Job request: 379
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- covid-vs-non-covid-deaths-research
- ID:
- efwzn5dwttv2apbo
This page shows the technical details of what happened when the authorised researcher Krishnan Bhaskaran 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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xvlqcswtgta3bixw - Error:
- Job exited with an error code
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- Job identifier:
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vm3liyao6w23bwtq - Error:
- Not starting as dependency failed
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rdugnfzvm4jsh376 - Error:
- Not starting as dependency failed
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- Job identifier:
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reppievdmoma6kn7 - Error:
- Not starting as dependency failed
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- Job identifier:
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owvnlsu3qvqtmwxz - Error:
- Not starting as dependency failed
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- Job identifier:
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jffhle4vtar6ljeu
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- Job identifier:
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jg6wvbyhqa5cp6dg
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- Job identifier:
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sb53a7krctx4vgzc - Error:
- No outputs found matching patterns: - analysis/output/cr_create_analysis_datasetMAIN.log
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- Job identifier:
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eyze6jokgsjo26te - Error:
- No outputs found matching patterns: - analysis/output/cr_create_analysis_dataset2019.log
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- Job identifier:
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hc42k3jo5febtt7t - Error:
- Not starting as dependency failed
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- Job identifier:
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nqy5euyxacwpfcgz - Error:
- Not starting as dependency failed
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dmxvygucq5h5k3ny - Error:
- Not starting as dependency failed
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7qo5hfdsto2qlbrx - Error:
- Not starting as dependency failed
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wc35ftnsaazqmdv6 - Error:
- Not starting as dependency failed
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zrma5nsrbsyhpovs - Error:
- Not starting as dependency failed
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- Job identifier:
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5l7iqrrap5a6ogzn - Error:
- Not starting as dependency failed
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5f2wx3b5kjp3pl7u - Error:
- Not starting as dependency failed
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gcehfrast4ozvjlx - Error:
- Not starting as dependency failed
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- Job identifier:
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2pwqjv4s7ilmxoyk - Error:
- Not starting as dependency failed
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- Job identifier:
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jh66dlrvef2wydxw - Error:
- Not starting as dependency failed
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- Job identifier:
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muwvfjrlzqi77cji - Error:
- Not starting as dependency failed
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 100000
actions:
generate_cohortMAIN:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_cohort2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
outputs:
highly_sensitive:
cohort: output/input_2019.csv
generate_cohortSEPT2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sept2020
outputs:
highly_sensitive:
cohort: output/input_sept2020.csv
generate_flowchartdata:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
outputs:
highly_sensitive:
cohort: output/input_flow_chart.csv
crMAIN:
run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do MAIN
needs: [generate_cohortMAIN]
outputs:
highly_sensitive:
data: analysis/cr_create_analysis_dataset_MAIN_STSET.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_datasetMAIN.log
crSEPT2020:
run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do SEPT2020
needs: [generate_cohortSEPT2020]
outputs:
highly_sensitive:
data: analysis/cr_create_analysis_dataset_SEPT2020_STSET.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_datasetSEPT2020.log
cr2019:
run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do 2019
needs: [generate_cohort2019]
outputs:
highly_sensitive:
data: analysis/cr_create_analysis_dataset_2019_STSET.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_dataset2019.log
imputedataMAIN:
run: stata-mp:latest analysis/an_impute_GENERAL.do MAIN
needs: [crMAIN]
outputs:
highly_sensitive:
data: analysis/an_impute_imputeddata_MAIN.dta
moderately_sensitive:
log: analysis/output/an_impute_MAIN.log
imputedataSEPT2020:
run: stata-mp:latest analysis/an_impute_GENERAL.do SEPT2020
needs: [crSEPT2020]
outputs:
highly_sensitive:
data: analysis/an_impute_imputeddata_SEPT2020.dta
moderately_sensitive:
log: analysis/output/an_impute_SEPT2020.log
imputedata2019:
run: stata-mp:latest analysis/an_impute_GENERAL.do 2019
needs: [cr2019]
outputs:
highly_sensitive:
data: analysis/an_impute_imputeddata_2019.dta
moderately_sensitive:
log: analysis/output/an_impute_2019.log
descriptive_table1:
run: stata-mp:latest analysis/an_tablecontent_PublicationDescriptivesTable.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_tablecontent_PublicationDescriptivesTable.txt
absoluterisksbycause:
run: stata-mp:latest analysis/an_covid_vs_othercauses_abs_AGE.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_covid_vs_othercauses_abs_AGE.log
graph: analysis/output/an_covid_vs_othercauses_abs_AGE_GRAPH.svg
estimates: analysis/output/an_covid_vs_othercauses_abs_AGE_ESTIMATES.dta
agesexmodelsMAIN:
run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_agesex_MAIN.log
models: analysis/output/models/an_covidvsnoncovid_agesex_MAIN*.ster
agesexmodelsSEPT2020:
run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do SEPT2020
needs: [crSEPT2020]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_agesex_SEPT2020.log
models: analysis/output/models/an_covidvsnoncovid_agesex_SEPT2020*.ster
agesexmodels2019:
run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do 2019
needs: [cr2019]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_agesex_2019.log
models: analysis/output/models/an_covidvsnoncovid_agesex_2019*.ster
agesexmodelsSA_anyonDC:
run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_anywhereonDC
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC.log
models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC*.ster
agesexmodelsSA_u071only:
run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_u071only
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_u071only.log
models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_u071only*.ster
fullmodelsMAIN:
run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do MAIN
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_full_MAIN.log
models: analysis/output/models/an_covidvsnoncovid_full_MAIN*.ster
fullmodelsSEPT2020:
run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do SEPT2020
needs: [crSEPT2020]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_full_SEPT2020.log
models: analysis/output/models/an_covidvsnoncovid_full_SEPT2020*.ster
fullmodels2019:
run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do 2019
needs: [cr2019]
outputs:
moderately_sensitive:
log: analysis/output/an_covidvsnoncovid_full_2019.log
models: analysis/output/models/an_covidvsnoncovid_full_2019*.ster
ethnicity_model_and_graph:
run: stata-mp:latest analysis/an_ethnicitybycod_logisticversion.do
needs: [imputedataMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_ethnicitybycod_logisticversion.log
graph: analysis/output/an_ethnicitybycod_logisticversion.svg
deathsonly_models:
run: stata-mp:latest analysis/an_deathsonlyanalysis.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: analysis/output/an_deathsonlyanalysis.log
models: analysis/output/models/an_deathsonlyanalysis_*.ster
run_model:
run: stata-mp:latest analysis/model.do
needs: [generate_cohortMAIN]
outputs:
moderately_sensitive:
log: logs/model.log
run_all:
needs:
- run_model
# In order to be valid this action needs to define a run commmand and some
# output. We don't really care what these are but the below does the trick.
# In a future release of the platform, this special action won't need to be
# defined at all.
run: cohortextractor:latest --version
outputs:
moderately_sensitive:
whatever: project.yaml
Timeline
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Created:
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Started:
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Finished:
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Runtime: 00:03:49
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
- Backend
- TPP
- Workspace
- covid-vs-non-covid-deaths-research
- Requested by
- Krishnan Bhaskaran
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 63505ab
- Requested actions
-
-
generate_cohort2019 -
crMAIN -
crSEPT2020 -
cr2019 -
imputedataMAIN -
imputedataSEPT2020 -
imputedata2019 -
descriptive_table1 -
absoluterisksbycause -
agesexmodelsMAIN -
agesexmodelsSEPT2020 -
agesexmodels2019 -
agesexmodelsSA_anyonDC -
agesexmodelsSA_u071only -
fullmodelsMAIN -
fullmodelsSEPT2020 -
fullmodels2019 -
ethnicity_model_and_graph -
deathsonly_models
-
Code comparison
Compare the code used in this job request