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Job request: 9426

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
long_term_kidney_outcomes_after_covid
ID:
e2yqikinfwbtk3w5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Viyaasan Mahalingasivam 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:
    extract_covid_all
    Status:
    Status: Failed
    Job identifier:
    ppynf24m2xdehp47
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    covid_all_descriptive
    Status:
    Status: Failed
    Job identifier:
    jfyqhsj2q5nugtoq
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:

# Match covid_all_for_matching to comparators in potential_historical_general_population and potential_contemporary_general_population
# https://docs.opensafely.org/case-control-studies/

# Extract data for covid_all_for_matching
  extract_covid_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_all_for_matching
    outputs:
      highly_sensitive:
        cohort: output/input_covid_all_for_matching.csv

  covid_all_descriptive:
    run: stata-mp:latest analysis/covid_all_for_matching.do
    needs: [extract_covid_all]
    outputs:
      highly_sensitive:
        analysis_dataset: output/covid_all_for_matching.dta
      moderately_sensitive:
        svg1: output/krt_outcome_covid_severity.svg 
        svg2: output/krt_outcome_covid_acute_kidney_injury.svg 
        svg3: output/krt_outcome_covid_krt.svg
        svg4: output/krt_outcome_covid_vax_status.svg
        svg5: output/krt_outcome_calendar_period.svg
        svg6: output/mortality_covid_severity.svg 
        svg7: output/mortality_covid_acute_kidney_injury.svg 
        svg8: output/mortality_covid_krt.svg
        svg9: output/mortality_covid_vax_status.svg
        svg10: output/mortality_calendar_period.svg
        svg11: output/aki_covid_severity.svg 
        svg12: output/aki_covid_acute_kidney_injury.svg 
        svg13: output/aki_covid_krt.svg
        svg14: output/aki_covid_vax_status.svg
        svg15: output/aki_calendar_period.svg
        log: logs/covid_all_for_matching.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:05:39

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

Job request

Status
Failed
Backend
TPP
Workspace
long_term_kidney_outcomes_after_covid
Requested by
Viyaasan Mahalingasivam
Branch
main
Force run dependencies
No
Git commit hash
c7adb44
Requested actions
  • run_all

Code comparison

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