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
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 |
|---|---|---|
| ea7cf6od46vp6izy | succeeded | anSUMM |
| duisf7z5dkvwkfbl | succeeded | crMAIN |
Pipeline
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
State
State is inferred from the related Jobs.
Status: Succeeded
Timings
Timings set to UTC timezone.
- Created:
- Started:
- Finished:
- Runtime: 00:09:57