Job request: 8143
- Organisation:
- Bennett Institute
- Workspace:
- mabs-main
- ID:
- itfkzktlbxekkc2p
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
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- Job identifier:
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wekzjumcsip3g5md
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- Job identifier:
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zecobnbxym7g4vuu
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- Job identifier:
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24xqmfik2n2enjcp
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- Job identifier:
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fk6sni2g7a25t672
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- Job identifier:
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vqi34acoyfos7vcf
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- Job identifier:
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gvz76czqxqhjux6r
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- Job identifier:
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zkclgzbsigybgmrz
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- Job identifier:
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nfxu32vgbu6ygnxc
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: 15/02/2022
#
################################################################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract 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 ----
data_process:
run: r:latest analysis/process/process_data.R
needs: [extract_data]
outputs:
highly_sensitive:
data: output/data/data_processed*.rds
# Data summaries ----
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
# Sensitivity anslysis ----
sa_symptomatic_test:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/sa_symptomatic_test.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/coverage/sa_symptomatic_test.html
# Report ----
report_data:
run: r:latest analysis/descriptive/coverage_report_data.R
needs: [data_process]
outputs:
moderately_sensitive:
redacted_tables: output/coverage/table_*.csv
unredacted_tables: output/coverage/for-checks/table_*.csv
# Variation by STP ----
stp_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/mabs-and-abs-by-stp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/variation/mabs-and-abs-by-stp.html
csvs: output/variation/figure_*.csv
# Obs vs exp ----
obs_vs_exp_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/obs-vs-exp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/variation/obs-vs-exp.html
# Crude count of outcomes ----
outcomes_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/crude_outcomes.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/effectiveness/counts")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/effectiveness/counts/crude_outcomes.html
Timeline
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Created:
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Started:
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Finished:
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Runtime: 00:58:34
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Code comparison
Compare the code used in this Job Request