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Job request: 9690
- ID:
ftwlfdrgqxikhn3m
- Workspace: bmi-short-data-report-segmented
This page shows the technical details of what happened when authorised researcher Robin Park requested one or more actions to be run against real patient data in the BMI Short Data Report 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
ID | Status | Action |
---|---|---|
ms5grwxhadilxw66 | failed | execute_validation_analyses_all_definitions |
Pipeline
Show Hide project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input.feather
generate_study_population_derived_bmi:
run: cohortextractor:latest generate_cohort --study-definition study_definition_derived_bmi --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_derived_bmi.feather
generate_study_population_recorded_bmi:
run: cohortextractor:latest generate_cohort --study-definition study_definition_recorded_bmi --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_recorded_bmi.feather
generate_study_population_snomed_hw:
run: cohortextractor:latest generate_cohort --study-definition study_definition_snomed_hw --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_snomed_hw.feather
generate_study_population_ctv3_hw:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ctv3_hw --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_ctv3_hw.feather
preprocess_derived_bmi_input:
run: python:latest python analysis/preprocess_bmi_inputs.py "derived_bmi" --output-format feather
needs: [generate_study_population_derived_bmi]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_derived_bmi.feather
preprocess_recorded_bmi_input:
run: python:latest python analysis/preprocess_bmi_inputs.py "recorded_bmi" --output-format feather
needs: [generate_study_population_recorded_bmi]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_recorded_bmi.feather
preprocess_computed_bmi_input:
run: python:latest python analysis/preprocess_hw_inputs.py "height" "weight" "snomed" "computed_bmi" --output-format feather
needs: [generate_study_population_snomed_hw]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_computed_bmi.feather
preprocess_backend_computed_bmi_input:
run: python:latest python analysis/preprocess_hw_inputs.py "height_backend" "weight_backend" "ctv3" "backend_computed_bmi" --output-format feather
needs: [generate_study_population_ctv3_hw]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_backend_computed_bmi.feather
join_cohorts:
run: >
cohort-joiner:v0.0.35
--lhs output/data/input_processed*.feather
--rhs output/data/input.feather
--output-dir output/joined
needs: [generate_study_population, preprocess_derived_bmi_input, preprocess_recorded_bmi_input, preprocess_computed_bmi_input, preprocess_backend_computed_bmi_input]
outputs:
highly_sensitive:
cohort: output/joined/input_processed*.feather
preprocess_age_dates:
run: python:latest python analysis/preprocess_age_dates.py --output-format feather
needs: [join_cohorts]
outputs:
highly_sensitive:
cohort1: output/joined/input_processed_backend_computed_bmi.feather
cohort2: output/joined/input_processed_computed_bmi.feather
cohort3: output/joined/input_processed_derived_bmi.feather
cohort4: output/joined/input_processed_recorded_bmi.feather
execute_validation_analyses_derived_bmi:
run: python:latest python analysis/validation_script_single_definition.py "derived_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/derived_bmi/*.csv
execute_validation_analyses_recorded_bmi:
run: python:latest python analysis/validation_script_single_definition.py "recorded_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/recorded_bmi/*.csv
execute_validation_analyses_computed_bmi:
run: python:latest python analysis/validation_script_single_definition.py "computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/computed_bmi/*.csv
execute_validation_analyses_backend_computed_bmi:
run: python:latest python analysis/validation_script_single_definition.py "backend_computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/backend_computed_bmi/*.csv
execute_validation_analyses_high_computed_bmi:
run: python:latest python analysis/validation_script_high_bmi.py "computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/high_computed_bmi/*.csv
execute_validation_analyses_high_backend_computed_bmi:
run: python:latest python analysis/validation_script_high_bmi.py "backend_computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/high_backend_computed_bmi/*.csv
execute_validation_analyses_all_definitions:
run: python:latest python analysis/validation_script_all_definitions.py
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/comparison/*.csv
consolidate_analyses:
run: python:latest python analysis/consolidate_analyses.py
needs: [execute_validation_analyses_derived_bmi, execute_validation_analyses_recorded_bmi, execute_validation_analyses_backend_computed_bmi, execute_validation_analyses_computed_bmi]
outputs:
moderately_sensitive:
tables: output/validation/formatted_tables/*.csv
State
State is inferred from the related Jobs.
Status: Failed
Timings
Timings set to UTC timezone.
- Created:
- Started:
- Finished:
- Runtime: 00:13:38
Config
-
- Backend:
-
TPP
-
- Workspace:
- bmi-short-data-report-segmented
-
- Branch:
separate-study-definitions
-
- Creator:
- robinyjpark
-
- Force run dependencies:
- False
-
- Git Commit Hash:
- 16bc921
-
Requested actions:
execute_validation_analyses_all_definitions