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Job request: 622

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-thrombosis
ID:
6tnoj3kwcm5e4icg
View repo View project.yaml

This page shows the technical details of what happened when 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 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

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_covid_community_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
    outputs:
      highly_sensitive:
        cohort: output/input_covid_community.csv

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

  generate_measure_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 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

  covid_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_covid_cohort]
    outputs:
      moderately_sensitive:
        outcome_dist: output/tabfig/outcome_distribution_covid.csv
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta

  covid_community_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
    needs: [generate_covid_community_cohort]
    outputs:
      moderately_sensitive: 
        outcome_dist: output/tabfig/outcome_distribution_covid_community.csv
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid_community.dta

  pneumonia_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_pneumonia_cohort]
    outputs:
      moderately_sensitive:
        outcome_dist: output/tabfig/outcome_distribution_pneumonia.csv
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta

  covid_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [covid_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid.csv

  covid_comm_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
    needs: [covid_community_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_community.csv

  pneumonia_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_pneumonia.csv

  baseline_characteristics:
    run: stata-mp:latest analysis/400_baseline_characteristics.do
    needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        tables: output/tabfig/an_descriptiveTable_*.txt

  append_cohorts:
    run: stata-mp:latest analysis/300_cr_data_management_matching.do
    needs: [covid_rates_cohort, pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        log: output/append_cohorts.txt
      highly_sensitive: 
        dataset: output/combined_covid_pneumonia.dta

  cox_models:
    run: stata-mp:latest analysis/302_cox_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cox_models.txt
      highly_sensitive: 
        dataset: output/tabfig/cox_model_summary.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:50

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
4563261
Requested actions
  • covid_rates_cohort
  • covid_community_rates_cohort
  • pneumonia_rates_cohort
  • covid_rates
  • covid_comm_rates
  • pneumonia_rates
  • baseline_characteristics
  • append_cohorts
  • cox_models

Code comparison

Compare the code used in this Job Request