Job request: 10555
- Organisation:
- University of Bristol
- Workspace:
- vaccine-effectiveness-in-children
- ID:
- 6w26ozfantlxn2d2
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:
-
fm3u2kaiownwfz6h
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_treated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_treated --output-format feather
outputs:
highly_sensitive:
cohort: output/input_treated.feather
data_process_treated:
run: r:latest analysis/data_process_treated.R over12
needs:
- generate_study_treated
outputs:
highly_sensitive:
rds: output/data/data_treated_eligible.rds
moderately_sensitive:
flowchart: output/data/flowchart_treated_eligible.csv
## matching round 1
generate_study_control_potential1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_potential --output-format feather --index-date-range "2021-09-20 to 2021-09-20 by week"
outputs:
highly_sensitive:
cohort: output/input_control_potential_2021-09-20.feather
data_process_control_potential1:
run: r:latest analysis/data_process_control.R over12 1
needs:
- generate_study_control_potential1
outputs:
highly_sensitive:
rds: output/data/data_control_potential1.rds
matching1:
run: r:latest analysis/matching.R over12 1
needs:
- data_process_treated
- data_process_control_potential1
outputs:
highly_sensitive:
rds1: output/match/data_potential_matchstatus1.rds
rds2: output/match/data_potential_matched1.rds
csv: output/match/potential_matched_controls1.csv.gz
generate_study_match_control1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_match1 --output-format feather
needs:
- matching1
outputs:
highly_sensitive:
cohort: output/input_control_match1.feather
matching_filter1:
run: r:latest analysis/matching_filter.R over12 1
needs:
- matching1
- generate_study_match_control1
outputs:
highly_sensitive:
rds1: output/match/data_matchstatus_allrounds1.rds
rds2: output/match/data_match_actual1.rds
# ## matching round 2
# generate_study_control_potential1:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_control_potential --output-format feather --index-date-range "2021-10-04 to 2021-10-04 by week"
# outputs:
# highly_sensitive:
# cohort: output/input_control_potential_2021-10-04.feather
# data_process_control_potential2:
# run: r:latest analysis/data_process_control.R over12 2
# needs:
# - generate_study_control_potential2
# outputs:
# highly_sensitive:
# rds: output/data/data_control_potential2.rds
# matching2:
# run: r:latest analysis/matching.R over12 2
# needs:
# - data_matching_filter1
# - data_process_treated
# - data_process_control_potential2
# outputs:
# highly_sensitive:
# rds1: output/match/data_potential_matchstatus2.rds
# rds2: output/match/data_potential_matched2.rds
# csv: output/match/potential_matched_controls2.csv.gz
# generate_study_match_control2:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_control_match2 --output-format feather
# needs:
# - matching2
# outputs:
# highly_sensitive:
# cohort: output/input_control_match2.feather
# matching_filter2:
# run: r:latest analysis/matching_filter.R over12 2
# needs:
# - matching_filter1
# - matching2
# - generate_study_match_control2
# outputs:
# highly_sensitive:
# rds1: output/match/data_matchstatus_allrounds2.rds
# rds2: output/match/data_match_actual2.rds
# ## combine together
# matching_combine:
# run: r:latest analysis/matching_combine.R over12
# needs:
# - matching_filter1
# - matching_filter2
# outputs:
# highly_sensitive:
# rds: output/match/data_match_all.rds
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:25
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- vaccine-effectiveness-in-children
- Requested by
- Will Hulme
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- c1cc0f1
- Requested actions
-
-
matching_filter1
-
Code comparison
Compare the code used in this Job Request