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Job request: 13037

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
a25sg2mrzyv2dazg
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Colm Andrews 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

  • Action:
    combine_ons
    Status:
    Status: Succeeded
    Job identifier:
    pl7cuq5dhnrbpzth

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data: codelists/ethnicity_*.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/data/input.feather

  generate_dataset_report:
    run: >
      dataset-report:v0.0.9
        --input-files output/data/input.feather
        --output-dir output/data
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        dataset_report: output/data/input.html

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/5_group/tables/*.csv
        figures: output/simplified_output/5_group/figures/*.png

  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/16_group/tables/simpl*.csv

  combine_ons:
    run: r:latest analysis/combine_ons.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        data: output/ons/ethnic_group*.csv
        data2: output/ons/ethnic_group_NA*.csv
        data3: output/ons/data_check*.csv

  ons_plot:
    run: r:latest analysis/ons_plots.R
    needs: [combine_ons]
    outputs:
      moderately_sensitive:
        plot_na: output/ons/na_removed/ethnicity_*.png

  iqr: 
    run: r:latest analysis/iqr.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        full: output/simplified_output/5_group/tables/range_fullset.csv
        registered: output/simplified_output/5_group/tables/range_registered.csv    
        figures: output/simplified_output/5_group/figures/density*.svg    

## Only to be run locally
  generate_report:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
    outputs:
      moderately_sensitive:
        notebook: output/draft_report_ethnicity.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:05:18

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ethnicity-short-data-report-notebook
Requested by
Colm Andrews
Branch
notebook
Force run dependencies
No
Git commit hash
2c9e444
Requested actions
  • combine_ons

Code comparison

Compare the code used in this Job Request