Job request: 22753
- Organisation:
- Bennett Institute
- Workspace:
- the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
- ID:
- noeaotausqtljndl
This page shows the technical details of what happened when authorised researcher Chris Wood 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
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Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_ethnicity_01HW38MAP18PWK35KP7T46DST1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-dir output/01HW38MAP18PWK35KP7T46DST1 --output-format=feather
outputs:
highly_sensitive:
cohort: output/01HW38MAP18PWK35KP7T46DST1/input_ethnicity.feather
generate_study_population_weekly_01HW38MAP18PWK35KP7T46DST1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--param codelist_1_frequency="weekly"
--param breakdowns=""
--index-date_range="2024-04-01 to 2024-04-01 by week"
--output-dir=output/01HW38MAP18PWK35KP7T46DST1
--output-format=feather
--output-file=output/01HW38MAP18PWK35KP7T46DST1/input_weekly_2024-04-01.feather
outputs:
highly_sensitive:
cohort: output/01HW38MAP18PWK35KP7T46DST1/input_weekly_2024-04-01.feather
generate_study_population_01HW38MAP18PWK35KP7T46DST1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range="2019-09-01 to 2024-03-31 by month"
--output-dir=output/01HW38MAP18PWK35KP7T46DST1
--output-format=feather
outputs:
highly_sensitive:
cohort: output/01HW38MAP18PWK35KP7T46DST1/input_*.feather
join_cohorts_01HW38MAP18PWK35KP7T46DST1:
run: >
cohort-joiner:v0.0.38
--lhs output/01HW38MAP18PWK35KP7T46DST1/input_20*.feather
--rhs output/01HW38MAP18PWK35KP7T46DST1/input_ethnicity.feather
--output-dir output/01HW38MAP18PWK35KP7T46DST1/joined
needs: [generate_study_population_01HW38MAP18PWK35KP7T46DST1, generate_study_population_ethnicity_01HW38MAP18PWK35KP7T46DST1]
outputs:
highly_sensitive:
cohort: output/01HW38MAP18PWK35KP7T46DST1/joined/input_20*.feather
generate_measures_01HW38MAP18PWK35KP7T46DST1:
run: >
python:latest -m analysis.measures
--breakdowns=sex
--breakdowns=age
--breakdowns=ethnicity
--breakdowns=imd
--breakdowns=region
--input-dir="output/01HW38MAP18PWK35KP7T46DST1/joined"
--output-dir="output/01HW38MAP18PWK35KP7T46DST1"
needs: [join_cohorts_01HW38MAP18PWK35KP7T46DST1]
outputs:
moderately_sensitive:
measure: output/01HW38MAP18PWK35KP7T46DST1/measure_all.csv
decile_measure: output/01HW38MAP18PWK35KP7T46DST1/measure_practice_rate_deciles.csv
top_5_table_01HW38MAP18PWK35KP7T46DST1:
run: >
python:latest python analysis/top_5.py
--codelist-1-path="interactive_codelists/codelist_1.csv"
--codelist-2-path="interactive_codelists/codelist_2.csv"
--output-dir="output/01HW38MAP18PWK35KP7T46DST1"
needs: [generate_measures_01HW38MAP18PWK35KP7T46DST1]
outputs:
moderately_sensitive:
table_1: output/01HW38MAP18PWK35KP7T46DST1/top_5_code_table_1.csv
table_2: output/01HW38MAP18PWK35KP7T46DST1/top_5_code_table_2.csv
tables_for_checking: output/01HW38MAP18PWK35KP7T46DST1/for_checking/top_5*.csv
plot_measure_01HW38MAP18PWK35KP7T46DST1:
run: >
python:latest python analysis/plot_measures.py
--breakdowns=sex
--breakdowns=age
--breakdowns=ethnicity
--breakdowns=imd
--breakdowns=region
--input-dir output/01HW38MAP18PWK35KP7T46DST1
--output-dir output/01HW38MAP18PWK35KP7T46DST1
needs: [generate_measures_01HW38MAP18PWK35KP7T46DST1]
outputs:
moderately_sensitive:
measure: output/01HW38MAP18PWK35KP7T46DST1/plot_measure*.png
data: output/01HW38MAP18PWK35KP7T46DST1/for_checking/plot_measure_for_checking.csv
deciles: output/01HW38MAP18PWK35KP7T46DST1/deciles_chart.png
event_counts_01HW38MAP18PWK35KP7T46DST1:
run: >
python:latest -m analysis.event_counts --input-dir="output/01HW38MAP18PWK35KP7T46DST1" --output-dir="output/01HW38MAP18PWK35KP7T46DST1"
needs: [join_cohorts_01HW38MAP18PWK35KP7T46DST1, generate_study_population_weekly_01HW38MAP18PWK35KP7T46DST1]
outputs:
moderately_sensitive:
measure: output/01HW38MAP18PWK35KP7T46DST1/event_counts.json
generate_report_01HW38MAP18PWK35KP7T46DST1:
run: >
python:latest python analysis/render_report.py
--output-dir="output/01HW38MAP18PWK35KP7T46DST1"
needs: [event_counts_01HW38MAP18PWK35KP7T46DST1, top_5_table_01HW38MAP18PWK35KP7T46DST1, plot_measure_01HW38MAP18PWK35KP7T46DST1]
outputs:
moderately_sensitive:
notebook: output/01HW38MAP18PWK35KP7T46DST1/report.html
Timeline
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Created:
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Started:
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Finished:
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Runtime: 16:12:38
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
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Succeeded
- Backend
- TPP
- Requested by
- Chris Wood
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 95b70f8
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request