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Job request: 8492

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
long-covid-symptoms
ID:
oryb3qfuwrjd3pog
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Kevin Wing 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: 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 103:38:10

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

Job information

Status
Failed
Backend
TPP
Workspace
long-covid-symptoms
Requested by
Kevin Wing
Branch
master
Force run dependencies
No
Git commit hash
9f4d438
Requested actions
  • run_all

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