Job request: 14530
- Organisation:
- University of Surrey
- Workspace:
- adtinjectables
- ID:
- c6tk7rzxddinuswa
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:
-
phwmmt3eq56zdwuu
-
- Job identifier:
-
oaaropetrlkwykpr
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_ADT_rates_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2015-01-01 to 2018-12-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/inpu*.feather
generate_ADT_rates_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2019-01-01 to 2022-12-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/inp*.feather
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs:
[
generate_ADT_rates_1,
generate_ADT_rates_2,
generate_ethnicity,
]
outputs:
highly_sensitive:
cohort: output/measures/in*.feather
generate_measures_ADT:
run: cohortextractor:latest generate_measures --study-definition study_definition_rates --skip-existing --output-dir=output/measures
needs:
[
generate_ADT_rates_1,
generate_ADT_rates_2,
join_ethnicity,
]
outputs:
moderately_sensitive:
measure_csv1: output/measures/measure_ADT_inj*_rate.csv
measure_csv2: output/measures/measure_ADT_inj1*_rate.csv
measure_csv3: output/measures/measure_ADT_inj3*_rate.csv
measure_csv4: output/measures/measure_ADT_inj6*_rate.csv
measure_csv5: output/measures/measure_ADTinjbyRegion*_rate.csv
measure_csv6: output/measures/measure_ADTinjbyIMD*_rate.csv
measure_csv7: output/measures/measure_ADTinjbyEthnicity*_rate.csv
measure_csv8: output/measures/measure_ADTinjbyAge*_rate.csv
measure_csv9: output/measures/measure_ADT_oral*_rate.csv
measure_csv10: output/measures/measure_ADToralbyRegion*_rate.csv
measure_csv11: output/measures/measure_ADToralbyIMD*_rate.csv
measure_csv12: output/measures/measure_ADToralbyEthnicity*_rate.csv
measure_csv13: output/measures/measure_ADToralbyAge*_rate.csv
describe_trends:
run: r:latest analysis/Descriptive_trends.R
needs:
[
generate_measures_ADT,
generate_study_population
]
outputs:
moderately_sensitive:
fig1: output/ADT_inj_rat.png
fig2: output/ADT_inj1_ra.png
fig3: output/ADT_inj3_ra.png
fig4: output/ADT_inj6_ra.png
fig5: output/ADTinjbyReg.png
fig6: output/ADTinjbyIMD.png
fig7: output/ADTinjbyEth.png
fig8: output/ADTinjbyAge.png
fig9: output/ADT_oral_ra.png
fig10: output/ADToralbyRe.png
fig11: output/ADToralbyIM.png
fig12: output/ADToralbyEt.png
fig13: output/ADToralbyAg.png
csv1: output/ADT_inj_rat_rounded.csv
csv2: output/ADT_inj1_ra_rounded.csv
csv3: output/ADT_inj3_ra_rounded.csv
csv4: output/ADT_inj6_ra_rounded.csv
csv5: output/ADTinjbyReg_rounded.csv
csv6: output/ADTinjbyIMD_rounded.csv
csv7: output/ADTinjbyEth_rounded.csv
csv8: output/ADTinjbyAge_rounded.csv
csv9: output/ADT_oral_ra_rounded.csv
csv10: output/ADToralbyRe_rounded.csv
csv11: output/ADToralbyIM_rounded.csv
csv12: output/ADToralbyEt_rounded.csv
csv13: output/ADToralbyAg_rounded.csv
csv14: output/Table1.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 02:47:42
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- adtinjectables
- Requested by
- AgzLeman
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 4260bd4
- Requested actions
-
-
generate_study_population
-
describe_trends
-
Code comparison
Compare the code used in this Job Request