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Job request: 14356

Organisation:
University of Manchester
Workspace:
ab_adverse_drug_reaction
ID:
g3nr7hzxguikp7xp
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_case:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case
    outputs:
      highly_sensitive:
        cohort: output/input_case.csv

  generate_study_population_control:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control
    outputs:
      highly_sensitive:
        cohort: output/input_control.csv

  generate_study_population_sepsis_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sepsis_2019
    outputs:
      highly_sensitive:
        cohort: output/input_sepsis_2019.csv

  generate_study_population_sepsis_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sepsis_2020
    outputs:
      highly_sensitive:
        cohort: output/input_sepsis_2020.csv

  generate_study_population_sepsis_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sepsis_2021
    outputs:
      highly_sensitive:
        cohort: output/input_sepsis_2021.csv

  generate_study_population_sepsis_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sepsis_2022
    outputs:
      highly_sensitive:
        cohort: output/input_sepsis_2022.csv
### extract patient_id & index_date in case ###

  process_1:  
    run: r:latest analysis/process_1.R
    needs: [generate_study_population_case,generate_study_population_control]
    outputs:
      moderately_sensitive:
        table1: output/table_case_0.csv
        table2: output/table_case_1.csv
        table3: output/table_control_0.csv
        table4: output/table_control_1.csv
      highly_sensitive: 
        case_csv: output/case_csv.csv
        match_csv: output/match_csv.csv


  matching_1:
    run: python:latest python analysis/matching.py
    needs: [process_1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases.csv
        table2: output/matched_matches.csv
        table3: output/matched_combined.csv
      moderately_sensitive: 
        report1: output/matching_report.txt

  process_sepsis_2019:  
    run: r:latest analysis/process_sepsis_2019.R
    needs: [generate_study_population_sepsis_2019]
    outputs:
      moderately_sensitive:
        table1: output/table_sepsis_2019_0.csv
        table2: output/table_sepsis_2019_1.csv

  process_sepsis_2020:  
    run: r:latest analysis/process_sepsis_2020.R
    needs: [generate_study_population_sepsis_2020]
    outputs:
      moderately_sensitive:
        table1: output/table_sepsis_2020_0.csv
        table2: output/table_sepsis_2020_1.csv

  process_sepsis_2021:  
    run: r:latest analysis/process_sepsis_2021.R
    needs: [generate_study_population_sepsis_2021]
    outputs:
      moderately_sensitive:
        table1: output/table_sepsis_2021_0.csv
        table2: output/table_sepsis_2021_1.csv

  process_sepsis_2022:  
    run: r:latest analysis/process_sepsis_2022.R
    needs: [generate_study_population_sepsis_2022]
    outputs:
      moderately_sensitive:
        table1: output/table_sepsis_2022_0.csv
        table2: output/table_sepsis_2022_1.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:16:49

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
2556486
Requested actions
  • generate_study_population_sepsis_2019
  • generate_study_population_sepsis_2020
  • generate_study_population_sepsis_2021
  • generate_study_population_sepsis_2022
  • process_sepsis_2019
  • process_sepsis_2020
  • process_sepsis_2021
  • process_sepsis_2022

Code comparison

Compare the code used in this job request