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feat: add multiple refresh job definitions for ClinVar controls with year and month parameters
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‎src/mavedb/lib/workflow/definitions.py‎

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@@ -49,6 +49,151 @@ def annotation_pipeline_job_definitions() -> list[JobDefinition]:
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},
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"dependencies": [("submit_uniprot_mapping_jobs_for_score_set", DependencyType.SUCCESS_REQUIRED)],
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},
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# TODO#650: Simplify or automate the generation of these repetitive job definitions
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{
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"key": "refresh_clinvar_controls_201502",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2015,
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"month": 2,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_201601",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2016,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_201701",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2017,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_201801",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2018,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_201901",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2019,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202001",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2020,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202101",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2021,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202201",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2022,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202301",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2023,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202401",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2024,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202501",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2025,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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{
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"key": "refresh_clinvar_controls_202601",
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"function": "refresh_clinvar_controls",
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"type": JobType.MAPPED_VARIANT_ANNOTATION,
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"params": {
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"correlation_id": None, # Required param to be filled in at runtime
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"score_set_id": None, # Required param to be filled in at runtime
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"year": 2026,
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"month": 1,
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},
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"dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)],
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},
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]
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