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Job request: 1403

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
non-specific-immunity-m
ID:
oplmq4hxn4c3ifgg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Daniel Grint 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:
    anCOX
    Status:
    Status: Failed
    Job identifier:
    pddgu4hm6eq467c7
    Error:
    nonzero_exit: Job exited with an error code

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  feasibility:
    run: stata-mp:latest analysis/00_Test_runs_and_feasibility.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/00_Test_runs_and_feasibility.log
        figure1: output/00_spells.svg

  crMAIN:
    run: stata-mp:latest analysis/cr_analysis_dataset.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/cr_analysis_dataset.log
      highly_sensitive:
        data: analysis/cr_analysis_dataset.dta

  anSTP:
    run: stata-mp:latest analysis/an_stp.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/an_stp.log

  anCASE:
    run: stata-mp:latest analysis/an_ccount_crude.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_ccount_crude.log
        figure1: output/tpp_sgss_counts.svg
        figure2: output/tpp_type_counts.svg
        figure3: output/tpp_fp.svg

  anCOX:
    run: stata-mp:latest analysis/an_cox_models.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_models.log
#        figure1: output/unadj_cox_haz.svg
        figure1: output/unadj_cox_month.svg
#        figure2: output/utla_haz.svg
        figure3: output/unadj_cox_week.svg
        figure4: output/unadj_cox_week_nl.svg
        figure5: output/utla_cox_month.svg
        figure6: output/unadj_sgss_month.svg
        figure7: output/unadj_sgss_week.svg
        figure8: output/unadj_sgss_week_nl.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:27:50

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

Job request

Status
Failed
Backend
TPP
Workspace
non-specific-immunity-m
Requested by
Daniel Grint
Branch
master
Force run dependencies
No
Git commit hash
ce6c6fc
Requested actions
  • anCOX

Code comparison

Compare the code used in this job request