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Job request: 6220

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report
ID:
2332fwuwbeick2wt
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data1: codelists/group_1.csv
        data2: codelists/group_2.csv
        data3: codelists/group_3.csv
        data4: codelists/group_4.csv
        data5: codelists/group_5.csv
        data6: codelists/group_6.csv
        data7: codelists/group_7.csv
        data8: codelists/group_8.csv
        data9: codelists/group_9.csv
        data10: codelists/group_10.csv

  generate_cohort1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_cohort2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2
    outputs:
      highly_sensitive:
        cohort: output/input_2.csv
  
  generate_cohort3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_3
    outputs:
      highly_sensitive:
        cohort: output/input_3.csv

  generate_cohort4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_4
    outputs:
      highly_sensitive:
        cohort: output/input_4.csv

  generate_cohort5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_5
    outputs:
      highly_sensitive:
        cohort: output/input_5.csv

  generate_cohort6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_6
    outputs:
      highly_sensitive:
        cohort: output/input_6.csv

  generate_cohort7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_7
    outputs:
      highly_sensitive:
        cohort: output/input_7.csv

  generate_cohort8:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_8
    outputs:
      highly_sensitive:
        cohort: output/input_8.csv

  generate_cohort9:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_9
    outputs:
      highly_sensitive:
        cohort: output/input_9.csv

  generate_cohort10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_10
    outputs:
      highly_sensitive:
        cohort: output/input_10.csv

  initial_counts:
    run: r:latest analysis/01_describe_snomed_ethnicity.r
    needs: [split_codelist,generate_cohort1, generate_cohort2, generate_cohort3, generate_cohort4, generate_cohort5, generate_cohort6, generate_cohort7, generate_cohort8, generate_cohort9, generate_cohort10]
    outputs:      
      moderately_sensitive:
        table: output/for_release/snomed_ethnicity_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 14:02:52

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

Job information

Status
Failed
Backend
TPP
Workspace
ethnicity-short-data-report
Requested by
Colm Andrews
Branch
main
Force run dependencies
Yes
Git commit hash
f374e3f
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request