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Job request: 26393

Organisation:
NHS North Bristol Trust
Workspace:
fluoroquinolones_adverse_events
ID:
j4vomo42iynziqj2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jack Stanley 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:
    b6qc4jt6q7ie5bgk
  • Action:
    generate_measure
    Status:
    Succeeded
    Job identifier:
    wakdvrgkjs7ftn5t
  • Action:
    generate_cohort
    Status:
    Succeeded
    Job identifier:
    scvpxykldkcjuqpa
  • Action:
    run_model
    Status:
    Succeeded
    Job identifier:
    6adr5y2hzyncfw3g
  • Action:
    generate_report
    Status:
    Succeeded
    Job identifier:
    enqgzwi56s3acza3

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

 # generate_ctc_cases_tendinitis:
 #  run: ehrql:v1 generate-dataset analysis/ctc_definition_tendinitis.py --output output/ctc_data_cases_tendinitis.csv.gz
 #   outputs:
 #     highly_sensitive:
 #       dataset: output/ctc_data_cases_tendinitis.csv.gz

 # generate_ctc_potential_control_tendinitis:
 #  run: ehrql:v1 generate-dataset analysis/ctc_definition_tendinitis_potential_ctrl.py --output output/ctc_data_potential_controls_tendinitis.csv.gz
 #   outputs:
 #     highly_sensitive:
 #       dataset: output/ctc_data_potential_controls_tendinitis.csv.gz

 # match_tendinitis:
 #   run: >
 #     matching:v1.1.0
 #     --cases output/ctc_data_cases_tendinitis.csv.gz
 #    --controls output/ctc_data_potential_controls_tendinitis.csv.gz
 #   --config '{
 #     "matches_per_case": 3,
 #     "match_variables": {
 #     "sex": "category",
 #     "age": 5
    #   },
    #   "index_date_variable": "tendinitis_case_date",
    #   "generate_match_index_date": "no_offset"
    #   }'
    # needs: [generate_ctc_cases_tendinitis, generate_ctc_potential_control_tendinitis]
    # outputs:
    #   highly_sensitive:
    #     matched_cases: output/matched_cases.arrow
    #     matched_controls: output/matched_matches.arrow
    #     matched_combined: output/matched_combined.arrow
    #   moderately_sensitive:
    #     report: output/matching_report.txt

#measures - look at abx prescribing over time
  generate_measure:
    run: ehrql:v1 generate-measures analysis/measure_definition.py --output output/measures.csv 
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures.csv

  
  generate_report:
     run: r:v2 analysis/abx_time_series.R
     needs: [generate_measure]
     outputs:
      moderately_sensitive:
        chart1: output/time_plot/abx_quarter_time_plot.png
        chart2: output/time_plot/outcome_quarter_time_plot.png

  generate_cohort:
      run: r:v2 analysis/dataset_manipulate_cohort.R
      needs: [generate_dataset]
      outputs:
        highly_sensitive:
          chart1: output/dataset_formatted_cohort.csv
          chart2: output/cohort/n_events.md
          chart3: output/cohort/missingdata_count_df.md

  run_model:
    run: r:v2 analysis/iptw_coxph.R
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        chart1:  output/cohort/age_spline_check.png
        table1:  output/cohort/aictable_agespline.md
        chart2:  output/cohort/imd_decile_rough_check.png
        chart3:  output/cohort/n_hosp_appt_logoddsplot.png
        chart4:  output/cohort/ps_density_plot.png
        chart5 : output/cohort/ps_love_plot.png
        table2:  output/cohort/n_events_tendinitis_complete_covariates_dataset.md
        table3:  output/cohort/n_events_neuropathy_complete_covariates_dataset.md
        chart6:  output/cohort/cox_models_tendinitis_and_neuropathy_forest.png
        table 4:  output/cohort/all_cox_model_summaries.txt
        table 5:  output/cohort/cumulative_cox_results.md
        chart7:   output/cohort/km_tendinitis_combo_curve.png
        chart8:   output/cohort/km_neuropathy_combo_curve.png

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 5 100%
Failed 0 0%

5 / 5 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 60:31:20

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

Job request

Status
Succeeded
Backend
TPP
Workspace
fluoroquinolones_adverse_events
Requested by
Jack Stanley
Branch
main
Force run dependencies
Yes
Git commit hash
322bfc0
Requested actions
  • generate_dataset
  • generate_measure
  • generate_report
  • generate_cohort
  • run_model

Code comparison

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