Job request: 20857
- Organisation:
- University of Surrey
- Workspace:
- prostate_ca_incidence
- ID:
- 7a76quvrmhfvhqv4
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:
-
g3bo63klbvjo5ofs
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
# describe_trends:
# run: r:latest analysis/reclassEthnicity.R
# needs:
# [
# generate_ethnicity
# ]
# outputs:
# moderately_sensitive:
# fig1: output/input_ethnicity2.feather
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_rates_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2015-01-01 to 2019-06-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/inpu*.feather
generate_rates_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2019-07-01 to 2023-09-01 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_rates_1,
generate_rates_2,
generate_ethnicity,
]
outputs:
highly_sensitive:
cohort: output/measures/in*.feather
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_rates --skip-existing --output-dir=output/measures
needs:
[
generate_rates_1,
generate_rates_2,
join_ethnicity,
]
outputs:
moderately_sensitive:
measure_csv1: output/measures/measure_prevalence*_rate.csv
measure_csv2: output/measures/measure_prevalencebyIMD*_rate.csv
measure_csv3: output/measures/measure_prevalencebyEthnicity*_rate.csv
measure_csv4: output/measures/measure_prevalencebyAge*_rate.csv
measure_csv5: output/measures/measure_prevalencebyRegion*_rate.csv
measure_csv6: output/measures/measure_incidence*_rate.csv
measure_csv7: output/measures/measure_incidencebyIMD*_rate.csv
measure_csv8: output/measures/measure_incidencebyEthnicity*_rate.csv
measure_csv9: output/measures/measure_incidencebyAge*_rate.csv
measure_csv10: output/measures/measure_incidencebyRegion*_rate.csv
measure_csv11: output/measures/measure_mortality*_rate.csv
describe_trends:
run: r:latest analysis/Descriptive_trends.R
needs:
[
generate_measures,
generate_study_population
]
outputs:
moderately_sensitive:
Fig1: output/incidence.png
Fig2: output/prevalence.png
Fig3: output/died_prostate.png
Fig4: output/incidence_by_age_group.png
Fig5: output/incidence_by_ethnicity.png
Fig6: output/incidence_by_imd_cat.png
Fig7: output/incidence_by_region.png
Fig8: output/prevalenc_by_age_group.png
Fig9: output/prevalenc_by_ethnicity.png
Fig10: output/prevalenc_by_imd_cat.png
Fig11: output/prevalenc_by_region.png
csv1: output/Rates_rounded_prevalence.csv
csv2: output/Rates_rounded_prevalence_by_imd_cat.csv
csv3: output/Rates_rounded_prevalence_by_ethnicity.csv
csv4: output/Rates_rounded_prevalence_by_age_group.csv
csv5: output/Rates_rounded_prevalence_by_region.csv
csv6: output/Rates_rounded_incidence.csv
csv7: output/Rates_rounded_incidence_by_imd_cat.csv
csv8: output/Rates_rounded_incidence_by_ethnicity.csv
csv9: output/Rates_rounded_incidence_by_age_group.csv
csv10: output/Rates_rounded_incidence_by_region.csv
csv11: output/Rates_rounded_died_prostate.csv
csv12: output/Table1.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:37
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- prostate_ca_incidence
- Requested by
- AgzLeman
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 54a36fc
- Requested actions
-
-
describe_trends
-
Code comparison
Compare the code used in this Job Request