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Job request: 6438

Organisation:
Bennett Institute
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
xazvxfqtytqhczmj
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    generate_results_jun
    Status:
    Status: Failed
    Job identifier:
    7ceidfntalv3d42b
    Error:
    nonzero_exit: Job exited with error code 1

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: 00:01:12

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

Job request

Status
Failed
Backend
TPP
Workspace
vaccine-effectiveness-hospital-admissions-validation
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
62f23e8
Requested actions
  • generate_results_jun

Code comparison

Compare the code used in this job request