Job request: 1579
- Organisation:
- Bennett Institute
- Workspace:
- factors-associated-with-covid-19-vaccination-test
- ID:
- wbuzjchvnh2zlsmj
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:
-
atk7qpl6f6rr5lmh
-
- Job identifier:
-
tsxruyikn6doutop
-
- Job identifier:
-
5e4vmaqg5b27i5bl
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_all:
run: r:latest analysis/R/Scripts/00_process_data.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
# Models
cox_models:
run: r:latest analysis/R/Scripts/02_Models.R
needs: [generate_study_population, data_process_all]
outputs:
moderately_sensitive:
models: output/models/mod*.rds
tables: output/models/tab*.html
data: output/models/tab*.csv
plots: output/models/plot*.svg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:25:06
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Requested by
- Millie Green
- Branch
- wip
- Force run dependencies
- Yes
- Git commit hash
- 4bed285
- Requested actions
-
-
cox_models
-
Code comparison
Compare the code used in this Job Request
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