Merge pull request #1 from RobokopU24/packaging

Packaging

.github/workflows/pypi.yml

@@ -0,0 +1,70 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build Python 🐍 distributions
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.9"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/robokop-genetics
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+      - publish-to-testpypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/robokop-genetics
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+

.github/workflows/test.yml

@@ -0,0 +1,23 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+      - name: Run pytest
+        run: |
+          python -m pytest tests/test_normalization.py tests/test_services.py

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -0,0 +1,2 @@
+requests>=2.32.3
+redis>=5.0.4

robokop_genetics/services/clingen.py

@@ -81,7 +81,9 @@ def get_batch_of_synonyms(self, variant_curie_list: list):
             query_response: ClinGenQueryResponse = self.query_service(query_url, data=variant_pseudo_file)
             if query_response.success:
                 for allele_json in query_response.response_json:
-                    normalization_results.append(self.parse_result(allele_json))
+                    parsed_result = self.parse_result(allele_json)
+                    if parsed_result is not None:
+                        normalization_results.append(parsed_result)
             else:
                 for j in range(len(variant_subset)):
                     normalization_results.append(ClinGenSynonymizationResult(success=False,
@@ -131,7 +133,9 @@ def get_synonyms_by_parameter_matching(self, url_param: str, url_param_value: st
                                                                           error_message='Clingen returned a 200 status but no results.'))
             else:
                 for response_item in query_response.response_json:
-                    synonymization_results.append(self.parse_result(response_item))
+                    parsed_result = self.parse_result(response_item)
+                    if parsed_result is not None:
+                        synonymization_results.append(parsed_result)
                 if allele_preference:
                     filtered_syn_results = []
                     for syn_result in synonymization_results:
@@ -159,6 +163,13 @@ def parse_result(self, allele_json: dict):
                                                error_message=cg_error_description)
         try:
             variant_caid = allele_json['@id'].rsplit('/', 1)[1]
+            # clingen added Protein Allele IDs but we don't want them (for now)
+            if variant_caid.startswith('PA'):
+                return None
+                # we could do something like the following, but it's not really an error, let's just ignore them
+                # return ClinGenSynonymizationResult(success=False,
+                #                                    error_type='UnsupportedIdentifier',
+                #                                    error_message=f'Protein Allele IDs not supported {variant_caid}')
         except KeyError:
             return ClinGenSynonymizationResult(success=False,
                                                error_type='MissingIdentifier',

setup.py

@@ -5,19 +5,25 @@
 
 setuptools.setup(
     name="robokop-genetics",
-    version="0.4.1",
+    version="0.5.0",
     author="Evan Morris",
     author_email="[email protected]",
+    maintainer="Evan Morris",
+    maintainer_email="[email protected]",
     description="A package for Robokop genetics tools and services.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://github.com/ObesityHub/robokop-genetics",
+    url="https://github.com/RobokopU24/robokop-genetics",
     packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.8',
-    install_requires=["requests", "redis"]
-)
+    python_requires='>=3.9',
+    license="CC-0",
+    install_requires=[
+        "requests>=2.32.3",
+        "redis>=5.0.4"
+    ]
+)

tests/test_normalization.py

@@ -41,10 +41,15 @@ def test_one_at_a_time_normalization(genetics_normalizer):
     assert normalization_result['error_type'] == 'InefficientUsage'
 
     node_id = "CLINVARVARIANT:18390"
-    normalization_info = genetics_normalizer.get_sequence_variant_normalization(node_id).pop()
-    assert normalization_info["id"] == 'CAID:CA128085'
-    assert normalization_info["name"] == 'rs671'
-    assert 'DBSNP:rs671' in normalization_info["equivalent_identifiers"]
+    synonymization_results = genetics_normalizer.get_sequence_variant_normalization(node_id)
+    found_result = False
+    for normalization_info in synonymization_results:
+        if 'id' in normalization_info:
+            assert normalization_info["id"] == 'CAID:CA128085'
+            assert normalization_info["name"] == 'rs671'
+            assert 'DBSNP:rs671' in normalization_info["equivalent_identifiers"]
+            found_result = True
+    assert found_result
 
     # rs369602258 is tri-allelic - the following tests show how a specific allele can be normalized from a DBSNP
     # if no allele specified return all CAID and their synonym sets