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Job request: 24859

Organisation:
Bennett Institute
Workspace:
pifu-data-exploration
ID:
p45gjafaxhe5bjfz
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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

  • Action:
    generate_dataset_rheum
    Status:
    Status: Succeeded
    Job identifier:
    3csiok5xatfxlwc7
  • Action:
    generate_dataset
    Status:
    Status: Succeeded
    Job identifier:
    s3o2pjkqhmhm5iio
  • Action:
    measures
    Status:
    Status: Succeeded
    Job identifier:
    egrnnmyh5jl5xn2x
  • Action:
    time_series
    Status:
    Status: Succeeded
    Job identifier:
    cm6jw45wbkp6oxjb
  • Action:
    table
    Status:
    Status: Failed
    Job identifier:
    v5mksr7shs7hedc2
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_dataset_explore:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_explore.py --output output/dataset_explore.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_explore.csv.gz

  table_explore:
    run: r:latest analysis/process/data_exploration.R
    needs: [generate_dataset_explore]
    outputs:
      moderately_sensitive:
        table1: output/processed/table_explore.csv
        #table2: output/processed/table_pfu_explore.csv
        table3: output/processed/counts_explore.csv

  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_everyone.py --output output/dataset_everyone.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_everyone.csv.gz
  
  generate_dataset_rheum:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_rheum.py --output output/dataset_rheum.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_rheum.csv.gz

  measures:
    run: ehrql:v1 generate-measures analysis/measures.py --output output/measures/measures.csv
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures.csv

  table:
    run: r:latest analysis/process/pop_characteristics.R
    needs: [generate_dataset, generate_dataset_rheum]
    outputs:
      moderately_sensitive:
        table1: output/processed/table.csv
        table2: output/processed/table_pfu.csv
        table3: output/processed/table_rheum.csv
        table4: output/processed/visits_stats.csv

  time_series:
    run: r:latest analysis/process/measures_process.R
    needs: [measures]
    outputs:
      moderately_sensitive:
        timeseries1: output/processed/time_series_overall.csv
        timeseries2: output/processed/time_series_specialty.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 27:47:58

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

Job information

Status
Failed
Backend
TPP
Workspace
pifu-data-exploration
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
e2c7083
Requested actions
  • generate_dataset
  • generate_dataset_rheum
  • measures
  • table
  • time_series

Code comparison

Compare the code used in this Job Request