Job request: 1828
- Organisation:
- Bennett Institute
- Workspace:
- factors-associated-with-covid-19-vaccination
- ID:
- aylz6efpxrmqag3j
This page shows the technical details of what happened when authorised researcher Millie Green 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
-
- Job identifier:
-
inrp7deeswgo4yby
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: 1000000
actions:
# Extract data for study population flow chart
generate_study_population_flow_chart_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
outputs:
highly_sensitive:
cohort: output/input_flow_chart.csv
# Calculate numbers for study population flow chart
flow_chart:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population_flow_chart_data]
outputs:
moderately_sensitive:
html: output/Study_definition_flow_chart.html
# Extract study data
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
# Process data
data_process:
run: r:latest analysis/R/Scripts/00_process_data.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
data2: output/data/data_modelling.rds
# Summarise data
data_properties:
run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_all*.txt
# More data summaries
data_summaries:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population, data_process]
outputs:
moderately_sensitive:
html: output/Data_summaries.html
# Coxph models
cox_models:
run: r:latest analysis/R/Scripts/02_Models.R
needs: [generate_study_population, data_process]
outputs:
highly_sensitive :
models: output/models/testing/mod*.rds
# Coxme model
cox_models_sub:
run: r:latest analysis/R/Scripts/02_Models_sub_test.R
needs: [generate_study_population, data_process]
outputs:
highly_sensitive :
models: output/models/testing/mod_test*.rds
# Model summaries
cox_models_summaries:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population, data_process, cox_models, cox_models_sub]
outputs:
moderately_sensitive:
html: output/Model_comparisons.html
# Models
cox_model_final:
run: r:latest analysis/R/Scripts/03_Final_model.R
needs: [generate_study_population, data_process]
outputs:
highly_sensitive :
models: output/models/final/mod*.rds
moderately_sensitive:
tables: output/models/final/tab*.html
data: output/models/final/tab*.csv
plots: output/models/final/plot*.svg
# Results summary
results_summary:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Results_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population, data_process, cox_models]
outputs:
moderately_sensitive:
html: output/Results_summary.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:15:20
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Requested by
- Millie Green
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 16caf18
- Requested actions
-
-
results_summary
-
Code comparison
Compare the code used in this Job Request