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Job request: 10221

Organisation:
Bennett Institute
Workspace:
covid-mortality-over-time-imd
ID:
2ecuon3aezfyndmz
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Linda Nab 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

# Extract ethnicity
  generate_study_population_ethnicity:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_ethnicity 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

# SECOND PART OF STUDY
  generate_study_population_flowchart:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_flowchart
        --skip-existing 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv.gz

  # Process data flowchart
  process_data_flowchart:
    run: r:latest analysis/data_flowchart_process.R
    needs: [generate_study_population_flowchart]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_flowchart.rds
  
  # Skim data flowchart
  skim_data_flowchart:
    run: r:latest analysis/data_skim.R output/processed/input_flowchart.rds output/data_properties
    needs: [process_data_flowchart]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_flowchart_skim.txt
        txt2: output/data_properties/input_flowchart_coltypes.txt
        txt3: output/data_properties/input_flowchart_tabulate.txt

  # Numbers for flowchart
  calc_numbers_flowchart:
    run: r:latest analysis/flowchart.R
    needs: [process_data_flowchart]
    outputs:
      moderately_sensitive:
        cohort: output/tables/flowchart/wave1_flowchart.csv

  generate_study_population_wave1:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_wave1 
        --skip-existing 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave1.csv.gz

  generate_study_population_wave1_imd:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_wave1_imd
        --skip-existing 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave1_imd.csv.gz

  generate_study_population_wave2:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_wave2
        --skip-existing 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave2.csv.gz

  generate_study_population_wave3:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition_wave3
        --skip-existing 
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_wave3.csv.gz

# Join data
  join_cohorts_waves:
    run: >
      cohort-joiner:v0.0.7
        --lhs output/input_wave*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir=output/joined
    needs: [generate_study_population_wave1, generate_study_population_wave2, generate_study_population_wave3, generate_study_population_wave1_imd, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_wave*.csv.gz

# Process data
  process_data:
    run: r:latest analysis/data_process.R
    needs: [join_cohorts_waves]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_wave*.rds

# Skim data
  skim_data_wave1:
    run: r:latest analysis/data_skim.R output/processed/input_wave1.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_wave1_skim.txt
        txt2: output/data_properties/input_wave1_coltypes.txt
        txt3: output/data_properties/input_wave1_tabulate.txt

  # Skim data
  skim_data_wave1_imd:
    run: r:latest analysis/data_skim.R output/processed/input_wave1_imd.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_wave1_imd_skim.txt
        txt2: output/data_properties/input_wave1_imd_coltypes.txt
        txt3: output/data_properties/input_wave1_imd_tabulate.txt

  skim_data_wave2:
    run: r:latest analysis/data_skim.R output/processed/input_wave2.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_wave2_skim.txt
        txt2: output/data_properties/input_wave2_coltypes.txt
        txt3: output/data_properties/input_wave2_tabulate.txt

  skim_data_wave3:
    run: r:latest analysis/data_skim.R output/processed/input_wave3.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_wave3_skim.txt
        txt2: output/data_properties/input_wave3_coltypes.txt
        txt3: output/data_properties/input_wave3_tabulate.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:32:30

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-mortality-over-time-imd
Requested by
Linda Nab
Branch
explore-old-imd-data-extract
Force run dependencies
No
Git commit hash
947d309
Requested actions
  • generate_study_population_wave1_imd
  • join_cohorts_waves
  • process_data
  • skim_data_wave1
  • skim_data_wave1_imd

Code comparison

Compare the code used in this Job Request