Job request: 8492

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Kev Wing requested one or more actions to be run against real patient data in the long-covid-symptoms 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
tlmrwy2qddxaykq3 succeeded generate_community_cases_cohort
rmgktxand2aq7cq2 succeeded generate_potential_controls_contemporary
6pl3odfht3fnghaq failed match_contemporary

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 20000

actions:

# 1. EXTRACT DATA FOR EXPOSED AND POTENTIAL CONTROLS 
  generate_community_cases_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
    outputs:
      highly_sensitive:
        cohort: output/input_covid_community.csv


# 2. EXTRACT DATA FOR POTENTIAL COMPARATORS
# new extract potential comparators code... I guess I'll have to this twice for each control group
# or potentially 3 times: 2018 matches, 2019 matches, contemporary matches?

 # *** contemporary potential comparators
  generate_potential_controls_contemporary:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_potential_controls_contemporary
    outputs:
      highly_sensitive:
        cohort: output/input_potential_controls_contemporary.csv


# 3. MATCH CASES TO COMPARATORS
  # *** contemporary potential comparators
  match_contemporary:
    run: python:latest python analysis/match_contemporary.py
    needs: [generate_community_cases_cohort, generate_potential_controls_contemporary]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_contemporary.txt
      highly_sensitive:
        matched_cases: output/matched_cases_contemporary.csv
        matched_matches: output/matched_matches_contemporary.csv
        matched_all: output/matched_combined_contemporary.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 103:38:10

Config

  • Backend:
    TPP
  • Workspace:
    long-covid-symptoms
  • Branch:
    master
  • Creator:
    kevwing
  • Force run dependencies:
    False
  • Git Commit Hash:
    9f4d438
  • Requested actions:
    • run_all