Merge pull request #38 from tcmitchell/pysbol3-test

Add pySBOL3 tests for the SBOL3 files

Author: cjmyers

.github/workflows/python.yml

@@ -0,0 +1,35 @@
+name: Python SBOL3 Test
+
+on:
+  # Schedule a nightly build. Times are UTC
+  # See https://docs.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events
+  schedule:
+    # 5:15 am UTC (https://en.wikipedia.org/wiki/5:15)
+    - cron: '15 5 * * *'
+  push:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Default builds are on Ubuntu
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        # Only test on with the latest version of Python 3
+        python-version: ['3.x']
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: 'recursive'
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install sbol3
+    - name: Test with unittest
+      run: |
+        python -m unittest discover -s src/test/python

.gitignore

@@ -3,3 +3,5 @@
 /.project
 /.classpath
 /.travis.yml~
+/.idea
+__pycache__

src/test/python/test_roundtrip.py

@@ -0,0 +1,180 @@
+import logging
+import os
+import shutil
+import tempfile
+import unittest
+
+import rdflib
+import rdflib.compare
+
+import sbol3
+
+MODULE_LOCATION = os.path.dirname(os.path.abspath(__file__))
+# The SBOLTestSuite root is 3 directories up from this file
+SBOL_TEST_SUITE = os.path.join(MODULE_LOCATION, '..', '..', '..')
+SBOL3_LOCATION = os.path.join(SBOL_TEST_SUITE, 'SBOL3')
+TEST_RESOURCE_DIR = os.path.join(MODULE_LOCATION, 'resources')
+
+DEBUG_ENV_VAR = 'SBOL_TEST_DEBUG'
+
+
+class TestRoundTrip(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        # Skip reading these files
+        # No files are skipped at this time. All SBOLTestSuite files can
+        # be read.
+        cls.skip_reading = [
+        ]
+        # Skip round tripping these files
+        cls.skip_round_trip = [
+        ]
+        # Skip validating these files
+        cls.skip_validation = [
+        ]
+
+    def setUp(self):
+        sbol3.set_defaults()
+        # Create temp directory
+        self.temp_out_dir = tempfile.mkdtemp()
+        self.logger = logging.getLogger('sbol3.test')
+        if not self.logger.hasHandlers():
+            logging.basicConfig()
+        if DEBUG_ENV_VAR in os.environ:
+            self.logger.setLevel(logging.DEBUG)
+
+    def tearDown(self):
+        # Remove directory after the test
+        if self.temp_out_dir:
+            shutil.rmtree(self.temp_out_dir)
+            self.temp_out_dir = None
+        sbol3.set_defaults()
+
+    def test_BBa_F2620_PoPSReceiver(self):
+        sbol_path = os.path.join(SBOL3_LOCATION, 'BBa_F2620_PoPSReceiver',
+                                 'BBa_F2620_PoPSReceiver.ttl')
+        doc = sbol3.Document()
+        doc.read(sbol_path, sbol3.TURTLE)
+        uri = 'https://synbiohub.org/public/igem/BBa_F2620/SubComponent3/Range1'
+        range1 = doc.find(uri)
+        self.assertIsNotNone(range1)
+        self.assertEqual(1, range1.start)
+        self.assertEqual(53, range1.end)
+
+    def find_all_files(self, dirname: str):
+        for item in os.listdir(dirname):
+            item_path = os.path.join(dirname, item)
+            if os.path.isdir(item_path):
+                for f in self.find_all_files(item_path):
+                    yield f
+            elif os.path.isfile(item_path):
+                yield item_path
+            else:
+                print(f'{item} is neither file nor directory')
+
+    @staticmethod
+    def rdf_type(filename: str):
+        filename = os.path.basename(filename)
+        ext = os.path.splitext(filename)[1]
+        # drop the leading dot
+        ext = ext[1:]
+        ext_map = {
+            'nt': sbol3.NTRIPLES,
+            'ttl': sbol3.TURTLE,
+            'rdf': sbol3.RDF_XML,
+            'jsonld': sbol3.JSONLD,
+            'jsonld_expanded': sbol3.JSONLD,
+        }
+        if ext in ext_map:
+            return ext_map[ext]
+        else:
+            return None
+
+    def test_read_all(self):
+        # In lieu of round tripping the files, just make sure we can
+        # read them all.
+        #
+        # This was an early test, before the library was complete and
+        # the files could be round tripped.
+        skip_list = self.skip_reading
+        for f in self.find_all_files(SBOL3_LOCATION):
+            basename = os.path.basename(f)
+            if os.path.splitext(basename)[0] in skip_list:
+                # print(f'Skipping {f}')
+                continue
+            rdf_type = self.rdf_type(f)
+            if rdf_type is None:
+                # Skip file types we don't know
+                # print(f'Skipping {f} of type {rdf_type}')
+                continue
+            # print(f'Reading {f}')
+            doc = sbol3.Document()
+            doc.read(f, rdf_type)
+
+    def run_round_trip_file(self, test_path, file_format):
+        """Runs a round trip test on the file at the given path.
+        Path can be relative or absolute.
+        """
+        filename = os.path.basename(test_path)
+        test2_path = os.path.join(self.temp_out_dir, filename)
+        # Read the document, then write it back to disk
+        doc = sbol3.Document()
+        doc.read(test_path, file_format)
+        skip_list = self.skip_validation
+        basename = os.path.basename(test_path)
+        if os.path.splitext(basename)[0] not in skip_list:
+            # Validate files that are not in the skip list
+            report = doc.validate()
+            if report:
+                for item in report:
+                    print(item)
+                self.fail(f'got {len(report)} validation errors')
+
+        doc.write(test2_path, file_format)
+
+        # Read the newly written document and compare results
+        doc2 = sbol3.Document()
+        doc2.read(test2_path, file_format)
+        # TODO: what about Document.compare()?
+        # self.assertTrue(doc.compare(doc2))
+
+        # Now compare the graphs in RDF
+        g1 = rdflib.Graph()
+        g1.parse(test_path, format=file_format)
+        iso1 = rdflib.compare.to_isomorphic(g1)
+        g2 = rdflib.Graph()
+        g2.parse(test2_path, format=file_format)
+        iso2 = rdflib.compare.to_isomorphic(g2)
+        rdf_diff = rdflib.compare.graph_diff(iso1, iso2)
+        if rdf_diff[1] or rdf_diff[2]:
+            self.logger.warning('Detected %d different RDF triples in %s' %
+                                (len(rdf_diff[1]) + len(rdf_diff[2]), test_path))
+            if not self.logger.isEnabledFor(logging.DEBUG):
+                self.logger.warning('Set environment variable %s to see details',
+                                    DEBUG_ENV_VAR)
+            for stmt in rdf_diff[1]:
+                self.logger.debug('Only in original: %r', stmt)
+            for stmt in rdf_diff[2]:
+                self.logger.debug('Only in loaded: %r', stmt)
+            self.fail('Differences in RDF detected')
+
+    def test_sbol3_files(self):
+        test_dir = SBOL3_LOCATION
+        skip_list = self.skip_round_trip
+        for test_file in self.find_all_files(test_dir):
+            basename = os.path.basename(test_file)
+            if os.path.splitext(basename)[0] in skip_list:
+                self.logger.debug(f'Skipping {test_file}')
+                continue
+            file_format = self.rdf_type(test_file)
+            if not file_format:
+                continue
+            with self.subTest(filename=test_file):
+                self.setUp()
+                self.run_round_trip_file(test_file, file_format)
+                self.tearDown()
+
+
+if __name__ == '__main__':
+    unittest.main()