Job request: 16659
- Organisation:
- Bennett Institute
- Workspace:
- vax-fourth-dose-rd-baseline
- ID:
- ckqbw7qhi5plwikv
This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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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cjnsoomyalvyfx6u
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- Job identifier:
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bbgmca747ve5istw
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- Job identifier:
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twn2hah7gjz3hsyx
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- Job identifier:
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aeoc6p4j2wssuf4j
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- Job identifier:
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elri4b3un2xisynp
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- Job identifier:
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pkwqvptewrlknfdx
Pipeline
Show project.yaml
######################################
# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 10000
actions:
# Generate study population and extract baseline characteristics at Sep 3, 2022
generate_study_pop_baseline:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_baseline
--output-dir=feather
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_baseline.feather
# Data cleaning, defining exclusions, saving final study pop
data_process_baseline:
run: r:latest analysis/processing/data_processing_baseline.R
needs: [generate_study_pop_baseline]
outputs:
highly_sensitive:
cohort: output/cohort/cohort_*.csv
moderately_sensitive:
descriptive: output/descriptive/total_*.csv
# Extract outcomes based on final study pop
study_definition_outcomes:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_outcomes
--index-date-range "2022-09-03 to 2023-01-31 by week"
--output-dir=feather
--output-format=feather
needs: [data_process_baseline]
outputs:
highly_sensitive:
cohort: output/index/input_outcomes_*.feather
# Data cleaning of outcome data
data_process_outcomes:
run: r:latest analysis/processing/data_processing_outcomes.R
needs: [study_definition_outcomes]
outputs:
highly_sensitive:
primary_outcomes: output/cohort/primary_outcomes.csv
secondary_outcomes: output/cohort/secondary_outcomes.csv
# Plots of COVID booster uptake by age
booster_uptake:
run: r:latest analysis/descriptive/cumulative_vax_byage.R
needs: [data_process_baseline]
outputs:
moderately_sensitive:
rates_csv: output/cumulative_rates/final_*.csv
plot: output/cumulative_rates/plot_*.png
# Outcome plots #
covid_outcomes:
run: r:latest analysis/descriptive/covid_outcomes_byage.R
needs: [data_process_outcomes]
outputs:
moderately_sensitive:
measure_csv: output/covid_outcomes/primary_*.csv
plot: output/covid_outcomes/plot_outcomes_*.png
# Discontinuity of demographics
# demographics:
# run: r:latest analysis/descriptive/demographics_byage.R
# needs: [generate_study_pop_baseline, data_process_baseline]
# outputs:
# moderately_sensitive:
# measures_csv: output/descriptive/demographics_*.csv
# Flu vaccine uptake #
# flu_vax:
# run: r:latest analysis/descriptive/flu_vax_byage.R
# needs: [generate_study_pop]
# outputs:
# moderately_sensitive:
# measure_csv: output/cumulative_rates/flu_*.csv
# plot: output/cumulative_rates/plot_flu_vax_byage.png
# Outcome plots #
# covid_outcomes:
# run: r:latest analysis/descriptive/covid_outcomes_byage.R
# needs: [generate_study_pop]
# outputs:
# moderately_sensitive:
# measure_csv: output/covid_outcomes/covid_*.csv
# plot: output/covid_outcomes/plot_outcomes_*.png
# ITT analysis #
# IV analysis #
Timeline
-
Created:
-
Started:
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Finished:
-
Runtime: 12:27:20
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- vax-fourth-dose-rd-baseline
- Requested by
- Andrea Schaffer
- Branch
- Protocol-updates
- Force run dependencies
- No
- Git commit hash
- 712af2e
- Requested actions
-
-
generate_study_pop_baseline
-
data_process_baseline
-
study_definition_outcomes
-
data_process_outcomes
-
booster_uptake
-
covid_outcomes
-
Code comparison
Compare the code used in this Job Request