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Job request: 12824

Organisation:
Bennett Institute
Workspace:
unknown-codes-investigation
ID:
vqayvbha6coj7avd
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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: 1

actions:
  # query_APCS_Der_Diagnosis_All:
  #   run: >
  #     sqlrunner:latest
  #       queries/APCS.Der_Diagnosis_All.sql
  #       --output output/APCS.Der_Diagnosis_All.csv
  #   outputs:
  #     highly_sensitive:
  #       output: output/APCS.Der_Diagnosis_All.csv

  query_APCS_Der__Spell_Primary_Diagnosis:
    run: >
      sqlrunner:latest
        queries/APCS_Der.Spell_Primary_Diagnosis.sql
        --output output/gAPCS_Der.Spell_Primary_Diagnosis.csv
    outputs:
      highly_sensitive:
        output: output/gAPCS_Der.Spell_Primary_Diagnosis.csv

  query_CodedEvent__CTV3Code:
    run: >
      sqlrunner:latest
        queries/CodedEvent.CTV3Code.sql
        --output output/gCodedEvent.CTV3Code.csv
    outputs:
      highly_sensitive:
        output: output/gCodedEvent.CTV3Code.csv

  query_CodedEvent_SNOMED__ConceptID:
    run: >
      sqlrunner:latest
        queries/CodedEvent_SNOMED.ConceptID.sql
        --output output/gCodedEvent_SNOMED.ConceptID.csv
    outputs:
      highly_sensitive:
        output: output/gCodedEvent_SNOMED.ConceptID.csv

  # query_EC_Diagnosis_EC_Diagnosis_XX:
  #   run: >
  #     sqlrunner:latest
  #       queries/EC_Diagnosis.EC_Diagnosis_XX.sql
  #       --output output/EC_Diagnosis.EC_Diagnosis_XX.csv
  #   outputs:
  #     highly_sensitive:
  #       output: output/EC_Diagnosis.EC_Diagnosis_XX.csv

  # query_EC_Diagnosis_Discharge_Destination_SNOMED_CT:
  #   run: >
  #     sqlrunner:latest
  #       queries/EC_Diagnosis.Discharge_Destination_SNOMED_CT.sql
  #       --output output/EC_Diagnosis.Discharge_Destination_SNOMED_CT.csv
  #   outputs:
  #     highly_sensitive:
  #       output: output/EC_Diagnosis.Discharge_Destination_SNOMED_CT.csv

  # query_MedicationDictionary_DMD_ID:
  #   run: >
  #     sqlrunner:latest
  #       queries/MedicationDictionary.DMD_ID.sql
  #       --output output/MedicationDictionary.DMD_ID.csv
  #   outputs:
  #     highly_sensitive:
  #       output: output/MedicationDictionary.DMD_ID.csv

  # query_ONS_Deaths_icd10XX:
  #   run: >
  #     sqlrunner:latest
  #       queries/ONS_Deaths.icd10XX.sql
  #       --output output/ONS_Deaths.icd10XX.csv
  #   outputs:
  #     highly_sensitive:
  #       output: output/ONS_Deaths.icd10XX.csv

# This action (1) joins all different datasets
# (2) removes rows with count less than 10
# (3) rounds numbers to the nearest 10
  tidy_data:
    run: r:latest analysis/tidy_data.R
    needs:
      - query_APCS_Der__Spell_Primary_Diagnosis
      - query_CodedEvent__CTV3Code
      - query_CodedEvent_SNOMED__ConceptID
      # - query_APCS_Der_Diagnosis_All
      # - query_EC_Diagnosis_EC_Diagnosis_XX
      # - query_EC_Diagnosis_Discharge_Destination_SNOMED_CT
      # - query_MedicationDictionary_DMD_ID
      # - query_ONS_Deaths_icd10XX
    outputs:
      moderately_sensitive:
        output: output/output.csv

  generate_report:
    run: r:latest -e 'rmarkdown::render("analysis/report.Rmd", knit_root_dir = "/workspace", output_dir = "output/")'
    needs:
      - tidy_data
    outputs:
      moderately_sensitive:
        output: output/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:37

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

Job information

Status
Succeeded
Backend
TPP
Workspace
unknown-codes-investigation
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
a3a9554
Requested actions
  • generate_report

Code comparison

Compare the code used in this Job Request