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Job request: 5786

Organisation:
Bennett Institute
Workspace:
breakthrough-covid-updates-feb
ID:
mea7xltol43ozta2
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 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

  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    jc7gofsjdralmlsl
  • Action:
    simple_summaries
    Status:
    Status: Failed
    Job identifier:
    fqx6wlxrwg437s4j
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    t5ximlgho2rzgvl2
  • Action:
    flow_chart
    Status:
    Status: Failed
    Job identifier:
    32wxvxvrj3gzwea3
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    d5dy2tdl2wdpj5xt
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    fgugqbor2lmokkyp
  • Action:
    table_2
    Status:
    Status: Failed
    Job identifier:
    vnefzgb6wbvmxvun
  • Action:
    table_ckd
    Status:
    Status: Failed
    Job identifier:
    qkxg45hkgxgw3uup
  • Action:
    cummulative_incidence
    Status:
    Status: Failed
    Job identifier:
    xfgmwlqztefrnpi7
  • Action:
    figure_2
    Status:
    Status: Failed
    Job identifier:
    5zgrqszvt3jbf5a2

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: 16:15:07

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

Job information

Status
Failed
Backend
TPP
Workspace
breakthrough-covid-updates-feb
Requested by
Millie Green
Branch
updates-feb
Force run dependencies
No
Git commit hash
843cdec
Requested actions
  • generate_study_population
  • data_process
  • flow_chart
  • data_properties
  • simple_summaries
  • table_1
  • table_2
  • table_ckd
  • cummulative_incidence
  • figure_2

Code comparison

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