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Job request: 25261

Organisation:
Bennett Institute
Workspace:
pharmacy-first-report
ID:
o73qklxlhulcjz4h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Viveck Kingsley 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

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:
  generate_dataset_definition_tables:
    run: >
      ehrql:v1
       generate-dataset analysis/dataset_definition_tables.py
       --test-data-file analysis/test_dataset_definition_tables.py
       --dummy-data-file dummy_data/pf_tables_dataset.csv
       --output output/population/pf_tables.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/population/pf_tables.csv.gz

  create_tables:
    run: r:v2 analysis/create_tables.R
    needs: [generate_dataset_definition_tables]
    outputs:
      moderately_sensitive:
        dataset: output/population/pf_tables.csv

  generate_pf_statistics_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_descriptive_stats.py
      --dummy-tables dummy_tables
      --output output/measures/pf_descriptive_stats_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_descriptive_stats_measures.csv

  generate_pf_breakdown_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_breakdown.py
      --output output/measures/pf_breakdown_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_breakdown_measures.csv

  generate_pf_med_counts_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_med_counts.py
      --dummy-tables dummy_tables
      --output output/measures/pf_medications_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_medications_measures.csv

  tidy_med_measures:
    run: r:latest analysis/tidy_measures_med_counts.R
    needs: [generate_pf_med_counts_measures]
    outputs:
      moderately_sensitive:
        measure_pf_meds: output/measures/pf_medications_measures_tidy.csv

  generate_pf_opensafely_report:
    run: >
      r:v2 -e 'rmarkdown::render(
        "reports/pharmacy_first_report.Rmd",
        knit_root_dir = "/workspace",
        output_dir = "/workspace/output/report"
      )'
    needs:
      - generate_dataset_definition_tables
      - create_tables
      - generate_pf_statistics_measures
      - generate_pf_breakdown_measures
      - generate_pf_med_counts_measures
      - tidy_med_measures
    outputs:
      moderately_sensitive:
        html: output/report/pharmacy_first_report.html
        pf_demographics: output/report/data/df_demographics_table.csv
        pf_breakdowns: output/report/data/df_measures.csv
        pf_clinical_conditions: output/report/data/df_clinical_pathways_by_sex.csv
        pf_med_counts: output/report/data/df_pf_and_non_pf_med_counts.csv
        pf_consultations: output/report/data/df_pf_consultations.csv
        pf_descriptive_stats: output/report/data/df_pf_descriptive_stats.csv
        pf_counts: output/report/figures/figure1.png
        pf_by_sex: output/report/figures/figure2sex.png
        pf_by_age: output/report/figures/figure3age.png
        pf_by_imd: output/report/figures/figure4imd.png
        pf_by_region: output/report/figures/figure5region.png
        pf_by_ethnicity: output/report/figures/figure6ethnicity.png
        pf_completeness: output/report/figures/figure7.png

  generate_pf_opensafely_monthly_report:
    run: >
      r:v2 -e 'rmarkdown::render(
        "reports/pharmacy_first_monthly_report.Rmd",
        knit_root_dir = "/workspace",
        output_dir = "/workspace/output/report"
      )'
    needs:
      - create_tables
      - generate_pf_statistics_measures
      - generate_pf_breakdown_measures
      - generate_pf_med_counts_measures
      - tidy_med_measures
    outputs:
      moderately_sensitive:
        html: output/report/pharmacy_first_monthly_report.html
        pf_breakdowns: output/report/data/df_measures_updated.csv
        pf_med_counts: output/report/data/df_pf_and_non_pf_med_counts_updated.csv
        pf_consultations: output/report/data/df_pf_consultations_updated.csv
        pf_descriptive_stats: output/report/data/df_pf_descriptive_stats_updated.csv
        pf_counts: output/report/figures/figure1_updated.png
        pf_by_sex: output/report/figures/figure2sex_updated.png
        pf_by_age: output/report/figures/figure3age_updated.png
        pf_by_imd: output/report/figures/figure4imd_updated.png
        pf_by_region: output/report/figures/figure5region_updated.png
        pf_by_ethnicity: output/report/figures/figure6ethnicity_updated.png
        pf_completeness: output/report/figures/figure7_updated.png
        pf_clinical_conditions: output/report/figures/figure8clinicalpathways_updated.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:32:53

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

Job request

Status
Succeeded
Backend
TPP
Workspace
pharmacy-first-report
Requested by
Viveck Kingsley
Branch
main
Force run dependencies
Yes
Git commit hash
d29739c
Requested actions
  • generate_pf_opensafely_monthly_report

Code comparison

Compare the code used in this job request