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Job request: 10338

Organisation:
Bennett Institute
Workspace:
opensafely-interactive
ID:
sqtunuu6rvkxs2p2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher opensafely-interactive requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  codelist_report_02qRUrkRtlvitCp1nAfNfc:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelist.csv
        --start-date=2019-09-01
        --end-date=2022-07-06
        --output-dir output/02qRUrkRtlvitCp1nAfNfc
    outputs:
      moderately_sensitive:
        table: output/02qRUrkRtlvitCp1nAfNfc/counts_per_*.csv
        list_sizes: output/02qRUrkRtlvitCp1nAfNfc/list_sizes.csv
        patient_count_table: output/02qRUrkRtlvitCp1nAfNfc/patient_count.csv

  measures_02qRUrkRtlvitCp1nAfNfc:
    run: >
      python:latest python analysis/generate_measures.py
        --start-date=2019-09-01
        --end-date=2022-07-06
        --output-dir output/02qRUrkRtlvitCp1nAfNfc
        --low-count-threshold 100
        --rounding-base 10
    needs: [codelist_report_02qRUrkRtlvitCp1nAfNfc]
    outputs:
      moderately_sensitive:
        measure: output/02qRUrkRtlvitCp1nAfNfc/measure_counts_per_week_per_practice.csv
        events_count_table: output/02qRUrkRtlvitCp1nAfNfc/for_release/event_counts.csv
        practice_count_table: output/02qRUrkRtlvitCp1nAfNfc/for_release/practice_count.csv

  top_5_table_02qRUrkRtlvitCp1nAfNfc:
    run: >
      python:latest python analysis/top_codes_table.py
        --start-date=2019-09-01
        --end-date=2022-07-06
        --output-dir output/02qRUrkRtlvitCp1nAfNfc
        --low-count-threshold 100
        --rounding-base 10
    needs: [codelist_report_02qRUrkRtlvitCp1nAfNfc]
    outputs:
      moderately_sensitive:
        table: output/02qRUrkRtlvitCp1nAfNfc/for_release/top_5_code_table.csv

  deciles_charts_02qRUrkRtlvitCp1nAfNfc:
    run: >
      deciles-charts:v0.0.24
        --input-files output/02qRUrkRtlvitCp1nAfNfc/measure_counts_per_week_per_practice.csv
        --output-dir output/02qRUrkRtlvitCp1nAfNfc/for_release
    config:
      show_outer_percentiles: false
      tables:
        output: false
      charts:
        output: true
    needs: [measures_02qRUrkRtlvitCp1nAfNfc]
    outputs:
      moderately_sensitive:
        deciles_charts: output/02qRUrkRtlvitCp1nAfNfc/for_release/deciles_*.*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:24

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

Job information

Status
Succeeded
Backend
TPP
Workspace
opensafely-interactive
Requested by
opensafely-interactive
Branch
main
Force run dependencies
Yes
Git commit hash
b2a3afc
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request