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Job request: 23866

Organisation:
University of Manchester
Workspace:
main_pregnancy_sdr
ID:
67t4773ek7ns5y36
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Vicki Palin UoM 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:
    run_all
    Status:
    Status: Succeeded
    Job identifier:
    znvrda5fxo6pvs2p

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_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 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/AntenatalCohort_baseline_table_SDR_minmax.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          patient_nums: output/patient_numbers_AntenatalCohort_SDR_minmax.csv
          cohorts_minmax: output/SDR_table_minmax_AntenatalCohort.csv
          cohorts_meanSD: output/SDR_table_meanSD_AntenatalCohort.csv

# describe delivery code episodes - Antenatal Cohort
  describe_antenatal_cohort_delivery_episodes:
    run: r:latest analysis/AntenatalCohort_num_deliveries_each.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          by_NAs: output/df_count_NAs_for_del_episodes.csv
          not_missing_dates: output/df_count_del_episodes.csv

# describe outcomes for delivery episodes 
  describe_antenatal_cohort_outcomes:
    run: r:latest analysis/AntenatalCohort_outcomes.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          outcome_plot_data: output/raw_monthly_rates_outcomes.csv
          outcome_plot_data_rr: output/rr_monthly_rates_outcomes.csv
          outcome_plot: output/raw_monthly_outcome.jpeg
          outcome_plot_rr: output/rr_monthly_outcome.jpeg
          outcome_plot_rr_labels: output/rr_monthly_outcome_labels.jpeg

# describe covid positive and vaccination for delivery episodes 
  describe_antenatal_cohort_covidvacc:
    run: r:latest analysis/AntenatalCohort_covid_and_vacc_overtime.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          covid_plot_data: output/raw_monthly_rates_covid_and_vaccs.csv
          covid_plot_data_rr: output/rr_monthly_rates_covid_and_vaccs.csv
          covid_plot: output/raw_monthly_covid_rates.jpeg
          covid_plot_rr: output/rr_monthly_covid_rates.jpeg
          covid_plot_rr_labels: output/rr_monthly_covid_rates_labels.jpeg
          covid_SB: output/monthly_rates_covid_SB.csv
          covid_SB_plot: output/monthly_covid_SB.jpeg
          covid_SB_rr: output/rr_monthly_rates_covid_SB.csv
          covid_SB_plot_rr: output/rr_monthly_covid_SB.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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
Vicki Palin UoM
Branch
main
Force run dependencies
No
Git commit hash
9661a23
Requested actions
  • run_all

Code comparison

Compare the code used in this job request