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Job request: 25961

Organisation:
Bennett Institute
Workspace:
vaccines-data-quality
ID:
zfb3gperrpxxadc2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Qian Gao 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

  • Action:
    extract_covid
    Status:
    Pending
    Job identifier:
    g3bctjv6coeu37rl
  • Action:
    report_data_quality_covid
    Status:
    Pending
    Job identifier:
    3q43l2th2iq4zu56

Pipeline

Show project.yaml 
version: '5.0'

actions:
#########################
#  Flu vax data quality #
#########################
  design_elements_flu:
    run: r:v2 analysis/flu/0_flu_design.R
    needs: []
    outputs:
      moderately_sensitive:
        json: output/outputs_flu/design_elements/*.json
  
  extract_flu:
    run: ehrql:v1 generate-dataset analysis/flu/1_flu_dataset_definition.py
      --output output/outputs_flu/extract_flu:arrow
      #--dummy-data-file analysis/1-extract/dummy-data/dummy_varying.arrow
    needs: [design_elements_flu]
    outputs:
      highly_sensitive:
        cohort: output/outputs_flu/extract_flu/*.arrow

  report_data_quality_flu:
    run: r:v2 analysis/flu/2_flu_data_quality.R
    needs: [extract_flu]
    outputs:
      moderately_sensitive:
        csv: output/outputs_flu/flu_data_quality/*.csv


###########################
# COVID vax data quality  #
###########################

  extract_covid:
    run: ehrql:v1 generate-dataset analysis/covid/1_covid_dataset_definition.py
      --output output/covid/extract_covid:arrow
    outputs:
      highly_sensitive:
        cohort: output/covid/extract_covid/*.arrow

  report_data_quality_covid:
    run: r:v2 analysis/covid/2_covid_data_quality.R
    needs: [extract_covid]
    outputs:
      moderately_sensitive:
        csv: output/covid/covid_data_quality/*.csv

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
vaccines-data-quality
Requested by
Qian Gao
Branch
main
Force run dependencies
No
Git commit hash
7408d7c
Requested actions
  • extract_covid
  • report_data_quality_covid

Code comparison

Compare the code used in this job request