IMPC web api tasks migration #427
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…b_apiimpc_gene_diseases_mapperpy-to-use-airflow 399 migrate impc etljobsloadimpc web apiimpc gene diseases mapperpy to use airflow
…sk, use shared one
…b_apiimpc_batch_query_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_batch_query_mapper to use Airflow
…b_apiimpc_gene_search_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_gene_search_mapper to use Airflow
…b_apiimpc_idg_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_idg_mapper.py to use Airflow
…b_apiimpc_external_links_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_external_links_mapper to use Airflow
…b_apiimpc_gene_histopathology_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_external_links_mapper to use Airflow
…b_apiimpc_gene_images_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_gene_images_mapper to use Airflow
…b_apiimpc_phenotype_pleiotropy_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_phenotype_pleiotropy_mapper.py to use Airflow
…b_apiimpc_embryo_landing_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_embryo_landing_mapper.py to use Airflow
…b_apiimpc_gene_stats_results_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_gene_stats_results_mapper.py to use Airflow
francisco-ebi
commented
Sep 23, 2025
| "associationCurated", col("associationCurated").astype(BooleanType()) | ||
| ) | ||
|
|
||
| max_disease_df.coalesce(100).write.option("ignoreNullFields", "false").json( |
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Changed from repartition(500) to coalesce(100) for local development
francisco-ebi
commented
Sep 23, 2025
| impc_images_df.repartition(500).write.option("ignoreNullFields", "false").json( | ||
| output_path | ||
| ) | ||
| impc_images_df.coalesce(100).write.option("ignoreNullFields", "false").json( |
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Changed from repartition(500) to coalesce(100) for local development
francisco-ebi
commented
Sep 23, 2025
| stats_results_df = stats_results_df.withColumn( | ||
| "femaleMutantCount", col("femaleMutantCount").astype(IntegerType()) | ||
| ) | ||
| stats_results_df.distinct().coalesce(5).write.option( |
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Changed from repartition(1000) to coalesce(5) for local development
…b_apiimpc_gene_summary_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_gene_summary_mapper.py to use Airflow
francisco-ebi
commented
Sep 24, 2025
| "embryoExpressionObservationsAverage" | ||
| ), | ||
| ) | ||
| gene_avg_df.coalesce(10).write.option("ignoreNullFields", "false").json( |
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Changed from repartition(1) to coalesce(10) for local development
francisco-ebi
commented
Sep 24, 2025
| gene_avg_df.coalesce(10).write.option("ignoreNullFields", "false").json( | ||
| output_path + "_avgs" | ||
| ) | ||
| gene_df.coalesce(10).write.option("ignoreNullFields", "false").json( |
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Changed from repartition(100) to coalesce(10) for local development
…b_apiimpc_phenotype_search_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_phenotype_search_mapper.py to use Airflow
…b_apiimpc_phenotype_summary_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_phenotype_summary_mapper.py to use Airflow
…b_apiimpc_images_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_images_mapper.py to use Airflow
…b_apiimpc_histopathology_datasets_mapperpy-to-use-airflow Migrate impc_etl/jobs/load/impc_web_api/impc_histopathology_datasets_mapper.py to use Airflow
ficolo
requested changes
Sep 26, 2025
This was referenced Sep 26, 2025
ficolo
approved these changes
Sep 26, 2025
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Branch containing all migrated tasks related to the impc_web_api_mapper.py original task.
Added shared utils model