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Job request: 3957

Organisation:
Bennett Institute
Workspace:
aimpaper-analysis
ID:
kf62pynie34tli4w
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project.R 
  ## Edit and run create_project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Metadata for study design 
  ## # # # # # # # # # # # # # # # # # # # 

  design:
    run: r:latest analysis/00_design.R
    outputs:
      highly_sensitive:
        dates_json: analysis/lib/dates.json
        dates_rds: analysis/lib/dates.rds

  ## # # # # # # # # # # # # # # # # # # # 
  ## Study definition 
  ## # # # # # # # # # # # # # # # # # # # 

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

  ## # # # # # # # # # # # # # # # # # # # 
  ## Process the data 
  ## # # # # # # # # # # # # # # # # # # # 

  process_data:
    run: r:latest analysis/01_data_process.R
    needs:
    - design
    - study_definition
    outputs:
      highly_sensitive:
        data: output/data/data_processed_*.rds
        variables: analysis/lib/all_variables.rds
      moderately_sensitive:
        elig_dates: output/tables/elig_dates_tibble.csv
        death_counts: output/tables/death_count_*.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Summary tables for each jcvi_group 
  ## # # # # # # # # # # # # # # # # # # # 

  summary_table_02:
    run: r:latest analysis/02_summary_tables.R 02
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_02.csv

  summary_table_09:
    run: r:latest analysis/02_summary_tables.R 09
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_09.csv

  summary_table_11:
    run: r:latest analysis/02_summary_tables.R 11
    needs:
    - process_data
    outputs:
      moderately_sensitive:
        table: output/tables/summary_table_11.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Models for each jcvi_group and model_type 
  ## # # # # # # # # # # # # # # # # # # # 

  model_02_unadj:
    run: r:latest analysis/03_model.R 02 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_02_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_02_unadj.csv

  model_09_unadj:
    run: r:latest analysis/03_model.R 09 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_09_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_09_unadj.csv

  model_11_unadj:
    run: r:latest analysis/03_model.R 11 unadj
    needs:
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/model_11_unadj_*.rds
      moderately_sensitive:
        table: output/tables/table_11_unadj.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Cumulative incidence analysis 
  ## # # # # # # # # # # # # # # # # # # # 

  cml_inc_model_jcvi_group:
    run: r:latest analysis/04_cumulative_incidence.R jcvi_group
    needs:
    - design
    - study_definition
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/surv_model_jcvi_group.rds
      moderately_sensitive:
        cml_inc_plot: output/figures/cml_inc_plot_jcvi_group.png
        survtable: output/tables/survtable_jcvi_group.csv

  cml_inc_model_elig_date:
    run: r:latest analysis/04_cumulative_incidence.R elig_date
    needs:
    - design
    - study_definition
    - process_data
    outputs:
      highly_sensitive:
        model: output/models/surv_model_elig_date.rds
      moderately_sensitive:
        cml_inc_plot: output/figures/cml_inc_plot_elig_date.png
        survtable: output/tables/survtable_elig_date.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:45:11

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

Job request

Status
Succeeded
Backend
TPP
Workspace
aimpaper-analysis
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
a1ffe60
Requested actions
  • process_data
  • summary_table_02
  • summary_table_09
  • summary_table_11
  • model_02_unadj
  • model_09_unadj
  • model_11_unadj
  • cml_inc_model_jcvi_group
  • cml_inc_model_elig_date

Code comparison

Compare the code used in this job request