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Job request: 13015

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
lone_households
ID:
d6vm2cybyjhq34nm
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  # Study population for lone households and mental health outcomes
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-01 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv
  # Relative outcome measures
  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_*.csv
  # Model checks for normality, seasonal effects, lags, etc.
  check:
    run: stata-mp:latest analysis/modelcheck.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: output/modelcheck.txt
        figures: output/tabfig/checks_*.svg
  # Model coefficients from time series analysis     
  describe:
    run: stata-mp:latest analysis/timeseries.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: output/tsreg.txt
        tables: output/tabfig/tsreg_tables*.csv
        figures: output/tabfig/margin_*.svg
  # Line graphs
  graph:
    run: stata-mp:latest analysis/lines.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: output/lines.txt
        results: output/tabfig/lines_*.svg
  # Sensitivity analysis     
  sensitivity:
    run: stata-mp:latest analysis/sensitivity.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: output/sensitivity.txt
        tables: output/tabfig/sens_tables*.csv
        figures: output/tabfig/sens_mar_*.svg
        results: output/tabfig/senslin_*.svg
  # Generates study populations for baseline tables at 3 timepoints
  generate_study_population_tables_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2019-01-01.csv
  generate_study_population_tables_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2020-01-01.csv
  generate_study_population_tables_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2021-01-01.csv  
  # Baseline tables
  create_baseline_tables:
    run: stata-mp:latest analysis/baseline_tables.do  
    needs: [generate_study_population_tables_2019, generate_study_population_tables_2020, generate_study_population_tables_2021]  
    outputs:
      moderately_sensitive:
        log: logs/table1_descriptives.log
        tables: output/tables/baseline_table_*.csv
  # Self harm mortality graph
  create_selfharm_mortality:
    run: stata-mp:latest analysis/self_harm_graph.do  
    needs: [generate_study_population, calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/selfharm_mortgraph.log
        measure: output/measures/measure_self_harmDeath_rate_rounded.csv
        figures: output/tabfig/line_selfharmmort.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:26

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

Job information

Status
Succeeded
Backend
TPP
Workspace
lone_households
Requested by
Emily Herrett
Branch
main
Force run dependencies
No
Git commit hash
06731b3
Requested actions
  • create_selfharm_mortality

Code comparison

Compare the code used in this Job Request