Job request: 1447
- Organisation:
- Workspace:
- onlineconsultations_runmaster
- ID:
- beknkyejmdhvwrg3
This page shows the technical details of what happened when the authorised researcher Martina Fonseca 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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e5wfublwtj3rvwyk
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- Job identifier:
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mayf66ij44tmq43c - Error:
- nonzero_exit: Job exited with an error code
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- Job identifier:
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44ipjsuafy3mlqcd - Error:
- nonzero_exit: Job exited with an error code
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- Job identifier:
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l7h2jqcoypvjddo3 - Error:
- nonzero_exit: Job exited with an error code
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- Job identifier:
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4xnbtlh35es7pyyn - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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borzgig6iompnpwy - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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iraquvoae3nbbds5 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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5mga4uyix5bapn3t - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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ixxxmxkn6u5pix2j - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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pt2sihk4daiqgwsw - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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jpc4rbmvc6me3hee - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_cohorts_main:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ori
outputs:
highly_sensitive:
cohort: output/input_ori.csv
run_model:
run: r:latest analysis/01-createSDtables.R
needs: [generate_cohorts_main]
outputs:
moderately_sensitive:
log: logs/log-01-createSDtables.txt
#gtpng1: output/tables/gt_ocpop.png
#gtpng2: output/tables/gt_gpcpop.png
rdata1: output/tables/gt_ocpop.RData
rdata2: output/tables/gt_gpcpop.RData
#tb01: output/tables/tb01_gpcr_region.csv
#tb02: output/tables/tb02_gpcr_stp.csv # guidance says to not output identifiable regions
tb04: output/tables/tb04_gpcr_agesex.csv
tb05: output/tables/tb05_gpcr_ethnicity.csv
tb06: output/tables/tb06_gpcr_ruc.csv
tb07: output/tables/tb07_gpcr_care.csv
tb08: output/tables/tb08_gpcr_dis.csv
tb09: output/tables/tb09_gpcr_imd.csv
# https://docs.opensafely.org/en/latest/measures/
generate_cohorts_long:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/measures
outputs:
highly_sensitive:
cohort: output/measures/input_measures_bycode_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures_bycode --output-dir=output/measures
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
run_model_long:
run: r:latest analysis/03-createnattrends_codes.R
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
log: logs/log-03-createnattrends.txt
tb01: output/tables/sc03_tb01_nattrends.csv
fig01: output/plots/sc03_fig01_nattrends.svg
fig02: output/plots/sc03_fig02_nattrends.svg
fig03: output/plots/sc03_fig03_pracnatcoverage.svg
fig04: output/plots/sc03_fig04_pracbyregcoverage.svg
run_model_measures:
run: r:latest analysis/02-createtemporal.R
needs: [generate_cohorts_long,generate_measures]
outputs:
moderately_sensitive:
log: logs/log-02-createtemporal.txt
red_measures: output/tables/redacted_*.csv
#tb01: output/measures_gpc_pop.csv # redundant into. omit output
fig01: output/plots/plot_overall_gpc_pop.svg
#figall: output/plots/plot_each_*_practice.svg
figquant: output/plots/plot_quantiles_*_practice.svg
# run_model_measuresDEBUG:
# run: r:latest analysis/02-createtemporal_debug.R
# needs: [generate_cohorts_long,generate_measures]
# outputs:
# moderately_sensitive:
# log: logs/log-02-createtemporal-debug.txt
# #tb01: output/measures_gpc_pop_debug.csv
# #fig01: output/plots/plot_overall_gpc_pop_debug.svg
# #figall: output/plots/plot_each_debug_*_practice.svg
# #figquant: output/plots/plot_quantiles_debug_*_practice.svg
# #figquant2: output/plots/plot_quantiles2_debug_*_practice.svg
#run_model_redactedmeasures:
# run: r:latest analysis/02a-createredactedmeasure.R
# needs: [generate_cohorts_long,generate_measures]
# outputs:
# moderately_sensitive:
# log: logs/log-02a-createredactedmeasure.txt
# red_measures: output/tables/redacted2a_*.csv
### SRO template pipeline
SROtem_generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_*.csv
SROtem_generate_study_population_practice_count:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_practice_count.csv
SROtem_generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [SROtem_generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measure_*.csv
SROtem_get_patient_count:
run: python:latest python analysis/SROtem_get_patients_counts.py
needs: [SROtem_generate_study_population]
outputs:
moderately_sensitive:
text: output/patient_count.json
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/SRO-Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [SROtem_generate_measures, SROtem_generate_study_population_practice_count]
outputs:
moderately_sensitive:
notebook: output/SRO-Notebook.html
Timeline
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Created:
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Started:
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Finished:
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Runtime: 00:53:47
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- onlineconsultations_runmaster
- Requested by
- Martina Fonseca
- Branch
- master
- Force run dependencies
- Yes
- Git commit hash
- 1996903
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request