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Job request: 24716

Organisation:
UKHSA
Workspace:
main_branch
ID:
qulomiyj3g5evcgw
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

  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_msoa8.csv.gz
        df_all_counts3: output/dataset_processed/processed_counts_data_max_msoa7.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_msoa8.csv.gz
        df_all_counts6: output/dataset_processed/processed_counts_data_min_msoa7.csv.gz

  dataset_processing_subset:
    run: r:v2 analysis/dataset_processing_subset.R 
    needs:
    - generate_dataset
    - dataset_cleaning
    outputs:
      highly_sensitive:
        df_all_counts: output/dataset_processed/subset_processed_counts_data.csv.gz

  processed_data_overview:
    run: r:v2 analysis/raw_data_overview.R output/dataset_processed/processed_counts_data.csv.gz output/dataset_processed/overview/ FALSE
    needs:
    - generate_dataset
    - dataset_cleaning
    - dataset_processing
    outputs:
      moderately_sensitive:
        txt: output/dataset_processed/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_hist_png: output/dataset_processed/analysis/plots/all_hist_plot.png
        subset_processed_counts_data: output/dataset_processed/analysis/subset_processed_counts_data.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:34

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
8822669
Requested actions
  • dataset_processing

Code comparison

Compare the code used in this job request