Job request: 5359
- Organisation:
- Bennett Institute
- Workspace:
- mabs-draft-report
- ID:
- pe4eqcbfnkr5c4p4
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:
-
67ojqzgjl2viwkqq
Pipeline
Show project.yaml
################################################################################
#
# Description: This script defines the project pipeline - it specifys the
# execution orders for all the code in this repo using a series of
# actions.
#
# Author(s): M Green
# Date last updated: 31/01/2022
#
################################################################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract data ----
## Cohort data
extract_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/data/input.csv.gz
# Data processing ----
## Process data
data_process:
run: r:latest analysis/process/process_data.R
needs: [extract_data]
outputs:
highly_sensitive:
data: output/data/data_processed.rds
data_process2:
run: r:latest analysis/process/process_data2.R
needs: [data_process]
outputs:
highly_sensitive:
data: output/data/data_processed_clean.rds
data_process3:
run: r:latest analysis/process/process_data3.R
needs: [data_process]
outputs:
highly_sensitive:
data: output/data/data_processed_clean_test.rds
# Data summaries ----
flow_chart:
run: r:latest analysis/descriptive/flow_chart.R
needs: [data_process]
outputs:
moderately_sensitive:
data: output/data/flowchart.csv
data_properties:
run: r:latest analysis/descriptive/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
# Report ----
report_data:
run: r:latest analysis/descriptive/coverage_report_data.R
needs: [data_process]
outputs:
moderately_sensitive:
tables: output/reports/coverage/tables/table_*.csv
report_data2:
run: r:latest analysis/descriptive/coverage_report_data_v2.R
needs: [data_process3]
outputs:
moderately_sensitive:
tables: output/reports/coverage/table_*.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:03:09
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- mabs-draft-report
- Requested by
- Millie Green
- Branch
- draft-report
- Force run dependencies
- No
- Git commit hash
- 3637336
- Requested actions
-
-
report_data2
-
Code comparison
Compare the code used in this Job Request