refactor: reorder tasks in genetics_etl (#62)

Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
opentargets · Oct 29, 2024 · 41c73b6 · 41c73b6
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diff --git a/src/ot_orchestration/dags/config/genetics_etl.yaml b/src/ot_orchestration/dags/config/genetics_etl.yaml
@@ -1,4 +1,3 @@
-gwas_catalog_manifests_path: gs://gwas_catalog_data/manifests
 l2g_gold_standard_path: gs://genetics_etl_python_playground/input/l2g/gold_standard/curation.json
 release_dir: gs://ot_orchestration/releases/24.10_freeze5
 dataproc:
@@ -34,7 +33,7 @@ nodes:
         - gs://finngen_data/r11/study_index
       step.target_index_path: gs://ot_orchestration/releases/24.10_freeze5/gene_index
       step.disease_index_path: gs://open-targets-pre-data-releases/24.06/output/etl/parquet/diseases
-      step.valid_study_index_path: &valid_study_index gs://ot_orchestration/releases/24.10_freeze5/study_index
+      step.valid_study_index_path: gs://ot_orchestration/releases/24.10_freeze5/study_index
       step.invalid_study_index_path: gs://ot_orchestration/releases/24.10_freeze5/invalid_study_index
       step.biosample_index_path: gs://ot_orchestration/releases/24.10_freeze5/biosample_index
       step.invalid_qc_reasons:
@@ -51,15 +50,15 @@ nodes:
       - study_validation
     params:
       step: credible_set_validation
-      step.study_index_path: *valid_study_index
+      step.study_index_path: gs://ot_orchestration/releases/24.10_freeze5/study_index
       step.study_locus_path:
         - gs://gwas_catalog_top_hits/credible_sets/
         - gs://gwas_catalog_sumstats_pics/credible_sets/
         - gs://gwas_catalog_sumstats_susie/credible_set_clean/
         - gs://eqtl_catalogue_data/credible_set_datasets/eqtl_catalogue_susie/
         - gs://ukb_ppp_eur_data/credible_set_clean/
         - gs://finngen_data/r11/credible_set_datasets/susie/
-      step.valid_study_locus_path: &valid_credible_set gs://ot_orchestration/releases/24.10_freeze5/credible_set
+      step.valid_study_locus_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.invalid_study_locus_path: gs://ot_orchestration/releases/24.10_freeze5/invalid_credible_set
       step.invalid_qc_reasons:
         - DUPLICATED_STUDYLOCUS_ID
@@ -171,7 +170,7 @@ nodes:
     command: gs://genetics_etl_python_playground/initialisation/0.0.0/cli.py
     params:
       step: colocalisation
-      step.credible_set_path: *valid_credible_set
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.coloc_path: gs://ot_orchestration/releases/24.10_freeze5/colocalisation
       step.colocalisation_method: ECaviar
       step.session.spark_uri: yarn
@@ -181,7 +180,7 @@ nodes:
     command: gs://genetics_etl_python_playground/initialisation/0.0.0/cli.py
     params:
       step: colocalisation
-      step.credible_set_path: *valid_credible_set
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.coloc_path: gs://ot_orchestration/releases/24.10_freeze5/colocalisation/
       step.colocalisation_method: Coloc
       step.session.spark_uri: yarn
@@ -192,10 +191,10 @@ nodes:
     command: gs://genetics_etl_python_playground/initialisation/0.0.0/cli.py
     params:
       step: locus_to_gene_feature_matrix
-      step.credible_set_path: *valid_credible_set
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.variant_index_path: gs://ot_orchestration/releases/24.10_freeze5/variant_index
       step.colocalisation_path: gs://ot_orchestration/releases/24.10_freeze5/colocalisation
-      step.study_index_path: *valid_study_index
+      step.study_index_path: gs://ot_orchestration/releases/24.10_freeze5/study_index
       step.gene_index_path: gs://ot_orchestration/releases/24.10_freeze5/gene_index
       step.feature_matrix_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_feature_matrix
       +step.session.extended_spark_conf: "{spark.sql.autoBroadcastJoinThreshold:'-1'}"
@@ -213,7 +212,7 @@ nodes:
       step.wandb_run_name: "24.10"
       step.hf_hub_repo_id: opentargets/locus_to_gene
       step.model_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_model/classifier.skops
-      step.credible_set_path: *valid_credible_set
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.variant_index_path: gs://ot_orchestration/releases/24.10_freeze5/variant_index
       step.feature_matrix_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_feature_matrix
       step.gold_standard_curation_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_gold_standard.json
@@ -233,7 +232,7 @@ nodes:
       step.run_mode: predict
       step.predictions_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_predictions
       step.feature_matrix_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_feature_matrix
-      step.credible_set_path: *valid_credible_set
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
       step.session.spark_uri: yarn
     prerequisites:
       - l2g_train
@@ -243,8 +242,8 @@ nodes:
       step: locus_to_gene_evidence
       step.evidence_output_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_evidence
       step.locus_to_gene_predictions_path: gs://ot_orchestration/releases/24.10_freeze5/locus_to_gene_predictions
-      step.credible_set_path: *valid_credible_set
-      step.study_index_path: *valid_study_index
+      step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze5/credible_set
+      step.study_index_path: gs://ot_orchestration/releases/24.10_freeze5/study_index
       step.locus_to_gene_threshold: 0.05
       step.session.spark_uri: yarn
     prerequisites:

diff --git a/src/ot_orchestration/dags/genetics_etl.py b/src/ot_orchestration/dags/genetics_etl.py
@@ -5,7 +5,7 @@
 import time
 from pathlib import Path
 
-from airflow.decorators import task, task_group
+from airflow.decorators import task
 from airflow.models.baseoperator import chain
 from airflow.models.dag import DAG
 from airflow.providers.google.cloud.operators.cloud_batch import (
@@ -44,103 +44,13 @@
 SOURCE_CONFIG_FILE_PATH = Path(__file__).parent / "config" / "genetics_etl.yaml"
 config = read_yaml_config(SOURCE_CONFIG_FILE_PATH)
 nodes = config["nodes"]
-gwas_catalog_manifests_path = GCSPath(config["gwas_catalog_manifests_path"])
-l2g_gold_standard_path = GCSPath(config["l2g_gold_standard_path"])
-release_dir = GCSPath(config["release_dir"])
-variant_annotation_task_group_config = find_node_in_config(nodes, "variant_annotation")
+node_map = {}
 
 
 # FIXME: eventually this task group should have 2 steps only
 # - 1. transform variant sources to vcf files, collect and partition them by chunk size - should be done by a single gentropy step rather then
 # multiple tasks in the DAG (pending)
 # - 2. list new chunk vcf files and annotate them - batch job
-@task_group(group_id="variant_annotation")
-def variant_annotation():
-    """Variant annotation task group."""
-    task_config = find_node_in_config(
-        variant_annotation_task_group_config["nodes"], "variant_to_vcf"
-    )
-
-    google_batch_config = task_config["google_batch"]
-
-    commands = create_task_commands(
-        commands=google_batch_config["commands"],
-        params=task_config["params"],
-    )
-
-    task = create_task_spec(
-        image=google_batch_config["image"],
-        commands=commands,
-        resource_specs=google_batch_config["resource_specs"],
-        task_specs=google_batch_config["task_specs"],
-        entrypoint=google_batch_config["entrypoint"],
-    )
-
-    environment = google_batch_config["environment"]
-    batch_job = create_batch_job(
-        task=task,
-        task_env=create_task_env(environment),
-        policy_specs=google_batch_config["policy_specs"],
-    )
-    variant_to_vcf = CloudBatchSubmitJobOperator(
-        task_id="variant_to_vcf",
-        project_id=GCP_PROJECT_GENETICS,
-        region=GCP_REGION,
-        job_name=f"variant-to-vcf-job-{time.strftime('%Y%m%d-%H%M%S')}",
-        job=batch_job,
-        deferrable=False,
-    )
-
-    task_config = find_node_in_config(
-        config=variant_annotation_task_group_config["nodes"],
-        node_id="list_nonannotated_vcfs",
-    )["params"]
-
-    merged_vcfs = ConvertVariantsToVcfOperator(
-        task_id="list_nonannotated_vcfs",
-        tsv_files_glob=task_config["input_vcf_glob"],
-        output_path=task_config["output_path"],
-        chunk_size=task_config["chunk_size"],
-    )
-
-    task_config = find_node_in_config(
-        variant_annotation_task_group_config["nodes"], "vep_annotation"
-    )
-    task_config_params = task_config["params"]
-    vep_annotation = VepAnnotateOperator(
-        task_id=task_config["id"],
-        vcf_input_path=task_config_params["vcf_input_path"],
-        vep_output_path=task_config_params["vep_output_path"],
-        vep_cache_path=task_config_params["vep_cache_path"],
-        google_batch=task_config["google_batch"],
-    )
-    chain_dependencies(
-        nodes=variant_annotation_task_group_config["nodes"],
-        tasks_or_task_groups={
-            "variant_to_vcf": variant_to_vcf,
-            "list_nonannotated_vcfs": merged_vcfs,
-            "vep_annotation": vep_annotation,
-        },
-    )
-
-
-# Files to move:
-DATA_TO_MOVE = {
-    # GWAS Catalog manifest files:
-    "gwas_catalog_manifests": {
-        "source_bucket": gwas_catalog_manifests_path.bucket,
-        "source_object": gwas_catalog_manifests_path.path,
-        "destination_bucket": release_dir.bucket,
-        "destination_object": f"{release_dir.path}/manifests/",
-    },
-    # L2G gold standard:
-    "l2g_gold_standard": {
-        "source_bucket": l2g_gold_standard_path.bucket,
-        "source_object": l2g_gold_standard_path.path,
-        "destination_bucket": release_dir.bucket,
-        "destination_object": f"{release_dir.path}/locus_to_gene_gold_standard.json",
-    },
-}
 
 
 # This operator meant to fail the DAG if the release folder exists:
@@ -153,6 +63,18 @@ def variant_annotation():
     # 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:
+        l2g_gold_standard_path = GCSPath(config["l2g_gold_standard_path"])
+        release_dir = GCSPath(config["release_dir"])
+        # Files to move:
+        DATA_TO_MOVE = {
+            # L2G gold standard:
+            "l2g_gold_standard": {
+                "source_bucket": l2g_gold_standard_path.bucket,
+                "source_object": l2g_gold_standard_path.path,
+                "destination_bucket": release_dir.bucket,
+                "destination_object": f"{release_dir.path}/locus_to_gene_gold_standard.json",
+            },
+        }
         [
             GCSToGCSOperator(
                 task_id=f"move_{data_name}",
@@ -165,9 +87,80 @@ def variant_annotation():
         ]
 
     with TaskGroup(group_id="genetics_etl") as genetics_etl:
-        # Register all TaskGroups as nodes
-        node_map = {"variant_annotation": variant_annotation()}
-        # Register all standalone dataproc tasks
+        # ===== Variant annotation task group ======
+        with TaskGroup(group_id="variant_annotation") as variant_annotation:
+            variant_annotation_task_group_config = find_node_in_config(
+                nodes, "variant_annotation"
+            )
+
+            # ===== Convert variant datasource to vcf file step ======
+            task_config = find_node_in_config(
+                variant_annotation_task_group_config["nodes"],
+                node_id="variant_to_vcf",
+            )
+            google_batch_config = task_config["google_batch"]
+            commands = create_task_commands(
+                commands=google_batch_config["commands"],
+                params=task_config["params"],
+            )
+            task = create_task_spec(
+                image=google_batch_config["image"],
+                commands=commands,
+                resource_specs=google_batch_config["resource_specs"],
+                task_specs=google_batch_config["task_specs"],
+                entrypoint=google_batch_config["entrypoint"],
+            )
+            environment = google_batch_config["environment"]
+            batch_job = create_batch_job(
+                task=task,
+                task_env=create_task_env(environment),
+                policy_specs=google_batch_config["policy_specs"],
+            )
+            variant_to_vcf = CloudBatchSubmitJobOperator(
+                task_id="variant_to_vcf",
+                project_id=GCP_PROJECT_GENETICS,
+                region=GCP_REGION,
+                job_name=f"variant-to-vcf-job-{time.strftime('%Y%m%d-%H%M%S')}",
+                job=batch_job,
+                deferrable=False,
+            )
+
+            # ===== Partition vcf files into chunks step ======
+            task_config = find_node_in_config(
+                config=variant_annotation_task_group_config["nodes"],
+                node_id="list_nonannotated_vcfs",
+            )
+            merged_vcfs = ConvertVariantsToVcfOperator(
+                task_id="list_nonannotated_vcfs",
+                tsv_files_glob=task_config["params"]["input_vcf_glob"],
+                output_path=task_config["params"]["output_path"],
+                chunk_size=task_config["params"]["chunk_size"],
+            )
+            # ===== Perform VEP annotations on chunks step =====
+            task_config = find_node_in_config(
+                variant_annotation_task_group_config["nodes"],
+                node_id="vep_annotation",
+            )
+            task_config_params = task_config["params"]
+            vep_annotation = VepAnnotateOperator(
+                task_id=task_config["id"],
+                vcf_input_path=task_config_params["vcf_input_path"],
+                vep_output_path=task_config_params["vep_output_path"],
+                vep_cache_path=task_config_params["vep_cache_path"],
+                google_batch=task_config["google_batch"],
+            )
+
+            chain_dependencies(
+                nodes=variant_annotation_task_group_config["nodes"],
+                tasks_or_task_groups={
+                    "variant_to_vcf": variant_to_vcf,
+                    "list_nonannotated_vcfs": merged_vcfs,
+                    "vep_annotation": vep_annotation,
+                },
+            )
+            node_map["variant_annotation"] = variant_annotation
+        # ===== END Variant annotation task group ======
+
         tasks = [node for node in nodes if node.get("kind", "Task") == "Task"]
         # Build individual tasks and register them as nodes.
         for task in tasks: