Job request: 15354
- Organisation:
- University of Bristol
- Workspace:
- post-covid-respiratory
- ID:
- mmyry23w2g4emnbo
This page shows the technical details of what happened when the authorised researcher Alex Whitmarsh 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
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- Job identifier:
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hbkqdqc43c3e6i5d
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- Job identifier:
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eqgurskh4newnwqr
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- Job identifier:
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vq2q5zqmhavwn5j5
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- Job identifier:
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5757tbcpmokul6qa - Error:
- nonzero_exit: Job exited with an error: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
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- Job identifier:
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brz6jcc65vaabw46 - Error:
- nonzero_exit: Job exited with an error: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
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- Job identifier:
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soyijujwy3bxt2i5
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- Job identifier:
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riqrygj2uwrtbfau
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- Job identifier:
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pno27thucsctu44q - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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7a765hc7xdkyqkgp - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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wi7qczpxwgltj554 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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augp2uxirkxlkleh - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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akwl2qf6c7iafu3j - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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kfroz53tbz3r54pd - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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2se3ml6u54dmilof - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 10000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format feather
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_prelim.feather
generate_index_dates:
run: r:latest analysis/prelim.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
outputs:
highly_sensitive:
index_dates: output/index_dates.csv
generate_study_population_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax.csv.gz
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format csv.gz
needs:
- generate_index_dates
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_vax.csv.gz
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.csv.gz
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prevax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_stage0.txt
describe_venn: output/not-for-review/describe_venn_prevax.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_vax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_stage0.txt
descrive_venn: output/not-for-review/describe_venn_vax.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_stage0.txt
describe_venn: output/not-for-review/describe_venn_unvax.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
stage1_data_cleaning_all:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R all
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_*.csv
QA_rules: output/review/descriptives/QA_summary_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_*.csv
histograms: output/not-for-review/numeric_histograms_*.svg
highly_sensitive:
cohort: output/input_*.rds
describe_file-input_prevax_stage1:
run: r:latest analysis/describe_file.R input_prevax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_prevax_stage1.txt
describe_file-input_vax_stage1:
run: r:latest analysis/describe_file.R input_vax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_vax_stage1.txt
describe_file-input_unvax_stage1:
run: r:latest analysis/describe_file.R input_unvax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_unvax_stage1.txt
stage2_missing_table1_all:
run: r:latest analysis/descriptives/Stage2_missing_table1.R all
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
Missing_RangeChecks: output/not-for-review/Check_missing_range_*.csv
DateChecks: output/not-for-review/Check_dates_range_*.csv
Descriptive_Table: output/review/descriptives/Table1_*.csv
Timeline
-
Created:
-
Started:
-
Finished:
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Runtime: 60:15:26
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- post-covid-respiratory
- Requested by
- Alex Whitmarsh
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- b580ab0
- Requested actions
-
-
generate_study_population_prevax -
generate_study_population_vax -
generate_study_population_unvax -
preprocess_data_prevax -
preprocess_data_vax -
preprocess_data_unvax -
stage1_data_cleaning_all -
describe_file-input_prevax_stage1 -
describe_file-input_vax_stage1 -
describe_file-input_unvax_stage1 -
stage2_missing_table1_all
-
Code comparison
Compare the code used in this Job Request