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Job request: 27367

Organisation:
Bennett Institute
Workspace:
death-report_followup
ID:
mugeuvy5iupyezil
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Irene Kyomuhangi 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:
    apply_inclusion_exclusion
    Status:
    Pending
    Job identifier:
    iwhrtyw7gomqiqqs
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    extract_underlying_cause_summary
    Status:
    Pending
    Job identifier:
    zl6heeccngzichvu
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    extract_data
    Status:
    Pending
    Job identifier:
    hrqrwdjpukc45ddn
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    add_classifications
    Status:
    Pending
    Job identifier:
    nmcerqete6tgdrjc
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    analysis
    Status:
    Pending
    Job identifier:
    r5hffwek2n46rffq
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'

actions:

  extract_data:
    run: ehrql:v1 generate-dataset analysis/01_dataset_definition.py
      --dummy-data-file dummy_data/dummy_dataset.csv
      --output output/highly_sensitive/dataset_death_ons_tpp.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/highly_sensitive/dataset_death_ons_tpp.csv.gz

  apply_inclusion_exclusion:
    needs: [extract_data]
    run: r:v2 analysis/02_inclusion_exclusion_criteria.R
    outputs:
      highly_sensitive:
        cohort: output/02_cohort.csv
      moderately_sensitive:
        cohort_flow: output/02_cohort_flow.csv

  extract_underlying_cause_summary:
    needs: [apply_inclusion_exclusion]
    run: r:v2 analysis/03_extract_underlying_cause_summary.R
    outputs:
      moderately_sensitive:
        underlying_cause_summary: output/03_underlying_cause_summary.csv

  add_classifications:
    needs: [extract_underlying_cause_summary]
    run: r:v2 analysis/04_add_classifications.R
    outputs:
      moderately_sensitive:
        broad_cause_classification: output/04_broad_cause_classification.csv
        broad_cause_codes_for_review: output/04_broad_cause_codes_for_review.csv

  analysis:
    needs: [apply_inclusion_exclusion, add_classifications]
    run: r:v2 analysis/05_analysis.R
    outputs:
      moderately_sensitive:
        tpp_recording_diagnostic: output/05_tpp_recording_diagnostic.csv
        date_difference_validation: output/05_date_difference_validation.csv
        broad_cause_results: output/05_broad_cause_results.csv

Job statistics

Status Count Percentage
Pending 5 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 5 (0%) complete

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
death-report_followup
Requested by
Irene Kyomuhangi
Branch
main
Force run dependencies
Yes
Git commit hash
959fe62
Requested actions
  • run_all

Code comparison

Compare the code used in this job request