Job request: 21023
- Organisation:
- Bennett Institute
- Workspace:
- waiting-list
- ID:
- oj5fn24u6kt4wajc
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
-
- Job identifier:
-
tocbuqpagdhrgkgq
-
- Job identifier:
-
zq5cvajfbncpw3pq
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
##### Dataset definitions #####
# Closed (completed) RTT pathways
generate_dataset_clockstops:
run: ehrql:v0 generate-dataset analysis/dataset_definition_clockstops.py
--output output/data/dataset_clockstops.csv.gz
outputs:
highly_sensitive:
cohort: output/data/dataset_clockstops.csv.gz
# Open (incomplete) RTT pathways
# generate_dataset_openpathways:
# run: ehrql:v0 generate-dataset analysis/dataset_definition_openpathways.py
# --output output/data/dataset_openpathways.csv.gz
# outputs:
# highly_sensitive:
# cohort: output/data/dataset_openpathways.csv.gz
#### Check number of pathways over time ####
measures_checks:
run: ehrql:v0 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:v0 generate-measures analysis/measures_any_opioid.py
--output output/measures/measures_any_opioid.csv
--dummy-data-file dummy/dummy_any_opioid.csv
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_any_opioid.csv
measures_hi_opioid:
run: ehrql:v0 generate-measures analysis/measures_hi_opioid.py
--output output/measures/measures_hi_opioid.csv
--dummy-data-file dummy/dummy_hi_opioid.csv
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_hi_opioid.csv
# opioids_by_week:
# run: r:latest analysis/clockstops/opioids_by_week.R
# needs: [measures_any_opioid, measures_hi_opioid]
# outputs:
# moderately_sensitive:
# data: output/clockstops/opioid*.csv
# plots: output/clockstops/plo*.png
##### Analysis - closed pathways #####
checks_clockstops:
run: r:latest analysis/clockstops/checks_clockstops.R
needs: [generate_dataset_clockstops, measures_checks]
outputs:
moderately_sensitive:
data: output/clockstops/check*.csv
# final_cohort_clockstops:
# run: r:latest analysis/clockstops/final_cohort_clockstops.R
# needs: [generate_dataset_clockstops]
# outputs:
# highly_sensitive:
# cohort: output/data/cohort*.csv.gz
# full_stats_clockstops:
# run: r:latest analysis/clockstops/full_stats_clockstops.R
# needs: [final_cohort_clockstops]
# outputs:
# moderately_sensitive:
# data1: output/clockstops/rtt_dates.csv
# data2: output/clockstops/cat_var_dist.csv
# data3: output/clockstops/wait_time_pcent.csv
# data4: output/clockstops/wait_time.csv
# data5: output/clockstops/med_counts_by_period.csv
# plots: output/clockstops/plot_*.png
# ortho_stats_clockstops:
# run: r:latest analysis/clockstops/ortho_stats_clockstops.R
# needs: [final_cohort_clockstops]
# outputs:
# moderately_sensitive:
# data1: output/clockstops/rtt_dates_ortho.csv
# data2: output/clockstops/cat_var_dist_ortho.csv
# data3: output/clockstops/wait_time_pcent_ortho.csv
# data4: output/clockstops/wait_time_ortho.csv
# data5: output/clockstops/med_counts_by_period_ortho.csv
# plots: output/clockstops/plot*.png
##### Analysis - open pathways #####
# checks_openpathways:
# run: r:latest analysis/openpathways/checks_openpathways.R
# needs: [generate_dataset_openpathways]
# outputs:
# moderately_sensitive:
# data: output/openpathways/*.csv
# final_cohort_openpathways:
# run: r:latest analysis/openpathways/final_cohort_openpathways.R
# needs: [generate_dataset_openpathways]
# outputs:
# highly_sensitive:
# cohort: output/data/cohor*.csv.gz
# full_stats_openpathways:
# run: r:latest analysis/openpathways/full_stats_openpathways.R
# needs: [final_cohort_openpathways]
# outputs:
# moderately_sensitive:
# data1: output/openpathways/rtt_dates_open.csv
# data2: output/openpathways/cat_var_dist_open.csv
# data3: output/openpathways/wait_time_pcent_open.csv
# data4: output/openpathways/wait_time_open.csv
# data5: output/openpathways/med_counts_by_period_open.csv
# plots: output/openpathways/plot_*.png
# ortho_stats_openpathways:
# run: r:latest analysis/openpathways/ortho_stats_openpathways.R
# needs: [final_cohort_openpathways]
# outputs:
# moderately_sensitive:
# data1: output/openpathways/rtt_dates_ortho_open.csv
# data2: output/openpathways/cat_var_dist_ortho_open.csv
# data3: output/openpathways/wait_time_pcent_ortho_open.csv
# data4: output/openpathways/wait_time_ortho_open.csv
# data5: output/openpathways/med_counts_by_period_ortho_open.csv
# plots: output/openpathways/plot*.png
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:30:54
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- waiting-list
- Requested by
- Andrea Schaffer
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 575e552
- Requested actions
-
-
measures_checks
-
checks_clockstops
-
Code comparison
Compare the code used in this Job Request