Job request: 16269

Organisation:: Bennett Institute
Workspace:: opensafely-internal-interactive
ID:: 6ta44izha5sopnjx

This page shows the technical details of what happened when the authorised researcher Simon Davy 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:

generate_study_population_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

snphct5otgsu66qj

Error:

cancelled_by_user: Cancelled by user
Action:

generate_study_population_ethnicity_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

aytjq5hdswja3stf

Error:

nonzero_exit: Job exited with an error
Action:

generate_measures_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

xh3uevndkezekfe5

Error:

cancelled_by_user: Cancelled by user
Action:

deciles_chart_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

xqx35mc6xnowreca

Error:

cancelled_by_user: Cancelled by user
Action:

plot_measure_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

cxsbeyfxs6jqm4rk

Error:

cancelled_by_user: Cancelled by user
Action:

top_5_table_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

5nkes53xjeir2v46

Error:

cancelled_by_user: Cancelled by user
Action:

event_counts_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

qeukiuwrxl4unai6

Error:

cancelled_by_user: Cancelled by user
Action:

generate_report_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

fy6zhxnoaspaaahd

Error:

cancelled_by_user: Cancelled by user
Action:

join_cohorts_01GVE12SFQBN24ZKJN7NWZ9G0Q

Status:

Status: Failed

Job identifier:

td5ib73qe2yujsgv

Error:

dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-03-01"
      --output-dir output/01GVE12SFQBN24ZKJN7NWZ9G0Q --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/input_ethnicity.csv.gz


  generate_study_population_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_type="event"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_type="medication"
      --param codelist_1_frequency="monthly"
      --param time_value="3"
      --param time_scale="weeks"
      --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="2022-09-02 to 2023-03-01 by month"
      --output-dir=output/01GVE12SFQBN24ZKJN7NWZ9G0Q
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/input_*.csv.gz

  join_cohorts_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GVE12SFQBN24ZKJN7NWZ9G0Q/input_20*.csv.gz
        --rhs output/01GVE12SFQBN24ZKJN7NWZ9G0Q/input_ethnicity.csv.gz
        --output-dir output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined
    needs: [generate_study_population_01GVE12SFQBN24ZKJN7NWZ9G0Q, generate_study_population_ethnicity_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      highly_sensitive:
        cohort: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/input_20*.csv.gz

  generate_measures_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      python:latest -m analysis.measures
        --breakdowns="sex,age"
        --input_dir="output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined"
        --measure="med_review"

    needs: [join_cohorts_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        measure: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/measure*rate.csv
        decile_measure: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/measure*rate_deciles.csv

  top_5_table_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    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/01GVE12SFQBN24ZKJN7NWZ9G0Q"
    needs: [generate_measures_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        tables: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/top_5*.csv

  deciles_chart_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined/deciles_*.*

  plot_measure_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age"
        --output-dir output/01GVE12SFQBN24ZKJN7NWZ9G0Q
    needs: [generate_measures_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        measure: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/plot_measure*.png

  event_counts_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GVE12SFQBN24ZKJN7NWZ9G0Q/joined" --output_dir="output/01GVE12SFQBN24ZKJN7NWZ9G0Q"
    needs: [join_cohorts_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        measure: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/event_counts.json

  generate_report_01GVE12SFQBN24ZKJN7NWZ9G0Q:
    run: >
      python:latest python analysis/render_report.py
      --report-title="Medication Review - OpenSAFELY Service Restoration Observatory & DMARDs"
      --population="all"
      --breakdowns="sex,age"
      --codelist-1-name="Medication Review - OpenSAFELY Service Restoration Observatory"
      --codelist-2-name="DMARDs"
      --codelist-1-link="opensafely/medication-review-opensafely-service-restoration-observatory/24b50f64"
      --codelist-2-link="opensafely/dmards/2020-06-23"
      --time-value="3"
      --time-scale="weeks"
      --time-event="before"
      --start-date="2022-09-02"
      --end-date="2023-03-01"
      --num-practices=1000
      --request-id="01GVE12SFQBN24ZKJN7NWZ9G0Q"
    needs: [event_counts_01GVE12SFQBN24ZKJN7NWZ9G0Q, deciles_chart_01GVE12SFQBN24ZKJN7NWZ9G0Q, top_5_table_01GVE12SFQBN24ZKJN7NWZ9G0Q, plot_measure_01GVE12SFQBN24ZKJN7NWZ9G0Q]
    outputs:
      moderately_sensitive:
        notebook: output/01GVE12SFQBN24ZKJN7NWZ9G0Q/report.html

Timeline

Created: 2 years, 7 months ago 13 Mar 2023 17:42:56 UTC
Started: 2 years, 7 months ago 13 Mar 2023 17:41:59 UTC
Finished: 2 years, 7 months ago 13 Mar 2023 17:42:40 UTC
Runtime: 00:00:47

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: Simon Davy
Branch: main
Force run dependencies: Yes
Git commit hash: a682b09
Requested actions: run_all

Code comparison

Compare the code used in this job request