Job request: 2256
- Organisation:
- Bennett Institute
- Workspace:
- ncs-hospital-disruption
- ID:
- wsjznwbkwfxihx2k
This page shows the technical details of what happened when the 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 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:
-
laxf723hw5ojstqx
-
- Job identifier:
-
dco73z3sdbipmmi2
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 10000
actions:
generate_cohort_imd_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_imd_ethnicity
outputs:
highly_sensitive:
cohort: output/input_imd_ethnicity.csv
generate_cohort_1:
# week 1 2019 to 21 2019 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-12-31 to 2019-05-26 by week"
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_cohort_2:
# week 22 2019 to 42 2019 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-27 to 2019-10-20 by week"
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_cohort_3:
# week 43 2019 to 11 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-10-21 to 2020-03-15 by week"
outputs:
highly_sensitive:
cohort: output/inpu*.csv
generate_cohort_4:
# week 12 2020 to 32 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-16 to 2020-08-09 by week"
outputs:
highly_sensitive:
cohort: output/inp*.csv
generate_cohort_5:
# week 33 2020 to week 53 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-08-10 to 2021-01-03 by week"
outputs:
highly_sensitive:
cohort: output/in*.csv
join_ethnicity_imd:
run: python:latest python analysis/join_ethnicity_imd.py
needs: [generate_cohort_1, generate_cohort_2, generate_cohort_3, generate_cohort_4, generate_cohort_5, generate_cohort_imd_ethnicity]
outputs:
highly_sensitive:
cohort: output/i*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition
needs: [join_ethnicity_imd]
outputs:
moderately_sensitive:
measure: output/measure_*_rate.csv
measure_admission_method: output/measure_*_rate_admission_method.csv
calculate_measures_demographics:
run: python:latest python analysis/generate_measures_demographics.py
needs: [join_ethnicity_imd]
outputs:
moderately_sensitive:
csvs: output/measure_*_rate_*.csv
standardise_and_plot:
run: python:latest python analysis/time_series_plots.py
needs: [calculate_measures]
outputs:
moderately_sensitive:
tables: output/*_rate.csv
graph: output/time_series_plot.svg
standardise_and_plot_demographics:
run: python:latest python analysis/time_series_plots_demographics.py
needs: [calculate_measures, calculate_measures_demographics]
outputs:
moderately_sensitive:
tables: output/*_rate_*_breakdown.csv
tables_combined: output/combined_disease_breakdown_*.csv
graph: output/time_series_plot_*.svg
combined_graph: output/combined_diseases_time_series.svg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:05:13
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- ncs-hospital-disruption
- Requested by
- Louis Fisher
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 2d3b3bf
- Requested actions
-
-
standardise_and_plot
-
standardise_and_plot_demographics
-
Code comparison
Compare the code used in this Job Request