Job request: 1993
- Organisation:
- Bennett Institute
- Workspace:
- factors-associated-with-covid-19-vaccination-emis
- ID:
- dmpa2fe3fa3fd43e
This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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
-
- Job identifier:
-
vfjbzn5qxamsbtvk - Error:
- nonzero_exit: Job exited with an error code
-
- Job identifier:
-
ewcmnwwoiy4iu6g6 - Error:
- nonzero_exit: Job exited with an error code
-
- Job identifier:
-
wfuupjo4z7lcdqdc - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
vw2gxa36qhmgwmxe - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
5hrez7xnn2hmowx4 - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
6zwl6im3mijzr6cy - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
vtz5tlu5cijjgtvb - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
v5q7c72ijghaz5s5 - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
ntw5hb4l2igbutv6 - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
g3iwv75djwwjjtaz - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
ot3omnsweqi2r67n - Error:
- dependency_failed: Not starting as dependency failed
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]
outputs:
moderately_sensitive:
html: output/Model_comparisons.html
# Stratified cox model
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
# Strata summaries
strata_summary:
run: r:latest analysis/R/Scripts/04_Strata_Summary.R
needs: [data_process, cox_model_final]
outputs:
moderately_sensitive:
plots: output/models/final/plot_strata*.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_model_final]
outputs:
moderately_sensitive:
html: output/Results_summary.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:07:43
These timestamps are generated and stored using the UTC timezone on the EMIS backend.
Job information
- Status
-
Failed
- Backend
- EMIS
- Requested by
- Peter Inglesby
- Branch
- emis
- Force run dependencies
- No
- Git commit hash
- 3e351af
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request
- No previous Job Request available for comparison