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Job request: 24736

Organisation:
UKHSA
Workspace:
main_branch
ID:
756otrefyrmhqznw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Megan Griffiths 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

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv.gz

  raw_data_overview:
    run: r:v2 analysis/raw_data_overview.R output/dataset.csv.gz output/overview/ TRUE
    needs:
    - generate_dataset
    outputs:
      moderately_sensitive:
        txt: output/overview/dataset*.txt

  dataset_cleaning:
    run: r:v2 analysis/dataset_cleaning.R 
    needs:
    - generate_dataset
    outputs:
      highly_sensitive:
        df_clean: output/dataset_clean/dataset_clean.csv.gz
      moderately_sensitive:
        msoas: output/dataset_clean/dataset_msoas.csv

  clean_data_overview:
    run: r:v2 analysis/raw_data_overview.R output/dataset_clean/dataset_clean.csv.gz output/dataset_clean/overview/ TRUE
    needs:
    - generate_dataset
    - dataset_cleaning
    outputs:
      moderately_sensitive:
        txt: output/dataset_clean/overview/dataset*.txt

  dataset_processing:
    run: r:v2 analysis/dataset_processing.R 
    needs:
    - generate_dataset
    - dataset_cleaning
    outputs:
      highly_sensitive:
        df_all_counts1: output/dataset_processed/processed_counts_data_max_msoa9.csv.gz
        df_all_counts2: output/dataset_processed/processed_counts_data_max_district.csv.gz
        df_all_counts4: output/dataset_processed/processed_counts_data_min_msoa9.csv.gz
        df_all_counts5: output/dataset_processed/processed_counts_data_min_district.csv.gz
        df_all_counts3: output/dataset_processed/processed_counts_data_no_e_msoa9.csv.gz
        df_all_counts6: output/dataset_processed/processed_counts_data_no_e_district.csv.gz

      moderately_sensitive:
        df_all_counts_sub1: output/dataset_processed/subset/processed_counts_data_max_msoa9_sub.csv
        df_all_counts_sub2: output/dataset_processed/subset/processed_counts_data_max_district_sub.csv
        df_all_counts_sub4: output/dataset_processed/subset/processed_counts_data_min_msoa9_sub.csv
        df_all_counts_sub5: output/dataset_processed/subset/processed_counts_data_min_district_sub.csv
        df_all_counts_sub3: output/dataset_processed/subset/processed_counts_data_no_e_msoa9_sub.csv
        df_all_counts_sub6: output/dataset_processed/subset/processed_counts_data_no_e_district_sub.csv

  processed_data_overview1:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_max_msoa9.csv.gz output/dataset_processed/max_msoa9/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/max_msoa9/overview/dataset*.txt

  processed_data_overview2:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_max_district.csv.gz output/dataset_processed/max_district/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/max_district/overview/dataset*.txt

  processed_data_overview3:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_no_e_msoa9.csv.gz output/dataset_processed/no_e_msoa9/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/no_e_msoa9/overview/dataset*.txt

  processed_data_overview4:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_min_msoa9.csv.gz output/dataset_processed/min_msoa9/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/min_msoa9/overview/dataset*.txt

  processed_data_overview5:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_min_district.csv.gz output/dataset_processed/min_district/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/min_district/overview/dataset*.txt

  processed_data_overview6:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data_no_e_district.csv.gz output/dataset_processed/no_e_district/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/no_e_district/overview/dataset*.txt

  post_processing_analysis:
    run: r:v2 analysis/post_processing_analysis.R
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        column_bar_png: output/dataset_processed/min_msoa7/analysis/plots/all_bar_plot.png
        ethnic_box_png: output/dataset_processed/min_msoa7/analysis/plots/ethnicity_total_pop_boxplot.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:10:29

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

Job request

Status
Succeeded
Backend
TPP
Workspace
main_branch
Requested by
Megan Griffiths
Branch
main
Force run dependencies
No
Git commit hash
adf1643
Requested actions
  • generate_dataset
  • raw_data_overview
  • dataset_cleaning
  • clean_data_overview
  • dataset_processing
  • processed_data_overview1
  • processed_data_overview2
  • processed_data_overview3
  • processed_data_overview4
  • processed_data_overview5
  • processed_data_overview6

Code comparison

Compare the code used in this job request