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Job request: 6205

Organisation:
Bennett Institute
Workspace:
covid_mortality_over_time
ID:
cavtsvm22wfrgkh5
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    join_cohorts
    Status:
    Status: Failed
    Job identifier:
    foe3ul3festyf5th
    Error:
    nonzero_exit: Job exited with error code 2

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:v0.0.3
        --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: 00:00:44

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

Job request

Status
Failed
Backend
TPP
Workspace
covid_mortality_over_time
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
099fa94
Requested actions
  • join_cohorts

Code comparison

Compare the code used in this job request