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Job request: 9195

Organisation:
Bennett Institute
Workspace:
hypertension-sro-dev
ID:
ldkya6j7e44w4ixg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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:
    generate_study_population_hyp007
    Status:
    Status: Failed
    Job identifier:
    gqgsvs2j57lertcj
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_hyp001
    Status:
    Status: Failed
    Job identifier:
    bt3sfuogvxpynwyb
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_ethnicity
    Status:
    Status: Failed
    Job identifier:
    rozfk73f5wv7otzl
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_hyp003
    Status:
    Status: Failed
    Job identifier:
    sykalnhpbd6balad
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_measures_hyp003
    Status:
    Status: Failed
    Job identifier:
    rmkj4makeobcw4jw
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    yojuo2v6e53uovh3
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures_hyp007
    Status:
    Status: Failed
    Job identifier:
    hth7c3yq7bsfzumt
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures_hyp001
    Status:
    Status: Failed
    Job identifier:
    c72i26wwplgvd2z7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_deciles
    Status:
    Status: Failed
    Job identifier:
    hhonjlhpkzk3pyys
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  # Study populations
  # Extract latests ethnicity record for cohort
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output/indicators 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_ethnicity.feather

  # Extract cohort for indicator HYP001 by month 
  generate_study_population_hyp001:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp001 
      --index-date-range "2020-01-01 to 2020-10-01 by month" 
      --output-dir=output/indicators
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp001_*.feather

  # Extract cohort for indicator HYP003 by month 
  generate_study_population_hyp003:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp003 
      --index-date-range "2020-01-01 to 2020-10-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp003_*.feather
  
  # Extract cohort for indicator HYP007 by month 
  generate_study_population_hyp007:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp007 
      --index-date-range "2020-01-01 to 2020-10-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp007_*.feather

  join_ethnicity:
    run: >
      cohort-joiner:v0.0.27
        --lhs output/indicators/input_hyp*.feather
        --rhs output/indicators/input_ethnicity.feather
        --output-dir output/indicators/joined
    needs: [generate_study_population_ethnicity, generate_study_population_hyp001, generate_study_population_hyp003, generate_study_population_hyp007]
    outputs:
      highly_sensitive:
        cohort: output/indicators/joined/input_hyp*.feather

  # Measures
  # Generate measures for indicator HYP001 by month
  generate_measures_hyp001:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp001 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp001_*_rate.csv

 # Generate measures for indicator HYP003 by month
  generate_measures_hyp003:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp003 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp003_*_rate.csv

  # Generate measures for indicator HYP007 by month
  generate_measures_hyp007:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp007 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp007_*_rate.csv

  generate_deciles:
    run: >
      deciles-charts:v0.0.21
        --input-files output/indicators/joined/measure_*_*_rate.csv
        --output-dir output/indicators/joined/
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007]
    outputs:
      moderately_sensitive:
        deciles_charts: output/indicators/joined/deciles_chart_*_*_practice_breakdown_rate.png
        deciles_tables: output/indicators/joined/deciles_table_*_*_practice_breakdown_rate.csv
  
  # check_data:
  #   run: r:latest analysis/check_bp_recording_values_dates.R
  #   needs: [join_ethnicity]
  #   outputs:
  #     moderately_sensitive:
  #       table_count_csv: output/indicators/joined/data_check/tab_hyp*_*_2020_03_01.csv
  #       skim_txt: output/indicators/joined/data_check/skim_df_hyp*_2020_03_01.txt
  #       table_date_diff_csv: output/indicators/joined/data_check/tab_hyp*_num_bp_date_diff_2020_03_01.csv
  #       plot_date_diff: output/indicators/joined/data_check/plot_hyp*_num_bp_date_diff_2020_03_01.png

  # # Join all measure files for each indicator
  # join_measures:
  #   run: r:latest analysis/join_measures.R
  #   needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/indicators/joined/measures/measures_hyp*.csv

  # # Join all deciles (by practice) files for each indicator
  # join_deciles:
  #   run: r:latest analysis/join_deciles.R
  #   needs: [generate_deciles]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/indicators/joined/deciles/deciles_hyp_practice.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:32:01

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

Job request

Status
Failed
Backend
TPP
Workspace
hypertension-sro-dev
Requested by
Milan Wiedemann
Branch
dev
Force run dependencies
Yes
Git commit hash
51e06c2
Requested actions
  • run_all

Code comparison

Compare the code used in this job request