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Job request: 714

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
non-specific-immunity-m
ID:
7zveinnt6xt5hccr
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 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_cohort
    Status:
    Status: Succeeded
    Job identifier:
    tnoozgzyycbtf7q4
  • Action:
    feasibility
    Status:
    Status: Succeeded
    Job identifier:
    yjmrfrizsqdv7ln2

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: 04:00:10

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

Job information

Status
Succeeded
Backend
TPP
Workspace
non-specific-immunity-m
Requested by
Daniel Grint
Branch
master
Force run dependencies
No
Git commit hash
8c3972f
Requested actions
  • generate_cohort
  • feasibility

Code comparison

Compare the code used in this Job Request