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Job request: 2711

Organisation:
Bennett Institute
Workspace:
mechanical-valve-anticoag-updated
ID:
6am5eyoxqphcstth
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_study_population_1
    Status:
    Status: Failed
    Job identifier:
    m5xrjltlkaicz2tb
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_4
    Status:
    Status: Failed
    Job identifier:
    4ykjfz5vrngbwswd
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_3
    Status:
    Status: Failed
    Job identifier:
    dpo7fyhtfja4wkw6
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_2
    Status:
    Status: Failed
    Job identifier:
    7tt6vbxatedus3xj
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_ethnicity
    Status:
    Status: Failed
    Job identifier:
    db2aejmumy2vauu7
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    fare3zud3lwn2qrt
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    sswo7i4g6wxo3ls2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    patient_count
    Status:
    Status: Failed
    Job identifier:
    u3aqvx4j4sareidu
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    7v44scr4yqvprdb5
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 15000

actions:

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv
      
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2019-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
  
  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-01 to 2019-11-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input*.csv
  
  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-12-01 to 2020-06-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv
  
  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-05-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv
        
  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_4, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/in*.csv
        
  patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        csv: output/patient_count.csv

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

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity, generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg
        total_csv: output/doac_rate_total.csv
        csvs: output/current_doac_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 28:49:18

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

Job information

Status
Failed
Backend
EMIS
Workspace
mechanical-valve-anticoag-updated
Requested by
Louis Fisher
Branch
updates
Force run dependencies
No
Git commit hash
b0551d1
Requested actions
  • generate_study_population_ethnicity
  • generate_study_population_1
  • generate_study_population_2
  • generate_study_population_3
  • generate_study_population_4
  • join_ethnicity
  • patient_count
  • generate_measures
  • generate_notebook

Code comparison

Compare the code used in this Job Request