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Job request: 8097

Organisation:
NHSE/I
Workspace:
nhs_at_home_main
ID:
2jc5n7hjm6ynhucc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alexandra Benson 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_bp_breakdowns
    Status:
    Status: Failed
    Job identifier:
    hsdl3tb4rpfneire
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_bp_timeseries
    Status:
    Status: Failed
    Job identifier:
    kl5jirie5vumnzvq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_oximetry_breakdowns
    Status:
    Status: Failed
    Job identifier:
    64ykksvzlvkslca5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_proactive_breakdowns
    Status:
    Status: Failed
    Job identifier:
    oxhbtnkzhyjyonob
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_study_population_bp
    Status:
    Status: Failed
    Job identifier:
    5nb5peuue3xubrrz
    Error:
    nonzero_exit: Job exited with error code 5: Something went wrong with the database, please contact tech support
  • Action:
    generate_oximetry_timeseries
    Status:
    Status: Failed
    Job identifier:
    qx67ymtpxl2egk2o
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_study_population_proactive
    Status:
    Status: Failed
    Job identifier:
    okycaxim23gbfaco
    Error:
    nonzero_exit: Job exited with error code 4: New data is being imported into the database, please try again in a few hours
  • Action:
    generate_oximetry_regional_timeseries
    Status:
    Status: Failed
    Job identifier:
    kz6fupctba5emtuq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_bp_regional_timeseries
    Status:
    Status: Failed
    Job identifier:
    i2ggr7nqmebh5td6
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_proactive_timeseries
    Status:
    Status: Failed
    Job identifier:
    gwgoixzqj6m3mbjk
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_study_population_oximetry
    Status:
    Status: Failed
    Job identifier:
    7w6o55cy6bubu7bw
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_proactive_regional_timeseries
    Status:
    Status: Failed
    Job identifier:
    6clmgwljmxcnv3cp
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_study_population_oximetry:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_oximetry --index-date-range "2019-04-01 to 2022-05-12 by week"
    outputs:
      highly_sensitive:
        oximetry_cohort: output/input_oximetry*.csv

  generate_study_population_bp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_bp --index-date-range "2019-04-01 to 2022-05-12 by week"
    outputs:
      highly_sensitive:
        bp_cohort: output/input_bp*.csv

  generate_study_population_proactive:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_proactive --index-date-range "2019-04-01 to 2022-05-12 by week"
    outputs:
      highly_sensitive:
        proactive_cohort: output/input_proactive*.csv

  generate_oximetry_timeseries:
    run: python:latest python analysis/analysis_oximetry_timeseries.py
    needs: [generate_study_population_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_counts: output/oximetry_table_counts.csv
        oximetry_plot_timeseries: output/oximetry_plot_timeseries.png

  generate_oximetry_regional_timeseries:
    run: python:latest python analysis/analysis_oximetry_region.py
    needs: [generate_study_population_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_counts_region: output/oximetry_table_counts_*.csv
        oximetry_plot_timeseries_region: output/oximetry_plot_timeseries_region_*.png

  generate_oximetry_breakdowns:
    run: python:latest python analysis/analysis_oximetry_breakdowns.py
    needs: [generate_study_population_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_breakdowns: output/oximetry_table_code_*.csv
        oximetry_plot_breakdowns: output/oximetry_plot_code_*.png

  generate_bp_timeseries:
    run: python:latest python analysis/analysis_bp_timeseries.py
    needs: [generate_study_population_bp]
    outputs:
      moderately_sensitive:
        bp_table_counts: output/bp_table_counts.csv
        bp_plot_timeseries: output/bp_plot_timeseries.png

  generate_bp_regional_timeseries:
    run: python:latest python analysis/analysis_bp_region.py
    needs: [generate_study_population_bp]
    outputs:
      moderately_sensitive:
        bp_table_counts_region: output/bp_table_counts_*.csv
        bp_plot_timeseries_region: output/bp_plot_timeseries_region_*.png

  generate_bp_breakdowns:
    run: python:latest python analysis/analysis_bp_breakdowns.py
    needs: [generate_study_population_bp]
    outputs:
      moderately_sensitive:
        bp_table_breakdowns: output/bp_table_code_*.csv
        bp_plot_breakdowns: output/bp_plot_code_*.png

  generate_proactive_timeseries:
    run: python:latest python analysis/analysis_proactive_timeseries.py
    needs: [generate_study_population_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_counts: output/proactive_table_counts.csv
        proactive_plot_timeseries: output/proactive_plot_timeseries.png

  generate_proactive_regional_timeseries:
    run: python:latest python analysis/analysis_proactive_region.py
    needs: [generate_study_population_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_counts_region: output/proactive_table_counts_*.csv
        proactive_plot_timeseries_region: output/proactive_plot_timeseries_region_*.png

  generate_proactive_breakdowns:
    run: python:latest python analysis/analysis_proactive_breakdowns.py
    needs: [generate_study_population_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_breakdowns: output/proactive_table_code_*.csv
        proactive_plot_breakdowns: output/proactive_plot_code_*.png

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job request

Status
Failed
Backend
TPP
Workspace
nhs_at_home_main
Requested by
Alexandra Benson
Branch
main
Force run dependencies
Yes
Git commit hash
318f6ab
Requested actions
  • run_all

Code comparison

Compare the code used in this job request