Job request: 8883

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
5ou5t7rbrp6di4lz succeeded calculate_measures
5nqsdcvqdnqjejkd succeeded calculate_rate_ratios
fb7izfzkwumc5ugw succeeded create_kaplan_meier
e6p32y5ivkocomyk succeeded create_table_one
4bjvx6gazaht3szd succeeded create_table_two
qjxmmk2dgi6gfjqc succeeded generate_study_population
4k5yduxtimvj5mdo succeeded generate_study_population_ethnicity
cdcfxszzzqvis3ts succeeded generate_study_population_wave1
r3z4mh76t5zebgmc succeeded generate_study_population_wave2
h3t35gs277vsfqph succeeded generate_study_population_wave3
32pmsfs7fu54c3ox succeeded join_cohorts
2httd6j76xuo35p3 succeeded join_cohorts_waves
pgy73ikvqytjdjdx succeeded model_cox_ph
cqblmraqlksnaexw succeeded process_data
q3alnsjzt3jwprod succeeded process_subgroup_rates
a6pjwb6nvhwt7nue succeeded redact_rates
vk6t27q3efxkyal7 succeeded skim_data_wave1
goe4kced6h5xozus succeeded skim_data_wave2
4rnzhp5jpd4pr4kv succeeded skim_data_wave3
l2fzg6wlg2emd4vg succeeded standardise_crude_rates
4tmlf53o2aa7d5vf succeeded standardise_subgroup_rates
pccn7nrfaurqftvz succeeded visualise_crude_rates
vsl6m4u7lot2pk74 succeeded visualise_subgroup_rates
rw7qeev6gee6k6zv succeeded visualise_subgroup_ratios
nqp3jpkfmjrwvsa7 succeeded calculate_measures_ckd_rrt

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

# Calculate mortality rates ckd_rrt subgroup
  calculate_measures_ckd_rrt:
    run: r:latest analysis/measures_calc_ckd_rrt.R
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/joined/measure_ckd_rrt_mortality_rate.csv

# Redact rates
  redact_rates:
    run: r:latest analysis/utils/redact_rates.R
    needs: [calculate_measures, calculate_measures_ckd_rrt]
    outputs:
      moderately_sensitive:
        csvs: output/rates/redacted/*_redacted.csv       

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

# Standardise subgroup specific mortality rates
  standardise_subgroup_rates:
    run: r:latest analysis/subgroups_rates_standardise.R
    needs: [redact_rates]
    outputs:
      moderately_sensitive:
        csvs: output/rates/standardised/*_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/*.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: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 118:05:08

Config