Job request: 25054
- Organisation:
- Bennett Institute
- Workspace:
- pharmacy-first-report
- ID:
- 7mw2glsmknsung2p
This page shows the technical details of what happened when the authorised researcher Viveck Kingsley 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:
-
mj7j4psvluaoqhws
Pipeline
Show project.yaml
version: "3.0"
# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
population_size: 1000
actions:
generate_dataset_definition_tables:
run: >
ehrql:v1
generate-dataset analysis/dataset_definition_tables.py
--test-data-file analysis/test_dataset_definition_tables.py
--dummy-data-file dummy_data/pf_tables_dataset.csv
--output output/population/pf_tables.csv.gz
outputs:
highly_sensitive:
cohort: output/population/pf_tables.csv.gz
create_tables:
run: r:v2 analysis/create_tables.R
needs: [generate_dataset_definition_tables]
outputs:
moderately_sensitive:
dataset: output/population/pf_tables.csv
generate_pf_statistics_measures:
run: >
ehrql:v1 generate-measures analysis/measures_definition_pf_descriptive_stats.py
--dummy-tables dummy_tables
--output output/measures/pf_descriptive_stats_measures.csv
outputs:
moderately_sensitive:
measure: output/measures/pf_descriptive_stats_measures.csv
generate_pf_breakdown_measures:
run: >
ehrql:v1 generate-measures analysis/measures_definition_pf_breakdown.py
--output output/measures/pf_breakdown_measures.csv
outputs:
moderately_sensitive:
measure: output/measures/pf_breakdown_measures.csv
generate_pf_med_counts_measures:
run: >
ehrql:v1 generate-measures analysis/measures_definition_pf_med_counts.py
--dummy-tables dummy_tables
--output output/measures/pf_medications_measures.csv
outputs:
moderately_sensitive:
measure: output/measures/pf_medications_measures.csv
tidy_med_measures:
run: r:latest analysis/tidy_measures_med_counts.R
needs: [generate_pf_med_counts_measures]
outputs:
moderately_sensitive:
measure_pf_meds: output/measures/pf_medications_measures_tidy.csv
generate_pf_opensafely_report:
run: >
r:v2 -e 'rmarkdown::render(
"reports/pharmacy_first_report.Rmd",
knit_root_dir = "/workspace",
output_dir = "/workspace/output/report"
)'
needs:
- generate_dataset_definition_tables
- create_tables
- generate_pf_statistics_measures
- generate_pf_breakdown_measures
- generate_pf_med_counts_measures
- tidy_med_measures
outputs:
moderately_sensitive:
html: output/report/pharmacy_first_report.html
pf_demographics: output/report/data/df_demographics_table.csv
pf_breakdowns: output/report/data/df_measures.csv
pf_clinical_conditions: output/report/data/df_clinical_pathways_by_sex.csv
pf_med_counts: output/report/data/df_pf_and_non_pf_med_counts.csv
pf_consultations: output/report/data/df_pf_consultations.csv
pf_descriptive_stats: output/report/data/df_pf_descriptive_stats.csv
pf_counts: output/report/figures/figure1.png
pf_by_sex: output/report/figures/figure2sex.png
pf_by_age: output/report/figures/figure3age.png
pf_by_imd: output/report/figures/figure4imd.png
pf_by_region: output/report/figures/figure5region.png
pf_by_ethnicity: output/report/figures/figure6ethnicity.png
pf_completeness: output/report/figures/figure7.png
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:42
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- pharmacy-first-report
- Requested by
- Viveck Kingsley
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 549e81b
- Requested actions
-
-
generate_pf_opensafely_report
-
Code comparison
Compare the code used in this Job Request