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Job request: 22376

Organisation:
University of Bristol
Workspace:
post-covid-autoimmune-studydef
ID:
2gdfou5k2rcmafqh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jose Ignacio Cuitun Coronado 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: 150000

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 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  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.gz
        vax_eligible_dates: output/vax_eligible_dates.csv.gz

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

  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.gz

  ## Generate study population - 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 study population - 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

  ## Generate study population - vax 

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

  ## Generate study population history - prevax 

  generate_study_population_history_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax_history.csv.gz

  ## Generate study population history - unvax 

  generate_study_population_history_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax_history.csv.gz

  ## Generate study population history - vax 

  generate_study_population_history_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_history
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_vax_history.csv.gz

  ## Join stage1 and history data - prevax 

  stage1_data_cleaning_history_prevax:
    run: r:latest analysis/preprocess/stage1_history_patients.R prevax
    needs:
    - stage1_data_cleaning_prevax
    - generate_study_population_history_prevax
    outputs:
      highly_sensitive:
        cohort_final: output/input_prevax_new_stage1.rds

  ## Join stage1 and history data - unvax 

  stage1_data_cleaning_history_unvax:
    run: r:latest analysis/preprocess/stage1_history_patients.R unvax
    needs:
    - stage1_data_cleaning_unvax
    - generate_study_population_history_unvax
    outputs:
      highly_sensitive:
        cohort_final: output/input_unvax_new_stage1.rds

  ## Join stage1 and history data - vax 

  stage1_data_cleaning_history_vax:
    run: r:latest analysis/preprocess/stage1_history_patients.R vax
    needs:
    - stage1_data_cleaning_vax
    - generate_study_population_history_vax
    outputs:
      highly_sensitive:
        cohort_final: output/input_vax_new_stage1.rds

  ## Preprocess data - prevax 

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.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:
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.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:
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  ## Stage 1 - data cleaning - prevax 

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/stage1_data_cleaning.R prevax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_prevax
    outputs:
      moderately_sensitive:
        consort: output/consort_prevax.csv
        consort_midpoint6: output/consort_prevax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_prevax_stage1.rds

  ## Stage 1 - data cleaning - unvax 

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/stage1_data_cleaning.R unvax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_unvax
    outputs:
      moderately_sensitive:
        consort: output/consort_unvax.csv
        consort_midpoint6: output/consort_unvax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_unvax_stage1.rds

  ## Stage 1 - data cleaning - vax 

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/stage1_data_cleaning.R vax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        consort: output/consort_vax.csv
        consort_midpoint6: output/consort_vax_midpoint6.csv
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:18:30

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-autoimmune-studydef
Requested by
Jose Ignacio Cuitun Coronado
Branch
Explore_study_def
Force run dependencies
No
Git commit hash
be97f39
Requested actions
  • preprocess_data_unvax

Code comparison

Compare the code used in this Job Request