Job request: 7483

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 96 - Covid-19 related death over time 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

ID Status Action
m3vt543vhexekfjt failed generate_study_population
lepl2ydpkxqz6liu succeeded generate_study_population_ethnicity
6fgg4ji2d7awyln4 succeeded generate_study_population_wave1
bqoaltx6tx5zz2da succeeded generate_study_population_wave2
hi545zk2lhocnnzb succeeded generate_study_population_wave3
dw4j6lq7iapw7ldw failed join_cohorts
nyshpbl7qgbf64zw succeeded join_cohorts_waves
6sbkvw36frdvl6n3 succeeded process_data
w5krsa7xdkjspvps succeeded skim_data_wave1
6pk2jzvlfhibmtdx succeeded skim_data_wave2
z334b6vkykr2wqk4 succeeded skim_data_wave3

Pipeline

Show Hide 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 2022-02-01 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

# SECOND PART OF STUDY
  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_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_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_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

# Create table one
  create_table_one:
    run: r:latest analysis/table_one.R
    needs: [process_data]
    outputs:
      moderately_sensitive: 
        html: output/tables/table1.html

# Kaplan-Meier
  create_kaplan_meier:
    run: r:latest analysis/waves_kaplan_meier.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        pngs: output/figures/kaplan_meier/wave*_*.png

# COX ph models
  model_cox_ph:
    run: r:latest analysis/waves_model_survival.R
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        csvs1: output/tables/wave*_effect_estimates.csv
        csvs2: output/tables/wave*_ph_tests.csv
        csvs3: output/tables/wave*_log_file.csv

# Create table two
  create_table_two:
    run: r:latest analysis/table_two.R
    needs: [model_cox_ph]
    outputs:
      moderately_sensitive: 
        html: output/tables/table2.html

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 81:57:51

Config

  • Backend:
    TPP
  • Workspace:
    covid_mortality_over_time
  • Branch:
    main
  • Creator:
    LindaNab
  • Force run dependencies:
    False
  • Git Commit Hash:
    ce7c2f0
  • Requested actions:
    • generate_study_population
    • generate_study_population_ethnicity
    • join_cohorts
    • generate_study_population_wave1
    • generate_study_population_wave2
    • generate_study_population_wave3
    • join_cohorts_waves
    • process_data
    • skim_data_wave1
    • skim_data_wave2
    • skim_data_wave3