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Job request: 5834

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-updates-feb
ID:
uj7ix5siwimj2ixm
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    itfg5vikct6lb2rz
  • Action:
    figure_2
    Status:
    Status: Succeeded
    Job identifier:
    zrxpspzo6xna4f7o
  • Action:
    table_2
    Status:
    Status: Succeeded
    Job identifier:
    mq5fvbs3r3x7gbmh
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    7bdbssus3zv3ztwj
  • Action:
    flow_chart
    Status:
    Status: Succeeded
    Job identifier:
    byo3lyxzubvduz3b
  • Action:
    cummulative_incidence
    Status:
    Status: Succeeded
    Job identifier:
    fwa34ru24uotaks4
  • Action:
    simple_summaries
    Status:
    Status: Succeeded
    Job identifier:
    qqrhrmh3cp4hu6xj
  • Action:
    table_ckd
    Status:
    Status: Succeeded
    Job identifier:
    okay5ctpkqalm5nq
  • Action:
    table_1
    Status:
    Status: Succeeded
    Job identifier:
    o4qvzd4tnx3kld7a

Pipeline

Show project.yaml 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 100000

actions:
  
  # Extract data ----
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv
        
  # Process data ----
  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_processed.rds
        
  # Inclusion/exclusion flow chart ----
  flow_chart:
    run: r:latest analysis/flow_chart.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/flowchart.csv

  # Data properties ----      
  data_properties:
    run: r:latest analysis/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt

  # Data summaries ----
  simple_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/simple_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/markdown/simple_summaries.html
  
  # Table 1 ----
  table_1:
    run: r:latest analysis/table_1.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table: output/tables/table1*.html
  
  # Table 2 ----
  table_2:
    run: r:latest analysis/table_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table1: output/tables/table2.html
        table2: output/tables/table2_redacted.html
  
  table_ckd:
    run: r:latest analysis/table_ckd.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table1: output/tables/table_ckd.html
        table2: output/tables/table_ckd_redacted.html
        table3: output/tables/table2_ckd.html
        table4: output/tables/table2_ckd_redacted.html

        
  # Figure 1 ----
  cummulative_incidence:
    run: r:latest analysis/cumulative_incidence.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/surv_data*.csv
        
  # Figure 2 ----
  figure_2:
    run: r:latest analysis/figure_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        png: output/figures/figure2*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:18:16

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

Job request

Status
Succeeded
Backend
TPP
Workspace
breakthrough-covid-updates-feb
Requested by
Millie Green
Branch
updates-feb
Force run dependencies
No
Git commit hash
e11eb2e
Requested actions
  • data_process
  • flow_chart
  • data_properties
  • simple_summaries
  • table_1
  • table_2
  • table_ckd
  • cummulative_incidence
  • figure_2

Code comparison

Compare the code used in this job request