Skip to content

Job request: 12830

Organisation:
Bennett Institute
Workspace:
unknown-codes-investigation
ID:
rn7m3spzxvs4ve73
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 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

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: 00:01:31

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

Job request

Status
Succeeded
Backend
TPP
Workspace
unknown-codes-investigation
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
9a5f8ec
Requested actions
  • generate_report

Code comparison

Compare the code used in this job request