Job request: 22568
- Organisation:
- Bennett Institute
- Workspace:
- waiting-list
- ID:
- roilnzbok5rrd35x
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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37sg3ddunbsd55kb
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- Job identifier:
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dvkbwb6alnjatnkm - Error:
- nonzero_exit: Job exited with an error
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- Job identifier:
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imzcmbb7g3lkuhla
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- Job identifier:
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6hswbn3vwfdfarx7
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- Job identifier:
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u6cshhhs2glia7j6
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- Job identifier:
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g2ktps6uk6egncjo
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- Job identifier:
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oo74t5c7dshkbzcb
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- Job identifier:
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rqhgqvp5i2bca65f
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- Job identifier:
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fawoz262g7licdra - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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uhyyzz7cmyvu267t - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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3z6udch56ikawyy3 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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c3ni44namhr7aeaa - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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sh5kgfgvutciuclp - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
##### Dataset definitions #####
# Closed (completed) RTT pathways
generate_dataset_full:
run: ehrql:v1 generate-dataset analysis/dataset_definition_full.py
--output output/data/dataset_full.arrow
#--dummy-data-file dummy/dummy_ortho_clockstops.arrow
outputs:
highly_sensitive:
cohort: output/data/dataset_full.arrow
# Closed (completed) RTT pathways
generate_dataset_ortho:
run: ehrql:v1 generate-dataset analysis/dataset_definition_ortho.py
--output output/data/dataset_ortho.arrow
#--dummy-data-file dummy/dummy_ortho_clockstops.arrow
outputs:
highly_sensitive:
cohort: output/data/dataset_ortho.arrow
#### Check number of pathways over time ####
measures_checks:
run: ehrql:v1 generate-measures analysis/measures_checks.py
--output output/measures/measures_checks.csv
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_checks.csv
##### Opioid measures - closed pathways #####
measures_any_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_any_opioid.csv
--
--codelist "opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_any_opioid.csv
measures_long_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_long_opioid.csv
--
--codelist "long_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_long_opioid.csv
measures_short_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_short_opioid.csv
--
--codelist "short_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_short_opioid.csv
measures_weak_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_weak_opioid.csv
--
--codelist "weak_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_weak_opioid.csv
measures_strong_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_strong_opioid.csv
--
--codelist "strong_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_strong_opioid.csv
# Combine measures
opioids_by_week:
run: r:latest analysis/clockstops/opioids_by_week.R
needs: [measures_any_opioid, measures_weak_opioid, measures_strong_opioid, measures_long_opioid, measures_short_opioid]
outputs:
moderately_sensitive:
data: output/clockstops/opioid*.csv
##### Analysis - closed pathways #####
# checks_cohort_clockstops:
# run: r:latest analysis/clockstops/checks_cohort_clockstops.R
# needs: [generate_dataset_clockstops]
# outputs:
# moderately_sensitive:
# data: output/clockstops/check*.csv
final_cohort_exclusions:
run: r:latest analysis/clockstops/final_cohort_exclusions.R
needs: [generate_dataset_full, generate_dataset_ortho]
outputs:
highly_sensitive:
cohort: output/data/cohort*.csv.gz
moderately_sensitive:
#exclusions1: output/clockstops/cohort_full_exclusions.csv
exclusions2: output/clockstops/exclude*.csv
wait_time:
run: r:latest analysis/clockstops/wait_time.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/rtt_dates.csv
data2: output/clockstops/wait_by_group.csv
data3: output/clockstops/num_weeks.csv
frequency_tables_all:
run: r:latest analysis/clockstops/frequency_tables_all.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/cat_var_dist_ortho.csv
frequency_tables_routine:
run: r:latest analysis/clockstops/frequency_tables_routine.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/cat_var_dist_prior.csv
data2: output/clockstops/age_stats.csv
check_no_admission:
run: r:latest analysis/clockstops/check_no_admission.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/check_no_admission.csv
opioid_prescribing:
run: r:latest analysis/clockstops/opioid_prescribing.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/med_by_period.csv
data2: output/clockstops/med_by_period_wait.csv
data3: output/clockstops/total_rx_wait.csv
######################################################################################
Timeline
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Created:
-
Started:
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Finished:
-
Runtime: 41:55:19
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- waiting-list
- Requested by
- Andrea Schaffer
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 805f359
- Requested actions
-
-
generate_dataset_full -
generate_dataset_ortho -
measures_any_opioid -
measures_long_opioid -
measures_short_opioid -
measures_weak_opioid -
measures_strong_opioid -
opioids_by_week -
final_cohort_exclusions -
wait_time -
frequency_tables_all -
frequency_tables_routine -
opioid_prescribing
-
Code comparison
Compare the code used in this Job Request