This page shows the technical details of what happened when authorised researcher dgrint requested one or more actions to be run against real patient data in the SGTF-Omi 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
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.
Show Hide project.yaml
version: '3.0' expectations: population_size: 10000 actions: generate_cohort: run: cohortextractor:latest generate_cohort --study-definition study_definition outputs: highly_sensitive: cohort: output/input.csv crMAIN: run: stata-mp:latest analysis/cr_main.do needs: [generate_cohort] outputs: moderately_sensitive: log: logs/cr_main.log highly_sensitive: data: output/main.dta anSUMM: run: stata-mp:latest analysis/an_summary.do needs: [crMAIN] outputs: moderately_sensitive: log: logs/an_summary.log figure1: output/sgtf_perc_region.svg figure2: output/sgtf_perc_region.pdf anTAB1: run: stata-mp:latest analysis/an_table1.do needs: [crMAIN] outputs: moderately_sensitive: log: logs/an_table1.log table1text: output/table1.txt table1xlsx: output/table1.xlsx figure1: output/time_ae_hist.svg figure2: output/date_ae_hist.svg figure3: output/date_ae_hist1.svg figure4: output/ae_hist.svg figure5: output/ae_kden.svg anCOX: run: stata-mp:latest analysis/an_cox.do needs: [crMAIN] outputs: moderately_sensitive: log: logs/an_cox.log figure1: output/cox_shoen.svg figure2: output/cox_km.svg figure3: output/cox_cumhaz.svg figure4: output/cox_haz.svg table1text: output/table2.txt table1xlsx: output/table2.xlsx crIMP: run: stata-mp:latest analysis/cr_imputed.do needs: [crMAIN] outputs: moderately_sensitive: log: logs/cr_imputed.log highly_sensitive: data: output/main_imputed.dta anCOX_IMP: run: stata-mp:latest analysis/an_cox_imputed.do needs: [crIMP] outputs: moderately_sensitive: log: logs/an_cox_imputed.log highly_sensitive: data2: output/an_imputed_eth2.ster anRISK: run: stata-mp:latest analysis/an_risk.do needs: [crMAIN] outputs: moderately_sensitive: log: logs/an_risk.log table1text: output/table3.txt table1xlsx: output/table3.xlsx