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Job request: 11776

Organisation:
Bennett Institute
Workspace:
opioids-covid-research
ID:
ga5pnsyfou4jmwhy
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Colm Andrews 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

Pipeline

Show project.yaml 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 10000

actions:

  # Extract data ----
  
  ## Cohort data
  #generate_study_population_1:
  #  run: cohortextractor:latest generate_cohort
  #    --study-definition study_definition 
  #    --index-date-range "2018-01-01 to 2018-12-01 by month" 
  #    --output-dir=output 
  #    --output-format=csv
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/input_*.csv

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition 
      --index-date-range "2019-01-01 to 2019-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition 
      --index-date-range "2020-01-01 to 2020-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv

  #generate_study_population_4:
  #  run: cohortextractor:latest generate_cohort 
  #    --study-definition study_definition 
  #    --index-date-range "2021-01-01 to 2021-12-01 by month" 
  #    --output-dir=output 
  #    --output-format=csv
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/inp*.csv
  
  #generate_study_population_5:
  #  run: cohortextractor:latest generate_cohort 
  #    --study-definition study_definition 
  #    --index-date-range "2022-01-01 to 2022-03-01 by month" 
  #    --output-dir=output 
  #    --output-format=csv
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/in*.csv

  ## Ethnicity      
  generate_ethnicity_cohort:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_ethnicity
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv


  # Data processing ----
  
  ## Add ethnicity
  join_cohorts:
    run: >
      cohort-joiner:v0.0.48
        --lhs output/input_*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/data
    needs: [generate_study_population_2, 
      generate_study_population_3, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv

  ## Generate measures
  generate_measures:
    run: >
      cohortextractor:latest generate_measures 
        --study-definition study_definition 
        --output-dir output/data
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv

  ## Process data
  process_data:
   run: r:latest analysis/process/process_data.R
   needs: [generate_measures,join_cohorts]
   outputs:
      moderately_sensitive:
        measure_csv: output/joined/final_*.csv


  # Results ---

  ## Time series
  timeseries:
    run: r:latest analysis/descriptive/time_series.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        table: output/time series/timeseries_*.csv  
        plot: output/time series/graph_age.png

  ## Table 
  table:
    run: r:latest analysis/descriptive/table.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        table: output/tables/table_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 16:47:03

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

Job information

Status
Failed
Backend
TPP
Workspace
opioids-covid-research
Requested by
Colm Andrews
Branch
main
Force run dependencies
No
Git commit hash
e4cdb30
Requested actions
  • run_all

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