This page shows the technical details of what happened when authorised researcher John Tazare 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: 20000
actions:
generate_covid_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
outputs:
highly_sensitive:
cohort: output/input_covid.csv
generate_covid_community_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
outputs:
highly_sensitive:
cohort: output/input_covid_community.csv
generate_covid_general_population_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population
outputs:
highly_sensitive:
cohort: output/input_general_population.csv
generate_pneumonia_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
outputs:
highly_sensitive:
cohort: output/input_pneumonia.csv
matching:
run: python:latest python analysis/match_running.py
needs: [generate_covid_cohort, generate_covid_general_population_cohort]
outputs:
moderately_sensitive:
matching_report: output/matching_report_general_population.txt
highly_sensitive:
combined: output/matched_combined_general_population.csv
covid_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
needs: [generate_covid_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid.dta
covid_community_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
needs: [generate_covid_community_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid_community.dta
pneumonia_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
needs: [generate_pneumonia_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_pneumonia.dta
gen_pop_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "matched_combined_general_population"
needs: [matching]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_gen_population.dta
covid_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
needs: [covid_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid.csv
covid_comm_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
needs: [covid_community_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_community.csv
pneumonia_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
needs: [pneumonia_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_pneumonia.csv
gen_pop_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "gen_population"
needs: [gen_pop_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_gen_population.csv
baseline_characteristics:
run: stata-mp:latest analysis/400_baseline_characteristics.do
needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
outputs:
moderately_sensitive:
tables: output/tabfig/an_descriptiveTable_*.txt
append_cohorts:
run: stata-mp:latest analysis/300_cr_data_management_matching.do
needs: [covid_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
outputs:
moderately_sensitive:
log: output/append_cohorts.txt
highly_sensitive:
dataset: output/combined_covid_pneumonia.dta
dataset2: output/combined_covid_gen_population.dta
cox_models:
run: stata-mp:latest analysis/302_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv
Timeline
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Created:
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Started:
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Finished:
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Runtime:
These timestamps are generated and stored using the UTC timezone on the backend.
Job information
- Status
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Failed
Completed successfully
- Backend
- TPP
- Workspace
- post-covid-research
- Requested by
- John Tazare
- Branch
- master
- Force run dependencies
- Yes
- Git commit hash
- 63c6da5
- Requested actions
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run_all
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