Job request: 4328
- Organisation:
- University of Manchester
- Workspace:
- abrx_os_brit
- ID:
- ycj7g6j3vf6lnimx
This page shows the technical details of what happened when authorised researcher ali 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.
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Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
describe_overall_OS:
run: r:latest analysis/plot/overall_ab_prescribing_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/overall_line_os.png
boxplot: output/overallbox_os.png
describe_overall_brit:
run: r:latest analysis/plot/overall_ab_prescribing_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/overall_line_brit.png
boxplot: output/overallbox_brit.png
describe_overall_brit_os:
run: r:latest analysis/plot/overall_ab_prescribing_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/overall_line_brit_os.png
boxplot: output/overallbox_brit_os.png
describe_ab_type_brit:
run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
barchart: output/barchart_abtype_brit.png
describe_ab_type_brit_os:
run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
barchart: output/barchart_abtype_brit_os.png
describe_percentile_os:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_os.png
describe_percentile_brit:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_brit.png
describe_percentile_brit_os:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_brit_os.png
describe_starpu_os:
run: r:latest analysis/plot/starpu_ab_prescribing_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_os.png
boxplot: output/starpu_box_os.png
describe_starpu_brit:
run: r:latest analysis/plot/starpu_ab_prescribing_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_brit.png
boxplot: output/starpu_box_brit.png
describe_starpu_brit_os:
run: r:latest analysis/plot/starpu_ab_prescribing_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_brit_os.png
boxplot: output/starpu_box_brit_os.png
describe_b_n_brit:
run: r:latest analysis/plot/broad_narrow_bar_chart_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/broad_narrow_bar_chart_brit.png
describe_b_n_brit_os:
run: r:latest analysis/plot/broad_narrow_bar_chart_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/broad_narrow_bar_chart_brit_os.png
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/starpu.html
# figures: output/*
generate_notebook_starpu_brit_os:
run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu_brit_os.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
needs: [generate_measures]
outputs:
moderately_sensitive:
notebook: output/starpu_brit_os.html
figures: output/*
Timeline
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Created:
-
Started:
-
Finished:
-
Runtime: 13:44:48
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- abrx_os_brit
- Requested by
- ali
- Branch
- ABRX_comparison_OS_v_brit
- Force run dependencies
- Yes
- Git commit hash
- 46a9179
- Requested actions
-
-
run_all
-
Code comparison
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