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Job request: 10189

Organisation:
Bennett Institute
Workspace:
mab-av-non-user-main
ID:
bjts6ljtlcvi6ehk
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher John Tazare 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

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

  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed_day0.rds
        data2: output/data/data_processed_day5.rds

  data_properties_process_day0:
    run: r:latest analysis/data_properties.R output/data/data_processed_day0.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_day0_skim.txt
        txt2: output/data_properties/data_processed_day0_coltypes.txt
        txt3: output/data_properties/data_processed_day0_tabulate.txt

  data_properties_process_day5:
    run: r:latest analysis/data_properties.R output/data/data_processed_day5.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_day5_skim.txt
        txt2: output/data_properties/data_processed_day5_coltypes.txt
        txt3: output/data_properties/data_processed_day5_tabulate.txt

  crosstab_trt_outcomes:
    run: r:latest analysis/crosstab_trt_outcomes.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csvsday5: output/data_properties/day5_*.csv 
        csvsday0: output/data_properties/day0_*.csv

  table_1_day5:
    run: r:latest analysis/table_1.R day5
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/table1_redacted_day5.rds
      moderately_sensitive:
        table: output/tables/table1_redacted_day5.html

  cox_day5:
    run: r:latest analysis/cox_models.R day5
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5.rds
      moderately_sensitive:
        figure1: output/figs/*_overlap_plot_day5_before_restriction.png
        figure2: output/figs/*_overlap_plot_day5_after_restriction.png
        figure3: output/figs/*_cumInc_day5.png
        table1: output/tables/cox_models_day5.csv
        table2: output/tables/log_cox_models_day5.csv

  trt_pat_day5:
    run: r:latest analysis/treatment_distributions.R day5
    needs: [data_process]
    outputs:
      moderately_sensitive:
        figure: output/figs/day5_treatment_pattern.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:21

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mab-av-non-user-main
Requested by
John Tazare
Branch
main
Force run dependencies
No
Git commit hash
a16d19b
Requested actions
  • data_process
  • data_properties_process_day0
  • data_properties_process_day5
  • crosstab_trt_outcomes
  • table_1_day5
  • cox_day5
  • trt_pat_day5

Code comparison

Compare the code used in this Job Request