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Job request: 26522

Organisation:
University of Bristol
Workspace:
polypharmacy-deprescribing-dementia
ID:
zfg4zgmhm6i2ztg3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robert Porteous 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:
    clean_dataset_desc
    Status:
    Pending
    Job identifier:
    zqjiq3hpxqmnj4hd
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    clean_dataset_hist
    Status:
    Pending
    Job identifier:
    b4npexccdans6utr
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    create_prescription_gaps_table
    Status:
    Pending
    Job identifier:
    dkheowf4evuqk7c6
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    create_table_desc
    Status:
    Pending
    Job identifier:
    2jjdlyshergn3wud
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_dataset_desc
    Status:
    Pending
    Job identifier:
    tgymtni2czct2pu5
    Status message:
    waiting_db_maintenance: Waiting for database to finish maintenance
  • Action:
    generate_dataset_hist
    Status:
    Pending
    Job identifier:
    c2rvizsux6pf76dm
    Status message:
    waiting_db_maintenance: Waiting for database to finish maintenance

Pipeline

Show project.yaml 
version: '5.0'

actions:
  generate_dataset_prematch:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_prematch.py --output output/dataset/input_prematch.csv.gz --dummy-tables dummy_tables
    outputs:
      highly_sensitive:
        dataset: output/dataset/input_prematch.csv.gz

  clean_dataset_prematch:
    run: r:v2 analysis/dataset_clean/dataset_clean_prematch.R
    needs: [generate_dataset_prematch]
    outputs:
      highly_sensitive:
        dataset: output/dataset_clean/input_clean_prematch.csv.gz
      moderately_sensitive:
        flow_prematch: output/dataset_clean/flow_prematch.csv
        flow_prematch_midpoint6: output/dataset_clean/flow_prematch_midpoint6.csv
        describe_inex_prematch: output/describe/inex-prematch.txt
        describe_preprocessed_prematch: output/describe/preprocessed-prematch.txt
        describe_qa_prematch: output/describe/qa-prematch.txt
        describe_ref_prematch: output/describe/ref-prematch.txt

  generate_dataset_desc:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_desc.py --output output/dataset/input_desc.csv.gz --dummy-tables dummy_tables
    needs: [clean_dataset_prematch]
    outputs:
      highly_sensitive:
        dataset: output/dataset/input_desc.csv.gz

  clean_dataset_desc:
    run: r:v2 analysis/dataset_clean/dataset_clean_desc.R
    needs: [generate_dataset_desc]
    outputs:
      highly_sensitive:
        dataset: output/dataset_clean/input_clean_desc.rds
      moderately_sensitive:
        describe_preprocessed: output/describe/preprocessed-desc.txt
        describe_ref: output/describe/ref-desc.txt

  create_cum_inc_med_rev:
    run: r:v2 analysis/tables/create_table_cum_inc_med_rev.R
    needs: [clean_dataset_desc]
    outputs:
      moderately_sensitive:
        medication_review_incidence_table: output/tables/med_rev_cum_inc.csv
        medication_review_incidence_table_midpoint6: output/tables/med_rev_cum_inc_midpoint6.csv
        medication_review_incidence: output/plots/med_rev_cum_inc.png
        medication_review_incidence_midpoint6: output/plots/med_rev_cum_inc_midpoint6.png

  create_cum_inc_stop_any:
    run: r:v2 analysis/tables/create_table_cum_inc_stop_any.R
    needs: [clean_dataset_desc]
    outputs:
      moderately_sensitive:

        # Any antihypertensive stopping (30-day gap)
        stop_any_30_table: output/tables/stop_any_30_cum_inc.csv
        stop_any_30_table_midpoint6: output/tables/stop_any_30_cum_inc_midpoint6.csv
        stop_any_30_plot: output/plots/stop_any_30_cum_inc.png
        stop_any_30_plot_midpoint6: output/plots/stop_any_30_cum_inc_midpoint6.png

        # Any antihypertensive stopping (90-day gap)
        stop_any_90_table: output/tables/stop_any_90_cum_inc.csv
        stop_any_90_table_midpoint6: output/tables/stop_any_90_cum_inc_midpoint6.csv
        stop_any_90_plot: output/plots/stop_any_90_cum_inc.png
        stop_any_90_plot_midpoint6: output/plots/stop_any_90_cum_inc_midpoint6.png

        # Any antihypertensive stopping (180-day gap)
        stop_any_180_table: output/tables/stop_any_180_cum_inc.csv
        stop_any_180_table_midpoint6: output/tables/stop_any_180_cum_inc_midpoint6.csv
        stop_any_180_plot: output/plots/stop_any_180_cum_inc.png
        stop_any_180_plot_midpoint6: output/plots/stop_any_180_cum_inc_midpoint6.png


  generate_dataset_hist:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_hist.py --output output/dataset/input_hist.csv.gz --dummy-tables dummy_tables
    needs: [clean_dataset_prematch]
    outputs:
      highly_sensitive:
        dataset: output/dataset/input_hist.csv.gz

  clean_dataset_hist:
    run: r:v2 analysis/dataset_clean/dataset_clean_hist.R
    needs: [generate_dataset_hist]
    outputs:
      highly_sensitive:
        dataset: output/dataset_clean/input_clean_hist.rds
      moderately_sensitive:
        describe_preprocessed: output/describe/preprocessed-hist.txt
        describe_ref: output/describe/ref-hist.txt

  create_prescription_gaps_table:
   run: r:v2 analysis/tables/create_table_prescription_gaps.R
   needs: [clean_dataset_hist]
   outputs:
     moderately_sensitive:
       prescription_gaps: output/tables/prescription_gaps.csv
       prescription_gaps_midpoint6: output/tables/prescription_gaps_midpoint6.csv

  create_table1_cov:
    run: r:v2 analysis/tables/create_table1_cov.R
    needs: [clean_dataset_cov]
    outputs:
      moderately_sensitive:
        table_one_all_years: output/tables/table1_cov_all_years.csv
        table_one_midpoint6_all_years: output/tables/table1_cov_all_years_midpoint6.csv
        table_one_period_summary: output/tables/table1_cov_period_summary.csv
        table_one_period_summary_midpoint6: output/tables/table1_cov_period_summary_midpoint6.csv

  create_table_desc:
   run: r:v2 analysis/tables/create_table_desc.R
   needs: [clean_dataset_desc]
   outputs:
     moderately_sensitive: 
       descptive_measures_table: output/tables/table_desc_region.csv
       descptive_measures_table_midpoint6: output/tables/table_desc_region_midpoint6.csv

  generate_dataset_cov:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_cov.py --output output/dataset/input_cov.csv.gz --dummy-tables dummy_tables
    needs: [clean_dataset_prematch]
    outputs:
      highly_sensitive:
        dataset: output/dataset/input_cov.csv.gz

  clean_dataset_cov:
    run: r:v2 analysis/dataset_clean/dataset_clean_cov.R 
    needs: [generate_dataset_cov]
    outputs:
      highly_sensitive:
        dataset: output/dataset_clean/input_clean_cov.rds
      moderately_sensitive:
        describe_preprocessed: output/describe/preprocessed-cov.txt
        describe_ref: output/describe/ref-cov.txt

  # generate_project_dag:
  #   run: python:v2 python analysis/project_dag.py --yaml-path project.yaml --output-path project.dag.md
  #   outputs:
  #     moderately_sensitive:
  #       counts: project.dag.md

Job statistics

Status Count Percentage
Pending 6 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 6 (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
polypharmacy-deprescribing-dementia
Requested by
Robert Porteous
Branch
main
Force run dependencies
No
Git commit hash
ee56d08
Requested actions
  • generate_dataset_desc
  • clean_dataset_desc
  • generate_dataset_hist
  • clean_dataset_hist
  • create_prescription_gaps_table
  • create_table_desc

Code comparison

Compare the code used in this job request