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Job request: 27072

Organisation:
Department of Health and Social Care
Workspace:
sv-analysis
ID:
b3nva67dnjj7bp7v
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ailsa Prise 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:
    Pending
    Job identifier:
    si2pjmzbgacnud2o
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_base
    Status:
    Pending
    Job identifier:
    o5bxh6qcf4lp42uj
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_comorbidity
    Status:
    Pending
    Job identifier:
    er34753ysxbjrh7p
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    rates
    Status:
    Pending
    Job identifier:
    7co2s22yb7lweybn
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    rates_by_demographics
    Status:
    Pending
    Job identifier:
    turrgwe7zwocttdk
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    rates_comorbidity
    Status:
    Pending
    Job identifier:
    23p7g7v6pe3c3ljm
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    measures_demo_age
    Status:
    Pending
    Job identifier:
    nqpyb6o2m2l2ygqy
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_demo_imd
    Status:
    Pending
    Job identifier:
    vgtzua5g2qc2ebmv
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    measures_demo_sex
    Status:
    Pending
    Job identifier:
    3nytlrwalz7hqy6u
    Status message:
    waiting_on_db_workers: Waiting on available database workers

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_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_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]
    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 9 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 9 (0%) complete

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
sv-analysis
Requested by
Ailsa Prise
Branch
main
Force run dependencies
Yes
Git commit hash
e077a8e
Requested actions
  • generate_dataset
  • measures_base
  • measures_demo_age
  • measures_demo_imd
  • measures_demo_sex
  • measures_comorbidity
  • rates
  • rates_comorbidity
  • rates_by_demographics

Code comparison

Compare the code used in this job request