Job request: 16716

Organisation:: Bennett Institute
Workspace:: opensafely-internal-interactive
ID:: 5hnwhzxdf3kz7zcp

This page shows the technical details of what happened when the authorised researcher Catherine Stables 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:

plot_measure_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

jh3ku6qn5qsjkjoq

Error:

cancelled_by_user: Cancelled by user
Action:

top_5_table_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

eimkgxy5tafsvqgd

Error:

cancelled_by_user: Cancelled by user
Action:

deciles_chart_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

le6itythwfm3r3pm

Error:

cancelled_by_user: Cancelled by user
Action:

event_counts_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

jjfiu3rgx6tbtttu

Error:

cancelled_by_user: Cancelled by user
Action:

generate_study_population_ethnicity_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

yyjmsujngcox2uln

Error:

cancelled_by_user: Cancelled by user
Action:

generate_study_population_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

kdnxcilmiaos7757

Error:

cancelled_by_user: Cancelled by user
Action:

join_cohorts_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

swurzlmzt5ie2azt

Error:

cancelled_by_user: Cancelled by user
Action:

generate_measures_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

ls6royhkj5uhuth7

Error:

cancelled_by_user: Cancelled by user
Action:

generate_report_01GWHQX96BFQ43TJ9J342Y234M

Status:

Failed

Job identifier:

bynedokb5kojlwvn

Error:

cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GWHQX96BFQ43TJ9J342Y234M:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-03-15"
      --output-dir output/01GWHQX96BFQ43TJ9J342Y234M --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GWHQX96BFQ43TJ9J342Y234M/input_ethnicity.csv.gz


  generate_study_population_01GWHQX96BFQ43TJ9J342Y234M:
    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="event"
      --param codelist_1_frequency="monthly"
      --param time_value="5"
      --param time_scale="years"
      --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="2022-09-16 to 2023-03-15 by month"
      --output-dir=output/01GWHQX96BFQ43TJ9J342Y234M
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GWHQX96BFQ43TJ9J342Y234M/input_*.csv.gz

  join_cohorts_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GWHQX96BFQ43TJ9J342Y234M/input_20*.csv.gz
        --rhs output/01GWHQX96BFQ43TJ9J342Y234M/input_ethnicity.csv.gz
        --output-dir output/01GWHQX96BFQ43TJ9J342Y234M/joined
    needs: [generate_study_population_01GWHQX96BFQ43TJ9J342Y234M, generate_study_population_ethnicity_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      highly_sensitive:
        cohort: output/01GWHQX96BFQ43TJ9J342Y234M/joined/input_20*.csv.gz

  generate_measures_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      python:latest -m analysis.measures
        --breakdowns="sex,age,ethnicity,imd,region"
        --input_dir="output/01GWHQX96BFQ43TJ9J342Y234M/joined"
        --measure="med_review"

    needs: [join_cohorts_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        measure: output/01GWHQX96BFQ43TJ9J342Y234M/joined/measure*rate.csv
        decile_measure: output/01GWHQX96BFQ43TJ9J342Y234M/joined/measure*rate_deciles.csv

  top_5_table_01GWHQX96BFQ43TJ9J342Y234M:
    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/01GWHQX96BFQ43TJ9J342Y234M"
    needs: [generate_measures_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        tables: output/01GWHQX96BFQ43TJ9J342Y234M/joined/top_5*.csv

  deciles_chart_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GWHQX96BFQ43TJ9J342Y234M/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GWHQX96BFQ43TJ9J342Y234M/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GWHQX96BFQ43TJ9J342Y234M/joined/deciles_*.*

  plot_measure_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age,ethnicity,imd,region"
        --output-dir output/01GWHQX96BFQ43TJ9J342Y234M
    needs: [generate_measures_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        measure: output/01GWHQX96BFQ43TJ9J342Y234M/plot_measure*.png

  event_counts_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GWHQX96BFQ43TJ9J342Y234M/joined" --output_dir="output/01GWHQX96BFQ43TJ9J342Y234M"
    needs: [join_cohorts_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        measure: output/01GWHQX96BFQ43TJ9J342Y234M/event_counts.json

  generate_report_01GWHQX96BFQ43TJ9J342Y234M:
    run: >
      python:latest python analysis/render_report.py
      --output-dir="output/01GWHQX96BFQ43TJ9J342Y234M"
      --report-title="OpenPrescribing Measure: Co-amoxiclav, cephalosporins and quinolones (numerato & Chronic obstructive pulmonary disease (COPD) codes"
      --population="adults"
      --breakdowns="sex,age,ethnicity,imd,region"
      --codelist-1-name="OpenPrescribing Measure: Co-amoxiclav, cephalosporins and quinolones (numerato"
      --codelist-2-name="Chronic obstructive pulmonary disease (COPD) codes"
      --codelist-1-link="opensafely/co-amoxiclav-cephalosporins-and-quinolones/0d299a50"
      --codelist-2-link="nhsd-primary-care-domain-refsets/copd_cod/20210127"
      --time-value="5"
      --time-scale="years"
      --time-event="before"
      --start-date="2022-09-16"
      --end-date="2023-03-15"
    needs: [event_counts_01GWHQX96BFQ43TJ9J342Y234M, deciles_chart_01GWHQX96BFQ43TJ9J342Y234M, top_5_table_01GWHQX96BFQ43TJ9J342Y234M, plot_measure_01GWHQX96BFQ43TJ9J342Y234M]
    outputs:
      moderately_sensitive:
        notebook: output/01GWHQX96BFQ43TJ9J342Y234M/report.html

Timeline

Created: 3 years ago 27 Mar 2023 14:35:20 UTC
Finished: 3 years ago 27 Mar 2023 15:10:19 UTC
Runtime:

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

Job request

Status: Failed
Backend: TPP
Workspace: opensafely-internal-interactive
Requested by: Catherine Stables
Branch: main
Force run dependencies: Yes
Git commit hash: ca47298
Requested actions: run_all

Code comparison

Compare the code used in this job request