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Job request: 19449

Organisation:
University of Bristol
Workspace:
post-covid-autoimmune
ID:
saz6zq6zkoh7msvl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Yinghui Wei 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: 1000

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
        vax_eligible_dates: output/vax_eligible_dates.csv

  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_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_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_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

  ## 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
        describe_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:
    - vax_eligibility_inputs
    - preprocess_data_prevax
    outputs:
      moderately_sensitive:
        consort: output/consort_prevax.csv
        consort_rounded: output/consort_prevax_rounded.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_rounded: output/consort_unvax_rounded.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_rounded: output/consort_vax_rounded.csv
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

  ## Table 1 - prevax 

  table1_prevax:
    run: r:latest analysis/descriptives/table1.R prevax
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        table1: output/table1_prevax.csv
        table1_rounded: output/table1_prevax_rounded.csv

  ## Table 1 - unvax 

  table1_unvax:
    run: r:latest analysis/descriptives/table1.R unvax
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        table1: output/table1_unvax.csv
        table1_rounded: output/table1_unvax_rounded.csv

  ## Table 1 - vax 

  table1_vax:
    run: r:latest analysis/descriptives/table1.R vax
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        table1: output/table1_vax.csv
        table1_rounded: output/table1_vax_rounded.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 110:28:17

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post-covid-autoimmune
Requested by
Yinghui Wei
Branch
main
Force run dependencies
No
Git commit hash
236e860
Requested actions
  • generate_study_population_vax
  • preprocess_data_vax
  • stage1_data_cleaning_vax
  • table1_vax

Code comparison

Compare the code used in this job request