Job request: 10414
- Organisation:
- NHSE/I
- Workspace:
- nhs_at_home_main
- ID:
- 5og7hvx5wbnxjgiz
This page shows the technical details of what happened when the authorised researcher Alexandra Benson 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
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- Job identifier:
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ew5ewclov4yautjd
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- Job identifier:
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6req5bm5wt5m7doh - Error:
- nonzero_exit: Job exited with error code 5: Ran out of memory (limit for this job was 128.00GB)
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- Job identifier:
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o6xys5kw2qr2rmue - Error:
- nonzero_exit: Job exited with error code 5: Ran out of memory (limit for this job was 128.00GB)
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- Job identifier:
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i2qxdn7ubnjnrufh - Error:
- nonzero_exit: Job exited with error code 5: Ran out of memory (limit for this job was 128.00GB)
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- Job identifier:
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scsnhupl5tdyrk3s - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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ochvboxfh3ffa7ri - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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uwsh6e2rkund325g - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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lnjxhze25jdxqveu - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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ru2ofg37uitczeoz - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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xplkevwxxyq6h4df - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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nvtjh4xqhd4nejj5 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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i2neqw3njovthooj - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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r2onzb3xtsb2ah6b - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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x2duil6er7veeg2d - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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ybekzvhrzxkjlpl6 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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rrt4mpzckq7zjgrn - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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vm2owxrvyp4zub54 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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nfxur2zregsyaptb - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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qf2qtlvfj4zpznuf - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 1000
actions:
generate_study_definition_static:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_static
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_static.csv
# Oximetry
generate_study_population_oximetry:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_oximetry
--index-date-range "2019-04-01 to 2022-05-30 by week"
--with-end-date-fix
outputs:
highly_sensitive:
oximetry_cohort: output/oximetry/0.1_generate_study_population/input_oximetry*.csv
join_cohorts_oximetry:
run: cohort-joiner:v0.0.30
--lhs output/oximetry/0.1_generate_study_population/input_oximetry*.csv
--rhs output/input_static.csv
--output-dir output/oximetry/0.2_join_cohorts/
needs:
[generate_study_population_oximetry, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/oximetry/0.2_join_cohorts/input_oximetry*.csv
# BP
generate_study_population_bp:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_bp
--index-date-range "2019-04-01 to 2022-05-30 by week"
--with-end-date-fix
outputs:
highly_sensitive:
bp_cohort: output/bp/0.1_generate_study_population/input_bp*.csv
join_cohorts_bp:
run: cohort-joiner:v0.0.30
--lhs output/bp/0.1_generate_study_population/input_bp*.csv
--rhs output/input_static.csv
--output-dir output/bp/0.2_join_cohorts/
needs: [generate_study_population_bp, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/bp/0.2_join_cohorts/input_bp*.csv
# Proactive
generate_study_population_proactive:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_proactive
--index-date-range "2019-04-01 to 2022-05-30 by week"
--with-end-date-fix
outputs:
highly_sensitive:
proactive_cohort: output/proactive/0.1_generate_study_population/input_proactive*.csv
join_cohorts_proactive:
run: cohort-joiner:v0.0.30
--lhs output/proactive/0.1_generate_study_population/input_proactive*.csv
--rhs output/input_static.csv
--output-dir output/proactive/0.2_join_cohorts/
needs:
[generate_study_population_proactive, generate_study_definition_static]
outputs:
highly_sensitive:
cohort: output/proactive/0.2_join_cohorts/input_proactive*.csv
# Analysis
# Oximetry
generate_oximetry_timeseries:
run: python:latest python analysis/analysis_oximetry_timeseries.py
needs: [join_cohorts_oximetry]
outputs:
moderately_sensitive:
oximetry_table_counts: output/oximetry/0.3_analysis_outputs/oximetry_table_counts.csv
oximetry_plot_timeseries: output/oximetry/0.3_analysis_outputs/oximetry_plot_timeseries.png
generate_oximetry_regional_timeseries:
run: python:latest python analysis/analysis_oximetry_region.py
needs: [join_cohorts_oximetry]
outputs:
moderately_sensitive:
oximetry_table_counts_region: output/oximetry/0.3_analysis_outputs/oximetry_table_counts_*.csv
oximetry_plot_timeseries_region: output/oximetry/0.3_analysis_outputs/oximetry_plot_timeseries_region_*.png
generate_oximetry_breakdowns:
run: python:latest python analysis/analysis_oximetry_breakdowns.py
needs: [join_cohorts_oximetry]
outputs:
moderately_sensitive:
oximetry_table_breakdowns: output/oximetry/0.3_analysis_outputs/oximetry_table_code_*.csv
oximetry_plot_breakdowns: output/oximetry/0.3_analysis_outputs/oximetry_plot_code_*.png
generate_oximetry_codes_analysis:
run: python:latest python analysis/analysis_oximetry_codes.py
needs: [join_cohorts_oximetry]
outputs:
moderately_sensitive:
oximetry_table_code_counts: output/oximetry/0.3_analysis_outputs/oximetry_table_code_counts_*.csv
oximetry_table_code_combinations: output/oximetry/0.3_analysis_outputs/oximetry_table_code_combinations.csv
oximetry_table_code_populations: output/oximetry/0.3_analysis_outputs/oximetry_patient_id_total_*.csv
# Blood pressure
generate_bp_timeseries:
run: python:latest python analysis/analysis_bp_timeseries.py
needs: [join_cohorts_bp]
outputs:
moderately_sensitive:
bp_table_counts: output/bp/0.3_analysis_outputs/bp_table_counts.csv
bp_plot_timeseries: output/bp/0.3_analysis_outputs/bp_plot_timeseries.png
generate_bp_regional_timeseries:
run: python:latest python analysis/analysis_bp_region.py
needs: [join_cohorts_bp]
outputs:
moderately_sensitive:
bp_table_counts_region: output/bp/0.3_analysis_outputs/bp_table_counts_*.csv
bp_plot_timeseries_region: output/bp/0.3_analysis_outputs/bp_plot_timeseries_region_*.png
generate_bp_breakdowns:
run: python:latest python analysis/analysis_bp_breakdowns.py
needs: [join_cohorts_bp]
outputs:
moderately_sensitive:
bp_table_breakdowns: output/bp/0.3_analysis_outputs/bp_table_code_*.csv
bp_plot_breakdowns: output/bp/0.3_analysis_outputs/bp_plot_code_*.png
generate_bp_codes_analysis:
run: python:latest python analysis/analysis_bp_codes.py
needs: [join_cohorts_bp]
outputs:
moderately_sensitive:
bp_table_code_counts: output/bp/0.3_analysis_outputs/bp_table_code_counts_*.csv
bp_table_code_combinations: output/bp/0.3_analysis_outputs/bp_table_code_combinations.csv
bp_table_code_populations: output/bp/0.3_analysis_outputs/bp_patient_id_total_*.csv
# Proactive Care
generate_proactive_timeseries:
run: python:latest python analysis/analysis_proactive_timeseries.py
needs: [join_cohorts_proactive]
outputs:
moderately_sensitive:
proactive_table_counts: output/proactive/0.3_analysis_outputs/proactive_table_counts.csv
proactive_plot_timeseries: output/proactive/0.3_analysis_outputs/proactive_plot_timeseries.png
generate_proactive_regional_timeseries:
run: python:latest python analysis/analysis_proactive_region.py
needs: [join_cohorts_proactive]
outputs:
moderately_sensitive:
proactive_table_counts_region: output/proactive/0.3_analysis_outputs/proactive_table_counts_*.csv
proactive_plot_timeseries_region: output/proactive/0.3_analysis_outputs/proactive_plot_timeseries_region_*.png
generate_proactive_breakdowns:
run: python:latest python analysis/analysis_proactive_breakdowns.py
needs: [join_cohorts_proactive]
outputs:
moderately_sensitive:
proactive_table_breakdowns: output/proactive/0.3_analysis_outputs/proactive_table_code_*.csv
proactive_plot_breakdowns: output/proactive/0.3_analysis_outputs/proactive_plot_code_*.png
generate_proactive_codes_analysis:
run: python:latest python analysis/analysis_proactive_codes.py
needs: [join_cohorts_proactive]
outputs:
moderately_sensitive:
proactive_table_code_counts: output/proactive/0.3_analysis_outputs/proactive_table_code_counts_*.csv
proactive_table_code_combinations: output/proactive/0.3_analysis_outputs/proactive_table_code_combinations.csv
proactive_table_code_populations: output/proactive/0.3_analysis_outputs/proactive_patient_id_total_*.csv
Timeline
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Created:
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Started:
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Finished:
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Runtime: 56:12:14
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- nhs_at_home_main
- Requested by
- Alexandra Benson
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 354bdd5
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request