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Job request: 27346

Organisation:
Department of Health and Social Care
Workspace:
sv-analysis-measures-split
ID:
xafzyvfi5kburywf
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Adedeji Saheed Ademola 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:
    generate_dataset
    Status:
    Succeeded
    Job identifier:
    wuy6qe2uhgxw3grh
  • Action:
    measures_base
    Status:
    Pending
    Job identifier:
    g7a5ha4dgelp36wl
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_disorder
    Status:
    Pending
    Job identifier:
    ukvnoy72weknzp5f
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_ppp_and_contraceptives
    Status:
    Pending
    Job identifier:
    dgmvckee4dxc2hv4
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    rates_by_demographics
    Status:
    Pending
    Job identifier:
    e5ygsr2xj4hcc3o7
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    plots_ppp_and_contraceptives
    Status:
    Pending
    Job identifier:
    7z4nfpoztfhyezei
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    plots_last_resort_prescribing
    Status:
    Pending
    Job identifier:
    772j3s6iogldds6y
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    measures_demo_age
    Status:
    Pending
    Job identifier:
    q47hbh6uc2ufaf64
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_demo_imd
    Status:
    Pending
    Job identifier:
    effjmyszozgwauyj
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_demo_sex
    Status:
    Pending
    Job identifier:
    r5ibjkl3jakowzd7
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    plots_birth_and_pregnancy_events
    Status:
    Pending
    Job identifier:
    6mynwvrq4unzksfj
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    measures_demo_female_age_band
    Status:
    Pending
    Job identifier:
    g4h5f35pn52ydxia
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_comorbidity
    Status:
    Pending
    Job identifier:
    fhqreip22xhxnblm
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_birth_and_pregnancy_events
    Status:
    Pending
    Job identifier:
    anpbjlzmsdxxmkg3
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_epilepsy_prescribing
    Status:
    Pending
    Job identifier:
    ymco7hhnl4lhdtue
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    rates
    Status:
    Pending
    Job identifier:
    di5t4ym67aj2vuc5
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    rates_comorbidity
    Status:
    Pending
    Job identifier:
    agft7hlct42kl6oj
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'

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


  measures_base:
    run: ehrql:v1 generate-measures analysis/measures_base.py
      --output output/measures_base.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_base.csv

  measures_demo_age:
    run: ehrql:v1 generate-measures analysis/measures_demo_age.py
      --output output/measures_demo_age.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_demo_age.csv

  measures_demo_imd:
    run: ehrql:v1 generate-measures analysis/measures_demo_imd.py
      --output output/measures_demo_imd.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_demo_imd.csv

  measures_demo_sex:
    run: ehrql:v1 generate-measures analysis/measures_demo_sex.py
      --output output/measures_demo_sex.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_demo_sex.csv

  measures_demo_female_age_band:
    run: ehrql:v1 generate-measures analysis/measures_demo_female_age_band.py
      --output output/measures_demo_female_age_band.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_demo_female_age_band.csv

  measures_comorbidity:
    run: ehrql:v1 generate-measures analysis/measures_comorbidity.py
      --output output/measures_comorbidity.csv.gz
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      highly_sensitive:
        measure_csv: output/measures_comorbidity.csv.gz

  measures_disorder:
    run: ehrql:v1 generate-measures analysis/measures_disorder.py
      --output output/measures_disorder.csv.gz
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      highly_sensitive:
        measure_csv: output/measures_disorder.csv.gz

  measures_ppp_and_contraceptives:
    run: ehrql:v1 generate-measures analysis/measures_ppp_and_contraceptives.py
      --output output/measures_ppp_and_contraceptives.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_ppp_and_contraceptives.csv

  measures_birth_and_pregnancy_events:
    run: ehrql:v1 generate-measures analysis/measures_birth_and_pregnancy_events.py
      --output output/measures_birth_and_pregnancy_events.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_birth_and_pregnancy_events.csv

  measures_epilepsy_prescribing:
    run: ehrql:v1 generate-measures analysis/measures_epilepsy_prescribing.py
      --output output/measures_epilepsy_prescribing.csv
      --
      --start-date "2014-01-01"
      --intervals 144
    outputs:
      moderately_sensitive:
        measure_csv: output/measures_epilepsy_prescribing.csv

  rates:
    run: python:v2 analysis/rates_analysis.py
          --output output/monthly_sv_prescribed_female_cba.svg
          --output output/monthly_new_starters_female_cba.svg
          --output output/monthly_sv_prescribed.svg
          --output output/monthly_new_starters.svg
    needs: [measures_base]
    outputs:
      moderately_sensitive:
        plot_total: output/monthly_sv_prescribed.svg
        plot_new_starter: output/monthly_new_starters.svg
        plot_sv_prescribed_females_cba: output/monthly_sv_prescribed_female_cba.svg
        plot_new_starters_females_cba: output/monthly_new_starters_female_cba.svg
        sv_new_starter_females_cba_ppp_time_series: output/sv_new_starter_females_cba_ppp_time_series.svg
        sv_prescribed_females_cba_ppp_time_series: output/sv_prescribed_females_cba_ppp_time_series.svg

  rates_comorbidity:
    run: python:v2 analysis/sv_prescription_rates_by_condition.py
          --output output/prescription_rates_by_condition.svg
          --output output/prescription_rates_by_condition_interrupted_time_series.svg
    needs: [measures_comorbidity, measures_disorder]
    outputs:
      moderately_sensitive:
        plot_conditions: output/prescription_rates_by_condition.svg
        plot_conditions_interrupted_time_series: output/prescription_rates_by_condition_interrupted_time_series.svg

  rates_by_demographics:
    run: python:v2 analysis/sv_prescription_demographics_timeseries.py
          --output output/monthly_new_sv_starters_prescribed_ratio_by_sex.svg --output output/monthly_sv_conditions_prescribed_ratio_by_sex.svg
          --output output/monthly_new_sv_starters_prescribed_ratio_by_ethnicity.svg --output output/monthly_sv_conditions_prescribed_ratio_by_ethnicity.svg
          --output output/monthly_new_sv_starters_prescribed_ratio_by_age.svg --output output/monthly_sv_conditions_prescribed_ratio_by_age.svg
          --output output/monthly_new_sv_starters_prescribed_ratio_by_region.svg --output output/monthly_sv_conditions_prescribed_ratio_by_region.svg
          --output output/monthly_new_sv_starters_prescribed_ratio_by_imd_quintile.svg --output output/monthly_sv_conditions_prescribed_ratio_by_imd_quintile.svg
    needs: [measures_demo_age, measures_demo_imd, measures_demo_sex]
    outputs:
      moderately_sensitive:
        plot_sex_new_starter: output/monthly_new_sv_starters_prescribed_ratio_by_sex.svg
        plot_sex_sv_prescriptions: output/monthly_sv_conditions_prescribed_ratio_by_sex.svg
        plot_age_new_starter: output/monthly_new_sv_starters_prescribed_ratio_by_age.svg
        plot_age_sv_prescriptions: output/monthly_sv_conditions_prescribed_ratio_by_age.svg
        plot_imd_quintile_new_starter: output/monthly_new_sv_starters_prescribed_ratio_by_imd_quintile.svg
        plot_imd_quintile_sv_prescriptions: output/monthly_sv_conditions_prescribed_ratio_by_imd_quintile.svg
  
  plots_ppp_and_contraceptives:
    run: python:v2 analysis/plots_ppp_and_contraceptives.py
    needs: [measures_ppp_and_contraceptives, measures_base]
    outputs:
      moderately_sensitive:
        plot_contraceptive_use: output/monthly_contraceptive_use.svg
        plot_contraceptive_use_trendlines: output/monthly_contraceptive_use_trendlines.svg
        plot_new_starters_to_ppp_and_sv: output/new_starters_to_ppp_and_sv.svg
        plot_new_starters_to_ppp_and_sv_trendlines: output/new_starters_to_ppp_and_sv_trendlines.svg
        new_sv_starter_contraceptive_use: output/new_sv_starter_contraceptive_use.svg
        new_sv_starter_contraceptive_use_trendlines: output/new_sv_starter_contraceptive_use_trendlines.svg
        sv_prescription_females_cba_contraception_comparison: output/sv_prescription_females_cba_contraception_comparison.svg

  plots_birth_and_pregnancy_events:
    run: python:v2 analysis/birth_and_pregnancy_events_on_sv.py
    needs: [measures_birth_and_pregnancy_events]
    outputs:
      moderately_sensitive:
        plot_births_or_pregnancies_with_valproate_history_ppp: output/births_or_pregnancies_with_valproate_history_ppp_trendlines.svg
        plot_births_or_pregnancies_with_valproate_history_covid: output/births_or_pregnancies_with_valproate_history_covid_trendlines.svg
        plot_valproate_history_with_births_or_pregnancies_ppp_trendlines: output/valproate_history_with_births_or_pregnancies_ppp_trendlines.svg
        plot_valproate_history_with_births_or_pregnancies_covid_trendlines: output/valproate_history_with_births_or_pregnancies_covid_trendlines.svg
        plot_births_or_pregnancies_with_recent_valproate_history_ppp: output/births_or_pregnancies_with_recent_valproate_history_ppp_trendlines.svg
        plot_births_or_pregnancies_with_recent_valproate_history_covid: output/births_or_pregnancies_with_recent_valproate_history_covid_trendlines.svg

  plots_last_resort_prescribing:
    run: python:v2 analysis/last_resort_prescribing.py
    needs: [measures_epilepsy_prescribing]
    outputs:
      moderately_sensitive:
        plot_epilepsy_patient_prescribed_sv: output/epilepsy_patient_prescribed_sv.svg
        plot_prescribed_sv_has_epilepsy: output/prescribed_sv_has_epilepsy.svg
        plot_new_starter_prescribed_sv_as_first_epilepsy_med: output/new_starter_prescribed_sv_as_first_epilepsy_med.svg
        plot_new_starter_prescribed_sv_as_first_epilepsy_med_covid_trendlines: output/new_starter_prescribed_sv_as_first_epilepsy_med_covid_trendlines.svg
        plot_new_starter_prescribed_sv_as_first_epilepsy_med_ppp_trendlines: output/new_starter_prescribed_sv_as_first_epilepsy_med_ppp_trendlines.svg

Job statistics

Status Count Percentage
Pending 16 94.1%
Running 0 0%
Succeeded 1 5.9%
Failed 0 0%

1 / 17 (5.9%) complete

Timeline

  • Created:

  • Started:

  • Runtime: 01:11:09

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

Job request

Status
Running
Backend
TPP
Workspace
sv-analysis-measures-split
Requested by
Adedeji Saheed Ademola
Branch
measures_disorder
Force run dependencies
No
Git commit hash
ddf3fb1
Requested actions
  • generate_dataset
  • measures_base
  • measures_demo_age
  • measures_demo_imd
  • measures_demo_sex
  • measures_demo_female_age_band
  • measures_comorbidity
  • measures_disorder
  • measures_ppp_and_contraceptives
  • measures_birth_and_pregnancy_events
  • measures_epilepsy_prescribing
  • rates
  • rates_comorbidity
  • rates_by_demographics
  • plots_ppp_and_contraceptives
  • plots_birth_and_pregnancy_events
  • plots_last_resort_prescribing
  • run_all

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