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Job request: 17921

Organisation:
University of Manchester
Workspace:
ab_adverse_drug_reaction
ID:
sdluzr65ute5wls5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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: 30000

actions:

### study cohort ###
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_study_population_ae:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ae --index-date-range "2019-01-01 to 2023-03-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ae_*.csv.gz

  generate_measures_ae:
    run: cohortextractor:latest generate_measures --study-definition study_definition_ae --skip-existing --output-dir=output/measures
    needs: [generate_study_population_ae]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  ae_rate_table:  
    run: r:latest analysis/figure/ae_rate.R
    needs: [generate_measures_ae]
    outputs:
      moderately_sensitive:
        table1: output/ae_rate_table.csv
        table2: output/ae_rate_forplot.csv
        plot1: output/figure_ae_rate.jpeg

  infection_table:  
    run: r:latest analysis/figure/infection_table.R
    needs: [generate_measures_ae]
    outputs:
      moderately_sensitive:
        table1: output/infection_table.csv
        table2: output/infection_forplot.csv
        plot1: output/figure_infection.jpeg

  generate_study_population_2ae:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2ae --index-date-range "2019-01-01 to 2023-03-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_2ae_*.csv.gz

  generate_measures_2ae:
    run: cohortextractor:latest generate_measures --study-definition study_definition_2ae --skip-existing --output-dir=output/measures
    needs: [generate_study_population_2ae]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_2ae_*.csv

  ae_rate_42days_table:  
    run: r:latest analysis/figure/ae_rate_42days.R
    needs: [generate_measures_2ae]
    outputs:
      moderately_sensitive:
        table1: output/ae_rate_42days_table.csv
        table2: output/ae_rate_42days_forplot.csv
        plot1: output/figure_ae_42days_rate.jpeg

  ae_rate_42days_nocovid_table:  
    run: r:latest analysis/figure/ae_rate_42days_nocovid.R
    needs: [generate_measures_2ae]
    outputs:
      moderately_sensitive:
        table1: output/ae_rate_42days_nocovid_table.csv
        table2: output/ae_rate_42days_nocovid_forplot.csv
        plot1: output/figure_ae_42days_nocovid_rate.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:48

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ab_adverse_drug_reaction
Requested by
Billy Zhong
Branch
ab_sideeffect
Force run dependencies
No
Git commit hash
18b09e9
Requested actions
  • infection_table

Code comparison

Compare the code used in this job request