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Job request: 19251

Organisation:
Bennett Institute
Workspace:
opioids-covid-research
ID:
oj5boxbuuhwjbz3i
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 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

  • Action:
    measures_overall
    Status:
    Status: Failed
    Job identifier:
    3iqfwgnjrxe4hsbc
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_dataset_table
    Status:
    Status: Failed
    Job identifier:
    dvhhzzcnx5ttlspk
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
######################################
# This script defines the project pipeline - 
# it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################

version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_dataset_table:
    run: ehrql:v0 generate-dataset analysis/define_dataset_table.py 
      --output output/data/dataset_table.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_table.csv.gz  

  measures_overall:
    run: ehrql:v0 generate-measures analysis/measures_overall.py 
      --output output/measures/measures_overall.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_overall.csv
  
  # measures_overall_nocancer:
  #   run: ehrql:v0 generate-measures analysis/measures_overall_nocancer.py 
  #     --output output/measures/measures_overall_nocancer.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_overall_nocancer.csv
    
  measures_demo:
    run: ehrql:v0 generate-measures analysis/measures_demo.py 
      --output output/measures/measures_demo.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_demo.csv

  # measures_demo_nocancer:
  #   run: ehrql:v0 generate-measures analysis/measures_demo_nocancer.py 
  #     --output output/measures/measures_demo_nocancer.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_demo_nocancer.csv

  measures_type:
    run: ehrql:v0 generate-measures analysis/measures_type.py 
      --output output/measures/measures_type.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_type.csv

  # measures_type_nocancer:
  #   run: ehrql:v0 generate-measures analysis/measures_type_nocancer.py 
  #     --output output/measures/measures_type_nocancer.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures_type_nocancer.csv

  measures_carehome:
    run: ehrql:v0 generate-measures analysis/measures_carehome.py 
      --output output/measures/measures_carehome.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_carehome.csv
        
  # measures_carehome_sens:
  #   run: ehrql:v0 generate-measures analysis/measures_carehome_sens.py 
  #     --output output/measures/measures_carehome_sens.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_carehome_sens.csv
        
  
  # ## Cohort data
  # generate_study_population_1:
  #   run: cohortextractor:latest generate_cohort
  #     --study-definition study_definition
  #     --index-date-range "2018-01-01 to 2018-12-01 by month" 
  #     --output-dir=output 
  #     --output-format=csv
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_*.csv

  # generate_study_population_2:
  #   run: cohortextractor:latest generate_cohort 
  #     --study-definition study_definition
  #     --index-date-range "2019-01-01 to 2019-12-01 by month" 
  #     --output-dir=output 
  #     --output-format=csv
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input*.csv

  # generate_study_population_3:
  #   run: cohortextractor:latest generate_cohort 
  #     --study-definition study_definition
  #     --index-date-range "2020-01-01 to 2020-12-01 by month" 
  #     --output-dir=output 
  #     --output-format=csv
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/inpu*.csv

  # generate_study_population_4:
  #   run: cohortextractor:latest generate_cohort 
  #     --study-definition study_definition
  #     --index-date-range "2021-01-01 to 2021-12-01 by month" 
  #     --output-dir=output 
  #     --output-format=csv
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/inp*.csv
  
  # generate_study_population_5:
  #   run: cohortextractor:latest generate_cohort 
  #     --study-definition study_definition
  #     --index-date-range "2022-01-01 to 2022-03-01 by month" 
  #     --output-dir=output 
  #     --output-format=csv
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/in*.csv

  # ## Ethnicity      
  # generate_ethnicity_cohort:
  #   run: >
  #     cohortextractor:latest generate_cohort
  #       --study-definition study_definition_ethnicity
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_ethnicity.csv


  # # Data processing ----
  
  # ## Add ethnicity
  # join_cohorts:
  #   run: >
  #     cohort-joiner:v0.0.48
  #       --lhs output/input_*.csv
  #       --rhs output/input_ethnicity.csv
  #       --output-dir output/data
  #   needs: [generate_study_population_1,  generate_study_population_2, 
  #     generate_study_population_5, generate_study_population_3, 
  #     generate_study_population_4, generate_ethnicity_cohort]
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/data/input_*.csv 


  # ## Generate measures - full population
  # generate_measures:
  #   run: >
  #     cohortextractor:latest generate_measures 
  #       --study-definition study_definition
  #       --output-dir output/data
  #   needs: [join_cohorts]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/data/measure_*.csv


  ## Process data - time series
  # process_data_ts:
  #  run: r:latest analysis/process/process_data_ts.R
  #  needs: [measures_overall, measures_demo, measures_type, measures_carehome]
  #  outputs:
  #     moderately_sensitive:
  #       timeseries_csv: output/timeseries/ts_*.csv

  # ## Time series - rates and rounding
  # rounding_ts:
  #  run: r:latest analysis/process/rounding_ts.R
  #  needs: [process_data_ts]
  #  outputs:
  #     moderately_sensitive:
  #       timeseries_csv: output/timeseries/ts*.csv

  # ## Process data - table
  # process_data_table:
  #  run: r:latest analysis/process/process_data_table.R
  #  needs: [generate_dataset_table]
  #  outputs:
  #     highly_sensitive:
  #       table_csv: output/processed/final*.csv
  #       table2_csv: output/joined/final*.csv

  # ## Results table 
  # table:
  #   run: r:latest analysis/descriptive/table_stand.R
  #   needs: [process_data_table]
  #   outputs:
  #     moderately_sensitive:
  #       table: output/tables/table_*.csv

Timeline

  • Created:

  • Started:

  • Runtime:

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

Job request

Status
Failed
Backend
TPP
Workspace
opioids-covid-research
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
c2d9ac4
Requested actions
  • generate_dataset_table
  • measures_overall

Code comparison

Compare the code used in this job request