Job request: 9754
- Organisation:
- University of Nottingham
- Workspace:
- postopcovid
- ID:
- 234w3bkh4wy7fs3w
This page shows the technical details of what happened when authorised researcher Colin Crooks 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:
-
lbgyzkhwyyywhlcc
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
data_manage:
run: r:latest analysis/data_manage.R
needs: [generate_study_population]
outputs:
highly_sensitive:
cohort: output/cohort_long.feather
data_manage_postdisch_week:
run: r:latest analysis/data_manage_postdisch_weeks.R
needs: [generate_study_population,data_manage]
outputs:
highly_sensitive:
cohort_splits: output/cohort_postdisch_week_splits.feather
flowchart:
run: r:latest analysis/FlowChart.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
flowchart_data: output/flowchart.RData
flowchart_fig: output/Flowchart.pdf
table_demo:
run: r:latest analysis/Table_demo.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_demo: output/table_demo.RData
table_postopcovid_crude:
run: r:latest analysis/Table_postopcovid_crude.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_crude: output/postopcovid_crude.RData
table_postopcovid_crude_sub:
run: r:latest analysis/Table_postopcovid_crude_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_crude: output/postopcovid_crude_sub.RData
table_postopcovid_adjusted:
run: r:latest analysis/Table_postopcovid_adjusted.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_adjusted: output/postopcovid_adjusted.RData
model_adjusted: output/postopcovidmodel.csv
model_adjusted_waves: output/postopcovidmodelwaves.csv
table_postopcovid_adjusted_sub:
run: r:latest analysis/Table_postopcovid_adjusted_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_adjusted_sub: output/postopcovid_adjusted_sub.RData
model_adjusted_sub: output/postopcovidmodelsub.csv
model_adjusted_waves_sub: output/postopcovidmodelwavessub.csv
table_postopcovid_tv:
run: r:latest analysis/Table_postopcovid_tv.R
needs: [generate_study_population, data_manage,data_manage_postdisch_week]
outputs:
moderately_sensitive:
table_tv: output/postopcovid_tv.RData
model_VTE_tv: output/postopVTEmodelsplit.csv
model_COVID_tv: output/postopcovidmodelsplit.csv
table_postopcovid_tv_sub:
run: r:latest analysis/Table_postopcovid_tv_sub.R
needs: [generate_study_population, data_manage,data_manage_postdisch_week]
outputs:
moderately_sensitive:
table_tv_sub: output/postopcovid_tv_sub.RData
model_VTE_tv_sub: output/postopVTEmodelsplitsub.csv
model_COVID_tv_sub: output/postopcovidmodelsplitsub.csv
table_postopLOS:
run: r:latest analysis/Table_postoplos.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_los: output/postoplos.RData
model_los: output/postopLOSmodel.csv
table_postopLOS_sub:
run: r:latest analysis/Table_postoplos_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_los_sub: output/postoplos_sub.RData
model_los_sub: output/postopLOSmodel_sub.csv
table_postopVTE:
run: r:latest analysis/Table_postopVTE.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_VTE: output/postopVTE.RData
model_VTE: output/postopVTEmodel.csv
table_postopVTE_sub:
run: r:latest analysis/Table_postopVTE_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_VTE_sub: output/postopVTE_sub.RData
model_VTE_sub: output/postopVTEmodelsub.csv
table_postopmortality:
run: r:latest analysis/Table_postopmortality.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_mortality: output/postopmortality.RData
model_mortality: output/postopdiedmodel.csv
table_postopmortality_sub:
run: r:latest analysis/Table_postopmortality_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_mortality_sub: output/postopmortality_sub.RData
model_mortality_sub: output/postopdiedmodelsub.csv
table_postopreadmit:
run: r:latest analysis/Table_postop_readmit.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_readmit: output/postopreadmit.RData
model_readmit: output/postopreadmitmodel.csv
table_postopreadmit_sub:
run: r:latest analysis/Table_postop_readmit_sub.R
needs: [generate_study_population, data_manage]
outputs:
moderately_sensitive:
table_readmit_sub: output/postopreadmit_sub.RData
model_readmit_sub: output/postopreadmitmodelsub.csv
report:
run: r:latest -e 'rmarkdown::render("analysis/Results.rmd", output_dir = "/workspace/output/",knit_root_dir = "/workspace",)'
needs: [generate_study_population, data_manage, data_manage_postdisch_week,
flowchart,
table_demo,
table_postopcovid_crude,
table_postopcovid_adjusted,
table_postopcovid_tv,
table_postopLOS,
table_postopVTE,
table_postopmortality,
table_postopreadmit,
table_postopcovid_crude_sub,
table_postopcovid_adjusted_sub,
table_postopcovid_tv_sub,
table_postopLOS_sub,
table_postopVTE_sub,
table_postopmortality_sub,
table_postopreadmit_sub]
outputs:
moderately_sensitive:
results_report: output/Results.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:11:42
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- postopcovid
- Requested by
- Colin Crooks
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- ab7aef8
- Requested actions
-
-
table_postopVTE_sub
-
Code comparison
Compare the code used in this Job Request