Job request: 19165
- Organisation:
- Bennett Institute
- Workspace:
- opioids-covid-research
- ID:
- bes5m65dxsltigg2
This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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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a2wmqrl7bhfmtfgb - Error:
- cancelled_by_user: Cancelled by user
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- Job identifier:
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k5b6mnxjxu6hssn6 - Error:
- cancelled_by_user: Cancelled by user
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- Job identifier:
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ckbspsg2bgk4vxh7 - Error:
- cancelled_by_user: Cancelled by user
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- Job identifier:
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pw3pisgvmj3xokfq - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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hnjbzkoj7cmiei46 - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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rr7shke2f5woh57w - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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rjiofdbbh27ytqnn - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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zapxgzh4nddypaqe - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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naxwtwk7yeh66fgy - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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3xpcmccwe5x4j4en - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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2l5mgubdkautfhcp - Error:
- cancelled_by_user: Cancelled by user
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- Job identifier:
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kqkvnwgip5ozkled - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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ufnlw32dqhka3hjt - Error:
- cancelled_by_user: Cancelled by user
Pipeline
Show project.yaml
######################################
# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 10000
actions:
generate_dataset_apr22:
run: ehrql:v0 generate-dataset analysis/define_dataset_apr22.py --output output/dataset_apr22.csv.gz
outputs:
highly_sensitive:
cohort: output/dataset_apr22.csv.gz
generate_dataset_may22:
run: ehrql:v0 generate-dataset analysis/define_dataset_may22.py --output output/dataset_may22.csv.gz
outputs:
highly_sensitive:
cohort: output/dataset_may22.csv.gz
generate_dataset_jun22:
run: ehrql:v0 generate-dataset analysis/define_dataset_jun22.py --output output/dataset_jun22.csv.gz
outputs:
highly_sensitive:
cohort: output/dataset_jun22.csv.gz
measures_overall:
run: ehrql:v0 generate-measures analysis/measures_overall.py --output output/measures_overall.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_overall.csv
measures_overall_nocancer:
run: ehrql:v0 generate-measures analysis/measures_overall_nocancer.py --output output/measures_overall_nocancer.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_overall_nocancer.csv
measures_demo:
run: ehrql:v0 generate-measures analysis/measures_demo.py --output output/measures_demo.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_demo.csv
measures_demo_nocancer:
run: ehrql:v0 generate-measures analysis/measures_demo_nocancer.py --output output/measures_demo_nocancer.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_demo_nocancer.csv
measures_type:
run: ehrql:v0 generate-measures analysis/measures_type.py --output output/measures_type.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_type.csv
measures_type_nocancer:
run: ehrql:v0 generate-measures analysis/measures_type_nocancer.py --output output/measures_type_nocancer.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_type_nocancer.csv
measures_sens:
run: ehrql:v0 generate-measures analysis/measures_sens.py --output output/measures_sens.csv
outputs:
moderately_sensitive:
measure_csv: output/measures_sens.csv
# ## Cohort data
# generate_study_population_1:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2018-01-01 to 2018-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_2:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2019-01-01 to 2019-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/input*.csv
# generate_study_population_3:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2020-01-01 to 2020-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/inpu*.csv
# generate_study_population_4:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2021-01-01 to 2021-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/inp*.csv
# generate_study_population_5:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2022-01-01 to 2022-03-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/in*.csv
# ## Ethnicity
# generate_ethnicity_cohort:
# run: >
# cohortextractor:latest generate_cohort
# --study-definition study_definition_ethnicity
# outputs:
# highly_sensitive:
# cohort: output/input_ethnicity.csv
# # Data processing ----
# ## Add ethnicity
# join_cohorts:
# run: >
# cohort-joiner:v0.0.48
# --lhs output/input_*.csv
# --rhs output/input_ethnicity.csv
# --output-dir output/data
# needs: [generate_study_population_1, generate_study_population_2,
# generate_study_population_5, generate_study_population_3,
# generate_study_population_4, generate_ethnicity_cohort]
# outputs:
# highly_sensitive:
# cohort: output/data/input_*.csv
# ## Generate measures - full population
# generate_measures:
# run: >
# cohortextractor:latest generate_measures
# --study-definition study_definition
# --output-dir output/data
# needs: [join_cohorts]
# outputs:
# moderately_sensitive:
# measure_csv: output/data/measure_*.csv
## Process data - time series
process_data_ts:
run: r:latest analysis/process/process_data_ts.R
needs: [measures_overall, measures_overall_nocancer, measures_demo, measures_demo_nocancer, measures_type, measures_type_nocancer, measures_sens]
outputs:
moderately_sensitive:
ts_csv: output/processed/final_*.csv
## Process data - table
process_data_table:
run: r:latest analysis/process/process_data_table.R
needs: [generate_dataset_apr22, generate_dataset_may22, generate_dataset_jun22]
outputs:
highly_sensitive:
table_csv: output/processed/final*.csv
# # Results ---
# ## Time series
# timeseries:
# run: r:latest analysis/descriptive/time_series_stand.R
# needs: [process_data_ts]
# outputs:
# moderately_sensitive:
# table: output/time series/ts_*.csv
# ## Time series graphs
# # graphs:
# # run: r:latest analysis/descriptive/graphs.R
# # needs: [timeseries]
# # outputs:
# # moderately_sensitive:
# # plot: output/time series/graphs/graph*.png
# ## Table
table:
run: r:latest analysis/descriptive/table_stand.R
needs: [process_data_table]
outputs:
moderately_sensitive:
table: output/tables/table_*.csv
Timeline
-
Created:
-
Started:
-
Runtime: 00:28:15
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- opioids-covid-research
- Requested by
- Andrea Schaffer
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 71403f9
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request