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Job request: 13022

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
7n4yyokbtizycg4r
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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_report
    Status:
    Status: Succeeded
    Job identifier:
    2q5shrd4gpqpldfu
  • Action:
    combine_ons
    Status:
    Status: Succeeded
    Job identifier:
    6utlrki3q3ny6rws
  • Action:
    ons_plot
    Status:
    Status: Succeeded
    Job identifier:
    ythn6i5gdb5wifhl

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

  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: 00:06:20

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ethnicity-short-data-report-notebook
Requested by
Colm Andrews
Branch
notebook
Force run dependencies
No
Git commit hash
49f7938
Requested actions
  • combine_ons
  • ons_plot
  • generate_report

Code comparison

Compare the code used in this job request