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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 the authorised researcher Kevin Wing 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

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 request

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

Code comparison

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