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Job request: 23950

Organisation:
University of Manchester
Workspace:
main_pregnancy_sdr
ID:
wuqgpknyrmz6k4ou
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 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: 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
          antenatal_plot_code_freq_sup: output/antenatalCohort_box-and-whisker_code_counts_outliers_supressed.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
          cohort_check: output/SDR_table_minmax_CHECK.csv
          cohorts_minmax_redacted: output/SDR_table_minmax_AntenatalCohort_REDACTED.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 delivery code Frequency
  describe_delivery_codes_frequency:
    run: r:latest analysis/AntenatalCohort_table_del_codes_freq.R
    needs: [generate_study_population_AnyCode_SDR]
    outputs:
      moderately_sensitive:
          feqtb: output/table_del_codes.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
          covid_SB_plot_rr_labels: output/rr_monthly_covid_SB_labels.jpeg
          both_covid_and_vacc: output/rr_monthly_rates_covid_BOTH.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:05

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

Job information

Status
Succeeded
Backend
TPP
Workspace
main_pregnancy_sdr
Requested by
Vicki Palin UoM
Branch
main
Force run dependencies
No
Git commit hash
c4faa94
Requested actions
  • describe_antenatal_cohort_plots
  • describe_SDR_cohort_with_any_antenatal_code_minmax_meanSD

Code comparison

Compare the code used in this Job Request