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Job request: 5153

Organisation:
University of Bristol
Workspace:
post-covid-vaccinated
ID:
bf4hpzj7hxh44qpe
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Venexia 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: 500000


actions:
  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated --output-format feather
    needs: [vax_eligibility_inputs] 
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data:
    run: r:latest analysis/preprocess_data.R
    needs: [generate_study_population_index, generate_study_population_vaccinated, generate_study_population_electively_unvaccinated]
    outputs:
      moderately_sensitive:
        describe: output/describe_*.txt
      highly_sensitive:
        cohort: output/input_*.rds
        venn: output/venn_*.rds

  stage1_data_cleaning_electively_unvaccinated:
    run: r:latest analysis/Stage1_data_cleaning.R electively_unvaccinated
    needs: [preprocess_data]
    outputs:
      moderately_sensitive:
        refactoring: output/meta_data_factors_electively_unvaccinated.csv
        QA_rules: output/qa_summary_electively_unvaccinated.csv
        IE_criteria: output/cohort_flow_electively_unvaccinated.csv
      highly_sensitive:
        cohort: output/input_electively_unvaccinated_stage1.rds

  stage1_data_cleaning_vaccinated:
    run: r:latest analysis/Stage1_data_cleaning.R vaccinated
    needs: [preprocess_data]
    outputs:
      moderately_sensitive:
        refactoring: output/meta_data_factors_vaccinated.csv
        QA_rules: output/qa_summary_vaccinated.csv
        IE_criteria: output/cohort_flow_vaccinated.csv
      highly_sensitive:
        cohort: output/input_vaccinated_stage1.rds

  stage2_missing_table1_electively_unvaccinated:
    run: r:latest analysis/Stage2_missing_table1.R output/input_electively_unvaccinated_stage1.rds electively_unvaccinated
    needs: [stage1_data_cleaning_electively_unvaccinated]
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/Check_missing_range_electively_unvaccinated.csv
        DateChecks: output/Check_dates_range_electively_unvaccinated.csv
        Descriptive_Table: output/Table1_electively_unvaccinated.csv

  stage2_missing_table1_vaccinated:
    run: r:latest analysis/Stage2_missing_table1.R output/input_vaccinated_stage1.rds vaccinated
    needs: [stage1_data_cleaning_vaccinated]
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/Check_missing_range_vaccinated.csv
        DateChecks: output/Check_dates_range_vaccinated.csv
        Descriptive_Table: output/Table1_vaccinated.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:30:11

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post-covid-vaccinated
Requested by
Venexia Walker
Branch
main
Force run dependencies
No
Git commit hash
6205675
Requested actions
  • preprocess_data

Code comparison

Compare the code used in this job request