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Job request: 6570

Organisation:
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
kl37tc5fecxhvu6m

This page shows the technical details of what happened when 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 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

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_prim_cov]
    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_2, 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: 00:01:59

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

Job information

Status
Failed
Backend
TPP
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
8fecce0
Requested actions
  • generate_results_jun
  • generate_results_oct