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Job request: 25817

Organisation:
Bennett Institute
Workspace:
migration-short-data-report
ID:
utaajaz27xrgwoho
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Yamina Boukari requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_full_study_cohort:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_full_study_cohort.py --output output/cohorts/full_study_cohort.arrow
    outputs:
      highly_sensitive:
         dataset: output/cohorts/full_study_cohort.arrow

  generate_dataset_for_census_2021:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_census_cohorts.py 
      --output output/cohorts/census_2021_study_cohort.arrow
      --
      --census-date "2021-03-21"
    outputs:
      highly_sensitive:
        dataset: output/cohorts/census_2021_study_cohort.arrow

  generate_dataset_for_census_2011:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_census_cohorts.py 
      --output output/cohorts/census_2011_study_cohort.arrow
      --
      --census-date "2011-03-27"
    outputs:
      highly_sensitive:
        dataset: output/cohorts/census_2011_study_cohort.arrow

  generate_pre_birth_migration_code_cohort:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_migration_code_before_birth_cohort.py --output output/cohorts/migration_code_before_birth_cohort.arrow
    outputs:
      highly_sensitive:
         dataset: output/cohorts/migration_code_before_birth_cohort.arrow  

  # generate_demographics_full_study_table:
  #   run: r:latest analysis/process_full_cohort_data.R 
  #   needs:
  #   - generate_full_study_cohort
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/demographics_full_study_cohort.csv


  generate_demographics_full_study_table_2cat:
    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_2cat.csv mig_status_2_cat
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_full_study_cohort_2cat.csv

  generate_demographics_full_study_table_3cat:
    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_3cat.csv mig_status_3_cat
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_full_study_cohort_3cat.csv

  generate_demographics_full_study_table_6cat:
    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_6cat.csv mig_status_6_cat
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_full_study_cohort_6cat.csv

  generate_demographics_census_2011_study_table_mig_2cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2011_study_cohort.arrow output/tables/demographics_census_2011_cohort_2cat.csv mig_status_2_cat
    needs:
    - generate_dataset_for_census_2011
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2011_cohort_2cat.csv

  generate_demographics_census_2011_study_table_mig_3cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2011_study_cohort.arrow output/tables/demographics_census_2011_cohort_3cat.csv mig_status_3_cat
    needs:
    - generate_dataset_for_census_2011
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2011_cohort_3cat.csv

  generate_demographics_census_2011_study_table_mig_6cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2011_study_cohort.arrow output/tables/demographics_census_2011_cohort_6cat.csv mig_status_6_cat
    needs:
    - generate_dataset_for_census_2011
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2011_cohort_6cat.csv

  generate_demographics_census_2021_study_table_2cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_2cat.csv mig_status_2_cat
    needs:
    - generate_dataset_for_census_2021
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2021_cohort_2cat.csv

  generate_demographics_census_2021_study_table_3cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_3cat.csv mig_status_3_cat
    needs:
    - generate_dataset_for_census_2021
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2021_cohort_3cat.csv
  
  generate_demographics_census_2021_study_table_6cat:
    run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_6cat.csv mig_status_6_cat
    needs:
    - generate_dataset_for_census_2021
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2021_cohort_6cat.csv

  generate_date_of_uk_entry_description:
    run: r:latest analysis/date_of_entry_to_uk.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/date_of_uk_entry_description.csv

  generate_annual_migrant_counts:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts.py --output output/tables/annual_migrant_counts.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_migrant_counts.csv

  generate_annual_migrant_counts_2cat:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_2cat.py --output output/tables/annual_migrant_counts_2cat.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_migrant_counts_2cat.csv

  generate_annual_migrant_counts_3cat:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_3cat.py --output output/tables/annual_migrant_counts_3cat.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_migrant_counts_3cat.csv 
  
  generate_annual_migrant_counts_6cat:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_6cat.py --output output/tables/annual_migrant_counts_6cat.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_migrant_counts_6cat.csv

  generate_annual_migrant_counts_migration_status_types:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_migration_status_types.py --output output/tables/annual_migrant_counts_migration_status_types.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_migrant_counts_migration_status_types.csv

  generate_migration_coding_summary:
    run: r:latest analysis/migration_coding.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/migration_coding_summary.csv

  generate_migration_code_combinations_summary:
    run: r:latest analysis/migration_coding_combinations.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/migration_code_combinations_summary.csv

  generate_migration_code_before_birth_combinations_summary:
    run: r:latest analysis/migration_code_before_birth_combinations.R
    needs:
    - generate_pre_birth_migration_code_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/migration_code_combinations_before_birth_summary.csv

  generate_date_variable_checks_summary:
    run: r:latest analysis/date_variable_checks.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/date_variable_checks.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:13:50

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Succeeded
Backend
TPP
Workspace
migration-short-data-report
Requested by
Yamina Boukari
Branch
main
Force run dependencies
No
Git commit hash
3383295
Requested actions
  • generate_demographics_full_study_table_2cat
  • generate_demographics_full_study_table_3cat
  • generate_demographics_full_study_table_6cat

Code comparison

Compare the code used in this job request