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Job request: 3755

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19-master
ID:
e3kpvg3gnymmavt5
View repo View project.yaml

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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:
    extract_data
    Status:
    Status: Succeeded
    Job identifier:
    iqxscsanmq7gb4lw
  • Action:
    extract_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    nv6ywi5gs5vqhlxa
  • Action:
    join_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    d6qiocukvcz5qdcf
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    5gmvcmkmunlv4ddn
  • Action:
    table_1
    Status:
    Status: Succeeded
    Job identifier:
    cbezuje54howewq2
  • Action:
    summary_figures
    Status:
    Status: Succeeded
    Job identifier:
    arzuhcx6d6gqzaka
  • Action:
    table_2
    Status:
    Status: Succeeded
    Job identifier:
    tlcgeedo75lel7xc

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 "2019-03-01 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
  
  ## Process data
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_ethnicity, join_ethnicity]
    outputs:
      moderately_sensitive:
        data: output/data/data_*.rds
 
  # Results ----
  
  ## 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
        
  ## 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 17:25:28

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

Job information

Status
Succeeded
Backend
TPP
Workspace
antipsychotics-prescribing-during-covid-19-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
03458de
Requested actions
  • extract_data
  • extract_ethnicity
  • join_ethnicity
  • data_process
  • summary_figures
  • table_1
  • table_2

Code comparison

Compare the code used in this Job Request