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Job request: 18483

Organisation:
University of Manchester
Workspace:
antibiotic-adverse-event
ID:
6mia4trax5fb4w5p
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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: 30000

actions:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
### study cohort ###

### UTI ###

  generate_study_population_case_uti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti
    outputs:
      highly_sensitive:
        cohort: output/input_case_uti.csv

  generate_study_population_control_uti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_uti
    outputs:
      highly_sensitive:
        cohort: output/input_control_uti.csv

  matching_uti:
    run: python:latest python analysis/matching_uti.py
    needs: [generate_study_population_case_uti,generate_study_population_control_uti]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_uti.csv
        table2: output/matched_matches_uti.csv
        table3: output/matched_combined_uti.csv
      moderately_sensitive: 
        report1: output/matching_report_uti.txt
### UTI var ###
  generate_study_population_case_uti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti_abvar
    needs: [matching_uti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_uti_abvar.csv

  generate_study_population_control_uti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_uti_abvar
    needs: [matching_uti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_uti_abvar.csv

  generate_study_population_case_uti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti_othvar
    needs: [matching_uti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_uti_othvar.csv

  generate_study_population_control_uti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_uti_othvar
    needs: [matching_uti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_uti_othvar.csv

  generate_study_population_case_uti_type:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti_type
    needs: [matching_uti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_uti_type.csv

### URTI ###

  generate_study_population_case_urti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti
    outputs:
      highly_sensitive:
        cohort: output/input_case_urti.csv

  generate_study_population_control_urti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_urti
    outputs:
      highly_sensitive:
        cohort: output/input_control_urti.csv

  matching_urti:
    run: python:latest python analysis/matching_urti.py
    needs: [generate_study_population_case_urti,generate_study_population_control_urti]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_urti.csv
        table2: output/matched_matches_urti.csv
        table3: output/matched_combined_urti.csv
      moderately_sensitive: 
        report1: output/matching_report_urti.txt

### URTI var ###
  generate_study_population_case_urti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti_abvar
    needs: [matching_urti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_urti_abvar.csv

  generate_study_population_control_urti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_urti_abvar
    needs: [matching_urti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_urti_abvar.csv

  generate_study_population_case_urti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti_othvar
    needs: [matching_urti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_urti_othvar.csv

  generate_study_population_control_urti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_urti_othvar
    needs: [matching_urti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_urti_othvar.csv

  generate_study_population_case_urti_type:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti_type
    needs: [matching_urti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_urti_type.csv

### LRTI ###

  generate_study_population_case_lrti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti
    outputs:
      highly_sensitive:
        cohort: output/input_case_lrti.csv

  generate_study_population_control_lrti:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_lrti
    outputs:
      highly_sensitive:
        cohort: output/input_control_lrti.csv

  matching_lrti:
    run: python:latest python analysis/matching_lrti.py
    needs: [generate_study_population_case_lrti,generate_study_population_control_lrti]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_lrti.csv
        table2: output/matched_matches_lrti.csv
        table3: output/matched_combined_lrti.csv
      moderately_sensitive: 
        report1: output/matching_report_lrti.txt

### LRTI var ###
  generate_study_population_case_lrti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti_abvar
    needs: [matching_lrti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_lrti_abvar.csv

  generate_study_population_control_lrti_abvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_lrti_abvar
    needs: [matching_lrti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_lrti_abvar.csv

  generate_study_population_case_lrti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti_othvar
    needs: [matching_lrti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_lrti_othvar.csv

  generate_study_population_control_lrti_othvar:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_lrti_othvar
    needs: [matching_lrti]
    outputs:
      highly_sensitive:
        cohort: output/input_control_lrti_othvar.csv

  generate_study_population_case_lrti_type:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti_type
    needs: [matching_lrti]
    outputs:
      highly_sensitive:
        cohort: output/input_case_lrti_type.csv


### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###

  case_othvar_process:
    run: r:latest analysis/casecontrol/case_othvar_process.R
    needs: [generate_study_population_case_uti_othvar,generate_study_population_case_urti_othvar,
    generate_study_population_case_lrti_othvar]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_case_*_othvar.rds

  control_othvar_process:
    run: r:latest analysis/casecontrol/control_othvar_process.R
    needs: [generate_study_population_control_uti_othvar,generate_study_population_control_urti_othvar,
    generate_study_population_control_lrti_othvar]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_control_*_othvar.rds

  case_abvar_process:
    run: r:latest analysis/casecontrol/case_abvar_process.R
    needs: [generate_study_population_case_uti_abvar,generate_study_population_case_urti_abvar,
    generate_study_population_case_lrti_abvar]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_case_*_abvar.rds

  control_abvar_process:
    run: r:latest analysis/casecontrol/control_abvar_process.R
    needs: [generate_study_population_control_uti_abvar,generate_study_population_control_urti_abvar,
    generate_study_population_control_lrti_abvar]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_control_*_abvar.rds

  model_process:
    run: r:latest analysis/casecontrol/model_process.R
    needs: [matching_uti,matching_urti,matching_lrti,case_othvar_process,control_othvar_process,case_abvar_process,control_abvar_process]
    outputs:
      highly_sensitive: 
        rds1: output/processed/model_*.rds

  model_OR:
    run: r:latest analysis/casecontrol/model_OR.R
    needs: [model_process]
    outputs:
      moderately_sensitive: 
        csv: output/*_model_result.csv

  model_table:
    run: r:latest analysis/casecontrol/model_table.R
    needs: [model_process]
    outputs:
      moderately_sensitive: 
        csv1: output/table_1_*_case.csv
        csv2: output/table_1_*_control.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:45

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

Job information

Status
Succeeded
Backend
TPP
Workspace
antibiotic-adverse-event
Requested by
Billy Zhong
Branch
ab_sideeffect_2
Force run dependencies
No
Git commit hash
36beadb
Requested actions
  • generate_study_population_case_uti_type
  • generate_study_population_case_urti_type
  • generate_study_population_case_lrti_type

Code comparison

Compare the code used in this Job Request