Skip to content

Job request: 16359

Organisation:
PrescQIPP
Workspace:
the_effects_of_covid-19_on_doac_prescribing
ID:
zm5pe3ekeytmewgs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rachel Seeley 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

  • Action:
    generate_study_population_2
    Status:
    Status: Failed
    Job identifier:
    p7pm5i7irqnx62p2
    Error:
    nonzero_exit: Job exited with an error: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
  • Action:
    generate_study_population_1
    Status:
    Status: Failed
    Job identifier:
    qtg22s66cm22ww22
    Error:
    nonzero_exit: Job exited with an error: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
  • Action:
    generate_dose
    Status:
    Status: Failed
    Job identifier:
    4nppl4rpnhakraru
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    filter_population
    Status:
    Status: Failed
    Job identifier:
    44txlc3ktgn7mrpk
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    m5kw6dbwtqwbwxnb
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    vcu3vdowy36ajbwk
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-01-01 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 2023-02-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_dose:
    run: python:latest python analysis/calculate_dose_scaled_back.py
    needs: [generate_study_population_1, generate_study_population_2]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
  
  filter_population:
    run: python:latest python analysis/filter_population.py
    needs: [generate_dose]
    outputs:
      highly_sensitive:
        cohort: output/filtered/input*.feather
  
  #generate_study_population_ethnicity:
  #run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv
  #outputs:
  #highly_sensitive:
  #cohort: output/input_ethnicity.csv

  #join_ethnicity:
  #run: python:latest python analysis/join_ethnicity.py
  #needs: [generate_study_population, generate_study_population_ethnicity]
  #outputs:
  #highly_sensitive:
  #cohort: output/input*.csv

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

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output/filtered --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/filtered/report.html
        plots: output/filtered/*.png
        tables: output/filtered/*.csv

  
   
  #generate_dose_match:
  #run: python:latest python analysis/dose_match.py
  #needs: [generate_measures]
  #outputs:
  #moderately_sensitive:
  #figure: output/dose_match.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 26:44:27

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

Job request

Status
Failed
Backend
TPP
Workspace
the_effects_of_covid-19_on_doac_prescribing
Requested by
Rachel Seeley
Branch
main
Force run dependencies
Yes
Git commit hash
8260fd6
Requested actions
  • run_all

Code comparison

Compare the code used in this job request