Job request: 14269
- Organisation:
- University of Surrey
- Workspace:
- pancreaticcancer_enzyme_rx
- ID:
- h5klsggkuzus4uue
This page shows the technical details of what happened when the 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 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:
-
ea7omlyxyvvj24dg
-
- Job identifier:
-
qsioon7loai3hgau
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 2022-12-01 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
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/Test1_R.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: 00:00:27
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
- 258b8c8
- Requested actions
-
-
describe_ERx_rates
-
generate_report
-
Code comparison
Compare the code used in this Job Request