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Job request: 713

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
non-specific-immunity-m
ID:
a3wrvspnwlvix3xg
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:
    feasibility
    Status:
    Status: Succeeded
    Job identifier:
    2u4ux64p6fctu4fr

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_utla_cox_haz.svg
        figure2: output/utla_haz.svg
        figure3: output/unadj_utla_cox_week.svg
        figure4: output/unadj_utla_cox_week_nl.svg
        figure5: output/reg_utla_cox_haz.svg
        figure6: output/unadj_utla_sgss_haz.svg
        figure7: output/unadj_utla_sgss_week.svg
        figure8: output/unadj_utla_sgss_week_nl.svg



  run_all:
    needs: [feasibility]
    # In order to be valid this action needs to define a run commmand and some
    # output. We don't really care what these are but the below does the trick.
    # In a future release of the platform, this special action won't need to be
    # defined at all.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:21:41

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

Job request

Status
Succeeded
Backend
TPP
Workspace
non-specific-immunity-m
Requested by
Daniel Grint
Branch
master
Force run dependencies
No
Git commit hash
e77d528
Requested actions
  • feasibility

Code comparison

Compare the code used in this job request