Job request: 5407

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the post-covid-vaccinated 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

ID Status Action
p4a27frlqsiyosha failed generate_study_population_electively_unvaccinated
qxop2fswpcoz5xqo failed generate_study_population_index
ble76jkn3y4vsodt failed generate_study_population_vaccinated
g7jzvbg7oarcuxrd failed preprocess_data
kzd5mc6ywpuyjgmg failed stage1_data_cleaning_both
kisrhnwxsp4g6rdh failed stage2_missing_table1_both
7zoynrixgwj4fffc succeeded vax_eligibility_inputs
epwx5i33cnwmrhdx succeeded active_analyses

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:

  population_size: 500000

actions:
  active_analyses:
    run: r:latest analysis/active_analyses.R
    outputs:
      highly_sensitive:
        active_analyses: output/active_analyses.rds

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated --output-format feather
    needs: [vax_eligibility_inputs] 
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data:
    run: r:latest analysis/preprocess_data.R
    needs: [generate_study_population_index, generate_study_population_vaccinated, generate_study_population_electively_unvaccinated]
    outputs:
      moderately_sensitive:
        describe: output/describe_*.txt
      highly_sensitive:
        cohort: output/input_*.rds
        venn: output/venn_*.rds

  stage1_data_cleaning_both:
    run: r:latest analysis/Stage1_data_cleaning.R both
    needs: [preprocess_data]
    outputs:
      moderately_sensitive:
        refactoring: output/meta_data_factors_*.csv
        QA_rules: output/QA_summary_*.csv
        IE_criteria: output/Cohort_flow_*.csv
      highly_sensitive:
        cohort: output/input_*_stage1.rds

  stage2_missing_table1_both:
    run: r:latest analysis/Stage2_missing_table1.R both
    needs: [stage1_data_cleaning_both]
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/Check_missing_range_*.csv
        DateChecks: output/Check_dates_range_*.csv
        Descriptive_Table: output/Table1_*.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 25:05:05

Config