Job request: 15801

Organisation:: Bennett Institute
Workspace:: opensafely-internal-interactive
ID:: luoelynxujcjlitd

This page shows the technical details of what happened when the authorised researcher George Hickman 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

Action:

generate_study_population_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

n3gc52frfuqvyf37
Action:

create_notebook_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

ow7rjylhmesjf46b
Action:

generate_study_population_ethnicity_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

wf43s4ebq3uvjv2w
Action:

join_cohorts_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

nfixsb2suq55upbv
Action:

event_counts_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

cnjoepwx6qlmlhwx
Action:

generate_measures_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

4fynezaymle7h4mh
Action:

deciles_chart_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Failed

Job identifier:

th66eguec64qhfld
Action:

top_5_table_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

zxtekob5zyyxqvlv
Action:

plot_measure_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Succeeded

Job identifier:

jnfq7cflumzcf3jg
Action:

generate_notebook_01GT24EY1R04S1Q80YR2MEARHW

Status:

Status: Failed

Job identifier:

vuyuoxbphx7rvyyd

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GT24EY1R04S1Q80YR2MEARHW:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity 
      --param end_date="2023-02-15"
      --output-dir output/01GT24EY1R04S1Q80YR2MEARHW --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GT24EY1R04S1Q80YR2MEARHW/input_ethnicity.csv.gz


  generate_study_population_01GT24EY1R04S1Q80YR2MEARHW:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_system="snomed"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_system="snomed"
      --param codelist_1_frequency="monthly"
      --param time_value="5"
      --param time_scale="years"
      --param time_event="before"
      --param codelist_2_comparison_date="event_1_date"
      --param operator="AND"
      --param population="all"
      --param breakdowns="sex,age"
      --index-date-range="2019-09-01 to 2023-02-15 by month"
      --output-dir=output/01GT24EY1R04S1Q80YR2MEARHW
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GT24EY1R04S1Q80YR2MEARHW/input_*.csv.gz

  join_cohorts_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GT24EY1R04S1Q80YR2MEARHW/input_20*.csv.gz
        --rhs output/01GT24EY1R04S1Q80YR2MEARHW/input_ethnicity.csv.gz
        --output-dir output/01GT24EY1R04S1Q80YR2MEARHW/joined
    needs: [generate_study_population_01GT24EY1R04S1Q80YR2MEARHW, generate_study_population_ethnicity_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      highly_sensitive:
        cohort: output/01GT24EY1R04S1Q80YR2MEARHW/joined/input_20*.csv.gz

  generate_measures_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      python:latest python analysis/measures.py
        --breakdowns="sex,age"
        --input_dir="output/01GT24EY1R04S1Q80YR2MEARHW/joined"
        --measure="med_review"

    needs: [join_cohorts_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        measure: output/01GT24EY1R04S1Q80YR2MEARHW/joined/measure*rate.csv
        decile_measure: output/01GT24EY1R04S1Q80YR2MEARHW/joined/measure*rate_deciles.csv

  top_5_table_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="codelists/codelist_1.csv"
      --codelist-2-path="codelists/codelist_2.csv"
      --output-dir="output/01GT24EY1R04S1Q80YR2MEARHW"
    needs: [generate_measures_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        tables: output/01GT24EY1R04S1Q80YR2MEARHW/joined/top_5*.csv

  deciles_chart_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GT24EY1R04S1Q80YR2MEARHW/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GT24EY1R04S1Q80YR2MEARHW/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GT24EY1R04S1Q80YR2MEARHW/joined/deciles_*.*

  plot_measure_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age"
        --output-dir output/01GT24EY1R04S1Q80YR2MEARHW
    needs: [generate_measures_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        measure: output/01GT24EY1R04S1Q80YR2MEARHW/plot_measure*.png

  event_counts_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GT24EY1R04S1Q80YR2MEARHW/joined" --output_dir="output/01GT24EY1R04S1Q80YR2MEARHW"
    needs: [join_cohorts_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        measure: output/01GT24EY1R04S1Q80YR2MEARHW/event_counts.json

  create_notebook_01GT24EY1R04S1Q80YR2MEARHW:
    run: >
      python:latest python analysis/create_notebook.py
      --output-dir "output/01GT24EY1R04S1Q80YR2MEARHW"
      --codelist-1-description="None"
      --codelist-2-description="None"
      --codelist-1-link="https://codelists.opensafely.org/codelist/opensafely/dmards/2020-06-23"
      --codelist-2-link="https://codelists.opensafely.org/codelist/opensafely/medication-review-opensafely-service-restoration-observatory/24b50f64"
      --report-title="Medication Review Report"
      --measure-description="Medication Review"
      --population="all"
      --breakdowns="sex,age"
    outputs:
      moderately_sensitive:
        notebook: output/01GT24EY1R04S1Q80YR2MEARHW/report.ipynb

  generate_notebook_01GT24EY1R04S1Q80YR2MEARHW:
    run: jupyter:latest jupyter nbconvert /workspace/output/01GT24EY1R04S1Q80YR2MEARHW/report.ipynb --execute --to html --output-dir=/workspace/output/01GT24EY1R04S1Q80YR2MEARHW --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook_01GT24EY1R04S1Q80YR2MEARHW, event_counts_01GT24EY1R04S1Q80YR2MEARHW, deciles_chart_01GT24EY1R04S1Q80YR2MEARHW, top_5_table_01GT24EY1R04S1Q80YR2MEARHW, plot_measure_01GT24EY1R04S1Q80YR2MEARHW]
    outputs:
      moderately_sensitive:
        notebook: output/01GT24EY1R04S1Q80YR2MEARHW/report.html

Timeline

Created: 1 year, 9 months ago 24 Feb 2023 16:35:26 UTC
Started: 1 year, 9 months ago 24 Feb 2023 16:52:09 UTC
Finished: 1 year, 9 months ago 25 Feb 2023 14:15:36 UTC
Runtime: 15:45:33

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

Job information

Status: Failed
Backend: TPP
Workspace: opensafely-internal-interactive
Requested by: George Hickman
Branch: main
Force run dependencies: Yes
Git commit hash: cb3b6e1
Requested actions: run_all

Code comparison

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