Skip to content

Job request: 15450

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
cwtitx5q2zyya4zn
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

Pipeline

Show project.yaml 
### CTV3, PRIMIS, SNOMED analysis

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_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_5 --output-file output/extract_5/input_5.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_5/input_5.feather

  generate_dataset_report_5:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_5/input_5.feather
        --output-dir output/extract_5
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_5/input_5.html

  generate_study_population_16:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_16 --output-file output/extract_16/input_16.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_16/input_16.feather

  generate_dataset_report_16:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_16/input_16.feather
        --output-dir output/extract_16
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_16/input_16.html

  generate_study_population_time:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_time --output-file output/extract_time/input_time.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_time/input_time.feather

  generate_dataset_report_time:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_time/input_time.feather
        --output-dir output/extract_time
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_time/input_time.html

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/5_group/tables/*.csv

  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population_16]
    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_16]
    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

######## SUS
  execute_simple_validation_analyses_sus:
    run: python:latest python analysis/sus/simple_validation_script_sus.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/5_group/tables/*.csv
#        figures: output/sus/simplified_output/5_group/figures/*.png

  execute_simple_validation_analyses_16_sus:
    run: python:latest python analysis/sus/simple_validation_script_16_sus.py
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive: 
        tables: output/sus/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

  # local_simple_run:
  #   run: python:latest python analysis/local_simple_run_sot.py
  #   outputs:
  #     moderately_sensitive: 
  #       tables: output/released/*.csv

################## over time

  time_tables:
    run: r:latest analysis/time/times.R
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        data: output/time/*.csv
        plots: output/time/*.png

##### draft report
  generate_draft_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: 00:00:24

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
55fd44e
Requested actions
  • generate_draft_report

Code comparison

Compare the code used in this Job Request