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Job request: 26658

Organisation:
Bennett Institute
Workspace:
raw_medicines_sdr
ID:
ebntv5zycbozzpqc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Em Prestige 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:
    generate_dataset
    Status:
    Succeeded
    Job identifier:
    eszldrmwixnd6rwk
  • Action:
    active_prescriptions_checks
    Status:
    Succeeded
    Job identifier:
    2yhbv6o3tbri3pdt

Pipeline

Show project.yaml 
version: '5.0'

actions:
  generate_dataset:
    run: >
      ehrql:v1 generate-dataset
      analysis/dataset_definition.py 
      --test-data-file analysis/test_dataset_definition.py
      --dummy-tables dummy_tables
      --output output/dataset.arrow
    outputs:
      highly_sensitive:
        dataset: output/dataset.arrow

  check_dataset:
    run: r:v2 analysis/dataset_checks.R
    needs:
      - generate_dataset
    outputs:
      moderately_sensitive:
        skim: output/dataset_skim.txt
        checks: output/dataset_check.csv
        missing: output/dataset_missing.csv
        status: output/dataset_status.csv
        status_issues: output/dataset_status_issues.csv
        status_reps: output/dataset_status_repeats.csv
        dates: output/dataset_date_outliers.csv
        dates_check: output/dataset_date_outliers_check.csv
        indexes: output/dataset_date_indexes.csv
        indexes_check: output/dataset_date_indexes_check.csv
        plots: output/sample_*.png
        demographics: output/meds_by_*.csv
        text_miss: output/missing_quantities.csv
        text_sum: output/quantity_sums_*.csv
        tex_sum_vis: output/quantity_summary_plot.png
        dmd_sum_vis: output/dmd_summary_plot.png

  active_prescriptions_checks:
    run: r:v2 analysis/active_prescriptions_checks.R
    needs:
      - generate_dataset
    outputs:
      moderately_sensitive:
        active_prescriptions_skim: output/active_prescriptions_skim.txt

  quantity_checks:
    run: r:v2 analysis/quantity_checks.R
    needs:
      - generate_dataset
    outputs:
      moderately_sensitive:
        quantity_skim: output/quantity_uoms.csv
        quantity_plots: output/*_plot.png

  generic_prescription_checks:
    run: r:v2 analysis/generic_prescription_checks.R
    needs:
      - generate_dataset
    outputs:
      moderately_sensitive:
        generic_prescription_skim: output/generic_prescriptions/generic_prescriptions_skim.txt
        generic_prescription_counts: output/generic_prescriptions/*_prescribing.csv
        generic_prescription_missing: output/generic_prescriptions/missing_quantities.csv
        generic_prescription_uoms: output/generic_prescriptions/*_quantity_uoms.csv
        generic_prescription_plots: output/generic_prescriptions/*_plot.png

  generate_measures:
    run: >
        ehrql:v1 generate-measures
        analysis/measures_definition.py
        --dummy-tables dummy_tables
        --output output/measures/:csv
    outputs:
      moderately_sensitive:
        dataset: output/measures/*.csv

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 2 100%
Failed 0 0%

2 / 2 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:19:35

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

Job request

Status
Succeeded
Backend
TPP
Workspace
raw_medicines_sdr
Requested by
Em Prestige
Branch
main
Force run dependencies
No
Git commit hash
b2c18dd
Requested actions
  • generate_dataset
  • active_prescriptions_checks

Code comparison

Compare the code used in this job request