Job request: 2423
- Organisation:
- Bennett Institute
- Workspace:
- comparative-ve-research_main
- ID:
- 7zbbtp7okhbtlxxs
This page shows the technical details of what happened when the authorised researcher Will Hulme requested one or more actions to be run against real patient data within a secure environment.
By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.
The output security levels are:
-
highly_sensitive
- Researchers can never directly view these outputs
- Researchers can only request code is run against them
-
moderately_sensitive
- Can be viewed by an approved researcher by logging into a highly secure environment
- These are the only outputs that can be requested for public release via a controlled output review service.
Jobs
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- Job identifier:
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kelrmvwhilc6uwzq - Error:
- nonzero_exit: Job exited with an error code
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- Job identifier:
-
ec3nsyu4oe4gqcjo
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- Job identifier:
-
yz6hqtl6iox4pyzy - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
cfmv5l3fayjigqsg - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
qxod65e5knfbjakt - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
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2rfwlrki74asgfqd - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
y3jfmq3vfg4yx64k - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
baet2byfr3ttj6bk - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
p6ergmncrlwixppk - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
katwngcx4uawai4m - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
bxdetds2qt4ravnq - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
design:
run: r:latest analysis/process/design.R
outputs:
moderately_sensitive:
metadata: output/data/metadata*
extract:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format feather
outputs:
highly_sensitive:
cohort: output/input.feather
data_process:
run: r:latest analysis/process/data_process.R
needs: [extract]
outputs:
highly_sensitive:
data1: output/data/data_processed.rds
data2: output/data/data_long_vax_dates.rds
data_properties:
run: r:latest analysis/process/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data*.txt
data_selection:
run: r:latest analysis/process/data_selection.R
needs: [data_process]
outputs:
highly_sensitive:
data: output/data/data_cohort.rds
data_az: output/data/data_vax_az_withoutdate.csv
data_pfizer: output/data/data_vax_pfizer_withoutdate.csv
data_az_date: output/data/data_vax_az_withdate.csv
data_pfizer_date: output/data/data_vax_pfizer_withdate.csv
moderately_sensitive:
flow: output/data/flowchart.csv
#######################################
## MATCHING
#######################################
matchwithoutdate_recipients:
run: python:latest python analysis/matching/matchwithoutdate.py
needs: [data_selection]
outputs:
highly_sensitive:
cases: output/data/matched_cases_withoutdate.csv
matches: output/data/matched_matches_withoutdate.csv
combined: output/data/matched_combined_withoutdate.csv
moderately_sensitive:
report: output/data/matching_report_withoutdate.txt
matchwithoutdate_process:
run: r:latest analysis/matching/match_process.R withoutdate
needs: [design, matchwithoutdate_recipients, data_selection]
outputs:
highly_sensitive:
data: output/data/data_matches_withoutdate.rds
moderately_sensitive:
report: output/matching/matching_balance_withoutdate.html
matchwithdate_recipients:
run: python:latest python analysis/matching/matchwithdate.py
needs: [data_selection]
outputs:
highly_sensitive:
cases: output/data/matched_cases_withdate.csv
matches: output/data/matched_matches_withdate.csv
combined: output/data/matched_combined_withdate.csv
moderately_sensitive:
report: output/data/matching_report_withdate.txt
matchwithdate_process:
run: r:latest analysis/matching/match_process.R withdate
needs: [design, matchwithdate_recipients, data_selection]
outputs:
highly_sensitive:
data: output/data/data_matches_withdate.rds
moderately_sensitive:
report: output/matching/matching_balance_withdate.html
#######################################
## COMPARATIVE EFFECTIVENESS MODELS
## positive test outcome
#######################################
model1_postest:
run: r:latest analysis/models/model_cox.R postest
needs: [design, matchwithoutdate_process]
outputs:
highly_sensitive:
models: output/postest/model*.rds
moderately_sensitive:
logs: output/postest/log*.txt
model1_covidadmitted:
run: r:latest analysis/models/model_cox.R covidadmitted
needs: [design, matchwithoutdate_process]
outputs:
highly_sensitive:
models: output/covidadmitted/model*.rds
moderately_sensitive:
logs: output/covidadmitted/log*.txt
Timeline
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Created:
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Started:
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Finished:
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Runtime: 00:50:15
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
- Backend
- TPP
- Workspace
- comparative-ve-research_main
- Requested by
- Will Hulme
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- e1436d2
- Requested actions
-
-
run_all
-
Code comparison
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