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Job request: 7815

Organisation:
Bennett Institute
Workspace:
long-covid-sick-notes
ID:
hsm5soa5us46dkro
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Walker 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_covid_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2020 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_covid_2020.csv

  generate_study_population_covid_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2021 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_covid_2021.csv

  generate_study_population_general_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2019 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_2019.csv

  generate_study_population_general_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2020 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_2020.csv

  generate_study_population_general_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2021 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_2021.csv

  generate_study_population_pneumonia_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia_2019 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_pneumonia_2019.csv

  matching_2019:
    run: python:latest python analysis/match_running.py "2019" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_2019]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2019.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2019.csv

  matching_2020:
    run: python:latest python analysis/match_running.py "2020" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_2020]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2020.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2020.csv

  matching_2021:
    run: python:latest python analysis/match_running.py "2021" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2021, generate_study_population_general_2021]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_general_2021.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_general_2021.csv

  reconcile_sick_note_spells_covid_2020:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2020" "input"
    needs: [generate_study_population_covid_2020]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_covid_2020_with_duration.csv

  reconcile_sick_note_spells_covid_2021:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2021" "input"
    needs: [generate_study_population_covid_2021]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_covid_2021_with_duration.csv

  reconcile_sick_note_spells_general_2019:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_general_2019" "matched_matches"
    needs: [matching_2019]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_general_2019_with_duration.csv

  reconcile_sick_note_spells_general_2020:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_general_2020" "matched_matches"
    needs: [matching_2020]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_general_2020_with_duration.csv

  reconcile_sick_note_spells_general_2021:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_general_2021" "matched_matches"
    needs: [matching_2021]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_general_2021_with_duration.csv

  reconcile_sick_note_spells_pneumonia_2019:
    run: python:latest python analysis/reconcile_sick_note_spells.py "_pneumonia_2019" "input"
    needs: [generate_study_population_pneumonia_2019]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/cohorts/input_pneumonia_2019_with_duration.csv

  covid_2020_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_2020" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_covid_2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_covid_2020.dta

  covid_2021_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_2021" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_covid_2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_covid_2021.dta

  general_2019_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "general_2019" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_general_2019.dta

  general_2020_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "general_2020" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2020]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_general_2020.dta

  general_2021_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "general_2021" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_general_2021]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_general_2021.dta

  pneumonia_2019_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia_2019" --output-dir=output/cohorts
    needs: [reconcile_sick_note_spells_pneumonia_2019]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohorts/cohort_rates_pneumonia_2019.dta

  covid_2020_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "covid_2020" --output-dir=output/tabfig
    needs: [covid_2020_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_2020.csv

  covid_2021_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "covid_2021" --output-dir=output/tabfig
    needs: [covid_2021_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_2021.csv

  general_2019_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "general_2019" --output-dir=output/tabfig
    needs: [general_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_general_2019.csv

  general_2020_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "general_2020" --output-dir=output/tabfig
    needs: [general_2020_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_general_2020.csv

  general_2021_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "general_2021" --output-dir=output/tabfig
    needs: [general_2021_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_general_2021.csv

  pneumonia_2019_rates:
    run: stata-mp:latest analysis/100_cr_simple_rates.do "pneumonia_2019" --output-dir=output/tabfig
    needs: [pneumonia_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_pneumonia_2019.csv

  append_cohorts:
    run: stata-mp:latest analysis/200_cr_data_management_matching.do --output-dir=output/cohorts
    needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, pneumonia_2019_rates_cohort, general_2021_rates_cohort, general_2020_rates_cohort, general_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        log: output/cohorts/append_cohorts.txt
      highly_sensitive: 
        dataset: output/cohorts/combined_covid_2020_pneumonia.dta
        dataset2: output/cohorts/combined_covid_2021_pneumonia.dta
        dataset3: output/cohorts/combined_covid_2020_general_2019.dta
        dataset4: output/cohorts/combined_covid_2021_general_2019.dta
        dataset5: output/cohorts/combined_covid_general_2020.dta
        dataset6: output/cohorts/combined_covid_general_2021.dta

  cox_models:
    run: stata-mp:latest analysis/201_cox_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cohorts/cox_models.txt
        dataset: output/tabfig/cox_model_summary.csv

  describe_duration_diagnoses:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/describe_duration_diagnoses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, general_2019_rates_cohort, general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort]
    outputs:
      moderately_sensitive:
        notebook: output/describe_duration_diagnoses.html
        table: output/tabfig/med_mean_overall.csv
        table2: output/tabfig/med_mean_age_group.csv
        table3: output/tabfig/med_mean_sex.csv
        table4: output/tabfig/med_mean_ethnicity.csv
        table5: output/tabfig/med_mean_imd.csv
        table6: output/tabfig/med_mean_region.csv
        subplots: output/tabfig/diag_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 159:04:18

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

Job request

Status
Succeeded
Backend
TPP
Workspace
long-covid-sick-notes
Requested by
Alex Walker
Branch
master
Force run dependencies
No
Git commit hash
324a24e
Requested actions
  • generate_study_population_covid_2020
  • generate_study_population_covid_2021
  • generate_study_population_pneumonia_2019
  • matching_2019
  • matching_2020
  • matching_2021
  • reconcile_sick_note_spells_covid_2020
  • reconcile_sick_note_spells_covid_2021
  • reconcile_sick_note_spells_general_2019
  • reconcile_sick_note_spells_general_2020
  • reconcile_sick_note_spells_general_2021
  • reconcile_sick_note_spells_pneumonia_2019
  • covid_2020_rates_cohort
  • covid_2021_rates_cohort
  • general_2019_rates_cohort
  • general_2020_rates_cohort
  • general_2021_rates_cohort
  • pneumonia_2019_rates_cohort
  • covid_2020_rates
  • covid_2021_rates
  • general_2019_rates
  • general_2020_rates
  • general_2021_rates
  • pneumonia_2019_rates
  • append_cohorts
  • cox_models
  • describe_duration_diagnoses

Code comparison

Compare the code used in this job request