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Job request: 4070

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19-master
ID:
cnz2dam6dakoqonn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Simon Davy 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 
######################################

# 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 ----
  
  ## Cohort data
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.feather
  
  ## Ethnicity      
  extract_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.feather
  
  # Data processing ----
  
  ## Add ethnicity
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [extract_data, extract_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather
        
  ## Generate measures
  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv
  
  ## Process data
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        data: output/data/data_*.csv
 
  # Results ----
        
  # ## Table 1
  # table_1:
  #   run: r:latest analysis/descriptive/table_1.R
  #   needs: [data_process]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/tables/table1.csv
  # 
  # ## Table 2
  # table_2:
  #   run: r:latest analysis/descriptive/table_2.R
  #   needs: [data_process]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/tables/table2*.csv
        
  # ## Figures
  # summary_figures:
  #   run: r:latest analysis/descriptive/summary_plots.R
  #   needs: [data_process]
  #   outputs:
  #     moderately_sensitive:
  #       plot1: output/figures/total_*.png
  #       plot2: output/figures/new_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:18:32

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

Job information

Status
Succeeded
Backend
EMIS
Workspace
antipsychotics-prescribing-during-covid-19-master
Requested by
Simon Davy
Branch
master
Force run dependencies
No
Git commit hash
22b4586
Requested actions
  • extract_ethnicity

Code comparison

Compare the code used in this Job Request