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Job request: 15622

Organisation:
University of Liverpool
Workspace:
flucats
ID:
aym4evw2a5u27et3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  
  generate_study_population_conscious_level_blood_pressure:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=altered_conscious_level,blood_pressure
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_clinical_concern_dehydration:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=causing_clinical_concern,dehydration_or_shock
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_heart_rate_resp_rate:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=heart_rate,respiratory_rate
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz

  generate_study_population_ox_temp:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=oxygen_saturation,temperature
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_study_population_who_dem:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=who_performance_score,demographic_variables
    outputs:
      highly_sensitive:
        cohort: output/in*.csv.gz

  generate_study_population_resp:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_v2
      --index-date-range "2020-03-01 to 2021-06-01 by month"
      --output-format=csv.gz
      --with-end-date-fix
      --param varset=severe_respiratory_distress,respiratory_exhaustion
    outputs:
      highly_sensitive:
        cohort: output/i*.csv.gz


  generate_study_population_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_end.csv.gz


  # join_cohorts_monthly:
  #   run: >
  #     cohort-joiner:v0.0.44
  #       --lhs output/input_v2*.csv.gz
  #       --rhs output/input_end.csv.gz
  #       --output-dir output/joined
  #   needs: [
  #     generate_study_population_conscious_level_blood_pressure,
  #     generate_study_population_clinical_concern_dehydration,
  #     generate_study_population_heart_rate_resp_rate,
  #     generate_study_population_ox_temp,
  #     generate_study_population_who_dem,
  #     generate_study_population_resp,
  #     generate_study_population_end
  #     ]
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/joined/input_20*.csv.gz



  # combined_input_files:
  #   run: python:latest python analysis/combine_input_files.py
  #   needs: [join_cohorts_monthly]
  #   outputs:
  #     highly_sensitive:
  #       attrition: output/joined/input_all_py.csv.gz

  # column_counts:
  #   run: python:latest python analysis/test_column_counts.py
  #   needs: [generate_study_population_v2_conscious_level]
  #   outputs:
  #     moderately_sensitive:
  #       counts: output/column_counts/*.csv

  # generate_first_outputs:
  #   run: r:latest analysis/flucats_descriptive_basic.R
  #   needs: [combined_input_files]
  #   outputs:
  #     moderately_sensitive:
  #       attrition: output/attrition.csv
  #       histogram_age: output/age_hist.png
  #       date_plot: output/weekly_template.png
  #       flucat_tables: output/flucat*.csv
  #       sex_table: output/sex_table.csv
  #       region_table: output/region_table.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:42:08

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

Job request

Status
Failed
Backend
EMIS
Workspace
flucats
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
3660966
Requested actions
  • generate_study_population_conscious_level_blood_pressure

Code comparison

Compare the code used in this job request