Skip to content

Job request: 6210

Workspace:
covid_mortality_over_time
ID:
qeoix5aayxm45apb

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

  • Action:
    join_cohorts
    Status:
    Status: Succeeded
    Job identifier:
    rysprknznpl7vchs

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 2020-04-01 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
0a613ff
Requested actions
  • join_cohorts