Job request: 1833

Organisation:: The London School of Hygiene & Tropical Medicine
Workspace:: post-admissions-admissions-kb
ID:: drzqnfnlhrojtuhr

This page shows the technical details of what happened when authorised researcher Krishnan Bhaskaran 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.

Jobs

Action:

create_covid

Status:

Status: Succeeded

Job identifier:

53hrwhxw6aecmnvl
Action:

create_2019pool02

Status:

Status: Succeeded

Job identifier:

vlgqlktiou3s6vzj
Action:

create_2019pool12

Status:

Status: Succeeded

Job identifier:

7w73y4k43klgrbuj
Action:

create_2019pool07

Status:

Status: Succeeded

Job identifier:

ozjymvrfckq776vu
Action:

create_2019pool10

Status:

Status: Succeeded

Job identifier:

3bdfe4pa27c47ock
Action:

create_2019pool03

Status:

Status: Succeeded

Job identifier:

4fgwc6bm525m37zi
Action:

create_2019pool04

Status:

Status: Succeeded

Job identifier:

pxsdoufymp5s6ive
Action:

create_2019pool05

Status:

Status: Succeeded

Job identifier:

lohyu2y624pshz6i
Action:

create_2019pool09

Status:

Status: Succeeded

Job identifier:

hfjz7bkmum6tblk5
Action:

create_flu2017_19

Status:

Status: Succeeded

Job identifier:

dygawsugzyhgdylj
Action:

create_2019pool06

Status:

Status: Succeeded

Job identifier:

i3laehwxhu7s5vu2
Action:

create_2019pool08

Status:

Status: Succeeded

Job identifier:

m276hsrexkdxvuxj
Action:

create_2019pool11

Status:

Status: Succeeded

Job identifier:

heembqscu23f6x7u

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_pop_covdischarged:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covdischarged
    outputs:
      highly_sensitive:
        cohort: output/input_covdischarged.csv

  generate_study_pop_pneum2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneum2019
    outputs:
      highly_sensitive:
        cohort: output/input_pneum2019.csv

  generate_study_pop_flu2017_19:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flu2017_19
    outputs:
      highly_sensitive:
        cohort: output/input_flu2017_19.csv

        
  generate_2019pool02:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool02
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool02.csv        

  generate_2019pool02_ALT:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019 --index-date-range "2019-02-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2019_2019-02-01.csv        

  generate_2019pool03:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool03
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool03.csv        

  generate_2019pool04:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool04
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool04.csv        

  generate_2019pool05:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool05
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool05.csv        

  generate_2019pool06:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool06
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool06.csv        

  generate_2019pool07:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool07
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool07.csv        

  generate_2019pool08:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool08
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool08.csv        
           
  generate_2019pool09:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool09
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool09.csv        

  generate_2019pool10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool10
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool10.csv        
      
  generate_2019pool11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool11
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool11.csv        

  generate_2019pool12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool12
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool12.csv        
                   
  create_covid:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do COVID
    needs: [generate_study_pop_covdischarged]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_COVID.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_COVID.log

  create_pneum2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do PNEUM 
    needs: [generate_study_pop_pneum2019]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_PNEUM.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_PNEUM.log
 
  create_flu2017_19:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do FLU 
    needs: [generate_study_pop_flu2017_19]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_FLU.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_FLU.log

  create_2019pool02:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 02
    needs: [generate_2019pool02]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_02.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_02.log

  create_2019pool03:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 03
    needs: [generate_2019pool03]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_03.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_03.log

  create_2019pool04:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 04
    needs: [generate_2019pool04]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_04.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_04.log

  create_2019pool05:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 05
    needs: [generate_2019pool05]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_05.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_05.log

  create_2019pool06:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 06
    needs: [generate_2019pool06]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_06.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_06.log

  create_2019pool07:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 07
    needs: [generate_2019pool07]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_07.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_07.log

  create_2019pool08:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 08
    needs: [generate_2019pool08]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_08.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_08.log

  create_2019pool09:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 09
    needs: [generate_2019pool09]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_09.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_09.log

  create_2019pool10:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 10
    needs: [generate_2019pool10]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_10.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_10.log

  create_2019pool11:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 11
    needs: [generate_2019pool11]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_11.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_11.log

  create_2019pool12:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 12
    needs: [generate_2019pool12]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_12.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_12.log


  getmatches2019:
    run: stata-mp:latest analysis/cr_getmatches2019.do
    needs:
      - create_covid
      - create_2019pool02
      - create_2019pool03
      - create_2019pool04
      - create_2019pool05
      - create_2019pool06
      - create_2019pool07
      - create_2019pool08
      - create_2019pool09
      - create_2019pool10
      - create_2019pool11
      - create_2019pool12
    outputs:
      highly_sensitive:
        cohort: analysis/cr_getmatches2019.dta
      moderately_sensitive:
        log: analysis/output/cr_getmatches2019.log

  appenddata:
    run: stata-mp:latest analysis/cr_append_process_data.do
    needs:
      - create_covid
      - create_pneum2019
      - create_flu2017_19
      - getmatches2019
    outputs:
      highly_sensitive:
        cohort: analysis/cr_append_process_data.dta
      moderately_sensitive:
        log: analysis/output/cr_append_process_data.log

  andescriptives_models:
    run: stata-mp:latest analysis/model_descriptives_models.do
    needs: 
      - generate_study_pop_covdischarged
      - appenddata
    outputs:
      moderately_sensitive:
        logs: analysis/output/*.log 
        tables: analysis/output/an_*.txt
        figures: analysis/output/an_cumulativeincidence*.svg
        timefig: analysis/output/an_desc*.svg
        models: analysis/output/models/an_cox*.ster

  anprocess_forestplots:
    run: stata-mp:latest analysis/model_forestplots.do
    needs: [andescriptives_models]
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_*.svg 
      
  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_study_pop_covdischarged]
    outputs:
      moderately_sensitive:
        log: logs/model.log

Timeline

Created: 3 years ago 26 Apr 2021 16:19:40 UTC
Started: 3 years ago 26 Apr 2021 16:20:00 UTC
Finished: 3 years ago 26 Apr 2021 22:32:47 UTC
Runtime: 07:21:32

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status: Succeeded
Backend: TPP
Workspace: post-admissions-admissions-kb
Requested by: Krishnan Bhaskaran
Branch: master
Force run dependencies: No
Git commit hash: 50d7dd1
Requested actions: create_covid

create_flu2017_19

create_2019pool02

create_2019pool03

create_2019pool04

create_2019pool05

create_2019pool06

create_2019pool07

create_2019pool08

create_2019pool09

create_2019pool10

create_2019pool11

create_2019pool12

Code comparison

Compare the code used in this Job Request