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Job request: 15054

Organisation:
Bennett Institute
Workspace:
winter-pressures
ID:
s3dzxs5rmbad5bl5

This page shows the technical details of what happened when authorised researcher Colm Andrews requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

Pipeline

Show project.yaml
version: "3.0"

expectations:
  population_size: 5000

actions:
  # Other data
  # ----------
  # Add actions for other data to this section. Prefix them with a suitable name; place
  # scripts in a similarly named sub-directory of the analysis directory; write outputs
  # to a similarly named sub-directory of the output directory.
  #
  # For example, let's call our other data "metrics". We would prefix our actions
  # "metrics_"; we would place our scripts in analysis/metrics; we would write outputs
  # to output/metrics.

  # Metrics data
  # ------------
  metrics_generate_study_dataset_winter:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --index-date-range '2021-12-01 to 2022-03-30 by month' --output-dir=output/metrics
      --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_*.feather

  metrics_generate_study_dataset_summer:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --index-date-range '2021-06-01 to 2022-09-30 by month' --output-dir=output/metrics
      --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input*.feather

  metrics_generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
      --output-dir=output/metrics
    needs:
    - metrics_generate_study_dataset_summer
    - metrics_generate_study_dataset_winter
    outputs:
      highly_sensitive:
        measure_csv: output/metrics/measure_*_rate.csv

  # Appointments data
  # -----------------
  appointments_generate_dataset_sql:
    run: >
      sqlrunner:latest
        analysis/appointments/dataset_query.sql
        --output output/appointments/dataset_long.csv.gz
        --dummy-data-file analysis/appointments/dummy_dataset_long.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/appointments/dataset_long.csv.gz

  # appointments_generate_dataset:
  #   run: >
  #     databuilder:v0
  #       generate-dataset
  #       analysis/appointments/dataset_definition.py
  #       --output output/appointments/dataset_wide.arrow
  #   outputs:
  #     highly_sensitive:
  #       dataset: output/appointments/dataset_wide.arrow

  # appointments_get_freq_na_values:
  #   run: >
  #     python:latest
  #       python
  #       -m analysis.appointments.get_freq_na_values
  #   needs: [appointments_generate_dataset]
  #   outputs:
  #     moderately_sensitive:
  #       dataset: output/appointments/freq_na_values.csv

  # appointments_reshape_dataset:
  #   run: >
  #     python:latest
  #       python
  #       -m analysis.appointments.reshape_dataset
  #   needs: [appointments_generate_dataset]
  #   outputs:
  #     highly_sensitive:
  #       dataset: output/appointments/dataset_long.arrow

  appointments_generate_measure:
    run: >
      python:latest
        python
        -m analysis.appointments.generate_measure
    needs: [appointments_generate_dataset_sql]
    outputs:
      moderately_sensitive:
        measure: output/appointments/measure_median_lead_time_in_days.csv

  appointments_generate_deciles_charts:
    run: >
      deciles-charts:v0.0.33
        --input-files output/appointments/measure_*.csv
        --output-dir output/appointments
    config:
      show_outer_percentiles: true
    needs: [appointments_generate_measure]
    outputs:
      moderately_sensitive:
        deciles_charts: output/appointments/deciles_chart_*.png
        deciles_tables: output/appointments/deciles_table_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:07:55

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

Job information

Status
Failed
Backend
TPP
Workspace
winter-pressures
Requested by
Colm Andrews
Branch
main
Force run dependencies
No
Git commit hash
a6f8504
Requested actions
  • metrics_generate_study_dataset_winter
  • metrics_generate_study_dataset_summer
  • metrics_generate_measures

Code comparison

Compare the code used in this Job Request