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Job request: 465

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-thrombosis
ID:
mamjyn2mn4cm4s33
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 20000

actions:
  generate_covid_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
    outputs:
      highly_sensitive:
        cohort: output/input_covid.csv

  generate_pneumonia_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
    outputs:
      highly_sensitive:
        cohort: output/input_pneumonia.csv

  generate_control_2019_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2019
    outputs:
      highly_sensitive:
        cohort: output/input_control_2019.csv

  generate_control_2020_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2020
    outputs:
      highly_sensitive:
        cohort: output/input_control_2020.csv

  generate_measure_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2020-10-01 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measures*.csv

  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_measures
    needs: [generate_measure_cohort]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_rate.csv

  draw_timeseries:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        graph: output/event_count_time_series.svg

  000_covid:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_covid_cohort]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_covid.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta

  000_pneumonia:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_pneumonia_cohort]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_pneumonia.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta

  201_covid:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [000_covid]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_covid.csv

  201_pneumonia:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [000_pneumonia]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_pneumonia.csv

  matching_control_2019:
    run: python:latest python analysis/match_running.py "control_2019"
    needs: [generate_covid_cohort, generate_control_2019_cohort]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2019.txt
      highly_sensitive:
        combined: output/matched_combined_control_2019.csv

  matching_control_2020:
    run: python:latest python analysis/match_running.py "control_2020"
    needs: [generate_covid_cohort, generate_control_2020_cohort]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2020.txt
      highly_sensitive:
        combined: output/matched_combined_control_2020.csv

  matching_data_management:
    run: stata-mp:latest analysis/300_cr_data_management_matching.do 
    needs: [generate_covid_cohort, generate_pneumonia_cohort, matching_control_2019, matching_control_2020]
    outputs:
      highly_sensitive:
        combined3: output/matched_combined_pneumonia.dta
        combined4: output/matched_combined_control_2019.dta
        combined5: output/matched_combined_control_2020.dta

  301_pneumonia:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "pneumonia"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_pneumonia.dta

  301_control_2019:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2019"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_control_2019.dta

  301_control_2020:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2020"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_control_2020.dta

  302_pneumonia:
    run: stata-mp:latest analysis/302_cox_models.do "pneumonia"
    needs: [301_pneumonia]
    outputs:
      moderately_sensitive:
        log: output/cox_model_pneumonia.log
        combined1: output/tabfig/cox_model_summary_pneumonia.csv

  302_control_2019:
    run: stata-mp:latest analysis/302_cox_models.do "control_2019"
    needs: [301_control_2019]
    outputs:
      moderately_sensitive:
        log: output/cox_model_control_2019.log
        combined1: output/tabfig/cox_model_summary_control_2019.csv

  302_control_2020:
    run: stata-mp:latest analysis/302_cox_models.do "control_2020"
    needs: [301_control_2020]
    outputs:
      moderately_sensitive:
        log: output/cox_model_control_2020.log
        combined1: output/tabfig/cox_model_summary_control_2020.csv

  400_baseline_characteristics:
    run: stata-mp:latest analysis/400_baseline_characteristics.do
    needs: [301_pneumonia, 301_control_2019, 301_control_2020]
    outputs:
      moderately_sensitive:
        tables: output/tabfig/an_descriptiveTable_*.txt

  401_survival_curves_pneumonia:
    run: stata-mp:latest analysis/401_survival_curves.do "pneumonia"
    needs: [301_pneumonia]
    outputs:
      moderately_sensitive:
        covid: output/tabfig/survcurv_*pneumonia.svg

  # 401_survival_curves_control_2019:
  #   run: stata-mp:latest analysis/401_survival_curves.do "control_2019"
  #   needs: [301_control_2019]
  #   outputs:
  #     moderately_sensitive:
  #       covid: output/tabfig/survcurv_*control_2019.svg

  # 401_survival_curves_control_2020:
  #   run: stata-mp:latest analysis/401_survival_curves.do "control_2020"
  #   needs: [301_control_2020]
  #   outputs:
  #     moderately_sensitive:
  #       covid: output/tabfig/survcurv_*control_2020.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:11:19

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-thrombosis
Requested by
Alex Walker
Branch
master
Force run dependencies
No
Git commit hash
7b586c8
Requested actions
  • generate_measure_cohort
  • calculate_measures
  • draw_timeseries

Code comparison

Compare the code used in this Job Request