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Job request: 24425

Organisation:
University of Bristol
Workspace:
post-covid-respiratory-v1
ID:
wggaqml5wtayzfap
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Zoe (Mengxuan) Zou 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

  • Action:
    clean_data_prevax
    Status:
    Status: Succeeded
    Job identifier:
    hjrzdyi3tkrwag66
  • Action:
    clean_data_unvax
    Status:
    Status: Succeeded
    Job identifier:
    nu6tyn322wu6jxbr
  • Action:
    clean_data_vax
    Status:
    Status: Succeeded
    Job identifier:
    frd2jtebzilufp7z
  • Action:
    table1_unvax
    Status:
    Status: Succeeded
    Job identifier:
    mscp7n3tki6ccrn3
  • Action:
    table1_prevax
    Status:
    Status: Succeeded
    Job identifier:
    ryqk2sqymqaogfue
  • Action:
    table1_vax
    Status:
    Status: Succeeded
    Job identifier:
    sn24d2uo64e3plpz

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 - 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

  ## 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

  ## 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 - 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

  ## 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

  ## Table 1 - prevax 

  table1_prevax:
    run: r:latest analysis/table1/table1.R prevax 18;40;60;80;111
    needs:
    - clean_data_prevax
    outputs:
      moderately_sensitive:
        table1: output/table1/table1_prevax.csv
        table1_midpoint6: output/table1/table1_prevax_midpoint6.csv

  ## Table 1 - unvax 

  table1_unvax:
    run: r:latest analysis/table1/table1.R unvax 18;40;60;80;111
    needs:
    - clean_data_unvax
    outputs:
      moderately_sensitive:
        table1: output/table1/table1_unvax.csv
        table1_midpoint6: output/table1/table1_unvax_midpoint6.csv

  ## Table 1 - vax 

  table1_vax:
    run: r:latest analysis/table1/table1.R vax 18;40;60;80;111
    needs:
    - clean_data_vax
    outputs:
      moderately_sensitive:
        table1: output/table1/table1_vax.csv
        table1_midpoint6: output/table1/table1_vax_midpoint6.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:39:28

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-respiratory-v1
Requested by
Zoe (Mengxuan) Zou
Branch
main
Force run dependencies
No
Git commit hash
efb5969
Requested actions
  • clean_data_prevax
  • clean_data_unvax
  • clean_data_vax
  • table1_prevax
  • table1_unvax
  • table1_vax

Code comparison

Compare the code used in this Job Request