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Job request: 6408

Organisation:
Bennett Institute
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
nzwhnypd73aohuum
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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: 1000

actions:
 
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range  "2021-06-01 to 2021-06-01 by month" --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_prim_cov:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prim_cov --index-date-range  "2021-06-01 to 2021-06-01 by month" --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_prim_cov_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range  "2021-10-01 to 2021-10-01 by month" --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_prim_cov_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prim_cov --index-date-range  "2021-10-01 to 2021-10-01 by month" --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_prim_cov*.csv.gz

  generate_results_jun:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/generate_results_jun.ipynb --execute --to html --template basic --output-dir=/workspace/output/jun --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_study_population_2, generate_study_population_prim_cov, generate_study_population_prim_cov_2]
    outputs:
      moderately_sensitive:
        notebook: output/jun/generate_results_jun.html
        tables: output/jun/summary_tabl*.csv
        id_tables: output/jun/identification_table_*.csv
        cm: output/jun/cm_*.jpeg

  generate_results_oct:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/generate_results_oct.ipynb --execute --to html --template basic --output-dir=/workspace/output/oct --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_study_population, generate_study_population_2, generate_study_population_prim_cov, generate_study_population_prim_cov_2]
    outputs:
      moderately_sensitive:
        notebook: output/oct/generate_results_oct.html
        tables: output/oct/summary_tabl*.csv
        id_tables: output/oct/identification_table_*.csv
        cm: output/oct/cm_*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:11

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vaccine-effectiveness-hospital-admissions-validation
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
e0b091f
Requested actions
  • generate_results_jun
  • generate_results_oct

Code comparison

Compare the code used in this Job Request