Merge pull request #33 from linkml/fix-funowl-version

fix funowl version

.github/workflows/pypi-publish.yaml

@@ -9,45 +9,28 @@ jobs:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
 
-    #----------------------------------------------
-    #       check-out repo and set-up python     
-    #----------------------------------------------
     steps:
-    - uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2.2.2
-      with:
-        python-version: 3.9
-
-    #----------------------------------------------
-    #          install & configure poetry         
-    #----------------------------------------------
-    - name: Install Poetry
-      uses: snok/install-poetry@v1.1.6
-      with:
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-
-    #----------------------------------------------
-    #            install dependencies
-    #----------------------------------------------
-    - name: Install dependencies
-      run: poetry install --no-interaction
-
-    #----------------------------------------------
-    #                 build dist
-    #----------------------------------------------
-    - name: Build source and wheel archives
-      run: |
-        poetry version $(git describe --tags --abbrev=0)
-        poetry build
-
-    #----------------------------------------------
-    #          publish package to PyPI     
-    #----------------------------------------------
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.2.2
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v3.1.0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pip install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: |
+          poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

docs/usage.md

@@ -22,7 +22,7 @@ Minimally you need to specify two inputs:
 To convert:
 
 ```bash
-linkml-data2owl -s my_schema.yaml my_data.{yaml,json,tsv,rdf} -o my_ontology.owl.ttl 
+linkml-data2owl -s my_schema.yaml my_data.{yaml,json,tsv,rdf} -o my_ontology.ofn
 ```
 
 For all options, see:

linkml_owl/dumpers/owl_dumper.py

@@ -1,3 +1,4 @@
+import sys
 from collections import defaultdict
 from typing import Optional, List, Set, Any, Union, Dict, Tuple
 from dataclasses import dataclass, field
@@ -15,7 +16,7 @@
 from linkml_runtime.index.object_index import ObjectIndex
 from linkml_runtime.utils.inference_utils import infer_all_slot_values, infer_slot_value, Config
 
-from rdflib import URIRef
+from rdflib import URIRef, Graph
 
 from linkml_runtime.linkml_model.meta import ClassDefinition, SchemaDefinition, SlotDefinition, Definition, \
     ClassDefinitionName
@@ -168,20 +169,26 @@ def to_ontology_document(self, element: Union[YAMLRoot, List[YAMLRoot]], schema:
             doc.prefixDeclarations.append(Prefix(pfx.prefix_prefix, pfx.prefix_reference))
         return doc
 
-    def dumps(self, element: YAMLRoot, schema: SchemaDefinition = None, schemaview: SchemaView = None, iri=None) -> str:
+    def dumps(self, element: YAMLRoot, schema: SchemaDefinition = None, schemaview: SchemaView = None, iri=None, output_type=None) -> str:
         """
         Dump a linkml instance tree to a function syntax OWL ontology string
 
         :param element:
         :param schema:
         :param schemaview:
         :param iri:
+        :param output_type:
         :return:
         """
         if schemaview:
             schema = schemaview.schema
         doc = self.to_ontology_document(element, schema, iri=iri)
-        return str(doc)
+        if output_type == "ttl":
+            g = Graph()
+            doc.to_rdf(g)
+            return g.serialize(format="ttl")
+        else:
+            return str(doc)
 
     def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_object=True) -> Any:
         """
@@ -296,7 +303,7 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
                             axiom_annotations.append(Annotation(ann_slot_iri, ann_val))
             # templates
             for tmpl in owl_templates:
-                self.add_axioms_from_template(tmpl, element)
+                self.add_axioms_from_template(tmpl, element, schema=schema)
             if schema_level_slot.slot_uri is not None:
                 slot_uri = self._get_IRI_str(schema_level_slot.slot_uri)
             else:
@@ -524,8 +531,9 @@ def _get_inferred_slot_annotations(self, slot: SlotDefinition, ann_key: str,
         anc_slots = [slot]
         sv = self.schemaview
         for anc_c in sv.class_ancestors(class_name, reflexive=True):
-            induced_slot = sv.induced_slot(slot.name, anc_c)
-            anc_slots.append(induced_slot)
+            if slot.name in sv.class_slots(anc_c):
+                induced_slot = sv.induced_slot(slot.name, anc_c)
+                anc_slots.append(induced_slot)
         for a in sv.slot_ancestors(slot.name, reflexive=True):
             anc_slots.append(sv.get_slot(a))
         for s in anc_slots:
@@ -634,20 +642,20 @@ def parse_axioms_string(self, owl_str: str, schemaview: SchemaView = None) -> On
         for prefix, url in schemaview.namespaces().items():
             prefix_lines.append(f'Prefix( {prefix}: = <{url}> )')
         header = "\n".join(prefix_lines)
-        owl_str = f'{header}\nOntology(\n{owl_str}\n)'
+        owl_str = f'{header}\nOntology(<http://example.org>\n{owl_str}\n)'
         logging.debug(owl_str)
         try:
             doc = to_python(owl_str)
         except Exception as e:
             logging.error(f'Error parsing generated OWL: {owl_str}')
             raise e
-        from funowl.writers.FunctionalWriter import FunctionalWriter
-        from rdflib import Graph
-        g = Graph()
-        for p in doc.prefixDeclarations:
-            g.namespace_manager.bind(p.prefixName, p.fullIRI)
-        fw = FunctionalWriter(g=g)
-        owl_str_roundtrip = doc.to_functional(fw)
+        #from funowl.writers.FunctionalWriter import FunctionalWriter
+        #from rdflib import Graph
+        #g = Graph()
+        #for p in doc.prefixDeclarations:
+        #    g.namespace_manager.bind(p.prefixName, p.fullIRI)
+        #fw = FunctionalWriter(g=g)
+        #owl_str_roundtrip = doc.to_functional(fw)
         #logging.debug(f'ROUNDTRIP = {owl_str_roundtrip}')
         return doc
 
@@ -686,6 +694,12 @@ def tr(e: YAMLRoot):
         else:
             d["tr"] = tr
         jt = Template(tstr)
+
+        def _tr(x):
+            fw = FunctionalWriter()
+            expr = self.transform(x, schema)
+            return expr.to_functional(fw)
+        d["tr"] = _tr
         owl_str = jt.render(**d)
         axioms = self.parse_axioms_string(owl_str).ontology.axioms
         self.ontology.axioms += axioms
@@ -724,34 +738,42 @@ def populate_missing_values(self, element: YAMLRoot):
               help="Path to python datamodel module")
 @click.option("--format", "-f",
               help="Input format (will be inferred from file suffix if not specified)")
-@click.option('-o', '--output', required=True,
+@click.option('-o', '--output',
+              type=click.File(mode="w"),
+              default=sys.stdout,
               help="Path to OWL functional syntax output")
+@click.option('-O', '--output-type',
+              type=click.Choice(["ofn", "ttl"]),
+              help="Output format")
 @click.option("--autofill/--no-autofill",
               default=False,
               show_default=True,
               help="If True, fill missing data slots using string_serialization")
 @click.argument('inputfile')
-def cli(inputfile: str, schema: str, target_class, module, output, format, autofill: bool, verbose: int, quiet: bool, **args):
+def cli(inputfile: str, schema: str, target_class, module, output, output_type, format, autofill: bool, verbose: int, quiet: bool, **args):
     """
     Dump LinkML instance data as OWL
 
     Examples:
 
     Convert a CSV to OWL
 
-        linkml-data2owl -s tests/inputs/owl_dumper_test.yaml tests/inputs/parts.csv -o parts.ofn
+        linkml-data2owl -s owl_dumper_test.yaml parts.csv -o parts.ofn
 
-        Note in this example, there must be a class type designator column `@type` in the CSV
+    Note in this example, there must be a class type designator column `@type` in the CSV
 
     Convert a CSV to OWL, homogeneous classes:
 
-        linkml-data2owl -C EquivGenusAndPartOf -s tests/inputs/owl_dumper_test.yaml \
-            tests/inputs/parts_implicit_type.csv -o parts.ofn
+        linkml-data2owl -C EquivGenusAndPartOf -s owl_dumper_test.yaml \
+            parts_implicit_type.csv -o parts.ofn
 
     Convert YAML or JSON to OWL:
 
-        linkml-data2owl -s tests/inputs/owl_dumper_test.yaml tests/inputs/owl_dumper_test_data.yaml -o ont.ofn
+        linkml-data2owl -s owl_dumper_test.yaml owl_dumper_test_data.yaml -o ont.ofn
 
+    More documentation:
+
+        https://linkml.io/linkml-owl/
     """
     logger = logging.getLogger()
     if verbose >= 2:
@@ -775,12 +797,8 @@ def cli(inputfile: str, schema: str, target_class, module, output, format, autof
     dumper = OWLDumper()
     if autofill:
         dumper.autofill = True
-    doc = dumper.dumps(element, schemaview=sv)
-    if output is None:
-        print(str(doc))
-    else:
-        with open(output, 'w') as stream:
-            stream.write(str(doc))
+    doc = dumper.dumps(element, schemaview=sv, output_type=output_type)
+    output.write(str(doc))
 
 
 if __name__ == '__main__':