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ferzcamferzcam
authoredNov 20, 2024··
Merge pull request #91 from bio-ontology-research-group/develop
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‎.github/workflows/python-package_3_10.yml

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‎.github/workflows/python-package_3_11.yml

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‎.github/workflows/python-package_3_12.yml

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‎.github/workflows/python-package_3_9.yml

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‎.github/workflows/unittests.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python Unit Tests
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on:
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push:
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branches: [ "main", develop ]
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pull_request:
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branches: [ "main", develop ]
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jobs:
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python-3-9:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.9"]
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: anaconda-client-env
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environment-file: envs/environment_3_9.yml
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auto-activate-base: false
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channels: conda-forge
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use-mamba: true
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install flake8 nose pinocchio nose-exclude coverage
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
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- name: Test with nose
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run: |
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nosetests tests
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python-3-10:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.10"]
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: anaconda-client-env
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environment-file: envs/environment_3_10.yml
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auto-activate-base: false
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channels: conda-forge
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use-mamba: true
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install flake8 pytest coverage pytest-faulthandler
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pytest -m "not slow" -p no:faulthandler
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python-3-11:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.11"]
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: anaconda-client-env
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environment-file: envs/environment_3_11.yml
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auto-activate-base: false
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channels: conda-forge
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use-mamba: true
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install flake8 pytest coverage pytest-faulthandler
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pytest -m "not slow" -p no:faulthandler
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python-3-12:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.12"]
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: anaconda-client-env
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environment-file: envs/environment_3_12.yml
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auto-activate-base: false
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channels: conda-forge
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use-mamba: true
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install flake8 pytest coverage pytest-faulthandler
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pytest -m "not slow" -p no:faulthandler

‎docs/source/conf.py

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copyright = '2023, Bio-Ontology Research Group'
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author = 'BORG'
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release = '1.0.1'
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version = '1.0.1'
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release = '1.0.2-dev'
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version = '1.0.2-dev'
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# -- General configuration
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extensions = [

‎docs/source/index.rst

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**mOWL** can be installed from `source code <https://github.com/bio-ontology-research-group/mowl>`_ or from `PyPi <https://pypi.org/project/mowl-borg/>`_. For more details on installation check out the how to :doc:`install/index` section of the project.
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.. note::
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This version of documentation corresponds to mOWL-1.0.1.
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This version of documentation corresponds to mOWL-1.0.2-dev.
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mOWL, JPype and the JVM

‎mowl/projection/edge.py

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from pykeen.triples import TriplesFactory
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from deprecated.sphinx import versionadded, deprecated
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from deprecated.sphinx import versionadded, deprecated, versionchanged
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import numpy as np
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import torch as th
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@@ -69,14 +69,15 @@ def getEntitiesAndRelations(edges):
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return Edge.get_entities_and_relations(edges)
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@staticmethod
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@versionchanged(version="1.0.2", reason="Method return type changed to tuple of lists")
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def get_entities_and_relations(edges):
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'''
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:param edges: list of edges
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:type edges: :class:`Edge`
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:returns: Returns a 2-tuple containing the list of entities (heads and tails) and the \
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list of relations
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:rtype: (Set of str, Set of str)
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:rtype: (list of str, list of str)
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'''
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entities = set()
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entities |= {edge.src, edge.dst}
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relations |= {edge.rel}
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entities = sorted(list(entities))
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relations = sorted(list(relations))
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return (entities, relations)
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@staticmethod
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"""
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if entity_to_id is None or relation_to_id is None:
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classes, relations = Edge.getEntitiesAndRelations(edges)
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classes, relations = set(classes), set(relations)
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if entity_to_id is None:
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entity_to_id = {v: k for k, v in enumerate(list(classes))}
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entity_to_id = {v: k for k, v in enumerate(classes)}
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if relation_to_id is None:
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relation_to_id = {v: k for k, v in enumerate(list(relations))}
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relation_to_id = {v: k for k, v in enumerate(relations)}
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def map_edge(edge):
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return [entity_to_id[edge.src], relation_to_id[edge.rel], entity_to_id[edge.dst]]

‎tests/projection/test_edge.py

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ents, rels = Edge.get_entities_and_relations([edge1, edge2])
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self.assertEqual(ents, {"src1", "src2", "dst1", "dst2"})
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self.assertEqual(rels, {"rel1", "rel2"})
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self.assertEqual(ents, ["dst1", "dst2", "src1", "src2"])
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self.assertEqual(rels, ["rel1", "rel2"])
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def test_zip_method(self):
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"""This checks if Edge.zip method works correctly"""

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