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Job request: 6617

Organisation:
Bennett Institute
Workspace:
covid_mortality_over_time
ID:
dtbpkb4m4owoni6h
View repo View project.yaml

This page shows the technical details of what happened when the 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 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 
version: '3.0'

expectations:
  population_size: 1000

actions:

# Extract data
# When argument --index-date-range is changed, change has to be made in ./analysis/config.json too
  generate_study_population:
    run: >
      cohortextractor:latest generate_cohort 
        --study-definition study_definition 
        --skip-existing 
        --output-format=csv.gz 
        --index-date-range "2020-03-01 to 2021-12-01 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

# 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

# Join data
  join_cohorts:
    run: >
      cohort-joiner:v0.0.7
        --lhs output/input_202*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir=output/joined
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_202*.csv.gz

# Calculate mortality rates (crude + subgroup specific)
  calculate_measures:
    run: >
      cohortextractor:latest generate_measures 
        --study-definition study_definition
        --skip-existing
        --output-dir=output/joined
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/joined/measure_*_mortality_rate.csv

# Standardise crude mortality rate
  standardise_crude_rates:
    run: r:latest analysis/crude_rates_standardise.R
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        csvs: output/rates/crude_*monthly_std.csv 

# Standardise subgroup specific mortality rates
  standardise_subgroup_rates:
    run: r:latest analysis/subgroups_rates_standardise.R
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        csvs: output/rates/*_monthly_std.csv

# Process subgroup specific mortality rates
  process_subgroup_rates:
    run: r:latest analysis/utils/process_rates.R
    needs: [standardise_subgroup_rates, standardise_subgroup_rates]
    outputs:
      moderately_sensitive:
        csvs: output/rates/processed/*_monthly_std.csv

# Calculate standardised rate ratios
  calculate_rate_ratios:
    run: r:latest analysis/subgroups_ratios.R
    needs: [standardise_subgroup_rates, process_subgroup_rates]
    outputs:
      moderately_sensitive:
        csvs: output/ratios/*.csv

# Plot and save graphs depicting the crude rates
  visualise_crude_rates:
    run: r:latest analysis/crude_rates_visualise.R
    needs: [standardise_crude_rates]
    outputs:
      moderately_sensitive:
        pngs: output/figures/rates_crude/*.png

# Plot and save graphs depicting the subgroup specific mortality rates
  visualise_subgroup_rates:
    run: r:latest analysis/subgroups_rates_visualise.R
    needs: [standardise_subgroup_rates, process_subgroup_rates]
    outputs:
      moderately_sensitive:
        pngs: output/figures/rates_subgroups/*.png

# Plot and save graphs depicting the subgroup specific mortality ratios
  visualise_subgroup_ratios:
    run: r:latest analysis/subgroups_ratios_visualise.R
    needs: [calculate_rate_ratios]
    outputs:
      moderately_sensitive:
        pngs: output/figures/ratios_subgroups/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:38

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

Job information

Status
Failed
Backend
TPP
Workspace
covid_mortality_over_time
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
9db5c0d
Requested actions
  • standardise_crude_rates
  • standardise_subgroup_rates
  • process_subgroup_rates
  • calculate_rate_ratios
  • visualise_crude_rates
  • visualise_subgroup_rates
  • visualise_subgroup_ratios

Code comparison

Compare the code used in this Job Request