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Job request: 5201

Organisation:
Bennett Institute
Workspace:
mabs-not-weekly-test
ID:
u6umzciattjo4drs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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 
################################################################################
#
# Description: This script defines the project pipeline - it specifys the 
#              execution orders for all the code in this repo using a series of 
#              actions.
#
# Author(s): M Green
# Date last updated: 31/01/2022
#
################################################################################

version: '3.0'

expectations:
  population_size: 100000

actions:
  
  # Extract data ----

  ## Cohort data
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-12-13 to 2022-01-24 by week" --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv.gz
  
 ## Cohort data - not weekly
  extract_data_not_weekly:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_not_weekly --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input_not_weekly.csv # use csv temporarily to avoid match with wildcard in previous output
  
  # Data processing ----

  ## Process data
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_data_not_weekly]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
  
  ## Inclusion/exclusion flow chart
  flow_chart:
    run: r:latest analysis/descriptive/flow_chart.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/flowchart.csv

  ## Data properties     
  data_properties:
    run: r:latest analysis/descriptive/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt
  
  
  # Report ----
  
  ## Data, figures and tables
  report_data:
    run: r:latest reports/coverage/report_data.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table1: reports/coverage/tables/report_stats.csv
        table2: reports/coverage/tables/table_elig_treat_redacted.csv
        table3: reports/coverage/tables/table_demo_clinc_breakdown_redacted.html
        figure1: reports/coverage/figures/cum_treatment_plot.png
        figure2: reports/coverage/figures/cum_eligiblity_plot.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:32:44

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabs-not-weekly-test
Requested by
Helen Curtis
Branch
helen-edits
Force run dependencies
No
Git commit hash
bdf758e
Requested actions
  • extract_data_not_weekly
  • data_process
  • flow_chart
  • data_properties

Code comparison

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