Job request: 17105
- Organisation:
- Bennett Institute
- Workspace:
- pincer-measures
- ID:
- 4x2an4hptdtud5o6
This page shows the technical details of what happened when the authorised researcher Rose Higgins 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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vusqqw25ripctuy3
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- Job identifier:
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vcrqikyc4bmj4733
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- Job identifier:
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22elcf7r32wsbqtn
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- Job identifier:
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vxtvno4ljtlhxxsr
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- Job identifier:
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xxp5ozh5zfyy37yn
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- Job identifier:
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nmnxxwaj7axpmfiu
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- Job identifier:
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s2hlbwzqukr7c3px
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- Job identifier:
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wikoxb3rylyrywe4
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- Job identifier:
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ofwnwxxhrhtiplyu
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 5000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2020-05-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-01 to 2021-02-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/input*.feather
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-01 to 2021-09-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/inpu*.feather
generate_study_population_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-10-01 to 2022-02-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/in*.feather
generate_study_population_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-03-01 to 2023-03-01 by month" --output-format feather
outputs:
highly_sensitive:
cohort: output/i*.feather
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
join_ethnicity_region:
run: python:latest python analysis/join_ethnicity_region.py
needs:
[
generate_study_population_1,
generate_study_population_2,
generate_study_population_3,
generate_study_population_4,
generate_study_population_5,
generate_study_population_ethnicity,
]
outputs:
highly_sensitive:
cohort: output/inp*.feather
filter_population:
run: python:latest python analysis/filter_population.py
needs: [join_ethnicity_region]
outputs:
highly_sensitive:
cohort: output/input_filtered_*.feather
check_asthma:
run: python:latest python analysis/asthma_check.py
needs: [filter_population]
outputs:
moderately_sensitive:
check: output/asthma_check.json
calculate_numerators:
run: python:latest python analysis/calculate_numerators.py
needs: [filter_population]
outputs:
highly_sensitive:
cohort: output/indicator_e_f_*.feather
calculate_composite_indicators:
run: python:latest python analysis/composite_indicators.py
needs: [calculate_numerators, filter_population]
outputs:
moderately_sensitive:
counts: output/*_composite_measure.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [filter_population]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
generate_measures_demographics:
run: python:latest python analysis/calculate_measures.py
needs: [calculate_numerators, filter_population]
outputs:
moderately_sensitive:
counts: output/indicator_measure_*.csv
measure_csv: output/measure*_rate.csv
demographics: output/demographics_summary_*.csv
produce_stripped_measures:
run: python:latest python analysis/stripped_measures.py
needs:
[
generate_measures,
generate_measures_demographics
]
outputs:
moderately_sensitive:
measures: output/measure_stripped_*.csv
generate_summary_counts:
run: python:latest python analysis/summary_statistics.py
needs:
[
filter_population,
generate_measures,
generate_measures_demographics,
calculate_numerators,
]
outputs:
moderately_sensitive:
patient_count: output/patient_count_*.json
practice_count: output/practice_count_*.json
summary: output/indicator_summary_statistics_*.json
generate_plots:
run: python:latest python analysis/plot_measures.py
needs:
[
generate_measures,
generate_measures_demographics,
calculate_composite_indicators,
]
outputs:
moderately_sensitive:
counts: output/figures/plot_*.jpeg
combined: output/figures/combined_plot_*.png
demographics: output/demographic_aggregates.csv
medians: output/medians.json
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_plots, generate_summary_counts]
outputs:
moderately_sensitive:
notebook: output/report.html
generate_notebook_updating:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_plots, generate_summary_counts]
outputs:
moderately_sensitive:
notebook: output/report_updating.html
generate_dem_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/demographic_report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_plots]
outputs:
moderately_sensitive:
notebook: output/demographic_report.html
plot_Q1_comparisons:
run: r:latest analysis/generate_demographic_slope_plot.R
needs: [generate_plots]
outputs:
moderately_sensitive:
plots: output/figures/SLOPE_*.png
run_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml
test_population:
run: python:latest python analysis/test_population.py
needs: [filter_population]
outputs:
moderately_sensitive:
counts: output/population_counts.csv
count: output/patient_count_check.json
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 33:23:26
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- pincer-measures
- Requested by
- Rose Higgins
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 421f8d7
- Requested actions
-
-
generate_study_population_5
-
join_ethnicity_region
-
filter_population
-
calculate_numerators
-
calculate_composite_indicators
-
generate_measures
-
generate_summary_counts
-
generate_plots
-
generate_notebook_updating
-
Code comparison
Compare the code used in this Job Request