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Job request: 17341

Organisation:
Bennett Institute
Workspace:
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
ID:
qwmhmi3wldte7li4
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Chris Wood 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: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-03-31"
      --output-dir output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_ethnicity.csv.gz

  generate_study_population_weekly_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="interactive_codelists/codelist_1.csv"
      --param codelist_1_type="medication"
      --param codelist_2_path="interactive_codelists/codelist_2.csv"
      --param codelist_2_type="medication"
      --param codelist_1_frequency="weekly"
      --param time_value="0"
      --param time_ever="False"
      --param time_scale="weeks"
      --param time_event="before"
      --param codelist_2_comparison_date="end_date"
      --param operator="AND"
      --param population="adults"
      --param breakdowns=""
      --index-date_range="2023-04-10 to 2023-04-10 by week"
      --output-dir=output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ
      --output-format=csv.gz
      --output-file=output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_weekly_2023-04-10.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_weekly_2023-04-10.csv.gz

  generate_study_population_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="interactive_codelists/codelist_1.csv"
      --param codelist_1_type="medication"
      --param codelist_2_path="interactive_codelists/codelist_2.csv"
      --param codelist_2_type="medication"
      --param codelist_1_frequency="monthly"
      --param time_value="0"
      --param time_ever="False"
      --param time_scale="weeks"
      --param time_event="before"
      --param codelist_2_comparison_date="end_date"
      --param operator="AND"
      --param population="adults"
      --param breakdowns="sex,age,ethnicity,imd,region"
      --index-date-range="2019-09-01 to 2023-03-31 by month"
      --output-dir=output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_*.csv.gz

  join_cohorts_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_20*.csv.gz
        --rhs output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/input_ethnicity.csv.gz
        --output-dir output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined
    needs: [generate_study_population_01GYWGZWA5ZMCCS2SQ6Z26TKVQ, generate_study_population_ethnicity_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      highly_sensitive:
        cohort: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined/input_20*.csv.gz

  generate_measures_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      python:latest -m analysis.measures
        --breakdowns=sex
        --breakdowns=age
        --breakdowns=ethnicity
        --breakdowns=imd
        --breakdowns=region
        --input-dir="output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined"

    needs: [join_cohorts_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      moderately_sensitive:
        measure: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined/measure_all.csv
        decile_measure: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined/measure_practice_rate_deciles.csv

  top_5_table_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="interactive_codelists/codelist_1.csv"
      --codelist-2-path="interactive_codelists/codelist_2.csv"
      --output-dir="output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ"
    needs: [generate_measures_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      moderately_sensitive:
        tables: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/joined/top_5*.csv

  plot_measure_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns=sex
        --breakdowns=age
        --breakdowns=ethnicity
        --breakdowns=imd
        --breakdowns=region
        --output-dir output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ
    needs: [generate_measures_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      moderately_sensitive:
        measure: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/plot_measure*.png
        deciles: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/deciles_chart.png

  event_counts_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      python:latest python analysis/event_counts.py --input-dir="output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ" --output-dir="output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ"
    needs: [join_cohorts_01GYWGZWA5ZMCCS2SQ6Z26TKVQ, generate_study_population_weekly_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      moderately_sensitive:
        measure: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/event_counts.json

  generate_report_01GYWGZWA5ZMCCS2SQ6Z26TKVQ:
    run: >
      python:latest python analysis/render_report.py
      --output-dir="output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ"
      --population="adults"
      --breakdowns=sex
      --breakdowns=age
      --breakdowns=ethnicity
      --breakdowns=imd
      --breakdowns=region
      --codelist-1-name="Amoxicillin (oral)"
      --codelist-2-name="Oral prednisolone codes"
      --codelist-1-link="opensafely/amoxicillin-oral/164af813"
      --codelist-2-link="primis-covid19-vacc-uptake/astrxm2/v1.5.3"
      --time-value="0"
      --time-scale="weeks"
      --time-event="before"
      --start-date="2019-09-01"
      --end-date="2023-03-31"
    needs: [event_counts_01GYWGZWA5ZMCCS2SQ6Z26TKVQ, top_5_table_01GYWGZWA5ZMCCS2SQ6Z26TKVQ, plot_measure_01GYWGZWA5ZMCCS2SQ6Z26TKVQ]
    outputs:
      moderately_sensitive:
        notebook: output/01GYWGZWA5ZMCCS2SQ6Z26TKVQ/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 33:11:01

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

Job request

Status
Succeeded
Backend
TPP
Workspace
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
Requested by
Chris Wood
Branch
main
Force run dependencies
Yes
Git commit hash
1f334e1
Requested actions
  • run_all

Code comparison

Compare the code used in this job request