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Job request: 27454

Organisation:
Bennett Institute
Workspace:
migration-short-data-report
ID:
chzy7dddx7p3quk4
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_annual_migration_coding_counts
    Status:
    Pending
    Job identifier:
    j5zztssmxcrjm3nm
    Status message:
    waiting_on_db_workers: Waiting on available database workers

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 1 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 1 (0%) complete

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
migration-short-data-report
Requested by
Yamina Boukari
Branch
main
Force run dependencies
No
Git commit hash
dca0832
Requested actions
  • generate_annual_migration_coding_counts

Code comparison

Compare the code used in this job request