Job request: 19757
- Organisation:
- University of Manchester
- Workspace:
- adverse-event-prediction-model
- ID:
- mawra6bdiyn5awdk
This page shows the technical details of what happened when the authorised researcher Billy Zhong 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:
-
uxlodghufr2ofub7
-
- Job identifier:
-
nfa53aoeiiyosnhq
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 30000
actions:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
### study cohort ###
generate_study_population_period_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1
outputs:
highly_sensitive:
cohort: output/input_period_1.csv
period_1_process:
run: r:latest analysis/period_1_process.R
needs: [generate_study_population_period_1]
outputs:
highly_sensitive:
csv1: output/period_1a.csv
csv2: output/period_1_*.csv
generate_study_population_period_1b:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1b
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1b.csv
period_1b_quickcheck:
run: r:latest analysis/period_1b_quickcheck.R
needs: [generate_study_population_period_1b]
outputs:
moderately_sensitive:
csv1: output/period_1b_quickcheck.csv
generate_study_population_period_1c:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1c
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1c.csv
generate_study_population_period_1d:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1d
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1d.csv
generate_study_population_period_1e:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1e
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1e.csv
generate_study_population_period_1f:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1f
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1f.csv
generate_study_population_period_1g:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1g
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1g.csv
generate_study_population_period_1h:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1h
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1h.csv
generate_study_population_period_1i:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1i
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1i.csv
generate_study_population_period_1j:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1j
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1j.csv
generate_study_population_period_1k:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1k
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1k.csv
generate_study_population_period_1l:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1l
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1l.csv
generate_study_population_period_1m:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1m
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1m.csv
generate_study_population_period_1n:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1n
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1n.csv
generate_study_population_period_1o:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1o
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1o.csv
generate_study_population_period_1p:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1p
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1p.csv
generate_study_population_period_1q:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1q
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1q.csv
generate_study_population_period_1r:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1r
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1r.csv
generate_study_population_period_1s:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1s
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1s.csv
generate_study_population_period_1t:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1t
needs: [period_1_process]
outputs:
highly_sensitive:
cohort: output/input_period_1t.csv
period_1a_id:
run: r:latest analysis/period_1a_id.R
needs: [generate_study_population_period_1]
outputs:
highly_sensitive:
csv1: output/period_1a_id.csv
generate_study_population_period_1a:
run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1a
needs: [period_1a_id]
outputs:
highly_sensitive:
cohort: output/input_period_1a.csv
process_cox_dataset:
run: r:latest analysis/process_cox_dataset.R
needs: [generate_study_population_period_1a,generate_study_population_period_1b,generate_study_population_period_1c,generate_study_population_period_1d,
generate_study_population_period_1e,generate_study_population_period_1f,generate_study_population_period_1g,generate_study_population_period_1h,
generate_study_population_period_1i,generate_study_population_period_1j,generate_study_population_period_1k,generate_study_population_period_1l,
generate_study_population_period_1m,generate_study_population_period_1n,generate_study_population_period_1o,generate_study_population_period_1p,
generate_study_population_period_1q,generate_study_population_period_1r,generate_study_population_period_1s,generate_study_population_period_1t]
outputs:
highly_sensitive:
rds: output/processed_data.rds
process_kaplan_meier_plot:
run: r:latest analysis/prediction/kaplan_meier_plot.R
needs: [process_cox_dataset]
outputs:
moderately_sensitive:
plot1: output/KM_overall_with_CI.jpeg
csv1: output/surv_df.csv
process_kaplan_meier_plot_by_infection:
run: r:latest analysis/prediction/kaplan_meier_plot_by_infection.R
needs: [process_cox_dataset]
outputs:
moderately_sensitive:
plot1: output/KM_by_*_with_CI.jpeg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:07:03
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- adverse-event-prediction-model
- Requested by
- Billy Zhong
- Branch
- ae_prediction
- Force run dependencies
- No
- Git commit hash
- f70fc9d
- Requested actions
-
-
process_kaplan_meier_plot
-
process_kaplan_meier_plot_by_infection
-
Code comparison
Compare the code used in this Job Request