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Job request: 24419

Organisation:
University of Bristol
Workspace:
post-covid-renal-v1
ID:
fqt22wlyqy2dplm6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Emily Eyles 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: 5000

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 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Define study dates 

  study_dates:
    run: r:latest analysis/study_dates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json

  ## Generate dates for all cohorts 

  generate_dates:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_dates.py
      --output output/dataset_definition/index_dates.csv.gz
    needs:
    - study_dates
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/index_dates.csv.gz

  ## Generate cohort - prevax 

  generate_cohort_prevax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_prevax.py
      --output output/dataset_definition/input_prevax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_prevax.csv.gz

  ## Generate cohort - vax 

  generate_cohort_vax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_vax.py
      --output output/dataset_definition/input_vax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_vax.csv.gz

  ## Generate cohort - unvax 

  generate_cohort_unvax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_unvax.py
      --output output/dataset_definition/input_unvax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_unvax.csv.gz

  ## Clean data - prevax, with describe = TRUE 

  clean_data_prevax:
    run: r:latest analysis/dataset_clean/dataset_clean.R prevax TRUE
    needs:
    - study_dates
    - generate_cohort_prevax
    outputs:
      moderately_sensitive:
        describe_raw: output/describe/prevax_raw.txt
        describe_venn: output/describe/prevax_venn.txt
        describe_preprocessed: output/describe/prevax_preprocessed.txt
        flow: output/dataset_clean/flow_prevax.csv
        flow_midpoint6: output/dataset_clean/flow_prevax_midpoint6.csv
      highly_sensitive:
        venn: output/dataset_clean/venn_prevax.rds
        cohort_clean: output/dataset_clean/input_prevax_clean.rds

  ## Clean data - vax, with describe = TRUE 

  clean_data_vax:
    run: r:latest analysis/dataset_clean/dataset_clean.R vax TRUE
    needs:
    - study_dates
    - generate_cohort_vax
    outputs:
      moderately_sensitive:
        describe_raw: output/describe/vax_raw.txt
        describe_venn: output/describe/vax_venn.txt
        describe_preprocessed: output/describe/vax_preprocessed.txt
        flow: output/dataset_clean/flow_vax.csv
        flow_midpoint6: output/dataset_clean/flow_vax_midpoint6.csv
      highly_sensitive:
        venn: output/dataset_clean/venn_vax.rds
        cohort_clean: output/dataset_clean/input_vax_clean.rds

  ## Clean data - unvax, with describe = TRUE 

  clean_data_unvax:
    run: r:latest analysis/dataset_clean/dataset_clean.R unvax TRUE
    needs:
    - study_dates
    - generate_cohort_unvax
    outputs:
      moderately_sensitive:
        describe_raw: output/describe/unvax_raw.txt
        describe_venn: output/describe/unvax_venn.txt
        describe_preprocessed: output/describe/unvax_preprocessed.txt
        flow: output/dataset_clean/flow_unvax.csv
        flow_midpoint6: output/dataset_clean/flow_unvax_midpoint6.csv
      highly_sensitive:
        venn: output/dataset_clean/venn_unvax.rds
        cohort_clean: output/dataset_clean/input_unvax_clean.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:03:14

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post-covid-renal-v1
Requested by
Emily Eyles
Branch
main
Force run dependencies
No
Git commit hash
3999835
Requested actions
  • clean_data_prevax
  • clean_data_vax
  • clean_data_unvax

Code comparison

Compare the code used in this job request