Job request: 3053
- Organisation:
- Bennett Institute
- Workspace:
- breakthrough-covid-master
- ID:
- dtehws6xgi5z4a5v
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:
-
d4whwi5ageewqmt6
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 ----
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input.csv
# Process data ----
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data: output/data/data_all.rds
# Data properties ----
data_properties:
run: r:latest analysis/data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_all*.txt
# Data summaries ----
data_summaries:
run: r:latest -e 'rmarkdown::render("analysis/data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [generate_study_population, data_process]
outputs:
moderately_sensitive:
html: output/markdown/data_summaries.html
# Table 1 ----
table_1:
run: r:latest analysis/table_1.R
needs: [data_process]
outputs:
moderately_sensitive:
table: output/tables/table1*.html
# Figure 1 ----
figure_1:
run: r:latest analysis/cumulative_incidence.R
needs: [data_process]
outputs:
moderately_sensitive:
svg: output/figures/cumulative_incidence_positive_test*.svg
# Table 2 ----
table_2:
run: r:latest analysis/table_2.R
needs: [data_process]
outputs:
moderately_sensitive:
table: output/tables/table2*.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:40
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- breakthrough-covid-master
- Requested by
- Millie Green
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 0c54129
- Requested actions
-
-
table_1
-
Code comparison
Compare the code used in this Job Request