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Job request: 22324

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
m7sqkxy6euqb6p2k
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  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

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  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

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  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


######## 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


  report_tables:
    run: python:latest python analysis/report_tables.py
    needs: [execute_simple_validation_analyses_16_sus, execute_simple_validation_analyses_sus,execute_simple_validation_analyses,execute_simple_validation_analyses_16]
    outputs:
      moderately_sensitive: 
        tables: output/report_tables/*.csv

  generate_ons_comparisons:
    run: r:latest analysis/sus/combine_ons_sus.R
    needs: [execute_simple_validation_analyses_16_sus,execute_simple_validation_analyses_sus]
    outputs:
      moderately_sensitive:
        csvs: output/sus/simplified_output/*/tables/ethnic_group*.csv

##### draft report
  generate_draft_report_rmd:
    run: r:latest -e 'rmarkdown::render("notebooks_r/report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/report")'
    needs: [generate_ons_comparisons,report_tables, execute_simple_validation_analyses,execute_simple_validation_analyses_16,execute_simple_validation_analyses_sus,execute_simple_validation_analyses_16_sus,generate_study_population_5]
    outputs:
      moderately_sensitive:
        html: output/report/report.html

#### move released files to output/released
###### run locally for manuscript
##### local notebook
  generate_local_runs:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/local_runs.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:
        csvs: output/released/made_locally/*.csv

  # process_ons_census_data:
  #   run: r:latest analysis/local/ons_process.R
  #   outputs:
  #     moderately_sensitive:
  #       csvs: data/*.csv.gz

  # generate_local_ons_comparisons:
  #   run: r:latest analysis/local/combine_ons_sus.R
  #   needs: [process_ons_census_data]
  #   outputs:
  #     moderately_sensitive:
  #       csvs: output/released/made_locally/ethnic_group*.csv
  #       tests: output/tests/*.csv

## create outputs for the manuscript
  ## library(hrbrthemes) not currently available on the OS R image
  # generate_manuscript_plots:
  #   run: r:latest analysis/local/local_manuscript_plots.R
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/released/made_locally/*.png

## create outputs for the appendix
# `row_group.as_column = TRUE` option not currently available on the OS R image
  # generate_appendix:
  #   run: r:latest analysis/local/appendix.R
  #   needs: [generate_local_runs]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/released/made_locally/*.html
  #       pdf: output/released/made_locally/*.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:49

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
7117274
Requested actions
  • generate_draft_report_rmd

Code comparison

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