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Job request: 24427

Organisation:
Bennett Institute
Workspace:
openpathology-main
ID:
o4psifmwvfwz752x
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jaidip Gill 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

Pipeline

Show project.yaml 
version: '4.0'

actions:

  generate_measures_alt_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/alt_tests/measures.arrow
        --
        --codelist codelists/opensafely-alanine-aminotransferase-alt-tests.csv
    outputs:
      highly_sensitive:
        measures: output/alt_tests/measures.arrow
  generate_processed_data_alt_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/alt_tests
        --codelist codelists/opensafely-alanine-aminotransferase-alt-tests.csv
    needs:
      [generate_measures_alt_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/alt_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/alt_tests/top_5_code_table.csv
        event_counts_table: output/alt_tests/event_counts.csv


  generate_measures_chol_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/chol_tests/measures.arrow
        --
        --codelist codelists/opensafely-cholesterol-tests.csv
    outputs:
      highly_sensitive:
        measures: output/chol_tests/measures.arrow
  generate_processed_data_chol_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/chol_tests
        --codelist codelists/opensafely-cholesterol-tests.csv
    needs:
      [generate_measures_chol_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/chol_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/chol_tests/top_5_code_table.csv
        event_counts_table: output/chol_tests/event_counts.csv


  generate_measures_hba1c_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/hba1c_tests/measures.arrow
        --
        --codelist codelists/opensafely-glycated-haemoglobin-hba1c-tests.csv
    outputs:
      highly_sensitive:
        measures: output/hba1c_tests/measures.arrow
  generate_processed_data_hba1c_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/hba1c_tests
        --codelist codelists/opensafely-glycated-haemoglobin-hba1c-tests.csv
    needs:
      [generate_measures_hba1c_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/hba1c_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/hba1c_tests/top_5_code_table.csv
        event_counts_table: output/hba1c_tests/event_counts.csv


  generate_measures_rbc_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/rbc_tests/measures.arrow
        --
        --codelist codelists/opensafely-red-blood-cell-rbc-tests.csv
    outputs:
      highly_sensitive:
        measures: output/rbc_tests/measures.arrow
  generate_processed_data_rbc_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/rbc_tests
        --codelist codelists/opensafely-red-blood-cell-rbc-tests.csv
    needs:
      [generate_measures_rbc_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/rbc_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/rbc_tests/top_5_code_table.csv
        event_counts_table: output/rbc_tests/event_counts.csv


  generate_measures_sodium_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/sodium_tests/measures.arrow
        --
        --codelist codelists/opensafely-sodium-tests-numerical-value.csv
    outputs:
      highly_sensitive:
        measures: output/sodium_tests/measures.arrow
  generate_processed_data_sodium_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/sodium_tests
        --codelist codelists/opensafely-sodium-tests-numerical-value.csv
    needs:
      [generate_measures_sodium_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/sodium_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/sodium_tests/top_5_code_table.csv
        event_counts_table: output/sodium_tests/event_counts.csv


  generate_measures_systol_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/systol_tests/measures.arrow
        --
        --codelist codelists/opensafely-systolic-blood-pressure-qof.csv
    outputs:
      highly_sensitive:
        measures: output/systol_tests/measures.arrow
  generate_processed_data_systol_tests:
    run: >
      python:latest 
        analysis/write_processed_csv_files.py
        --output-dir output/systol_tests
        --codelist codelists/opensafely-systolic-blood-pressure-qof.csv
    needs:
      [generate_measures_systol_tests]
    outputs:
      moderately_sensitive:
        decile_table: output/systol_tests/deciles_table_counts_per_week_per_practice.csv
        code_table: output/systol_tests/top_5_code_table.csv
        event_counts_table: output/systol_tests/event_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:42:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
openpathology-main
Requested by
Jaidip Gill
Branch
main
Force run dependencies
No
Git commit hash
121c5f6
Requested actions
  • generate_measures_hba1c_tests
  • generate_processed_data_hba1c_tests

Code comparison

Compare the code used in this job request