Job request: 2683
- Organisation:
- Bennett Institute
- Workspace:
- comparative-ve-research_main
- ID:
- xu5jjgxhsqmytnna
This page shows the technical details of what happened when the authorised researcher Will Hulme 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:
-
pgwkzskh63iwd5dz
-
- Job identifier:
-
tvyp35jmwlh27qhc
-
- Job identifier:
-
zn67kbbpovcugvpl
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
hcw_extract:
run: 'cohortextractor:latest generate_cohort --study-definition study_definition_hcw
--output-format feather '
outputs:
highly_sensitive:
cohort: output/input_hcw.feather
hcw_process:
run: 'r:latest analysis/hcw/process.R '
needs:
- hcw_extract
outputs:
highly_sensitive:
data: output/data/hcw_data_processed.rds
datavax: output/data/hcw_data_vax.rds
hcw_properties:
run: r:latest analysis/process/data_properties.R output/data/hcw_data_processed.rds
output/data_properties
needs:
- hcw_process
outputs:
highly_sensitive:
cohort: output/data_properties/hcw_data_processed.txt
hcw_descr:
run: 'r:latest analysis/hcw/descr.R '
needs:
- hcw_process
outputs:
moderately_sensitive:
png: output/hcw/*.png
svg: output/hcw/*.svg
html: output/hcw/*.html
csv: output/hcw/*.csv
design:
run: 'r:latest analysis/process/design.R '
outputs:
moderately_sensitive:
metadata: output/data/metadata*
extract:
run: 'cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather '
outputs:
highly_sensitive:
cohort: output/input.feather
data_process:
run: 'r:latest analysis/process/data_process.R '
needs:
- extract
outputs:
highly_sensitive:
cohort: output/data/data_processed.rds
data_properties:
run: r:latest analysis/process/data_properties.R output/data/data_processed.rds
output/data_properties
needs:
- data_process
outputs:
highly_sensitive:
cohort: output/data_properties/data_processed.txt
data_selection:
run: 'r:latest analysis/process/data_selection.R '
needs:
- data_process
outputs:
highly_sensitive:
data_allvax: output/data/data_cohort_allvax.rds
data: output/data/data_cohort.rds
moderately_sensitive:
flow: output/data/flowchart.csv
descr_table1:
run: 'r:latest analysis/descriptive/table1.R '
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table1*.html
csv: output/descriptive/tables/table1*.csv
descr_table1_allvax:
run: 'r:latest analysis/descriptive/table1_allvax.R '
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table1_allvax.html
csv: output/descriptive/tables/table1_allvax.csv
descr_irr:
run: r:latest analysis/descriptive/table_irr.R output/data/data_processed.rds
output/data_properties
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table_irr.html
csv: output/descriptive/tables/table_irr.csv
descr_km:
run: r:latest analysis/descriptive/km.R output/data/data_processed.rds output/data_properties
needs:
- design
- data_selection
outputs:
moderately_sensitive:
png: output/descriptive/km/plot_survival*.png
svg: output/descriptive/km/plot_survival*.svg
model_test_timesincevax:
run: r:latest analysis/models/model_cox.R test timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/test/timesincevax/data_cox_split.rds
models: output/test/timesincevax/model*.rds
moderately_sensitive:
logs: output/test/timesincevax/log*.txt
glance: output/test/timesincevax/glance*.csv
report_test_timesincevax:
run: r:latest analysis/models/report_cox.R test timesincevax
needs:
- design
- model_test_timesincevax
outputs:
moderately_sensitive:
svg: output/test/timesincevax/forest*.svg
png: output/test/timesincevax/forest*.png
csv: output/test/timesincevax/estimates*.csv
model_test_calendar:
run: r:latest analysis/models/model_cox.R test calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/test/calendar/data_cox_split.rds
models: output/test/calendar/model*.rds
moderately_sensitive:
logs: output/test/calendar/log*.txt
glance: output/test/calendar/glance*.csv
report_test_calendar:
run: r:latest analysis/models/report_cox.R test calendar
needs:
- design
- model_test_calendar
outputs:
moderately_sensitive:
svg: output/test/calendar/forest*.svg
png: output/test/calendar/forest*.png
csv: output/test/calendar/estimates*.csv
model_postest_timesincevax:
run: r:latest analysis/models/model_cox.R postest timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/postest/timesincevax/data_cox_split.rds
models: output/postest/timesincevax/model*.rds
moderately_sensitive:
logs: output/postest/timesincevax/log*.txt
glance: output/postest/timesincevax/glance*.csv
report_postest_timesincevax:
run: r:latest analysis/models/report_cox.R postest timesincevax
needs:
- design
- model_postest_timesincevax
outputs:
moderately_sensitive:
svg: output/postest/timesincevax/forest*.svg
png: output/postest/timesincevax/forest*.png
csv: output/postest/timesincevax/estimates*.csv
model_postest_calendar:
run: r:latest analysis/models/model_cox.R postest calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/postest/calendar/data_cox_split.rds
models: output/postest/calendar/model*.rds
moderately_sensitive:
logs: output/postest/calendar/log*.txt
glance: output/postest/calendar/glance*.csv
report_postest_calendar:
run: r:latest analysis/models/report_cox.R postest calendar
needs:
- design
- model_postest_calendar
outputs:
moderately_sensitive:
svg: output/postest/calendar/forest*.svg
png: output/postest/calendar/forest*.png
csv: output/postest/calendar/estimates*.csv
model_emergency_timesincevax:
run: r:latest analysis/models/model_cox.R emergency timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/emergency/timesincevax/data_cox_split.rds
models: output/emergency/timesincevax/model*.rds
moderately_sensitive:
logs: output/emergency/timesincevax/log*.txt
glance: output/emergency/timesincevax/glance*.csv
report_emergency_timesincevax:
run: r:latest analysis/models/report_cox.R emergency timesincevax
needs:
- design
- model_emergency_timesincevax
outputs:
moderately_sensitive:
svg: output/emergency/timesincevax/forest*.svg
png: output/emergency/timesincevax/forest*.png
csv: output/emergency/timesincevax/estimates*.csv
model_emergency_calendar:
run: r:latest analysis/models/model_cox.R emergency calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/emergency/calendar/data_cox_split.rds
models: output/emergency/calendar/model*.rds
moderately_sensitive:
logs: output/emergency/calendar/log*.txt
glance: output/emergency/calendar/glance*.csv
report_emergency_calendar:
run: r:latest analysis/models/report_cox.R emergency calendar
needs:
- design
- model_emergency_calendar
outputs:
moderately_sensitive:
svg: output/emergency/calendar/forest*.svg
png: output/emergency/calendar/forest*.png
csv: output/emergency/calendar/estimates*.csv
model_covidadmitted_timesincevax:
run: r:latest analysis/models/model_cox.R covidadmitted timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/covidadmitted/timesincevax/data_cox_split.rds
models: output/covidadmitted/timesincevax/model*.rds
moderately_sensitive:
logs: output/covidadmitted/timesincevax/log*.txt
glance: output/covidadmitted/timesincevax/glance*.csv
report_covidadmitted_timesincevax:
run: r:latest analysis/models/report_cox.R covidadmitted timesincevax
needs:
- design
- model_covidadmitted_timesincevax
outputs:
moderately_sensitive:
svg: output/covidadmitted/timesincevax/forest*.svg
png: output/covidadmitted/timesincevax/forest*.png
csv: output/covidadmitted/timesincevax/estimates*.csv
model_covidadmitted_calendar:
run: r:latest analysis/models/model_cox.R covidadmitted calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/covidadmitted/calendar/data_cox_split.rds
models: output/covidadmitted/calendar/model*.rds
moderately_sensitive:
logs: output/covidadmitted/calendar/log*.txt
glance: output/covidadmitted/calendar/glance*.csv
report_covidadmitted_calendar:
run: r:latest analysis/models/report_cox.R covidadmitted calendar
needs:
- design
- model_covidadmitted_calendar
outputs:
moderately_sensitive:
svg: output/covidadmitted/calendar/forest*.svg
png: output/covidadmitted/calendar/forest*.png
csv: output/covidadmitted/calendar/estimates*.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:03:13
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- comparative-ve-research_main
- Requested by
- Will Hulme
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 8da79e1
- Requested actions
-
-
hcw_process
-
hcw_properties
-
hcw_descr
-
Code comparison
Compare the code used in this Job Request