59,6 +59,22 @@
 }
 
 
+def check_gcp_folder_exists(bucket_name: str, folder_path: str) -> bool:
+    """Check if a folder exists in a Google Cloud bucket.
+
+    Args:
+        bucket_name (str): The name of the Google Cloud bucket.
+        folder_path (str): The path of the folder to check.
+
+    Returns:
+        bool: True if the folder exists, False otherwise.
+    """
+    client = storage.Client()
+    bucket = client.get_bucket(bucket_name)
+    blobs = bucket.list_blobs(prefix=folder_path)
+    return any(blobs)
+
+
 def create_cluster(
     cluster_name: str,
     master_machine_type: str = "n1-highmem-16",

src/airflow/dags/eqtl_preprocess.py

@@ -15,11 +15,11 @@
 AUTOSCALING = "eqtl-preprocess"
 PROJECT_ID = "open-targets-genetics-dev"
 
-EQTL_CATALOG_SUSIE_LOCATION = "gs://eqtl_catalog_data/ebi_ftp/susie"
-TEMP_DECOMPRESS_LOCATION = "gs://eqtl_catalog_data/susie_decompressed_tmp"
+EQTL_CATALOG_SUSIE_LOCATION = "gs://eqtl_catalogue_data/ebi_ftp/susie"
+TEMP_DECOMPRESS_LOCATION = "gs://eqtl_catalogue_data/susie_decompressed_tmp"
 DECOMPRESS_FAILED_LOG = f"{TEMP_DECOMPRESS_LOCATION}.log"
-STUDY_INDEX_PATH = "gs://eqtl_catalog_data/study_index"
-CREDIBLE_SET_PATH = "gs://eqtl_catalog_data/credible_set_datasets/susie"
+STUDY_INDEX_PATH = "gs://eqtl_catalogue_data/study_index"
+CREDIBLE_SET_PATH = "gs://eqtl_catalogue_data/credible_set_datasets/susie"
 
 with DAG(
     dag_id=Path(__file__).stem,

src/airflow/dags/finngen_preprocess.py

@@ -26,7 +26,7 @@
 )
 FINNGEN_FM_SUMMARIES = "gs://genetics_etl_python_playground/input/Finngen_susie_finemapping_r10/Finngen_susie_credset_summary_r10.tsv"
 FINNGEN_PREFIX = "FINNGEN_R10_"
-FINNGEN_FM_OUT = "gs://genetics_etl_python_playground/output/python_etl/parquet/XX.XX/finngen_susie_processed"
+FINNGEN_FM_OUT = f"{FINNGEN_BUCKET}/credible_set_datasets/finngen_susie"
 
 with DAG(
     dag_id=Path(__file__).stem,

src/airflow/dags/genetics_etl.py

@@ -0,0 +1,160 @@
+"""Test DAG to prototype data transfer."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import common_airflow as common
+from airflow.models.dag import DAG
+from airflow.operators.python import ShortCircuitOperator
+from airflow.providers.google.cloud.transfers.gcs_to_gcs import GCSToGCSOperator
+from airflow.utils.task_group import TaskGroup
+
+CLUSTER_NAME = "otg-etl"
+SOURCE_CONFIG_FILE_PATH = Path(__file__).parent / "configs" / "dag.yaml"
+
+# Release specific variables:
+RELEASE_VERSION = "24.03"
+RELEASE_BUCKET_NAME = "genetics_etl_python_playground"
+
+# Datasource paths:
+GWAS_CATALOG_BUCKET_NAME = "gwas_catalog_data"
+EQTL_BUCKET_NAME = "eqtl_catalogue_data"
+FINNGEN_BUCKET_NAME = "finngen_data"
+FINNGEN_RELEASE = "r10"
+
+# Files to move:
+DATA_TO_MOVE = {
+    # GWAS Catalog summary study index:
+    "gwas_catalog_study_index": {
+        "source_bucket": GWAS_CATALOG_BUCKET_NAME,
+        "source_object": "study_index",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/study_index/gwas_catalog",
+    },
+    # PICS credible sets from GWAS Catalog curated associations:
+    "gwas_catalog_curated_credible_set": {
+        "source_bucket": GWAS_CATALOG_BUCKET_NAME,
+        "source_object": "credible_set_datasets/gwas_catalog_curated",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_pics_from_curation",
+    },
+    # PICS credible sets from GWAS Catalog summary statistics:
+    "gwas_catalog_sumstats_credible_set": {
+        "source_bucket": GWAS_CATALOG_BUCKET_NAME,
+        "source_object": "credible_set_datasets/gwas_catalog_summary_stats",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_pics_from_summary_statistics",
+    },
+    # GWAS Catalog manifest files:
+    "gwas_catalog_manifests": {
+        "source_bucket": GWAS_CATALOG_BUCKET_NAME,
+        "source_object": "manifests",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/manifests",
+    },
+    # eQTL Catalog study index:
+    "eqtl_catalogue_study_index": {
+        "source_bucket": EQTL_BUCKET_NAME,
+        "source_object": "study_index",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/study_index/eqtl_catalogue",
+    },
+    # eQTL Catalog SuSiE credible sets:
+    "eqtl_catalogue_susie_credible_set": {
+        "source_bucket": EQTL_BUCKET_NAME,
+        "source_object": "credible_set_datasets/susie",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/eqtl_catalogue_susie",
+    },
+    # Finngen study index:
+    "finngen_study_index": {
+        "source_bucket": FINNGEN_BUCKET_NAME,
+        "source_object": f"{FINNGEN_RELEASE}/study_index",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/study_index/finngen",
+    },
+    # Finngen summary statistics:
+    "finngen_PICS_credible_set": {
+        "source_bucket": FINNGEN_BUCKET_NAME,
+        "source_object": f"{FINNGEN_RELEASE}/credible_set_datasets/finngen_pics",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/finngen_pics",
+    },
+    # Finngen SuSiE credible sets:
+    "finngen_susie_credible_set": {
+        "source_bucket": FINNGEN_BUCKET_NAME,
+        "source_object": f"{FINNGEN_RELEASE}/credible_set_datasets/finngen_susie_processed",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/finngen_susie",
+    },
+    # L2G gold standard:
+    "gold_standard": {
+        "source_bucket": "genetics_etl_python_playground",
+        "source_object": "input/l2g/gold_standard/curation.json",
+        "destination_bucket": RELEASE_BUCKET_NAME,
+        "destination_object": f"releases/{RELEASE_VERSION}/locus_to_gene_gold_standard.json",
+    },
+}
+
+
+# This operator meant to fail the DAG if the release folder exists:
+ensure_release_folder_not_exists = ShortCircuitOperator(
+    task_id="test_release_folder_exists",
+    python_callable=lambda bucket, path: not common.check_gcp_folder_exists(
+        bucket, path
+    ),
+    op_kwargs={
+        "bucket": RELEASE_BUCKET_NAME,
+        "path": f"releases/{RELEASE_VERSION}",
+    },
+)
+
+with DAG(
+    dag_id=Path(__file__).stem,
+    description="Open Targets Genetics ETL workflow",
+    default_args=common.shared_dag_args,
+    **common.shared_dag_kwargs,
+):
+    # Compiling tasks for moving data to the right place:
+    with TaskGroup(group_id="data_transfer") as data_transfer:
+        # Defining the tasks to execute in the task group:
+        [
+            GCSToGCSOperator(
+                task_id=f"move_{data_name}",
+                source_bucket=data["source_bucket"],
+                source_object=data["source_object"],
+                destination_bucket=data["destination_bucket"],
+                destination_object=data["destination_object"],
+            )
+            for data_name, data in DATA_TO_MOVE.items()
+        ]
+
+    with TaskGroup(group_id="genetics_etl") as genetics_etl:
+        # Parse and define all steps and their prerequisites.
+        tasks = {}
+        steps = common.read_yaml_config(SOURCE_CONFIG_FILE_PATH)
+        for step in steps:
+            # Define task for the current step.
+            step_id = step["id"]
+            this_task = common.submit_step(
+                cluster_name=CLUSTER_NAME,
+                step_id=step_id,
+                task_id=step_id,
+            )
+            # Chain prerequisites.
+            tasks[step_id] = this_task
+            for prerequisite in step.get("prerequisites", []):
+                this_task.set_upstream(tasks[prerequisite])
+
+        common.generate_dag(cluster_name=CLUSTER_NAME, tasks=list(tasks.values()))
+
+    # DAG description:
+    (
+        # Test that the release folder doesn't exist:
+        ensure_release_folder_not_exists
+        # Run data transfer:
+        >> data_transfer
+        # Once datasets are transferred, run the rest of the steps:
+        >> genetics_etl
+    )

src/gentropy/assets/schemas/l2g_feature_matrix.json

@@ -125,6 +125,30 @@
       "name": "sqtlColocLlrMaximumNeighborhood",
       "nullable": true,
       "type": "float"
+    },
+    {
+      "metadata": {},
+      "name": "tuqtlColocClppMaximum",
+      "nullable": true,
+      "type": "float"
+    },
+    {
+      "metadata": {},
+      "name": "tuqtlColocClppMaximumNeighborhood",
+      "nullable": true,
+      "type": "float"
+    },
+    {
+      "metadata": {},
+      "name": "tuqtlColocLlrMaximum",
+      "nullable": true,
+      "type": "float"
+    },
+    {
+      "metadata": {},
+      "name": "tuqtlColocLlrMaximumNeighborhood",
+      "nullable": true,
+      "type": "float"
     }
   ],
   "type": "struct"

src/gentropy/assets/schemas/pairwise_ld.json

@@ -0,0 +1,23 @@
+{
+  "fields": [
+    {
+      "metadata": {},
+      "name": "variantIdI",
+      "nullable": false,
+      "type": "string"
+    },
+    {
+      "metadata": {},
+      "name": "variantIdJ",
+      "nullable": false,
+      "type": "string"
+    },
+    {
+      "metadata": {},
+      "name": "r",
+      "nullable": false,
+      "type": "double"
+    }
+  ],
+  "type": "struct"
+}