Job request: 2711

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the Mechanical Valve Anticoag 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

ID Status Action
db2aejmumy2vauu7 failed generate_study_population_ethnicity
m5xrjltlkaicz2tb failed generate_study_population_1
7tt6vbxatedus3xj failed generate_study_population_2
dpo7fyhtfja4wkw6 failed generate_study_population_3
4ykjfz5vrngbwswd failed generate_study_population_4
sswo7i4g6wxo3ls2 failed join_ethnicity
u3aqvx4j4sareidu failed patient_count
fare3zud3lwn2qrt failed generate_measures
7v44scr4yqvprdb5 failed generate_notebook

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 28:49:18

Config

  • Backend:
    EMIS
  • Workspace:
    mechanical-valve-anticoag-updated
  • Branch:
    updates
  • Creator:
    LFISHER7
  • Force run dependencies:
    False
  • 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