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Job request: 4935

Organisation:
University of Manchester
Workspace:
amr_repeat_abs
ID:
x6vodxxzjmznopjv
View repo View project.yaml

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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  # generate_study_population:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/measures/input_*.csv.gz

  generate_study_population_repeat_ABs:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_repeat_ABs --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/repeat_ABs_data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/repeat_ABs_data/input_repeat_ABs_*.csv.gz

  generate_study_population_elderly:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_elderly 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_elderly.csv.gz

  # generate_measures:
  #   run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
  #   needs: [generate_study_population]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measure_*.csv
        
  describe_elderly_agedis:
    run: r:latest analysis/tables/gen_csv_age_check.R
    needs: [generate_study_population_elderly]
    outputs:
      moderately_sensitive:
        agetable: output/age_quant.csv

  # describe:
  #   run: r:latest analysis/plot/overall_ab_prescribing.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/overall.png
  #       boxplot: output/overallbox.png

  # describe_percentile:
  #   run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       percentile: output/overall_25th_75th_percentile.png

  # describe_starpu:
  #   run: r:latest analysis/plot/starpu_ab_prescribing.R
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/starpuline.png
  #       boxplot: output/starpubox.png
  
  # describe_infection_ab_UTI:
  #   run: r:latest analysis/plot/infection_ab_UTI.R
  #   needs: [generate_study_population, generate_measures]
  #   outputs:
  #      moderately_sensitive:
  #       plot: output/UTI.png
  
  generate_notebook_repeated_ABs:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/repeated_ABs.ipynb --execute --to html --output-dir=/workspace/output/repeat_ABs_outputs --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population_repeat_ABs]
    outputs:
      moderately_sensitive:
        notebook: output/repeat_ABs_outputs/repeated_ABs.html 
        figures: output/repeat_ABs_outputs/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 87:59:09

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

Job information

Status
Failed
Backend
TPP
Workspace
amr_repeat_abs
Requested by
ali
Branch
study_eval_repeated_abs
Force run dependencies
Yes
Git commit hash
8129962
Requested actions
  • generate_notebook_repeated_ABs

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