Job request: 21794
- Organisation:
- Bennett Institute
- Workspace:
- waiting-list
- ID:
- 5pf2n55h7rdi6wg4
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:
-
tqdsu446pexen4k4
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
##### Dataset definitions #####
# Closed (completed) RTT pathways
generate_dataset_clockstops:
run: ehrql:v1 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:v1 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 missing end date ####
# generate_dataset_clockstops_missing:
# run: ehrql:v1 generate-dataset analysis/dataset_definition_clockstops_missing.py
# --output output/data/dataset_clockstops_missing.csv.gz
# outputs:
# highly_sensitive:
# cohort: output/data/dataset_clockstops_missing.csv.gz
# checks_missing_clockstops:
# run: r:latest analysis/clockstops/checks_missing_clockstops.R
# needs: [generate_dataset_clockstops_missing]
# outputs:
# moderately_sensitive:
# data: output/clockstops/check_missing_dates.csv
#### 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
checks_overall_clockstops:
run: r:latest analysis/clockstops/checks_overall_clockstops.R
needs: [measures_checks]
outputs:
moderately_sensitive:
data: output/clockstops/chec*.csv
##### Opioid measures - closed pathways #####
measures_any_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid.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.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.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.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.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
# measures_opioid_weeks_during:
# run: ehrql:v1 generate-measures analysis/measures_opioid_weeks_during.py
# --output output/measures/measures_opioid_weeks_during.csv
# --dummy-data-file dummy/dummy_opioid_weeks_during.csv
# outputs:
# moderately_sensitive:
# measure_csv: output/measures/measures_opioid_weeks_during.csv
# measures_opioid_weeks_post:
# run: ehrql:v1 generate-measures analysis/measures_opioid_weeks_post.py
# --output output/measures/measures_opioid_weeks_post.csv
# --dummy-data-file dummy/dummy_opioid_weeks_post.csv
# outputs:
# moderately_sensitive:
# measure_csv: output/measures/measures_opioid_weeks_post.csv
# opioids_by_week_group:
# run: r:latest analysis/clockstops/opioids_by_week_group.R
# needs: [measures_opioid_weeks_during, measures_opioid_weeks_post]
# outputs:
# moderately_sensitive:
# data: output/clockstops/opioid_by_week_group.csv
# plots: output/clockstops/opioid_by_week_group*.png
##### 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_clockstops:
run: r:latest analysis/clockstops/final_cohort_clockstops.R
needs: [generate_dataset_clockstops]
outputs:
highly_sensitive:
cohort: output/data/cohort*.csv.gz
moderately_sensitive:
exclusions1: output/clockstops/cohort_full_exclusions.csv
exclusions2: output/clockstops/exclude_ortho.csv
ortho_clockstops_wait_time:
run: r:latest analysis/clockstops/ortho_clockstops_wait_time.R
needs: [final_cohort_clockstops]
outputs:
moderately_sensitive:
data1: output/clockstops/rtt_dates_ortho.csv
data2: output/clockstops/wait_time_pcent_ortho.csv
data3: output/clockstops/wait_time_ortho.csv
data4: output/clockstops/wait_by_group_ortho.csv
ortho_clockstops_freq_dist:
run: r:latest analysis/clockstops/ortho_clockstops_freq_dist.R
needs: [final_cohort_clockstops]
outputs:
moderately_sensitive:
data1: output/clockstops/cat_var_dist_ortho.csv
ortho_clockstops_prescribing:
run: r:latest analysis/clockstops/ortho_clockstops_prescribing.R
needs: [final_cohort_clockstops]
outputs:
moderately_sensitive:
data1: output/clockstops/med_by_period_ortho.csv
# full_stats_clockstops:
# run: r:latest analysis/clockstops/full_stats_clockstops.R
# needs: [final_cohort_clockstops]
# outputs:
# moderately_sensitive:
# data1: output/clockstops/rtt_dates_full.csv
# data2: output/clockstops/cat_var_dist_full.csv
# data3: output/clockstops/wait_time_pcent_full.csv
# data4: output/clockstops/wait_time_full.csv
# data5: output/clockstops/med_by_period_full.csv
# data6: output/clockstops/wait_by_group_full.csv
# plot1: output/clockstops/wait_time_full.png
# plot2: output/clockstops/rtt_dates_full.png
######################################################################################
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:48
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
- 6467662
- Requested actions
-
-
ortho_clockstops_prescribing
-
Code comparison
Compare the code used in this Job Request