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Job request: 19913

Organisation:
University of Bristol
Workspace:
post-covid-respiratory-repeat-events
ID:
tkelhjuh2hr6p4fy
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Whitmarsh 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: 10000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Generate vaccination eligibility information 

  vax_eligibility_inputs:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  ## Generate dummy data for study_definition - population_prelim 

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  ## Generate dates for all study cohorts 

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv

  ## Generate dummy data for study_definition - prevax 

  generate_study_population_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.csv.gz

  ## Generate dummy data for study_definition - vax 

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format csv.gz
    needs:
    - generate_index_dates
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_vax.csv.gz

  ## Generate dummy data for study_definition - unvax 

  generate_study_population_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax.csv.gz

  ## Preprocess data -prevax 

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_prevax.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  ## Preprocess data - vax 

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_stage0.txt
        descrive_venn: output/not-for-review/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  ## Preprocess data -unvax 

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  ## Stage 1 - Data cleaning - prevax 

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - preprocess_data_prevax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_prevax.csv
        QA_rules: output/review/descriptives/QA_summary_prevax.csv
        IE_criteria: output/review/descriptives/Cohort_flow_prevax.csv
        histograms: output/not-for-review/numeric_histograms_prevax.svg
      highly_sensitive:
        cohort: output/input_prevax_stage1.rds

  describe_file-input_prevax_stage1:
    run: r:latest analysis/describe_file.R input_prevax_stage1 rds
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_prevax_stage1.txt

  ## Stage 1 - Data cleaning - vax 

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
    needs:
    - preprocess_data_vax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_vax.csv
        QA_rules: output/review/descriptives/QA_summary_vax.csv
        IE_criteria: output/review/descriptives/Cohort_flow_vax.csv
        histograms: output/not-for-review/numeric_histograms_vax.svg
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

  describe_file-input_vax_stage1:
    run: r:latest analysis/describe_file.R input_vax_stage1 rds
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_vax_stage1.txt

  ## Stage 1 - Data cleaning - unvax 

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_unvax.csv
        QA_rules: output/review/descriptives/QA_summary_unvax.csv
        IE_criteria: output/review/descriptives/Cohort_flow_unvax.csv
        histograms: output/not-for-review/numeric_histograms_unvax.svg
      highly_sensitive:
        cohort: output/input_unvax_stage1.rds

  describe_file-input_unvax_stage1:
    run: r:latest analysis/describe_file.R input_unvax_stage1 rds
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_unvax_stage1.txt

  ## Stage 1 IDs 

  create_stage1_ids:
    run: r:latest analysis/preprocess/Stage1_ids.R
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        stage1_ids: output/stage1_ids.csv

  ## Study_definition - repeat events step 1 

  generate_study_population_repeat_events_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_repeat_events_1
      --output-file output/repeat_events/input_repeat_events_1.csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    - create_stage1_ids
    outputs:
      highly_sensitive:
        cohort: output/repeat_events/input_repeat_events_1.csv.gz

  ## Preflight - repeat events step 2 

  preflight_repeat_events_2:
    run: r:latest analysis/repeat_events/preflight_repeat_events.R 2
    needs:
    - generate_study_population_repeat_events_1
    outputs:
      moderately_sensitive:
        max_events: output/repeat_events/max_events.json
      highly_sensitive:
        out_date: output/repeat_events/out_date_2.csv.gz
        patient_ids: output/repeat_events/patient_ids_*.rds

  ## Study_definition - repeat events step 2 

  generate_study_population_repeat_events_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_repeat_events_x
      --output-file output/repeat_events/input_repeat_events_2.csv.gz --param step=2
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    - create_stage1_ids
    - preflight_repeat_events_2
    outputs:
      highly_sensitive:
        cohort: output/repeat_events/input_repeat_events_2.csv.gz

  ## Preflight - repeat events step 3 

  preflight_repeat_events_3:
    run: r:latest analysis/repeat_events/preflight_repeat_events.R 3
    needs:
    - generate_study_population_repeat_events_2
    - preflight_repeat_events_2
    outputs:
      highly_sensitive:
        out_date: output/repeat_events/out_date_3.csv.gz

  ## Study_definition - repeat events step 3 

  generate_study_population_repeat_events_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_repeat_events_x
      --output-file output/repeat_events/input_repeat_events_3.csv.gz --param step=3
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    - create_stage1_ids
    - preflight_repeat_events_2
    - preflight_repeat_events_3
    outputs:
      highly_sensitive:
        cohort: output/repeat_events/input_repeat_events_3.csv.gz

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:44:39

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-respiratory-repeat-events
Requested by
Alex Whitmarsh
Branch
main
Force run dependencies
No
Git commit hash
5336448
Requested actions
  • stage1_data_cleaning_prevax
  • stage1_data_cleaning_vax
  • stage1_data_cleaning_unvax
  • create_stage1_ids

Code comparison

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