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Job request: 3579

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vaccine-neuro-research
ID:
5jtpnhkyqv2rvjvh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Schultze requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 5000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_sccs_and_historical_cohort.csv

  apply_exclusion_criteria:
    run: stata-mp:latest analysis/apply_exclusion_criteria.do 
    needs: [generate_cohort] 
    outputs:
      moderately_sensitive: 
        log: output/logs/apply_exclusion_criteria.log
      highly_sensitive:
        cohort_controls: output/input_historical_controls.csv
        cohort_az_cases: output/input_AZ_cases.csv
        cohort_pfizer_cases: output/input_PF_cases.csv 
        cohort_moderna_cases: output/input_MOD_cases.csv 

  SCCS_first_dose_only_primary_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do AZ
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_AZ.log
        results: output/tables/results_summary_primary_AZ* 
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_AZ*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_AZ*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_AZ*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_AZ*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_AZ*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_AZ*

  SCCS_first_dose_only_primary_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do PF 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_PF.log
        results: output/tables/results_summary_primary_PF*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_PF*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_PF*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_PF*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_PF*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_PF*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_PF*

  SCCS_first_dose_only_primary_MOD:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do MOD 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_MOD.log
        results: output/tables/results_summary_primary_MOD*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_MOD*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_MOD*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_MOD*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_MOD*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_MOD*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_MOD*

  SCCS_baseline_tables_AZ:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_AZ.log
        tables: output/tables/table1_AZ* 

  SCCS_baseline_tables_PF:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_PF.log
        tables: output/tables/table1_PF* 

  SCCS_baseline_tables_MOD:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do MOD
    needs: [SCCS_first_dose_only_primary_MOD] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_MOD.log
        tables: output/tables/table1_MOD* 

  SCCS_assumption_checking_AZ:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_AZ.log
        plots_S1: output/plots/S1_exposure_centered_interval_AZ*
        plots_S2: output/plots/S2_censored_futime_AZ*

  SCCS_assumption_checking_PF:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_PF.log
        plots_S1: output/plots/S1_exposure_centered_interval_PF*
        plots_S2: output/plots/S2_censored_futime_PF*

  SCCS_assumption_checking_MOD:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do MOD
    needs: [SCCS_first_dose_only_primary_MOD] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_MOD.log
        plots_S1: output/plots/S1_exposure_centered_interval_MOD*
        plots_S2: output/plots/S2_censored_futime_MOD*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:50:11

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-neuro-research
Requested by
Anna Schultze
Branch
main
Force run dependencies
No
Git commit hash
b2975d0
Requested actions
  • apply_exclusion_criteria
  • SCCS_first_dose_only_primary_AZ
  • SCCS_first_dose_only_primary_PF
  • SCCS_first_dose_only_primary_MOD
  • SCCS_baseline_tables_AZ
  • SCCS_baseline_tables_PF
  • SCCS_baseline_tables_MOD
  • SCCS_assumption_checking_AZ
  • SCCS_assumption_checking_PF
  • SCCS_assumption_checking_MOD

Code comparison

Compare the code used in this Job Request