This page shows the technical details of what happened when authorised researcher Alex Walker requested one or more actions to be run against real patient data in the Post-COVID-19 Thrombosis 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
ID | Status | Action |
---|---|---|
yhekgoff3rnzm3ik | succeeded | covid_rates_cohort |
shiurfk2dt62qsy6 | succeeded | covid_community_rates_cohort |
zi2zyqsn2jmxmlam | succeeded | pneumonia_rates_cohort |
5snrlhxczohsfwkd | succeeded | gen_pop_rates_cohort |
4ho7ttcjo4xmjf4k | succeeded | covid_rates |
crvbxftbojpnuk7p | succeeded | covid_comm_rates |
56qujx7fl25xwhtt | succeeded | pneumonia_rates |
mi6nh5pjcc5lhoap | succeeded | gen_pop_rates |
zyvdgograzvqmymr | succeeded | baseline_characteristics |
za5kofme5t4odqlu | succeeded | append_cohorts |
zxfwjqfqy6sxxvzg | succeeded | cox_models |
Pipeline
Show Hide 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
State
State is inferred from the related Jobs.
Status: Succeeded
Timings
Timings set to UTC timezone.
- Created:
- Started:
- Finished:
- Runtime: 02:35:46
Config
-
- Backend:
-
TPP
-
- Workspace:
- post-covid-research
-
- Branch:
master
-
- Creator:
- alexwalkerepi
-
- Force run dependencies:
- False
-
- Git Commit Hash:
- c2a0f5a
-
Requested actions:
covid_rates_cohort
covid_community_rates_cohort
pneumonia_rates_cohort
gen_pop_rates_cohort
covid_rates
covid_comm_rates
pneumonia_rates
gen_pop_rates
baseline_characteristics
append_cohorts
cox_models