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Job request: 5211

Organisation:
Bennett Institute
Workspace:
mabs-not-weekly-test
ID:
ilns4iuib2vsqawv
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 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:
    extract_data_not_weekly
    Status:
    Status: Succeeded
    Job identifier:
    g6ghv4tuumn6n4ru
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    b7trskk5uttuwf7g
  • Action:
    flow_chart
    Status:
    Status: Succeeded
    Job identifier:
    74rmrs75jcjcgtgd
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    y623fdqhswsgkjwy
  • Action:
    report_data
    Status:
    Status: Succeeded
    Job identifier:
    faheyfttfirmpzsp

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: 00:53:03

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mabs-not-weekly-test
Requested by
Helen Curtis
Branch
helen-edits
Force run dependencies
No
Git commit hash
5811804
Requested actions
  • extract_data_not_weekly
  • data_process
  • flow_chart
  • data_properties
  • report_data

Code comparison

Compare the code used in this job request