Job request: 13921

Organisation:: Bennett Institute
Workspace:: medication_reviews
ID:: s4ixwzwmzybc23q5

This page shows the technical details of what happened when authorised researcher Chris Wood requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Action:

generate_allmedrev_codeuse_output

Status:

Status: Succeeded

Job identifier:

ifgh6kodkt4kobm7
Action:

run_tests

Status:

Status: Succeeded

Job identifier:

zagicp7o4gz4sufa
Action:

generate_codeuse_output

Status:

Status: Succeeded

Job identifier:

mgygbssadelvzsm4
Action:

generate_deciles_charts

Status:

Status: Succeeded

Job identifier:

iwp2hwheacwazb3f
Action:

redact_and_round

Status:

Status: Succeeded

Job identifier:

7qjls3mevb3p6wi7
Action:

generate_plots

Status:

Status: Succeeded

Job identifier:

tmiompxvizrauskb

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 3000

actions:

  generate_study_population:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --index-date-range "2019-04-01 to 2019-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_2019*.csv.gz

  generate_study_population_range2:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --index-date-range "2020-01-01 to 2020-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_2020*.csv.gz

  generate_study_population_range3:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --index-date-range "2021-01-01 to 2021-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_2021*.csv.gz

  generate_study_population_range4:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --index-date-range "2022-01-01 to 2022-03-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_2022*.csv.gz

  generate_study_population_allmedrev:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_allmedrev
        --index-date-range "2019-04-01 to 2019-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_allmedrev_2019*.csv.gz

  generate_study_population_allmedrev_range2:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_allmedrev
        --index-date-range "2020-01-01 to 2020-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort2: output/input_allmedrev_2020*.csv.gz

  generate_study_population_allmedrev_range3:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_allmedrev
        --index-date-range "2021-01-01 to 2021-12-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort3: output/input_allmedrev_2021*.csv.gz

  generate_study_population_allmedrev_range4:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_allmedrev
        --index-date-range "2022-01-01 to 2022-03-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort3: output/input_allmedrev_2022*.csv.gz

  generate_ethnicity_cohort:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_ethnicity
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  join_cohorts:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/input_20*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population, generate_study_population_range2, generate_study_population_range3, generate_study_population_range4, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz

  join_cohorts_allmedrev:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/input_allmedrev*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population_allmedrev, generate_study_population_allmedrev_range2, generate_study_population_allmedrev_range3, generate_study_population_allmedrev_range4, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_allmedrev_*.csv.gz

## generate Structured Medication Review Measures and plots

  generate_measures_mr_smr:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition
       --output-dir=output/joined
     needs: [join_cohorts]
     outputs:
       moderately_sensitive:
         mr_measure_csv: output/joined/measure_mr_*_rate.csv
         mr12m_measure_csv: output/joined/measure_mr12m_*_rate.csv
         smr_measure_csv: output/joined/measure_smr_*_rate.csv
         smr12m_measure_csv: output/joined/measure_smr12m_*_rate.csv

  generate_measures_all_reviews:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_allmedrev
       --output-dir=output/joined
     needs: [join_cohorts_allmedrev]
     outputs:
       moderately_sensitive:
         allmedrev_measure_csv: output/joined/measure_allmedrv_*_rate.csv
         allmedrev12m_measure_csv: output/joined/measure_allmedrv12m_*_rate.csv
         allmedrev_measure_asgrouped_csv: output/joined/measure_allmedrv_*_rate_agestandardgrouped.csv
         allmedrev12m_measure_asgrouped_csv: output/joined/measure_allmedrv12m_*_rate_agestandardgrouped.csv

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.33
        --input-files output/joined/measure_*_practice_rate.csv
        --output-dir output/joined
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_mr_smr, generate_measures_all_reviews]
    outputs:
      moderately_sensitive:
        deciles_charts: output/joined/deciles_*_*.*

  redact_and_round:
    run: python:latest python analysis/redact_and_round.py
    needs: [generate_measures_mr_smr, generate_codeuse_output, generate_allmedrev_codeuse_output, generate_measures_all_reviews]
    outputs:
      moderately_sensitive:
        cohort: output/redacted/redacted_measure_*.csv
        cohort_codeuse: output/redacted/redacted_totalcodeuse*.csv

  generate_plots:
    run: python:latest python analysis/plots.py
    needs: [redact_and_round, generate_deciles_charts]
    outputs:
      moderately_sensitive:
        percent_cohort: output/figures/*_*_rate_percentage.jpeg
        perthousand_cohort: output/figures/*_*_rate_perthousand.jpeg 

  generate_table_1:
    run: python:latest python analysis/table_1.py --study_def_paths="output/joined/input_allmedrev_*.csv.gz" --demographics="age_band,sex,region,imdQ5,ethnicity,learning_disability,care_home_type,addictivemeds_last12m,dmards_last12m,teratogenicmeds_last12m,highriskmeds_last12m" --outcome "had_anymedrev"
    needs: [join_cohorts_allmedrev]
    outputs:
      moderately_sensitive:
        counts: output/table_1.csv
        had_outcome: output/table_1_had_outcome.csv

  generate_codeuse_output:
    run: python:latest python analysis/code_use_summary.py --study_def_paths="output/joined/input_20*.csv.gz" --codelistfile="user-chriswood-medication-review.csv" --outputfile="codeuse"
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        code_counts: output/codeuse.csv
        total_code_counts: output/totalcodeuse.csv

  generate_allmedrev_codeuse_output:
    run: python:latest python analysis/code_use_summary.py --study_def_paths="output/joined/input_allmedrev_*.csv.gz" --codelistfile="user-chriswood-all-medication-reviews.csv" --outputfile="codeuse_allmedrev"
    needs: [join_cohorts_allmedrev]
    outputs:
      moderately_sensitive:
        code_counts: output/codeuse_allmedrev.csv
        total_code_counts: output/totalcodeuse_allmedrev.csv

  run_tests:
    run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
    outputs:
      moderately_sensitive:
        log: output/pytest.xml

Timeline

Created: 1 year, 5 months ago 13 Dec 2022 09:42:41 UTC
Started: 1 year, 5 months ago 13 Dec 2022 10:05:20 UTC
Finished: 1 year, 5 months ago 13 Dec 2022 13:05:22 UTC
Runtime: 04:17:56

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

Job information

Status: Succeeded
Backend: TPP
Workspace: medication_reviews
Requested by: Chris Wood
Branch: main
Force run dependencies: No
Git commit hash: 20957ac
Requested actions: generate_deciles_charts

redact_and_round

generate_plots

generate_codeuse_output

generate_allmedrev_codeuse_output

run_tests

Code comparison

Compare the code used in this Job Request