Job request: 9318
- Organisation:
- Bennett Institute
- Workspace:
- covid-vaccine-preliminary-study-master
- ID:
- rhr642euj7rd24pl
This page shows the technical details of what happened when the authorised researcher Lisa Hopcroft 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:
-
bdrvrmbzkftevpud
-
- Job identifier:
-
dpmodkyuglk3656k
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
# dummy population size must be at least 50000 to ensure the STP analysis can run successfully
actions:
### NB. THIS NEED ONLY BE RUN WHEN WE WANT TO REGENERATE COVERAGE STATISTICS
generate_whole_cohort_to_calculate_coverage:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ALL --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_ALL.csv.gz
calculate_stp_coverage:
run: python:latest lib/calculate_stp_coverage.py
needs: [generate_whole_cohort_to_calculate_coverage]
outputs:
moderately_sensitive:
coverage_calculation: lib/stp_tpp-coverage_total.csv
# generate_delivery_cohort:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/input_delivery.csv.gz
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
# needs: [calculate_stp_coverage, generate_delivery_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/population_characteristics.html
# ### first, second, third/booster doses
# figures: interim-outputs/figures/*
# tables: interim-outputs/tables/*
# # stp_tables: interim-outputs/stp/tables/*.csv
# fig_csvs_1: output/machine_readable_outputs/figure_csvs/*ethnicity*.csv
# fig_csvs_2: output/machine_readable_outputs/figure_csvs/*imd*.csv
# fig_csvs_3: output/machine_readable_outputs/figure_csvs/*psychosis*.csv
# fig_csvs_4: output/machine_readable_outputs/figure_csvs/*LD_*.csv
# fig_csvs_5: output/machine_readable_outputs/figure_csvs/*eligible*.csv
# text: interim-outputs/text/*
# generate_simple_report:
# run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --template basic --output=/workspace/output/opensafely_vaccine_report_overall_simple.html --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_delivery_cohort, generate_notebook]
# outputs:
# moderately_sensitive:
# notebook: output/opensafely_vaccine_report_overall_simple.html
# csvs: output/machine_readable_outputs/table_csvs/*
# generate_report_second_doses:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_notebook]
# outputs:
# moderately_sensitive:
# notebook: output/second_doses.html
# tables: output/machine_readable_outputs/second_doses/*.csv
# generate_report_third_doses:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/booster-third-doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_notebook]
# outputs:
# moderately_sensitive:
# notebook: output/booster-third-doses.html
# tables: output/machine_readable_outputs/third_doses/*.csv
# generate_u16_cohort:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_u16 --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/input_delivery_u16.csv.gz
# generate_u16_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics_u16.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
# needs: [calculate_stp_coverage, generate_u16_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/population_characteristics_u16.html
# figures: interim-outputs/u16/figures/*
# tables: interim-outputs/u16/tables/*
# fig_csvs: output/machine_readable_outputs/figure_csvs/*_u16*.csv
# text: interim-outputs/u16/text/*
# generate_u16_simple_report:
# run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/first_dose_u16.ipynb --execute --to html --template basic --output=/workspace/output/first_dose_u16.html --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_u16_cohort, generate_u16_notebook]
# outputs:
# moderately_sensitive:
# notebook: output/first_dose_u16.html
# csvs: output/machine_readable_outputs/table_csvs/*_u16*.csv
# generate_u16_report_second_doses:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses_u16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_u16_notebook]
# outputs:
# moderately_sensitive:
# notebook: output/second_doses_u16.html
# tables: output/machine_readable_outputs/second_doses/*_u16*.csv
# # generate_u16_report_third_doses:
# # run: jupyter:latest jupyter nbconvert /workspace/notebooks/booster-third-doses_u16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# # needs: [generate_u16_notebook]
# # outputs:
# # moderately_sensitive:
# # notebook: output/booster-third-doses_u16.html
# # tables: output/machine_readable_outputs/third_doses/*_u16*.csv
generate_booster_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_boosters --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_delivery_boosters.csv.gz
generate_booster_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics_boosters.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
needs: [calculate_stp_coverage, generate_booster_cohort]
outputs:
moderately_sensitive:
# notebook: output/population_characteristics_boosters.html
# figures_boosters: interim-outputs/spring_boosters/figures/*
# tables_boosters: interim-outputs/spring_boosters/tables/*
# fig_csvs_boosters: output/machine_readable_outputs/figure_csvs/*_spring_boosters*.csv
# text_boosters: interim-outputs/spring_boosters/text/*
test_pickles: interim-outputs/TEST_*.pickle
test_csvs: interim-outputs/TEST_*.csv
debug_booster_data:
run: python:latest analysis/debug_booster_data.py
needs: [generate_booster_notebook]
outputs:
moderately_sensitive:
coverage_calculation: interim-outputs/debug.txt
generate_spring_booster_report:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/spring-boosters.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_booster_notebook]
outputs:
moderately_sensitive:
notebook: output/spring-boosters.html
tables: output/machine_readable_outputs/spring_boosters/* spring booster *.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 03:27:56
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- covid-vaccine-preliminary-study-master
- Requested by
- Lisa Hopcroft
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- dccc854
- Requested actions
-
-
generate_booster_notebook
-
debug_booster_data
-
Code comparison
Compare the code used in this Job Request