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Job request: 1227

Organisation:
Bennett Institute
Workspace:
long-covid-descriptive
ID:
idg5qol2yumegfa5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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_measure_cohort_1
    Status:
    Status: Failed
    Job identifier:
    mlyjm7buey3tcvot
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_measure_cohort_2
    Status:
    Status: Failed
    Job identifier:
    spqwy67fcuh556y2
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_cohort
    Status:
    Status: Failed
    Job identifier:
    f5da4tpsx2d2exxs
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    standardise_and_plot
    Status:
    Status: Failed
    Job identifier:
    c6dfbeel6v344yte
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    count_by_strata
    Status:
    Status: Failed
    Job identifier:
    mn6b273fnpjoazuc
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    o762rodvqg66pn2n
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 500

actions:

  generate_measure_cohort_1:
    # week 45 2020 to 20 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2020-11-02 to 2021-01-03 by week"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_measure_cohort_2:
    # week 51 2020 to 03 2021 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2021-01-04 to 2021-03-07 by week"
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measure
    needs: [generate_measure_cohort_1, generate_measure_cohort_2]
    outputs:
      highly_sensitive:
        measure: output/measure_*_rate.csv

  standardise_and_plot:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        tables: output/*_rate.csv
        graph: output/time_series_plot.svg

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_cohort.csv

  count_by_strata:
    run: python:latest python analysis/all_time_counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        table: output/counts_table.csv
        code_table: output/first_long_covid_code.csv
        code_table2: output/all_long_covid_codes.csv
        practice_summ: output/practice_summ.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:26

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

Job request

Status
Failed
Backend
EMIS
Workspace
long-covid-descriptive
Requested by
Peter Inglesby
Branch
main
Force run dependencies
No
Git commit hash
0855d9b
Requested actions
  • run_all

Code comparison

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