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Job request: 1911

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
hh-classification-research
ID:
vnm3ebckqc4dftdn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kevin Wing 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.

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 100000

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

  W2_generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_W2
    outputs:
      highly_sensitive:
        cohort: output/input_W2.csv

  01_hhClassif_cr_analysis_dataset:
    run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do MAIN
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        allvars: output/hhClassif_analysis_datasetMAIN.dta
        allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityMAIN.dta
        allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*MAIN.dta 
        allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*MAIN.dta 
      moderately_sensitive:
        log: logs/01_hhClassif_cr_analysis_dataset.log

  01_hhClassif_cr_analysis_dataset_W2:
    run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do W2
    needs: [W2_generate_cohort]
    outputs:
      highly_sensitive:
        allvars: output/hhClassif_analysis_datasetW2.dta
        allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityW2.dta
        allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*W2.dta 
        allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*W2.dta 
      moderately_sensitive:
        log: logs/01_hhClassif_cr_analysis_dataset_W2.log

  02_hhClassif_an_data_checks:
    run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/02_hhClassif_an_data_checks.log

  02_hhClassif_an_data_checks_W2:
    run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do W2
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    outputs:
      moderately_sensitive:
        log: logs/02_hhClassif_an_data_checks_W2.log

  03_hhClassif_an_descriptive_table_1:
    run: stata-mp:latest analysis/03_hhClassif_an_descriptive_table_1.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/03_hhClassif_an_descriptive_table_1.log
        tableTxt: output/table1_hhClassif.txt
        tableExcel: output/table1_hhClassif.xlsx

  03_hhClassif_an_descriptive_table_1_W2:
    run: stata-mp:latest analysis/03_hhClassif_an_descriptive_table_1.do W2
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    outputs:
      moderately_sensitive:
        log: logs/03_hhClassif_an_descriptive_table_1_W2.log
        tableTxt: output/table1_hhClassif_W2.txt
        tableExcel: output/table1_hhClassif_W2.xlsx

  04_hhClassif_an_univariable_analysis:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/04_hhClassif_an_univariable_analysis_MAIN.log
        data: output/hhClassif_univariableAnalysis_*_ageband_*MAIN.ster

  04_hhClassif_an_univariable_analysis_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do W2
    outputs:
      moderately_sensitive:
        log: logs/04_hhClassif_an_univariable_analysis_W2.log
        data: output/hhClassif_univariableAnalysis_*_ageband_*W2.ster

  05_hhClassif_an_multivariable_analysis:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/05_hhClassif_an_multivariable_analysis_MAIN.log
        data: output/hhClassif_multivariableAllEthnicities_*_ageband_*MAIN.ster

  05_hhClassif_an_multivariable_analysis_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do W2
    outputs:
      moderately_sensitive:
        log: logs/05_hhClassif_an_multivariable_analysis_W2.log
        data: output/hhClassif_multivariableAllEthnicities_*_ageband_*W2.ster

  06_hhClassif_an_multivariable_analysis_eth5Interaction:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/06_hhClassif_an_eth5Interaction_analysis_MAIN.log
        data: output/hhClassif_multvariableAnalysisEth5Interaction_*_ageband_*MAIN.ster

  06_hhClassif_an_multivariable_analysis_eth5Interaction_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do W2
    outputs:
      moderately_sensitive:
        log: logs/06_hhClassif_an_eth5Interaction_analysis_W2.log
        data: output/hhClassif_multvariableAnalysisEth5Interaction_*_ageband_*W2.ster

  07_hhClassif_an_multivariable_analysis_perEth5Group:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_MAIN.log
        data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*MAIN.ster

  07_hhClassif_an_multivariable_analysis_perEth5Group_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do W2
    outputs:
      moderately_sensitive:
        log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_W2.log
        data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*W2.ster

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
JobRequestError: generate_cohort failed on a previous run and must be re-run
Backend
TPP
Workspace
hh-classification-research
Requested by
Kevin Wing
Branch
master
Force run dependencies
No
Git commit hash
e24616c
Requested actions
  • 01_hhClassif_cr_analysis_dataset
  • 01_hhClassif_cr_analysis_dataset_W2
  • 07_hhClassif_an_multivariable_analysis_perEth5Group
  • 07_hhClassif_an_multivariable_analysis_perEth5Group_W2

Code comparison

Compare the code used in this job request