Job request: 5133
- Organisation:
- University of Bristol
- Workspace:
- covid-ve-change-over-time-main
- ID:
- s5733356hqmpmvuj
This page shows the technical details of what happened when the authorised researcher Elsie Horne requested one or more actions to be run against real patient data within a secure environment.
By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.
The output security levels are:
-
highly_sensitive
- Researchers can never directly view these outputs
- Researchers can only request code is run against them
-
moderately_sensitive
- Can be viewed by an approved researcher by logging into a highly secure environment
- These are the only outputs that can be requested for public release via a controlled output review service.
Jobs
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- Job identifier:
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ljmo7qkdklioorhl
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- Job identifier:
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ij4wcyog4w6diwcz
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- Job identifier:
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xwdok7a26hnixnhi
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- Job identifier:
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7zwudgkjxkfpmqkq - Error:
- nonzero_exit: Job exited with error code 137: likely means it ran out of memory
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- Job identifier:
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lt3mkfno7icg22lz - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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p4dmeeqhb3fljz63 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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d7pchcuibnyhjmfr - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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hf7p47k5jhqulrt5 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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x5hnjmjkgdlhbbkn - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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anl25bijoqdd7drc - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
## ####################################
## preliminaries
## ####################################
design:
run: r:latest analysis/design.R
outputs:
moderately_sensitive:
study_dates_json: output/lib/study_parameters.json
study_dates_rds: output/lib/study_parameters.rds
jcvi_groups: output/lib/jcvi_groups.csv
elig_dates: output/lib/elig_dates.csv
regions: output/lib/regions.csv
model_varlist: output/lib/model_varlist.rds
outcomes: output/lib/outcomes.rds
subgroups: output/lib/subgroups.rds
## ####################################
## study definition
## ####################################
## generate dummy data for study_definition
dummy_data:
run: r:latest analysis/dummy_data.R
needs:
- design
outputs:
moderately_sensitive:
dummy_data: analysis/dummy_data.feather
## study definition
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather
dummy_data_file: analysis/dummy_data.feather
needs:
- design
- dummy_data
outputs:
highly_sensitive:
cohort: output/input.feather
## ####################################
## preprocessing
## ####################################
## process data from study_definition
data_input_process:
run: r:latest analysis/preprocess/data_input_process.R
needs:
- design
- dummy_data
- generate_study_population
outputs:
highly_sensitive:
data_all: output/data/data_*.rds
moderately_sensitive:
data_properties: output/tables/data_*_tabulate.txt
## apply eligiblity criteria from boxes a and b
data_eligible_ab:
run: r:latest analysis/preprocess/data_eligible_ab.R
needs:
- design
- data_input_process
outputs:
highly_sensitive:
data_eligible_a: output/data/data_eligible_a.rds
data_eligible_b: output/data/data_eligible_b.rds
moderately_sensitive:
eligibility_count: output/lib/eligibility_count_ab.csv
group_age_ranges: output/lib/group_age_ranges.csv
## ####################################
## second_vax_period
## ####################################
## identify second vaccination time periods
## create dataset for identifying second vaccination time periods
data_2nd_vax_dates:
run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
needs:
- design
- data_input_process
- data_eligible_ab
outputs:
highly_sensitive:
data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
second_vax_period_dates_rds: output/second_vax_period/data/second_vax_period_dates.rds
moderately_sensitive:
second_vax_period_dates_txt: output/second_vax_period/tables/second_vax_period_dates.txt
## plot second vaccination time periods
plot_2nd_vax_dates:
run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
needs:
- design
- data_eligible_ab
- data_2nd_vax_dates
outputs:
moderately_sensitive:
plots_by_region: output/second_vax_period/images/plot_by_region_*.png
## apply eligiblity criteria from boxes c, d and e
data_eligible_cde:
run: r:latest analysis/second_vax_period/data_eligible_cde.R
needs:
- design
- data_input_process
- data_eligible_ab
- data_2nd_vax_dates
outputs:
highly_sensitive:
data_eligible_e_vax: output/data/data_eligible_e_vax.rds
data_eligible_e_unvax: output/data/data_eligible_e_unvax.rds
data_eligible_e: output/data/data_eligible_e.csv
## ####################################
## study definition tests
## ####################################
## study definition tests
generate_covid_tests_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tests
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_tests.feather
## check the tests data as expected
check_tests:
run: r:latest analysis/tests/check_tests.R
needs:
- design
- generate_covid_tests_data
outputs:
moderately_sensitive:
covariate_distribution: output/tests/images/covariate_distribution.png
data_tests_tabulate: output/tests/tables/data_tests_tabulate.txt
Timeline
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Created:
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Started:
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Finished:
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Runtime: 11:54:39
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
- Backend
- TPP
- Workspace
- covid-ve-change-over-time-main
- Requested by
- Elsie Horne
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 92a5a93
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this job request