Merge pull request #84 from INCATools/list_issue

Bug fixes

.github/workflows/publish_to_pypi.yaml

@@ -1,4 +1,4 @@
-name: Publish Python distributions to PyPI
+name: Publish to PyPI
 
 on:
   # Allows you to run this workflow manually from the Actions tab
@@ -40,4 +40,4 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+        twine upload dist/*

.github/workflows/publish_to_test_pypi.yaml

@@ -0,0 +1,39 @@
+name: Publish to test PyPI
+
+# Expect this action to be triggered manually before
+
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build-and-publish:
+    name: Publish Python distributions to PyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install Deployment Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Install Project Dependencies
+      run: |
+        pip install -r requirements.txt
+    - name: Auto-Generate schema documentation
+      run: PYTHONPATH=./src:$PYTHONPATH python -m dosdp document --schema -o ./src/schema/
+    - name: Package Distribution
+      run: >-
+        python
+        setup.py
+        sdist
+        bdist_wheel
+    - name: Deploy Package
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_TEST_PASSWORD }}
+      run: |
+        twine upload --repository-url https://test.pypi.org/legacy/ dist/*

.github/workflows/tester.yaml

@@ -25,5 +25,7 @@ jobs:
         run: |
             python -m pip install --upgrade pip
             pip install -r requirements.txt
+      - name: Validate DOSDP Schema
+        run: python ./src/schema/schema_validator.py
       - name: Run Test
         run: PYTHONPATH=./src:$PYTHONPATH python -m unittest discover -s src -p '*_test.py'

setup.py

@@ -1,16 +1,32 @@
 import pathlib
 from setuptools import setup
 
+READTHEDOCS = "(http://incatools.github.io/dead_simple_owl_design_patterns/"
+relative_link_mapping = {"(docs/dosdp_schema.md)": READTHEDOCS + "dosdp_schema/)",
+                         "(docs/validator.md)": READTHEDOCS + "validator/)",
+                         "(docs/document.md)": READTHEDOCS + "document/)"}
+
+
+def update_relative_links(readme_content):
+    """
+    Relative links are broken in the pypi home page. So replace them with read the docs absolute links.
+    """
+    for key, value in relative_link_mapping.items():
+        readme_content = readme_content.replace(key, value)
+    return readme_content
+
+
 # The directory containing this file
 HERE = pathlib.Path(__file__).parent
 
 # The text of the README file
 README = (HERE / "README.md").read_text()
+README = update_relative_links(README)
 
 # This call to setup() does all the work
 setup(
     name="dosdp",
-    version="0.1.7.dev1",
+    version="0.1.9.dev1",
     description="The aim of this project is to specify a simple OWL design pattern system that can easily be consumed, whatever your code base.",
     long_description=README,
     long_description_content_type="text/markdown",

src/dosdp/validator.py

@@ -27,7 +27,7 @@ def test_jschema(validator, pattern):
     if not validator.is_valid(pattern):
         es = validator.iter_errors(pattern)
         for e in es:
-            warnings.warn(" => ".join([str(e.schema_path), str(e.message), str(e.context)]))
+            warnings.warn(str(e.message))
             is_valid = False
 
     return is_valid
@@ -200,6 +200,29 @@ def test_multi_clause_multi_list(pattern):
     return stat
 
 
+def test_annotation_properties(pattern):
+    """
+    Structurally tests whether an annotation property is declared before use.
+     Args:
+         pattern: schema in yaml format to validate
+
+    Returns: True if all used annotation properties are declared, False otherwise.
+    """
+    declared_annotations = set()
+    if 'annotationProperties' in pattern.keys(): declared_annotations.update(set(pattern['annotationProperties'].keys()))
+    expr = parse('annotations.[*].annotationProperty')
+    used_annotations = [match for match in expr.find(pattern)]
+
+    stat = True
+    if used_annotations:
+        for annotation_prop in used_annotations:
+            val = annotation_prop.value
+            if val not in declared_annotations:
+                warnings.warn("Annotation property '%s' didn't declared before use." % val)
+                stat = False
+    return stat
+
+
 def format_warning(message, category, filename, lineno, line=None):
     return '%s:%s: %s:%s\n' % (filename, lineno, category.__name__, message)
 
@@ -239,7 +262,8 @@ def validate(pattern):
 
     stat = True
     for pattern_doc in pattern_docs:
-        logging.info("Checking %s" % pattern_doc)
+        if len(pattern_docs) > 1:
+            logging.info("Checking %s" % pattern_doc)
         with open(pattern_doc, "r") as stream:
             try:
                 pattern = ryaml.load(stream)
@@ -249,6 +273,7 @@ def validate(pattern):
                 if not test_clause_nesting(pattern): stat = False
                 if not test_axiom_separator(pattern): stat = False
                 if not test_multi_clause_multi_list(pattern): stat = False
+                if not test_annotation_properties(pattern): stat = False
             except YAMLError as exc:
                 stat = False
                 logging.error('Failed to load pattern file: ' + pattern_doc)

src/schema/dosdp_schema.yaml

@@ -334,7 +334,7 @@ properties:
     doc_type: root
 
   examples:
-    type: list
+    type: array
     items: { type: string }
     description:  "A list of example terms implementing this pattern."
     doc_type: root
@@ -348,7 +348,7 @@ properties:
     doc_type: root
 
   tags:
-    type: list
+    type: array
     items: { type: string }
     description: >
        A list of strings used to tag a pattern for the purposes of arbitrary,

src/schema/schema_validator.py

@@ -0,0 +1,12 @@
+import os
+from ruamel.yaml import YAML
+from jsonschema import Draft7Validator
+
+SCHEMA_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../schema/dosdp_schema.yaml")
+
+
+ryaml = YAML(typ='safe')
+with open(SCHEMA_PATH) as stream:
+    dosdp_schema = ryaml.load(stream)
+
+Draft7Validator.check_schema(dosdp_schema)

src/schema/test/generic_test/schema_test.py

@@ -10,6 +10,8 @@
                                   "../positive_test_set/patterns/acute.yaml")
 POSITIVE_PATTERN_2 = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                   "../positive_test_set/patterns/multi_clause_schema.yaml")
+POSITIVE_PATTERN_3 = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                  "../positive_test_set/patterns/abnormallyHyperplasticAnatomicalEntity.yaml")
 NEGATIVE_PATTERN_1 = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                   "../negative_test_set/acute_negative.yaml")
 
@@ -38,6 +40,13 @@ def test_schema_validity1(self):
         # failing because def does not have a text
         self.assertEqual("{'vars': ['disease']} is not valid under any of the given schemas", next(es).message)
 
+    def test_array_validity(self):
+        self.assertTrue(pathlib.Path(SCHEMA).exists())
+
+        validator = Draft4Validator(self.read_yaml(SCHEMA))
+
+        self.assertTrue(validator.is_valid(self.read_yaml(POSITIVE_PATTERN_3)))
+
     def read_yaml(self, yaml_path):
         with open(yaml_path, "r") as stream:
             try:

src/schema/test/generic_test/validator_test.py

@@ -28,6 +28,10 @@
                                                         "../negative_test_set/multi_clause_with_multi_list.yaml")
 NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST2 = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                                          "../negative_test_set/multi_clause_with_multi_list2.yaml")
+NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                                      "../negative_test_set/undeclared_annotation_prop.yaml")
+NEGATIVE_PATTERN_SCHEMA = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                       "../negative_test_set/not_schema_compliant.yaml")
 
 
 class ValidatorTest(unittest.TestCase):
@@ -60,3 +64,9 @@ def test_axiom_separator(self):
     def test_single_list_per_multi_clause(self):
         self.assertFalse(validate(NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST))
         self.assertFalse(validate(NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST2))
+
+    def test_undeclared_annotation_prop(self):
+        self.assertFalse(validate(NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP))
+
+    def test_schema_validation(self):
+        self.assertFalse(validate(NEGATIVE_PATTERN_SCHEMA))

src/schema/test/negative_test_set/not_schema_compliant.yaml

@@ -0,0 +1,55 @@
+pattern_name: acute
+
+pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/acute.yaml
+
+description: 'This pattern is applied to diseases that are described as having an acute onset, i.e. the sudden appearance of disease manifestations over a short period of time.
+
+Examples: [acute bronchiolitis](http://purl.obolibrary.org/obo/MONDO_0020680),
+  [acute liver failure](http://purl.obolibrary.org/obo/MONDO_0019542)'
+
+contributors:
+- https://orcid.org/0000-0002-6601-2165
+- https://orcid.org/0000-0001-5208-3432
+
+classes:
+  acute: PATO:0000389
+  disease: MONDO:0000001
+
+relations:
+  has modifier: RO:0002573
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+  related_synonym: oio:hasRelatedSynonym
+
+vars:
+  disease: '''disease'''
+
+name:
+  text: acute %s
+  vars:
+  - disease
+
+# axioms is not valid
+axioms:
+- annotationProperty: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+annotations:
+#  property is not valid
+- property: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+def:
+  text: Acute form of %s.
+  vars:
+  - disease
+
+equivalentTo:
+  text: '%s and ''has modifier'' some ''acute'''
+  vars:
+  - disease

src/schema/test/negative_test_set/undeclared_annotation_prop.yaml

@@ -0,0 +1,47 @@
+pattern_name: acute
+
+pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/acute.yaml
+
+description: 'This pattern is applied to diseases that are described as having an acute onset, i.e. the sudden appearance of disease manifestations over a short period of time.
+
+Examples: [acute bronchiolitis](http://purl.obolibrary.org/obo/MONDO_0020680),
+  [acute liver failure](http://purl.obolibrary.org/obo/MONDO_0019542)'
+
+contributors:
+- https://orcid.org/0000-0002-6601-2165
+- https://orcid.org/0000-0001-5208-3432
+
+classes:
+  acute: PATO:0000389
+  disease: MONDO:0000001
+
+relations:
+  has modifier: RO:0002573
+
+annotationProperties:
+#  exact_synonym: oio:hasExactSynonym
+  related_synonym: oio:hasRelatedSynonym
+
+vars:
+  disease: '''disease'''
+
+name:
+  text: acute %s
+  vars:
+  - disease
+
+annotations:
+- annotationProperty: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+def:
+  text: Acute form of %s.
+  vars:
+  - disease
+
+equivalentTo:
+  text: '%s and ''has modifier'' some ''acute'''
+  vars:
+  - disease

src/schema/test/positive_test_set/patterns/abnormallyHyperplasticAnatomicalEntity.yaml

@@ -0,0 +1,50 @@
+pattern_name: abnormallyHyperplasticAnatomicalEntity.yaml
+
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyHyperplasticAnatomicalEntity.yaml
+
+description: 'Hyperplastic anatomical entity, for example, thyroid gland hyperplasia. The increase in size of the anatomical entitiy is due to an increase in cell number,'
+
+examples:
+  - http://purl.obolibrary.org/obo/HP_0008249
+  - http://purl.obolibrary.org/obo/MP_0000630
+  - http://purl.obolibrary.org/obo/MP_0013765
+
+contributors:
+  - https://orcid.org/0000-0001-8314-2140
+
+classes:
+  abnormal: PATO:0000460
+  anatomical_entity: UBERON:0001062
+  hyperplastic: PATO:0000644
+
+relations:
+  characteristic_of: RO:0000052
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+
+vars:
+  anatomical_entity: "'anatomical_entity'"
+
+name:
+  text: "%s hyperplasia"
+  vars:
+    - anatomical_entity
+
+annotations:
+  - annotationProperty: exact_synonym
+    text: "hyperplastic %s"
+    vars:
+      - anatomical_entity
+
+def:
+  text: "The increased size of the %s is due to an increase in cell number (hyperplasia)."
+  vars:
+    - anatomical_entity
+
+equivalentTo:
+  text: "'has_part' some ('hyperplastic' and ('characteristic_of' some %s) and ('has_modifier' some 'abnormal'))"
+  vars:
+    - anatomical_entity