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Job request: 8101

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-collateral
ID:
q7j5hbwcfwhi2agc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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:
    time_series_cvd
    Status:
    Status: Failed
    Job identifier:
    ufefbwueced26qmr
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    ysqmyfgh57ptjjyx
    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_study_population
    Status:
    Status: Failed
    Job identifier:
    hadejq23vjav5lqs
    Error:
    nonzero_exit: Job exited with error code 5: Something went wrong with the database, please contact tech support
  • Action:
    graphs_mh_cvd
    Status:
    Status: Failed
    Job identifier:
    icjrcswzwzwzoq7c
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    model_checks_cvd
    Status:
    Status: Failed
    Job identifier:
    5itujuqwhgnn7jv4
    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:
    model_checks_mh
    Status:
    Status: Failed
    Job identifier:
    wmrellzsseijwub5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    time_series_mh
    Status:
    Status: Failed
    Job identifier:
    nlemsai3zh3bidpz
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  # Generates study population for CV, mental health outcomes - start date = 2018-03-01
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv
  # Generates study population for diabetes outcomes
  generate_study_population_dm:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/dm --output-format=csv 
    outputs:
      highly_sensitive:
        cohort: output/measures/dm/input_dm_*.csv

  # Generates study population for respiratory outcomes
  generate_study_population_resp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/resp/input_resp_*.csv

  # Generates study population for mortality
  generate_study_population_mortality:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-01-31 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/mortality/input_mortality_*.csv
  
  # Generates study populations for baseline tables at 3 timepoints
  generate_study_population_tables_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2019-01-01.csv
  generate_study_population_tables_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2020-01-01.csv
  generate_study_population_tables_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2021-01-01.csv
  
  # Generates baseline tables
  create_baseline_tables:
    run: stata-mp:latest analysis/baseline_tables.do
    needs: [generate_study_population_tables_2019, generate_study_population_tables_2020, generate_study_population_tables_2021]
    outputs:
      highly_sensitive:
        output: output/measures/tables/baseline_table_*.xlsx

  # Generates summary measures for CV and mental health outcomes
  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_*_rate.csv
  # Generates summary measures for diabetes outcomes  
  calculate_measures_dm:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
    needs: [generate_study_population_dm]
    outputs:
      moderately_sensitive:
        measure: output/measures/dm/measure_dm_*_rate.csv

  # Generates summary measures for respiratory outcomes  
  calculate_measures_resp:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
    needs: [generate_study_population_resp]
    outputs:
      moderately_sensitive:
        measure: output/measures/resp/measure_*_rate.csv

  # Generates summary measures for mortality outcomes  
  calculate_measures_mortality:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
    needs: [generate_study_population_mortality]
    outputs:
      moderately_sensitive:
        measure: output/measures/mortality/measure_*_rate.csv
  
  # Generates graphs for CVD & mental health outcomes
  graphs_mh_cvd:
    run: stata-mp:latest analysis/graphs_mh_cvd.do 
    needs: [calculate_measures]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mh_cvd.log
        output: output/graphs/line_*.svg
     
  # Generates graphs for diabetes outcomes
  graphs_dm:
    run: stata-mp:latest analysis/graphs_dm.do 
    needs: [calculate_measures_dm]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_dm.log
        output: output/graphs/line_dm_*.svg
      highly_sensitive:
        output: output/collapsed/collapse_measure_dm_*
  # Generate graphs for respiratory outcomes
  graphs_resp:
    run: stata-mp:latest analysis/graphs_resp.do 
    needs: [calculate_measures_resp]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_resp.log
        output: output/graphs/line_resp_*.svg

  # Generate graphs for mortality
  graphs_mortality:
    run: stata-mp:latest analysis/graphs_mortality.do 
    needs: [calculate_measures_mortality]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mortality.log
        output: output/graphs/line_mortality_*.svg
      highly_sensitive:
        output: output/collapsed/collapse_measure_*
        
  # Running analysis scripts
  model_checks_dm:
    run: stata-mp:latest analysis/model_check_dm.do
    needs: [calculate_measures_dm]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_dm.log
        output: output/time_series/dm_*.svg

  model_checks_resp:
    run: stata-mp:latest analysis/model_check_resp.do
    needs: [calculate_measures_resp]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_resp.log
        output: output/time_series/resp_*.svg

  model_checks_cvd:
    run: stata-mp:latest analysis/model_check_cvd.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_cvd.log
        output: output/time_series/cvd_*.svg

  model_checks_mh:
    run: stata-mp:latest analysis/model_check_mh.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_mh.log
        output: output/time_series/mh_*.svg

  model_checks_mortality:
    run: stata-mp:latest analysis/model_check_mortality.do
    needs: [calculate_measures_mortality]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_mortality.log
        output: output/time_series/mortality_*.svg
  
  time_series_resp:
    run: stata-mp:latest analysis/time_series_resp.do
    needs: [calculate_measures_resp]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_resp.log
        output: output/time_series/tsreg_tables_resp.xlsx

  time_series_dm:
    run: stata-mp:latest analysis/time_series_dm.do
    needs: [calculate_measures_dm]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_dm.log
        output: output/time_series/tsreg_tables_dm.xlsx

  time_series_cvd:
    run: stata-mp:latest analysis/time_series_cvd.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_cvd.log
        output: output/time_series/tsreg_tables_cvd.xlsx

  time_series_mh:
    run: stata-mp:latest analysis/time_series_mh.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_mh.log
        output: output/time_series/tsreg_tables_mh.xlsx

  time_series_mortality:
    run: stata-mp:latest analysis/time_series_mortality.do
    needs: [calculate_measures_mortality]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_mortality.log
        output: output/time_series/tsreg_tables_mortality.xlsx

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
covid-collateral
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
bcc098c
Requested actions
  • generate_study_population
  • calculate_measures
  • graphs_mh_cvd
  • model_checks_cvd
  • model_checks_mh
  • time_series_cvd
  • time_series_mh

Code comparison

Compare the code used in this job request