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Job request: 24692

Organisation:
NHS England
Workspace:
adhd-pre-and-post-covid
ID:
2nymn6e77fo3n7cd
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kin Quan 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'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 5000

actions:
  generate_dataset:
    run: > 
      ehrql:v1 generate-dataset analysis/dataset_definition_dx_to_med_time.py
      --output output/adhd_dataset.csv.gz
    outputs:
      highly_sensitive:
        adhd_dataset: output/adhd_dataset.csv.gz

  generate_output_table:
    run: python:v2 python analysis/calculate_time_diff_from_dx_to_med.py
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        table1: output/adhd_dia_med_gap_weeks.csv
  
  generate_adhd_prevalence:
    run: > 
      ehrql:v1 generate-measures analysis/measures_definition.py 
      --output output/adhd_prevalence.csv
    outputs:
      moderately_sensitive:
        measure: output/adhd_prevalence.csv

  thin_slice_medication: 
    run: > 
      ehrql:v1 generate-measures analysis/medication_thin_slice_measures.py
      --output output/thin_slice_medication_measures.csv 
    outputs:
      moderately_sensitive:
        measure: output/thin_slice_medication_measures.csv

  Table_2_Prevalence_of_ADHD_Diagnosis:
    run: > 
      ehrql:v1 generate-measures analysis/Table_2_Prevalence_of_ADHD_Diagnosis.py
      --output output/Table_2_Prevalence_of_ADHD_Diagnosis.csv
    outputs:
      moderately_sensitive:
        measure: output/Table_2_Prevalence_of_ADHD_Diagnosis.csv

  Table_2_Prevalence_of_ADHD_Remission:
    run: > 
      ehrql:v1 generate-measures analysis/Table_2_Prevalence_of_ADHD_Remission.py 
      --output output/Table_2_Prevalence_of_ADHD_Remission.csv
    outputs:
      moderately_sensitive:
        measure: output/Table_2_Prevalence_of_ADHD_Remission.csv

  Table_3_with_ADHD_that_are_prescribed_ADHD_medication:
    run: > 
      ehrql:v1 generate-measures analysis/Table_3_with_ADHD_that_are_prescribed_ADHD_medication.py
      --output output/Table_3_with_ADHD_that_are_prescribed_ADHD_medication.csv 
    outputs:
      moderately_sensitive:
        measure: output/Table_3_with_ADHD_that_are_prescribed_ADHD_medication.csv
  
  Table_3_without_ADHD_that_are_prescribed_ADHD_medication:
    run: > 
      ehrql:v1 generate-measures analysis/Table_3_without_ADHD_that_are_prescribed_ADHD_medication.py
      --output output/Table_3_without_ADHD_that_are_prescribed_ADHD_medication.csv 
    outputs:
      moderately_sensitive:
        measure: output/Table_3_without_ADHD_that_are_prescribed_ADHD_medication.csv

  Table_3_are_prescribed_ADHD_medication_in_ADHD_group:
    run: > 
      ehrql:v1 generate-measures analysis/Table_3_are_prescribed_ADHD_medication_in_ADHD_group.py
      --output output/Table_3_are_prescribed_ADHD_medication_in_ADHD_group.csv 
    outputs:
      moderately_sensitive:
        measure: output/Table_3_are_prescribed_ADHD_medication_in_ADHD_group.csv

  Table_3_with_ADHD_that_are_NOT_prescribed_ADHD_medication:
    run: > 
      ehrql:v1 generate-measures analysis/Table_3_with_ADHD_that_are_NOT_prescribed_ADHD_medication.py
      --output output/Table_3_with_ADHD_that_are_NOT_prescribed_ADHD_medication.csv 
    outputs:
      moderately_sensitive:
        measure: output/Table_3_with_ADHD_that_are_NOT_prescribed_ADHD_medication.csv

  Table_3_NOT_prescribed_ADHD_medication_in_ADHD_group:
    run: > 
      ehrql:v1 generate-measures analysis/Table_3_NOT_prescribed_ADHD_medication_in_ADHD_group.py
      --output output/Table_3_NOT_prescribed_ADHD_medication_in_ADHD_group.csv 
    outputs:
      moderately_sensitive:
        measure: output/Table_3_NOT_prescribed_ADHD_medication_in_ADHD_group.csv

  Patient_table_5_dia_to_med:
    run: > 
      ehrql:v1 generate-dataset analysis/Patient_table_5_dia_to_med.py
      --output output/Patient_table_5_dia_to_med.csv.gz
    outputs:
      highly_sensitive:
        measure: output/Patient_table_5_dia_to_med.csv.gz

  Table_5_time_from_diagnosis_to_treatment:
    run: python:v2 python analysis/Table_5_time_from_diagnosis_to_treatment.py
    needs: [Patient_table_5_dia_to_med]
    outputs:
      moderately_sensitive:
        table1: output/Table_5_time_from_diagnosis_to_treatment.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 11:35:38

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

Job information

Status
Succeeded
Backend
TPP
Workspace
adhd-pre-and-post-covid
Requested by
Kin Quan
Branch
main
Force run dependencies
Yes
Git commit hash
466baf8
Requested actions
  • Table_2_Prevalence_of_ADHD_Diagnosis
  • Table_2_Prevalence_of_ADHD_Remission
  • Table_3_with_ADHD_that_are_prescribed_ADHD_medication
  • Table_3_without_ADHD_that_are_prescribed_ADHD_medication
  • Table_3_are_prescribed_ADHD_medication_in_ADHD_group
  • Table_3_with_ADHD_that_are_NOT_prescribed_ADHD_medication
  • Table_3_NOT_prescribed_ADHD_medication_in_ADHD_group
  • Patient_table_5_dia_to_med
  • Table_5_time_from_diagnosis_to_treatment

Code comparison

Compare the code used in this Job Request