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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 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:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    jc7gofsjdralmlsl
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    simple_summaries
    Status:
    Status: Failed
    Job identifier:
    fqx6wlxrwg437s4j
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    t5ximlgho2rzgvl2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    flow_chart
    Status:
    Status: Failed
    Job identifier:
    32wxvxvrj3gzwea3
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    d5dy2tdl2wdpj5xt
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    fgugqbor2lmokkyp
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_2
    Status:
    Status: Failed
    Job identifier:
    vnefzgb6wbvmxvun
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_ckd
    Status:
    Status: Failed
    Job identifier:
    qkxg45hkgxgw3uup
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    cummulative_incidence
    Status:
    Status: Failed
    Job identifier:
    xfgmwlqztefrnpi7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    figure_2
    Status:
    Status: Failed
    Job identifier:
    5zgrqszvt3jbf5a2
    Error:
    dependency_failed: Not starting as dependency failed

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 request

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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