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Job request: 23745

Organisation:
University of Manchester
Workspace:
main_pregnancy_sdr
ID:
bitpwvqg4cf52q2h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rose Higgins 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'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 1000

actions:
## Short data report work ##
  generate_study_population_SDR:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv.gz

  generate_study_population_AnyCode_SDR:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_any_antenatal.py --output output/dataset_anycode.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_anycode.csv.gz

### tables for DeliveryCode SDR cohort
  describe_SDR_cohort_with_delivery_codes:
    run: r:latest analysis/DeliveryCohort_baseline_table_SDR.R
    needs: [generate_study_population_SDR]
    outputs:
      moderately_sensitive:
          patient_numbers: output/patient_numbers_deliverycodes_cohort_SDR.csv
          cohort_contin_overall: output/SDR_table_continuous_vars_delcode_cohort.csv
          cohorts_catagorical_overall: output/SDR_table_categorical_delcode_cohort.csv

  describe_SDR_cohort_with_delivery_codes_minmax_meanSD:
    run: r:latest analysis/DeliveryCohort_baseline_table_SDR_minmax.R
    needs: [generate_study_population_SDR]
    outputs:
      moderately_sensitive:
          patient_nums: output/patient_numbers_deliverycodes_cohort_SDR_minmax.csv
          cohorts_minmax: output/SDR_table_minmax_delcode_cohort.csv
          cohorts_meanSD: output/SDR_table_meanSD_delcode_cohort.csv

### tables for any antenatal code 5 year cohort
  describe_SDR_cohort_with_any_antenatal_code:
    run: r:latest analysis/AntenatalCohort_baseline_table_SDR.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          patient_numbers: output/patient_numbers_antenatal_cohort_SDR.csv
          cohort_contin_overall: output/SDR_table_continuous_vars_antenatal_cohort.csv
          cohorts_catagorical_overall: output/SDR_table_categorical_antenatal_cohort.csv

# plots of antenatal data 
  describe_antenatal_cohort_plots: 
    run: r:latest analysis/AntenatalCohort_timeseries_plots.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          antenatal_first_csv: output/first_antenatal_codes_by_month_year.csv
          antenatal_first_plot: output/first_antenatal_codes_by_month_year.jpeg
          antenatal_plot_code_freq: output/antenatalCohort_box-and-whisker_code_counts.jpeg

  # describe_SDR_ cohort_with_any_antenatal_code_minmax_meanSD:
  #   run: r:latest analysis/DeliveryCohort_baseline_table_SDR_minmax.R
  #   needs: [generate_study_population_AnyCode_SDR]
  #   outputs:
  #     moderately_sensitive:
  #         patient_nums: output/patient_numbers_deliverycodes_cohort_SDR_minmax.csv
  #         cohorts_minmax: output/SDR_table_minmax_delcode_cohort.csv
  #         cohorts_meanSD: output/SDR_table_meanSD_delcode_cohort.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:38

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

Job request

Status
Succeeded
Backend
TPP
Workspace
main_pregnancy_sdr
Requested by
Rose Higgins
Branch
main
Force run dependencies
Yes
Git commit hash
ed6e5b3
Requested actions
  • generate_study_population_AnyCode_SDR

Code comparison

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