Job request: 14703
- Organisation:
- DataLab
- Workspace:
- sro-key-measures-dashboard
- ID:
- pzwq2ku4tuot7aje
This page shows the technical details of what happened when authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; 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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Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 1000
actions:
codelist_report_alt:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-alanine-aminotransferase-alt-tests.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/alt
outputs:
moderately_sensitive:
table: output/alt/counts_per_*.csv
list_sizes: output/alt/list_sizes.csv
patient_count_table: output/alt/patient_count.csv
codelist_report_asthma:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-asthma-annual-review-qof.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/asthma
outputs:
moderately_sensitive:
table: output/asthma/counts_per_*.csv
list_sizes: output/asthma/list_sizes.csv
patient_count_table: output/asthma/patient_count.csv
codelist_report_cholesterol:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-cholesterol-tests.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/cholesterol
outputs:
moderately_sensitive:
table: output/cholesterol/counts_per_*.csv
list_sizes: output/cholesterol/list_sizes.csv
patient_count_table: output/cholesterol/patient_count.csv
codelist_report_copd:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-chronic-obstructive-pulmonary-disease-copd-review-qof.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/copd
outputs:
moderately_sensitive:
table: output/copd/counts_per_*.csv
list_sizes: output/copd/list_sizes.csv
patient_count_table: output/copd/patient_count.csv
codelist_report_hba1c:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-glycated-haemoglobin-hba1c-tests.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/hba1c
outputs:
moderately_sensitive:
table: output/hba1c/counts_per_*.csv
list_sizes: output/hba1c/list_sizes.csv
patient_count_table: output/hba1c/patient_count.csv
codelist_report_medication_review:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-care-planning-medication-review-simple-reference-set-nhs-digital.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/medication_review
outputs:
moderately_sensitive:
table: output/medication_review/counts_per_*.csv
list_sizes: output/medication_review/list_sizes.csv
patient_count_table: output/medication_review/patient_count.csv
codelist_report_qrisk2:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-cvd-risk-assessment-score-qof.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/qrisk2/
outputs:
moderately_sensitive:
table: output/qrisk2/counts_per_*.csv
list_sizes: output/qrisk2/list_sizes.csv
patient_count_table: output/qrisk2/patient_count.csv
codelist_report_rbc:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-red-blood-cell-rbc-tests.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/rbc
outputs:
moderately_sensitive:
table: output/rbc/counts_per_*.csv
list_sizes: output/rbc/list_sizes.csv
patient_count_table: output/rbc/patient_count.csv
codelist_report_sodium:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-sodium-tests-numerical-value.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/sodium
outputs:
moderately_sensitive:
table: output/sodium/counts_per_*.csv
list_sizes: output/sodium/list_sizes.csv
patient_count_table: output/sodium/patient_count.csv
codelist_report_systolic_bp:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-systolic-blood-pressure-qof.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/systolic_bp
outputs:
moderately_sensitive:
table: output/systolic_bp/counts_per_*.csv
list_sizes: output/systolic_bp/list_sizes.csv
patient_count_table: output/systolic_bp/patient_count.csv
codelist_report_tsh:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelists/opensafely-thyroid-stimulating-hormone-tsh-testing.csv
--start-date=2019-01-01
--end-date=2023-01-17
--output-dir output/tsh
outputs:
moderately_sensitive:
table: output/tsh/counts_per_*.csv
list_sizes: output/tsh/list_sizes.csv
patient_count_table: output/tsh/patient_count.csv
measures:
run: >
python:latest python analysis/generate_measures.py
--input-dir output
--low-count-threshold 10
--rounding-base 5
--rounding-base-practice-count 10
needs: [codelist_report_alt,
codelist_report_asthma,
codelist_report_cholesterol,
codelist_report_copd,
codelist_report_hba1c,
codelist_report_medication_review,
codelist_report_qrisk2,
codelist_report_rbc,
codelist_report_sodium,
codelist_report_systolic_bp,
codelist_report_tsh]
outputs:
moderately_sensitive:
measure: output/*/measure_counts_per_week_per_practice.csv
events_count_table: output/*/event_counts.csv
practice_count_table: output/*/practice_count.csv
top_5_tables:
run: >
python:latest python analysis/top_codes_table.py
--input-dir output
--low-count-threshold 10
--rounding-base 10
needs: [codelist_report_alt,
codelist_report_asthma,
codelist_report_cholesterol,
codelist_report_copd,
codelist_report_hba1c,
codelist_report_medication_review,
codelist_report_qrisk2,
codelist_report_rbc,
codelist_report_sodium,
codelist_report_systolic_bp,
codelist_report_tsh,
measures]
outputs:
moderately_sensitive:
table: output/*/top_5_code_table.csv
table_count: output/*/top_5_code_table_with_count.csv
deciles_charts_alt:
run: >
deciles-charts:v0.0.33
--input-files output/alt/measure_counts_per_week_per_practice.csv
--output-dir output/alt
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/alt/deciles_*.*
deciles_charts_asthma:
run: >
deciles-charts:v0.0.24
--input-files output/asthma/measure_counts_per_week_per_practice.csv
--output-dir output/asthma
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/asthma/deciles_*.*
deciles_charts_cholesterol:
run: >
deciles-charts:v0.0.24
--input-files output/cholesterol/measure_counts_per_week_per_practice.csv
--output-dir output/cholesterol
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/cholesterol/deciles_*.*
deciles_charts_copd:
run: >
deciles-charts:v0.0.24
--input-files output/copd/measure_counts_per_week_per_practice.csv
--output-dir output/copd
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/copd/deciles_*.*
deciles_charts_hba1c:
run: >
deciles-charts:v0.0.24
--input-files output/hba1c/measure_counts_per_week_per_practice.csv
--output-dir output/hba1c
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/hba1c/deciles_*.*
deciles_charts_medication_review:
run: >
deciles-charts:v0.0.24
--input-files output/medication_review/measure_counts_per_week_per_practice.csv
--output-dir output/medication_review
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/medication_review/deciles_*.*
deciles_charts_qrisk2:
run: >
deciles-charts:v0.0.24
--input-files output/qrisk2/measure_counts_per_week_per_practice.csv
--output-dir output/qrisk2
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/qrisk2/deciles_*.*
deciles_charts_rbc:
run: >
deciles-charts:v0.0.24
--input-files output/rbc/measure_counts_per_week_per_practice.csv
--output-dir output/rbc
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/rbc/deciles_*.*
deciles_charts_sodium:
run: >
deciles-charts:v0.0.24
--input-files output/sodium/measure_counts_per_week_per_practice.csv
--output-dir output/sodium
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/sodium/deciles_*.*
deciles_charts_systolic_bp:
run: >
deciles-charts:v0.0.24
--input-files output/systolic_bp/measure_counts_per_week_per_practice.csv
--output-dir output/systolic_bp
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/systolic_bp/deciles_*.*
deciles_charts_tsh:
run: >
deciles-charts:v0.0.24
--input-files output/tsh/measure_counts_per_week_per_practice.csv
--output-dir output/tsh
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [measures]
outputs:
moderately_sensitive:
deciles_charts: output/tsh/deciles_*.*
generate_notebook_updating:
run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs:
[
measures,
top_5_tables,
deciles_charts_alt,
deciles_charts_asthma,
deciles_charts_cholesterol,
deciles_charts_copd,
deciles_charts_hba1c,
deciles_charts_medication_review,
deciles_charts_qrisk2,
deciles_charts_rbc,
deciles_charts_sodium,
deciles_charts_systolic_bp,
deciles_charts_tsh
]
outputs:
moderately_sensitive:
notebook: output/sentinel_measures_updating.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:18:37
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- sro-key-measures-dashboard
- Requested by
- Louis Fisher
- Branch
- updating-report-using-interactive
- Force run dependencies
- No
- Git commit hash
- b9dc8e0
- Requested actions
-
-
measures
-
deciles_charts_alt
-
deciles_charts_asthma
-
deciles_charts_cholesterol
-
deciles_charts_copd
-
deciles_charts_hba1c
-
deciles_charts_medication_review
-
deciles_charts_qrisk2
-
deciles_charts_rbc
-
deciles_charts_sodium
-
deciles_charts_systolic_bp
-
deciles_charts_tsh
-
generate_notebook_updating
-