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Job request: 27247

Organisation:
Bennett Institute
Workspace:
migration-short-data-report
ID:
d66nktisrn4usyeu
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

  • Action:
    generate_dataset_for_census_2011
    Status:
    Succeeded
    Job identifier:
    h6awe2jdbvi4bs4t
  • Action:
    generate_dataset_for_census_2021
    Status:
    Succeeded
    Job identifier:
    sxvth7rzqrgf7buq
  • Action:
    generate_full_study_cohort
    Status:
    Running
    Job identifier:
    k6ojf5cqw2a4bm6z
  • Action:
    generate_demographics_census_2011_study_table_mig_3cat_withdoe
    Status:
    Succeeded
    Job identifier:
    t4s5hihcjrd62duv
  • Action:
    generate_demographics_census_2021_study_table_3cat_withdoe
    Status:
    Succeeded
    Job identifier:
    6xnw5bzr2pa2iuuu
  • Action:
    generate_histogram_migration_codes_without_date_restrictions
    Status:
    Pending
    Job identifier:
    33w6addpjcr5np5i
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_migration_coding_summary
    Status:
    Pending
    Job identifier:
    eafh5k2anvmmiafe
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_demographics_full_study_table_migration_types
    Status:
    Pending
    Job identifier:
    xg7eamtmv4636s33
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_demographics_full_study_table_3cat_withdoe
    Status:
    Pending
    Job identifier:
    4gt77masdj2oyrpb
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_summary_migration_codes_without_date_restrictions
    Status:
    Pending
    Job identifier:
    7vtkvu7nsrmkocxp
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'

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_demographics_full_study_table_3cat_withdoe:
    run: r:v2 analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_full_study_cohort_3cat_withdoe.csv

  # generate_demographics_full_study_table_6cat_withdoe:
  #   run: r:v2 analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_6cat_withdoe.csv mig_status_6_cat_withdoe
  #   needs:
  #   - generate_full_study_cohort
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/demographics_full_study_cohort_6cat_withdoe.csv

  generate_demographics_full_study_table_migration_types:
    run: r:v2 analysis/process_full_cohort_data_migration_types.R 
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_full_study_cohort_migration_types.csv

  # generate_demographics_uk_entry_cohort:
  #   run: r:v2 analysis/process_date_of_uk_entry_cohort.R 
  #   needs:
  #   - generate_full_study_cohort
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/demographics_date_of_uk_entry_and_no_other_migration_info_cohort.csv

  generate_demographics_census_2011_study_table_mig_3cat_withdoe:
    run: r:v2 analysis/process_census_cohort_data.R output/cohorts/census_2011_study_cohort.arrow output/tables/demographics_census_2011_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
    needs:
    - generate_dataset_for_census_2011
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2011_cohort_3cat_withdoe.csv

  # generate_demographics_census_2011_study_table_mig_6cat_withdoe:
  #   run: r:v2 analysis/process_census_cohort_data.R output/cohorts/census_2011_study_cohort.arrow output/tables/demographics_census_2011_cohort_6cat_withdoe.csv mig_status_6_cat_withdoe
  #   needs:
  #   - generate_dataset_for_census_2011
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/demographics_census_2011_cohort_6cat_withdoe.csv

  generate_demographics_census_2021_study_table_3cat_withdoe:
    run: r:v2 analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
    needs:
    - generate_dataset_for_census_2021
    outputs:
      moderately_sensitive:
        csv: output/tables/demographics_census_2021_cohort_3cat_withdoe.csv
  
  # generate_demographics_census_2021_study_table_6cat_withdoe:
  #   run: r:v2 analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_6cat_withdoe.csv mig_status_6_cat_withdoe
  #   needs:
  #   - generate_dataset_for_census_2021
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/demographics_census_2021_cohort_6cat_withdoe.csv

  generate_age_summary_census_2011_mig_3cat_withdoe:
    run: r:v2 analysis/census_cohort_age_summary.R output/cohorts/census_2011_study_cohort.arrow output/tables/age_summary_census_2011_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
    needs:
    - generate_dataset_for_census_2011
    outputs:
      moderately_sensitive:
        csv: output/tables/age_summary_census_2011_cohort_3cat_withdoe.csv

  generate_age_summary_census_2021_mig_3cat_withdoe:
    run: r:v2 analysis/census_cohort_age_summary.R output/cohorts/census_2021_study_cohort.arrow output/tables/age_summary_census_2021_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
    needs:
    - generate_dataset_for_census_2021
    outputs:
      moderately_sensitive:
        csv: output/tables/age_summary_census_2021_cohort_3cat_withdoe.csv

  generate_date_of_uk_entry_description:
    run: r:v2 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_date_of_uk_entry_description_combinations:
    run: r:v2 analysis/date_of_entry_to_uk_combinations.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/date_of_uk_entry_combinations.csv

  generate_annual_migrant_counts_3cat_withdoe:
    run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_3cat_withdoe.py --output output/tables/annual_counts/3cat_withdoe/:csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_counts/3cat_withdoe/*.csv 
  
  # generate_annual_migrant_counts_6cat_withdoe:
  #   run: ehrql:v1 generate-measures analysis/generate_annual_migrant_counts_6cat_withdoe.py --output output/tables/annual_counts/6cat_withdoe/:csv
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/tables/annual_counts/6cat_withdoe/*.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_counts/migration_status_types/:csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_counts/migration_status_types/*.csv

  generate_migration_coding_summary:
    run: r:v2 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:v2 analysis/migration_coding_combinations.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/migration_code_combinations_summary.csv

  generate_date_variable_checks_summary:
    run: r:v2 analysis/date_variable_checks.R
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/date_variable_checks.csv

  generate_annual_migration_coding_counts:
    run: ehrql:v1 generate-measures analysis/annual_code_counts.py --output output/tables/annual_counts/migration_coding_occ_comparison.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_counts/migration_coding_occ_comparison.csv

  generate_primary_care_planned_encounters:
    run: ehrql:v1 generate-measures analysis/primary_care_activity_comparisons.py --output output/tables/annual_counts/primary_care_comparison.csv
    outputs:
      moderately_sensitive:
        csv: output/tables/annual_counts/primary_care_comparison.csv

  generate_histogram_migration_codes_without_date_restrictions:
    run: r:v2 analysis/histogram_migration_codes_without_date_restrictions.r
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        png: output/figures/histogram_migration_coding_no_restrictions.png

  generate_summary_migration_codes_without_date_restrictions:
    run: r:v2 analysis/summary_migration_codes_without_date_restrictions.r
    needs:
    - generate_full_study_cohort
    outputs:
      moderately_sensitive:
        csv: output/tables/summary_migration_coding_without_restrictions_by_mig_status.csv

Job statistics

Status Count Percentage
Pending 5 50%
Running 1 10%
Succeeded 4 40%
Failed 0 0%

4 / 10 (40%) complete

Timeline

  • Created:

  • Started:

  • Runtime: 01:09:05

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

Job request

Status
Running
Backend
TPP
Workspace
migration-short-data-report
Requested by
Yamina Boukari
Branch
main
Force run dependencies
Yes
Git commit hash
dca0832
Requested actions
  • generate_full_study_cohort
  • generate_dataset_for_census_2021
  • generate_dataset_for_census_2011
  • generate_demographics_full_study_table_3cat_withdoe
  • generate_demographics_full_study_table_migration_types
  • generate_demographics_census_2011_study_table_mig_3cat_withdoe
  • generate_demographics_census_2021_study_table_3cat_withdoe
  • generate_migration_coding_summary
  • generate_histogram_migration_codes_without_date_restrictions
  • generate_summary_migration_codes_without_date_restrictions

Code comparison

Compare the code used in this job request