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Job request: 16385

Organisation:
University of Manchester
Workspace:
main_pregnancy_tx_pathways
ID:
oqs6sgsorjg5tfum
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Vicki Palin UoM 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  # this is for number of matches
  # should delivery codes be in population?
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition 
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  #this is to generate a date file for each month
  generate_study_population_monthly:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_monthly 
      --index-date-range "2019-01-01 to today by month"
      --output-dir=output 
      --output-format csv.gz 
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  # this is to run measures
  # need to add first/last day of month to variables in study def?
  generate_study_population_measures:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_measures 
      --index-date-range "2019-01-01 to today by month" --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz 
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures --skip-existing --output-dir=output/measures
    needs: [generate_study_population_measures]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  describe_del_code_freq:
    run: r:latest analysis/del_code_frequency.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        hist1: output/del_code_histogram.jpeg
        table1: output/table_del_codes.csv

  describe_del_code_freq_with_names:
    run: r:latest analysis/del_code_frequency_with_names.R
    needs: [generate_study_population, describe_del_code_freq]
    outputs:
      moderately_sensitive:
        table1: output/table_del_codes_with_names.csv


  describe_pn_rate_plots:
    run: r:latest analysis/pn_check_using_measures.R
    needs: [generate_study_population_measures, generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/monthly_pn_rate_measures8wkcode.jpeg

#or does this go into command above
  describe_pn_rate_plots_by_age_cat:
    run: r:latest analysis/pn_check_using_measures_by_age_cat.R
    needs: [generate_study_population_measures, generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/monthly_pn_rate_measures8wkcode_by_age_cat.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 38:08:54

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

Job information

Status
Succeeded
Backend
TPP
Workspace
main_pregnancy_tx_pathways
Requested by
Vicki Palin UoM
Branch
main
Force run dependencies
No
Git commit hash
ec9eaa0
Requested actions
  • generate_study_population_measures

Code comparison

Compare the code used in this Job Request