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Job request: 9750

Organisation:
Bennett Institute
Workspace:
sro-measures
ID:
psrvh4iikjh72vjg
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    yft2pfwscfysysza
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    get_patient_count
    Status:
    Status: Failed
    Job identifier:
    aqnv3tyn5yeuckeh
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_notebook_updating
    Status:
    Status: Failed
    Job identifier:
    qmj3pwmajdoyoxcp
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    get_practice_count
    Status:
    Status: Failed
    Job identifier:
    gbmup6z4rmxkrwk7
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_measures_cleaned
    Status:
    Status: Failed
    Job identifier:
    5njkat2s3ngpfm7b
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2020-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2021-06-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-07-01 to 2021-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/in*.feather

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-01-01 to 2022-05-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/i*.feather


  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population_4, generate_study_population_5, join_ethnicity]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs:
      [
        generate_study_population_1,
        generate_study_population_2,
        generate_study_population_3,
        generate_study_population_ethnicity,
      ]
    outputs:
      highly_sensitive:
        cohort: output/inp*.feather

  get_practice_count:
    run: python:latest python analysis/get_practice_count.py
    needs: [join_ethnicity, generate_study_population_4, generate_study_population_5]
    outputs:
      moderately_sensitive:
        text: output/practice_count.json

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
    needs: [join_ethnicity, generate_study_population_4, generate_study_population_5]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv

  generate_measures_cleaned:
    run: python:latest python analysis/clean_measures.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_cleaned_*.csv


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs:
      [
        generate_measures,
        generate_measures_cleaned,
        get_practice_count,
        get_patient_count,
      ]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
        subplots: output/sentinel_measures_subplots.png
        code_tables: output/code_table_*.csv
        events_count: output/event_count.json

  generate_notebook_updating:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs:
      [
        generate_measures,
        generate_measures_cleaned,
        get_practice_count,
        get_patient_count,
      ]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_updating.html

#   run_tests:
#     run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
#     outputs:
#       moderately_sensitive:
#         log: output/pytest.xml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 143:41:49

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

Job information

Status
Failed
Backend
TPP
Workspace
sro-measures
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
0971603
Requested actions
  • get_patient_count
  • get_practice_count
  • generate_measures
  • generate_measures_cleaned
  • generate_notebook_updating

Code comparison

Compare the code used in this Job Request