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Job request: 20417

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt-cohort-profile
ID:
yal7dzcepp7imsiv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    extract_linked_tpp_info
    Status:
    Status: Failed
    Job identifier:
    s3o6gxi7yxy7ebbn
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    create_dummy_data
    Status:
    Status: Failed
    Job identifier:
    5tp7iytd3fvqn6vc
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    scrape_all_data
    Status:
    Status: Failed
    Job identifier:
    vgobrosls2433dtf
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_openprompt_survey1
    Status:
    Status: Failed
    Job identifier:
    gcx3xqmphan2h54g
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_openprompt_survey2
    Status:
    Status: Failed
    Job identifier:
    pbjcej7qxn4wf2h7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_openprompt_survey3
    Status:
    Status: Failed
    Job identifier:
    pi4cfban7b6evkrq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_openprompt_survey4
    Status:
    Status: Failed
    Job identifier:
    ckykb6m7nudyz7hy
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    datacombine_and_figure1
    Status:
    Status: Failed
    Job identifier:
    bfoj5hnp3nlohus2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    import_linked_tpp
    Status:
    Status: Failed
    Job identifier:
    r2g4j2wb22jkwirl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    export_table1_stats
    Status:
    Status: Failed
    Job identifier:
    kbi3v65ggpq7r6os
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    edit_dummy_data
    Status:
    Status: Failed
    Job identifier:
    bytuvcdirhlutwsi
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  create_dummy_data: 
    run: >
      ehrql:v0
        create-dummy-tables 
        analysis/dataset_definition.py output/dummydata 
        -- 
        --day=0
    outputs: 
      highly_sensitive:
        openprompt_dummy: output/dummydata/open_prompt.csv

  edit_dummy_data:
    run: > 
      r:latest
        analysis/dummy_data_editing/edit_automatic_dummy_data.R
    needs: [create_dummy_data]
    outputs: 
      highly_sensitive: 
        openprompt_dummy_edited: output/dummydata/dummy_edited/open_prompt.csv

  scrape_all_data: 
    run: >
      ehrql:v0
        generate-dataset
        analysis/scrape_data_response_dates.py
        --output output/openprompt_all.csv
        --dummy-tables output/dummydata/dummy_edited
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive: 
        openprompt_all: output/openprompt_all.csv

  generate_openprompt_survey1: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey1.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=0
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey1: output/openprompt_survey1.csv

  generate_openprompt_survey2: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey2.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=30
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey2: output/openprompt_survey2.csv

  generate_openprompt_survey3: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey3.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=60
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey3: output/openprompt_survey3.csv

  generate_openprompt_survey4: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey4.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=90
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey4: output/openprompt_survey4.csv

  extract_linked_tpp_info: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/add_tpp_data.py 
        --output output/openprompt_linked_tpp.csv.gz
    outputs:
      highly_sensitive:
        linked_tpp_data: output/openprompt_linked_tpp.csv.gz
  
  datacombine_and_figure1:
      run: >
        r:latest analysis/data_import/001_data_combine.R
      needs: [scrape_all_data, generate_openprompt_survey1, generate_openprompt_survey2, generate_openprompt_survey3, generate_openprompt_survey4]
      outputs: 
        highly_sensitive: 
          openprompt_combined: output/openprompt_raw.csv.gz
        moderately_sensitive:
          openprompt_raw_skim: output/data_properties/op_raw_skim.txt
          openprompt_raw_tab: output/data_properties/op_raw_tabulate.txt
          openprompt_mapped_skim: output/data_properties/op_mapped_skim.txt
          openprompt_mapped_tab: output/data_properties/op_mapped_tabulate.txt
          raw_summ_base_s: output/data_properties/op_baseline_skim.txt
          raw_summ_base_t: output/data_properties/op_baseline_tabulate.txt
          raw_summ_survey1_s: output/data_properties/op_survey1_skim.txt
          raw_summ_survey1_t: output/data_properties/op_survey1_tabulate.txt
          raw_summ_survey2_s: output/data_properties/op_survey2_skim.txt
          raw_summ_survey2_t: output/data_properties/op_survey2_tabulate.txt
          raw_summ_survey3_s: output/data_properties/op_survey3_skim.txt
          raw_summ_survey3_t: output/data_properties/op_survey3_tabulate.txt
          raw_summ_survey4_s: output/data_properties/op_survey4_skim.txt
          raw_summ_survey4_t: output/data_properties/op_survey4_tabulate.txt
          check_days_after_baseline: output/data_properties/sample_day_lags.pdf
          p1a_jpeg: output/plots/p1a_index_dates.jpeg
          p1a_tiff: output/plots/p1a_index_dates.tiff
          p1b_jpeg: output/plots/p1b_recorded_question_responses.jpeg
          p1b_tiff: output/plots/p1b_recorded_question_responses.tiff
          p1c_jpeg: output/plots/p1c_anyresponse_hist.jpeg
          p1c_tiff: output/plots/p1c_anyresponse_hist.tiff
          p1d_jpeg: output/plots/p1d_ltfu.jpeg
          p1d_tiff: output/plots/p1d_ltfu.tiff
          p1_jpeg: output/plots/p1_fup.jpeg
          p1_tiff: output/plots/p1_fup.tiff
  
  import_linked_tpp: 
    run:   
      r:latest analysis/data_import/002_import_linked_tpp.R
    needs: [extract_linked_tpp_info]
    outputs: 
      highly_sensitive: 
        linked_tpp_data_edited: output/openprompt_linked_tpp_edited.csv.gz
      moderately_sensitive:
        openprompt_tpp_skim: output/data_properties/op_tpp_skim.txt
        openprompt_tpp_tab: output/data_properties/op_tpp_tabulate.txt

  export_table1_stats: 
    run: 
      r:latest analysis/baseline_descriptive/001-table1stats.R
    needs: [datacombine_and_figure1, import_linked_tpp]
    outputs: 
      moderately_sensitive: 
        table1: output/tables/table1.html
        table1_stats: output/tables/table1_stats.csv

# Then need to run analysis/baseline_descriptive/002-map-making.R to produce the Figure 2 for the paper

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:21

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

Job information

Status
Failed
Backend
TPP
Workspace
openprompt-cohort-profile
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
No
Git commit hash
0dcf949
Requested actions
  • run_all

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