Job request: 16099
- Organisation:
- University of Surrey
- Workspace:
- pancreaticcancer_enzyme_rx
- ID:
- 77t2npblc7l2ojne
This page shows the technical details of what happened when authorised researcher AgzLeman 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:
-
whgv3bw7bqezblfp
-
- Job identifier:
-
cv565mmkhvmegpcd
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv
outputs:
highly_sensitive:
cohort: output/input.csv
generate_enzyme_replace_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2015-01-01 to 2018-08-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/inp*.feather
generate_enzyme_replace_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2023-01-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/in*.feather
generate_measures_enzymeRx:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs:
[
generate_enzyme_replace_1,
generate_enzyme_replace_2,
]
outputs:
moderately_sensitive:
measure_csv1: output/measures/measure_enzymeRx*_rate.csv
measure_csv2: output/measures/measure_ExByRegion*_rate.csv
describe_ERx_rates:
run: r:latest analysis/analysis_enzymeRx.R
needs: [generate_measures_enzymeRx]
outputs:
moderately_sensitive:
Fig1: output/ERx_number.png
Fig2: output/ERx_rates.png
Fig3: output/model_rates.png
Fig4: output/Region.png
Fig5: output/Figure_3A_East.png
Fig6: output/Figure_3B_East Midlands.png
Fig7: output/Figure_3C_London.png
Fig8: output/Figure_3D_North East.png
Fig9: output/Figure_3E_North West.png
Fig10: output/Figure_3F_South East.png
Fig11: output/Figure_3G_South West.png
Fig12: output/Figure_3H_West Midlands.png
Fig13: output/Figure_3I_Yorkshire and The Humber.png
csv3: output/ERx_Rates_rounded.csv
csv4: output/Region_rounded.csv
generate_report:
run: r:latest analysis/Produce_html.R
needs: [describe_ERx_rates]
outputs:
moderately_sensitive:
cohort: output/Report_file.html
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/reportEx.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [describe_ERx_rates]
# outputs:
# moderately_sensitive:
# notebook: output/reportEx.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:01:08
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- pancreaticcancer_enzyme_rx
- Requested by
- AgzLeman
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- cd444b2
- Requested actions
-
-
describe_ERx_rates
-
generate_report
-
Code comparison
Compare the code used in this Job Request