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Job request: 26029

Organisation:
Bennett Institute
Workspace:
death-report
ID:
bquiafuusgz3yxi6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Pesce 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:
    dataset_death_raw
    Status:
    Succeeded
    Job identifier:
    egwgggb3rnpcri5w
  • Action:
    dataset_death_processed
    Status:
    Succeeded
    Job identifier:
    wlini2jwvym27cym
  • Action:
    report_implausible_death_dates
    Status:
    Succeeded
    Job identifier:
    j2mcbhtgg7cmdnv3
  • Action:
    report_registration_at_death
    Status:
    Succeeded
    Job identifier:
    dnwbr5ddtnki3sjv
  • Action:
    report_death_source_comparison
    Status:
    Succeeded
    Job identifier:
    i7fck32s3vf5b5ab
  • Action:
    report_sources_date_agreement
    Status:
    Succeeded
    Job identifier:
    pxmpw6vtkmpfsqzk
  • Action:
    report_variation_source_by_practice
    Status:
    Succeeded
    Job identifier:
    wnpysszrr7mjirtt

Pipeline

Show project.yaml 
version: '5.0'

actions:

  dataset_death_raw:
    run: ehrql:v1 generate-dataset analysis/dataset_def/dataset_definition.py 
      --output output/highly_sensitive/dataset_death_TPP_ONS.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/highly_sensitive/dataset_death_TPP_ONS.csv.gz

  dataset_death_processed:
    run: r:v2 analysis/1_derive_key_variables.R 
    needs: [dataset_death_raw]
    outputs:
      highly_sensitive:
        csv: output/highly_sensitive/death_registration_processed.csv.gz
      moderately_sensitive:
        txt: output/analysis_tables/death_registration_processed_skim.txt
        csv: output/analysis_tables/table_source_raw.csv


  report_implausible_death_dates:
    run: r:v2 analysis/2_implausible_death_dates.R 
    needs: [dataset_death_processed]
    outputs:
      moderately_sensitive:
        death_implausible_source: output/analysis_tables/death_implausible_source.csv

  report_registration_at_death:
    run: r:v2 analysis/3_registration_at_death.R 
    needs: [dataset_death_processed]
    outputs:
      moderately_sensitive:
        registration_status_source: output/analysis_tables/registration_status_source.csv 
        reg_start_timing_source: output/analysis_tables/reg_start_timing_source.csv
        reg_end_timing_source: output/analysis_tables/reg_end_timing_source.csv

  report_death_source_comparison:
    run: r:v2 analysis/4_death_source_comparison.R 
    needs: [dataset_death_processed]
    outputs:
      moderately_sensitive:
        table_death_source: output/analysis_tables/table_death_source.csv
        table_death_source_25_26: output/analysis_tables/table_death_source_25_26.csv
        tpp_death_code_or_date: output/analysis_tables/tpp_death_code_or_date.csv
        table_death_source_overall_any_tpp: output/analysis_tables/table_death_source_overall_any_tpp.csv

  report_sources_date_agreement:
    run: r:v2 analysis/5_sources_date_agreement.R 
    needs: [dataset_death_processed]
    outputs:
      moderately_sensitive:
        table_ons_tpp_dates_diff: output/analysis_tables/table_ons_tpp_dates_diff.csv
  
  report_variation_source_by_practice:
    run: r:v2 analysis/6_variation_source_by_practice.R 
    needs: [dataset_death_processed]
    outputs:
      moderately_sensitive:
        table_practice_percentiles: output/analysis_tables/table_practice_percentiles.csv
  
# end----

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:17:10

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

Job request

Status
Succeeded
Backend
TPP
Workspace
death-report
Requested by
Martina Pesce
Branch
main
Force run dependencies
Yes
Git commit hash
013342b
Requested actions
  • dataset_death_raw
  • dataset_death_processed
  • report_implausible_death_dates
  • report_registration_at_death
  • report_death_source_comparison
  • report_sources_date_agreement
  • report_variation_source_by_practice

Code comparison

Compare the code used in this job request