Job request: 4564
- Organisation:
- Bennett Institute
- Workspace:
- med-safety-poc
- ID:
- r3x6vdw2j3fmre2w
This page shows the technical details of what happened when 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 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
-
- Job identifier:
-
7gila4tr36mq5jek
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 5000
actions:
generate_study_population_ce1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ce1_for_ce2 --index-date-range "2020-01-01 to 2020-12-01 by month"
outputs:
highly_sensitive:
cohort: output/ce1/input_ce1_for_ce2_*.csv
add_practice_ids:
run: python:latest python analysis/add_practice_ids.py
needs: [generate_study_population_ce1]
outputs:
moderately_sensitive:
cohort: output/ce1/input_expanded_*.csv
generate_study_population_ce2:
run: cohortextractor-v2:latest generate_cohort --cohort-definition analysis/study_definition_ce2.py --output output/ce2/input_ce2_*.csv --dummy-data-file output/ce1/input_expanded_ce1_for_ce2_*.csv
outputs:
highly_sensitive:
cohort: output/ce2/input_ce2_*.csv
validate_cohort_v2:
run: cohortextractor-v2:latest validate_cohort databricks --cohort-definition analysis/study_definition_ce2.py --output output/ce2/sql/generated_sql_*.sql
outputs:
moderately_sensitive:
cohort: output/ce2/sql/generated_sql_*.sql
# generate_measures:
# run: cohortextractor-v2:latest generate_measures --cohort-definition analysis/study_definition_ce2.py --output output/ce2/measure_ce2_*.csv --input=output/ce2/input_ce2_*.csv
# needs: [generate_study_population_ce2]
# outputs:
# moderately_sensitive:
# measure_csv: output/ce2/measure_ce2_*.csv
# generate_report:
# run: cohort-report:v2.0.2 output/ce1/input_2019-09-01.feather
# needs: [generate_study_population_ce1]
# config:
# output_path: output/ce1/cohort_reports_outputs
# outputs:
# moderately_sensitive:
# reports: output/ce1/cohort_reports_outputs/*.html
# generate_plots:
# run: python:latest python analysis/plot_measures.py
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# counts: output/ce2/figures/plot_*.jpeg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:17
These timestamps are generated and stored using the UTC timezone on the NHSD-REF backend.
Job information
- Status
-
Failed
- Backend
- NHSD-REF
- Workspace
- med-safety-poc
- Requested by
- Lisa Hopcroft
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- cf6bf2a
- Requested actions
-
-
generate_study_population_ce2
-
Code comparison
Compare the code used in this Job Request
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