Job request: 11455
- Organisation:
- Bennett Institute
- Workspace:
- asthma_sro
- ID:
- 4qvjt4gwooltovje
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
-
- Job identifier:
-
eufagjpjnnu7srxq - Error:
- nonzero_exit: Job exited with error code 5: Something went wrong with the database, please contact tech support
-
- Job identifier:
-
lhcbunoq5c5y4fbt - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
t37kywr3hpcyz66n - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
3imrovxqn3uuot65 - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
i4zpjejlht4m5hvb - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
tssmw5xnoakkzw67 - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
hghekakgfucxn25n - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
6i2z26mwf3qmvvhz - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
ry2jnc2gpbswktfs - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
xbcmhf5rophisqme - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
# Asthma register (ast_reg) Dictionary method actions
generate_study_population_ast_reg:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ast_reg
--index-date-range "2019-03-01 to 2022-03-31 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/input_ast_reg*.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv
join_ethnicity_ast_reg:
run: >
cohort-joiner:v0.0.46
--lhs output/input_ast*.csv
--rhs output/input_ethnicity.csv
--output-dir output/joined
needs: [generate_study_population_ethnicity, generate_study_population_ast_reg]
outputs:
highly_sensitive:
cohort: output/joined/input_ast*.csv
generate_measures_ast_reg:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_ast_reg
--output-dir=output/joined
needs: [join_ethnicity_ast_reg]
outputs:
moderately_sensitive:
measure_csv: output/joined/measure_ast_reg_*_rate.csv
join_measures_register:
run: python:latest python analysis/join_and_round.py
--input-list output/joined/measure_ast_reg_total_rate.csv
--input-list output/joined/measure_ast_reg_age_band_rate.csv
--input-list output/joined/measure_ast_reg_care_home_rate.csv
--input-list output/joined/measure_ast_reg_ethnicity_rate.csv
--input-list output/joined/measure_ast_reg_imd_rate.csv
--input-list output/joined/measure_ast_reg_learning_disability_rate.csv
--input-list output/joined/measure_ast_reg_region_rate.csv
--input-list output/joined/measure_ast_reg_sex_rate.csv
--output-dir output/joined/summary
--output-name "measure_register.csv"
needs: [generate_measures_ast_reg]
outputs:
moderately_sensitive:
# Only output the single summary file
measure_csv: output/joined/summary/measure_register.csv
calculate_rates_ast_reg:
run: python:latest python analysis/rate_calculations.py
needs: [generate_measures_ast_reg]
outputs:
moderately_sensitive:
tables: output/rate_table_*.csv
plots: output/plot_*.png
decile_chart: output/decile_chart.png
#############################
# Plotting
#############################
generate_qof_deciles_charts:
run: >
deciles-charts:v0.0.15
--input-files output/joined/measure_*_practice_rate.csv
--output-dir output/joined
config:
show_outer_percentiles: false
tables:
output: true
charts:
output: true
needs: [generate_measures_ast_reg]
outputs:
moderately_sensitive:
cohort: output/joined/deciles_*_*.*
generate_qof_groups:
run: >
python:latest python analysis/group_charts.py
--input-files output/joined/measure_ast_reg_*.csv
--output-dir output/joined
--date-lines "2019-03-31" "2020-03-31" "2021-03-31"
--scale "percentage"
needs: [generate_measures_ast_reg]
outputs:
moderately_sensitive:
cohort: output/joined/group_chart_*.png
generate_all_breakdowns:
run: >
python:latest python analysis/panel_plots.py
--input-file output/joined/summary/measure_register.csv
--measures-pattern "*_rate"
--output-dir output/joined/summary
--output-name "asthma_register_by_demographic_group"
--date-lines "2019-03-31" "2020-03-31" "2021-03-31"
--scale "percentage"
needs: [join_measures_register]
outputs:
moderately_sensitive:
cohort: output/joined/summary/asthma_register_by_demographic_group.png
generate_notebook_ast_reg:
run: jupyter:latest jupyter nbconvert /workspace/analysis/Table1_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [join_measures_register]
outputs:
moderately_sensitive:
notebook: output/Table1_notebook.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 07:25:13
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- asthma_sro
- Requested by
- Rose Higgins
- Branch
- master
- Force run dependencies
- Yes
- Git commit hash
- 570dbbf
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request