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Job request: 16450

Organisation:
Bennett Institute
Workspace:
vax-fourth-dose-rd-baseline
ID:
igf3hcmrlv63pdrj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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 
######################################

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

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


version: '3.0'

expectations:
  population_size: 100000

actions:

# Generate study population and extract baseline characteristics 
  generate_study_pop_baseline:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_baseline
      --index-date-range "2022-09-03" 
      --output-dir=feather 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_baseline_*.feather
        
# Generating study population at different index dates 
  generate_study_pop_index_1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_index
      --index-date-range "2022-09-03" 
      --output-dir=feather 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_index_*.feather
        
# # Generating study population at different index dates 
#   generate_study_pop_index_2:
#     run: cohortextractor:latest generate_cohort
#       --study-definition study_definition_index
#       --index-date-range "2022-10-15" 
#       --output-dir=feather 
#       --output-format=feather
#     outputs:
#       highly_sensitive:
#         cohort: output/input_index*.feather

# # Generating study population at different index dates 
#   generate_study_pop_index_3:
#     run: cohortextractor:latest generate_cohort
#       --study-definition study_definition_index
#       --index-date-range "2022-11-26" 
#       --output-dir=feather 
#       --output-format=feather
#     outputs:
#       highly_sensitive:
#         cohort: output/input_inde*.feather

# Data processing
  data_process_baseline:
    run: r:latest analysis/processing/data_processing_baseline.R
    needs: [generate_study_pop_baseline]
    outputs:
      highly_sensitive:
        cohort: output/cohort/cohort_*.csv
      moderately_sensitive:
        descriptive: output/descriptive/total_*.csv

# Data processing
  data_process_index:
    run: r:latest analysis/processing/data_processing_index.R
    needs: [generate_study_pop_index_1]
    outputs:
      moderately_sensitive:
        descriptive: output/descriptive/num_outcomes*.csv

# Discontinuity of demographics
  demographics:
   run: r:latest analysis/descriptive/demographics_byage.R
   needs: [generate_study_pop_baseline, data_process_baseline]
   outputs:
      moderately_sensitive:
        measures_csv: output/descriptive/demographics_*.csv


# Cumulative uptake of fourth dose #
  # cumulative_fourth_dose:
  #  run: r:latest analysis/descriptive/cumulative_vax_byage.R
  #  needs: [data_process]
  #  outputs:
  #     moderately_sensitive:
  #       rates_csv: output/cumulative_rates/final_*.csv 
  #       plot: output/cumulative_rates/plot_*.png

# Flu vaccine uptake #
  # flu_vax:
  #  run: r:latest analysis/descriptive/flu_vax_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/cumulative_rates/flu_*.csv
  #       plot: output/cumulative_rates/plot_flu_vax_byage.png


# Outcome plots #
  # covid_outcomes:
  #  run: r:latest analysis/descriptive/covid_outcomes_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/covid_outcomes/covid_*.csv
  #       plot: output/covid_outcomes/plot_outcomes_*.png
  

# ITT analysis #


# IV analysis #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:02:50

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vax-fourth-dose-rd-baseline
Requested by
Andrea Schaffer
Branch
Protocol-updates
Force run dependencies
Yes
Git commit hash
d0c6465
Requested actions
  • generate_study_pop_baseline
  • generate_study_pop_index_1
  • data_process_baseline
  • data_process_index
  • demographics

Code comparison

Compare the code used in this Job Request