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Job request: 13855

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report-notebook
ID:
zwyqugbap42gdgnq
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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:
    split_codelist
    Status:
    Status: Succeeded
    Job identifier:
    c5wi6p5qpi23lyxl
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    hn27mknowucqsyd6
    Error:
    nonzero_exit: Job exited with an error: Ran out of memory (limit for this job was 128.00GB)
  • Action:
    combine_ons
    Status:
    Status: Failed
    Job identifier:
    t34lrwnjdsjuvxey
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    ons_plot
    Status:
    Status: Failed
    Job identifier:
    irlcvucpnz33kpv7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    execute_simple_validation_analyses_16
    Status:
    Status: Failed
    Job identifier:
    iwe52prisuua7j3g
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    execute_simple_validation_analyses
    Status:
    Status: Failed
    Job identifier:
    xnq6goxm6kk6y6q3
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_dataset_report
    Status:
    Status: Failed
    Job identifier:
    aktxrkwczx5ujuci
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    time_tables
    Status:
    Status: Failed
    Job identifier:
    vlxwplctqtyuza2f
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
### CTV3, PRIMIS, SNOMED analysis

version: '3.0'

expectations:
  population_size: 1000

actions:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data: codelists/ethnicity_*.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-file output/extract/input.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract/input.feather

  generate_dataset_report:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract/input.feather
        --output-dir output/extract
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract/input.html

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/5_group/tables/*.csv

  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/16_group/tables/simpl*.csv

  combine_ons:
    run: r:latest analysis/combine_ons.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        data: output/ons/ethnic_group*.csv
        data2: output/ons/ethnic_group_NA*.csv
        data3: output/ons/data_check*.csv

  ons_plot:
    run: r:latest analysis/ons_plots.R
    needs: [combine_ons]
    outputs:
      moderately_sensitive:
        plot_na: output/ons/na_removed/ethnicity_*.png


# ## Only to be run locally
#   generate_report:
#     run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
#     needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
#     outputs:
#       moderately_sensitive:
#         notebook: output/draft_report_ethnicity.html

#   local_simple_run:
#     run: python:latest python analysis/local_simple_run.py
#     outputs:
#       moderately_sensitive: 
#         tables: output/from_jobserver/release_2022_11_18/made_locally/*.csv

# ######## SUS
#   execute_simple_validation_analyses_sus:
#     run: python:latest python analysis/sus/simple_validation_script_sus.py
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive: 
#         tables: output/sus/simplified_output/5_group/tables/*.csv
# #        figures: output/sus/simplified_output/5_group/figures/*.png

#   execute_simple_validation_analyses_16_sus:
#     run: python:latest python analysis/sus/simple_validation_script_16_sus.py
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive: 
#         tables: output/sus/simplified_output/16_group/tables/simpl*.csv

#   combine_ons:
#     run: r:latest analysis/combine_ons.R
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive:
#         data: output/ons/ethnic_group*.csv
#         data2: output/ons/ethnic_group_NA*.csv
#         data3: output/ons/data_check*.csv

#   ons_plot:
#     run: r:latest analysis/ons_plots.R
#     needs: [combine_ons]
#     outputs:
#       moderately_sensitive:
#         plot_na: output/ons/na_removed/ethnicity_*.png

#   iqr: 
#     run: r:latest analysis/iqr.R
#     needs: [generate_study_population]
#     outputs:
#       moderately_sensitive:
#         full: output/simplified_output/5_group/tables/range_fullset.csv
#         registered: output/simplified_output/5_group/tables/range_registered.csv    
#         figures: output/simplified_output/5_group/figures/density*.svg    

# ## Only to be run locally
#   generate_report:
#     run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
#     needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
#     outputs:
#       moderately_sensitive:
#         notebook: output/draft_report_ethnicity.html

#   local_simple_run:
#     run: python:latest python analysis/local_simple_run.py
#     outputs:
#       moderately_sensitive: 
#         tables: output/from_jobserver/release_2022_11_18/made_locally/*.csv

################## over time

  time_tables:
    run: r:latest analysis/time/times.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        data: output/time/*.csv
        plots: output/time/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 12:43:21

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

Job request

Status
Failed
Backend
TPP
Workspace
ethnicity-short-data-report-notebook
Requested by
Colm Andrews
Branch
notebook
Force run dependencies
Yes
Git commit hash
fc51411
Requested actions
  • run_all

Code comparison

Compare the code used in this job request