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Job request: 902

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
sgtf-cfr-research
ID:
smidr7fsxlo52h54
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:
    crMAIN
    Status:
    Status: Succeeded
    Job identifier:
    pf2fwh7it7dbzl47
  • Action:
    anSUMM
    Status:
    Status: Succeeded
    Job identifier:
    veo5i5ucxxwcppun
  • Action:
    anRISK_TAB1
    Status:
    Status: Succeeded
    Job identifier:
    dshiqbyi2wrkzavu
  • Action:
    anCOX_TAB1
    Status:
    Status: Succeeded
    Job identifier:
    t5etzxrcgnavk5mw
  • Action:
    anODDS_MOD
    Status:
    Status: Succeeded
    Job identifier:
    czp2umhqxei6eb63
  • Action:
    anCOX_MOD
    Status:
    Status: Succeeded
    Job identifier:
    tafeho2bgq4z3piy

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 150000

actions:

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

  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: output/cr_analysis_dataset.dta

  anSUMM:
    run: stata-mp:latest analysis/an_summary.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_summary.log
        figure1: output/sgtf_perc_region.svg

  anRISK_TAB1:
    run: stata-mp:latest analysis/an_risk28_table1.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_risk28_table1.log
        table1text: output/table1_risk28.txt
        table1xlsx: output/table1_risk28.xlsx

  anCOX_TAB1:
    run: stata-mp:latest analysis/an_cox_table1.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_table1.log
        table1text: output/table1_cox.txt
        table1xlsx: output/table1_cox.xlsx

#  anRISK_MOD:
#    run: stata-mp:latest analysis/an_risk_models.do
#    needs: [crMAIN]
#    outputs:
#      moderately_sensitive:
#        log: logs/an_risk_models.log

  anODDS_MOD:
    run: stata-mp:latest analysis/an_logit_models.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_logit_models.log

  anCOX_MOD:
    run: stata-mp:latest analysis/an_cox_models.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_models.log
        figure1: output/unadj_cox_shoen.svg
        figure2: output/unadj_cox_km.svg
        figure3: output/unadj_cox_haz.svg
        figure4: output/minadj_cox_shoen.svg
        figure5: output/minadj_cox_km.svg
        figure6: output/minadj_cox_haz.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:30:11

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sgtf-cfr-research
Requested by
Daniel Grint
Branch
master
Force run dependencies
No
Git commit hash
ab7386c
Requested actions
  • crMAIN
  • anSUMM
  • anRISK_TAB1
  • anCOX_TAB1
  • anODDS_MOD
  • anCOX_MOD

Code comparison

Compare the code used in this job request