Job request: 775
- Organisation:
- Bennett Institute
- Workspace:
- covid-vaccineeffectiveness-research_main
- ID:
- i3fkfwoa3klerfzt
This page shows the technical details of what happened when the authorised researcher Will Hulme 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:
-
eqstnpdz2wdifu7t
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
extract_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
#
# needs: [generate_delivery_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/population_characteristics.html
get_packages:
run: r:latest analysis/R/export_package_names.R
outputs:
moderately_sensitive:
cohort: output/available_packages.csv
process_data:
run: r:latest analysis/R/process_data.R
needs: [extract_data]
outputs:
highly_sensitive:
cohort1: output/data/data_processed.rds
cohort2: output/data/data_vaccinated.rds
moderately_sensitive:
summary1: output/data_summary/summary_extract.txt
summary2: output/data_summary/summary_processed.txt
summary3: output/data_summary/summary_vaccinated.txt
summary4: output/data_summary/type_extract.txt
summary5: output/data_summary/type_processed.txt
summary6: output/data_summary/type_vaccinated.txt
summarise_data:
run: r:latest analysis/R/summarise_data.R
needs: [process_data]
outputs:
moderately_sensitive:
summary1: output/variable_summary/categorical.txt
summary2: output/variable_summary/numeric.txt
summary3: output/variable_summary/date.txt
summarytables: output/variable_summary/tables/categorical_*.csv
summarystats: output/data_summary/summary_stats.json
vaccine_tables:
run: r:latest analysis/R/vaccine_type.R
needs: [process_data]
outputs:
moderately_sensitive:
tables: output/vaccine_type/tables/vaccine_type_*.csv
tte_tables:
run: r:latest analysis/R/tte_tables.R
needs: [process_data]
outputs:
moderately_sensitive:
tables: output/tte/tables/event_rates_*.csv
tte_plots:
run: r:latest analysis/R/tte_plots.R
needs: [process_data]
outputs:
moderately_sensitive:
plots: output/tte/figures/plot_*.svg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:01:29
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- covid-vaccineeffectiveness-research_main
- Requested by
- Will Hulme
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 4ab794a
- Requested actions
-
-
summarise_data
-
Code comparison
Compare the code used in this Job Request