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Job request: 6261

Organisation:
Bennett Institute
Workspace:
ethnicity-short-data-report
ID:
75zdk6sz2uex3znl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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:
    initial_counts
    Status:
    Status: Succeeded
    Job identifier:
    aghwrhablf72wu2f

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: 02:04:51

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ethnicity-short-data-report
Requested by
Colm Andrews
Branch
main
Force run dependencies
No
Git commit hash
f28ffd2
Requested actions
  • initial_counts

Code comparison

Compare the code used in this job request