Job Request: 2469 cop7auwjkzfhbaj7

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 Post-COVID-19 Outcomes 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.

State

State is inferred from the related Jobs
Status: succeeded

Config

Backend: tpp
Workspace: post-covid-competing-risks (reviewer-updates)
Creator: johntaz
Force run dependencies?: True
Git Commit Hash: e058078
Requested Actions:
  • run_all

Timings

Created: 1 month, 3 weeks ago
Started: 1 month, 3 weeks ago
Finished: 1 month, 3 weeks ago
Runtime: 46:54:36

Pipeline

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
moderately_sensitive:
out_dist: output/tabfig/outcomes_in_hosp_covid.csv
figs: output/tabfig/length_of_stay_covid.svg

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
moderately_sensitive:
out_dist: output/tabfig/outcomes_in_hosp_pneumonia.csv
figs: output/tabfig/length_of_stay_pneumonia.svg

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


fine_gray:
run: stata-mp:latest analysis/302_competing_events.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/competing_events.txt
dataset: output/tabfig/fine_gray_summary.csv
figs: output/tabfig/cumInc_*.svg

Jobs

ID Status Action
7kdclqxjglfojoou succeeded generate_covid_cohort View
soa7r77w6rzfrwta succeeded generate_covid_community_cohort View
zmhni6izprsslftz succeeded generate_covid_general_population_cohort View
cfkaby27lv3ajnkv succeeded generate_pneumonia_cohort View
dbcnosz77m7dlt62 succeeded matching View
x3mkfcmqtcwtthbq succeeded covid_rates_cohort View
f2gf5hxu3srrshvm succeeded covid_community_rates_cohort View
chjqlr2lmw2nvyqc succeeded pneumonia_rates_cohort View
bio3b22s4p4qffsy succeeded gen_pop_rates_cohort View
jgnf6umh377vjumc succeeded covid_rates View
rsyr6rekugaoga6w succeeded covid_comm_rates View
u6z3l4xiacoawydg succeeded pneumonia_rates View
nm5sfvbkxpxwr3qv succeeded gen_pop_rates View
6wqzsxrezsqcljcv succeeded baseline_characteristics View
jktpbbu5aqeogl6p succeeded append_cohorts View
3ke7gyi25g7wasy6 succeeded cox_models View
qahi4k6md263okr3 succeeded fine_gray View