workflow and last adaptations

Author: dachafra

.github/workflows/pypi-publish.yml

@@ -0,0 +1,49 @@
+name: Publish Python distribution to PyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry
+    - name: Build a binary wheel and a source tarball
+      run: |
+        poetry build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+      url: https://pypi.org/p/owl2yarrrml  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -1,4 +1,4 @@
-# Transforming your ontology to YARRRML mappings
+# Transforming your ontology into YARRRML mappings
 This script generates a YARRRML template from the input ontology. The transformations made are:
 
 | Ontology        | Mapping           
@@ -8,9 +8,24 @@ This script generates a YARRRML template from the input ontology. The transforma
 | Object Property | Join PredicateObjectMap in the TriplesMap corresponding to the class defined in the domain of the property and where the parentTriplesMap is the TriplesMap corresponding to the class defined in the range of the property | 
 
 ## How to execute it
-In order to avoid problems, we recommend that the input ontology follows RDF/XML syntax
 
+### Execution from CLI
+The input ontology can be serialized in NTRIPLES, RDF/XML or Turtle
+```bash
+python3 -m pip install owl2ready
+python3 owl2yarrrml -i paht/ontology.xml -o ouput_path/mapping.yml
+```
+
+### Execution as a library
+The ontology has to be provided in RDF/XML.
 ```python
-python3 -m pip install -r requirements.txt
-python3 translate.py -i ontology.xml -o mapping.yml
+import owl2yarrrml
+import owlready2
+ontology=owlready2.get_ontology("file://path/to/my/ontology.xml").load()
+yarrrml_content = owl2yarrrml.translate(ontology)
+
 ```
+
+## Authors
+CiTIUS - Universidade de Santiago de Compostela (2023-now) and Ontology Engineering Group - Universidad Politécnica de Madrid (2020-2023):
+- [David Chaves-Fraga](mailto:david.chaves@usc.es)

pyproject.toml

@@ -10,9 +10,10 @@ repository = "https://github.com/citius/owl2yarrrml"
 keywords = ["owl", "yarrrml", "rdf", "mapping", "ontology"]
 
 [tool.poetry.dependencies]
-python = ">3.12"
+python = ">3.8.1,<4.0.0"
 PyYAML = "^6.0"
 owlready2 = "^0.39.0"
+rdflib="^7.1.4"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.0.0"

src/owl2yarrrml/__init__.py

@@ -0,0 +1,8 @@
+
+from .translate import *
+
+
+def translate(ontology):
+    template = init_yarrrml()
+    construct_mapping(template, ontology)
+    return template

src/owl2yarrrml/__main__.py

@@ -1,9 +1,37 @@
+from . import translate
 import argparse
 import sys
 import yaml
 import os
-from .translate import translate
-import owlready2
+import tempfile
+from rdflib import Graph
+from owlready2 import World
+
+
+# Inline load_ontology logic
+def load_ontology(path_or_url: str):
+    """
+    Load ontology from a local file path or URL.
+    Supports Turtle by converting via rdflib, otherwise uses Owlready2 directly.
+    """
+    world = World()
+    ext = path_or_url.split('.')[-1].lower()
+
+    if ext in ("ttl", "turtle"):
+        # Parse Turtle to RDF/XML using rdflib
+        g = Graph()
+        g.parse(path_or_url, format="turtle")
+        with tempfile.NamedTemporaryFile(suffix=".owl", delete=False) as tmp:
+            tmp_path = tmp.name
+            g.serialize(destination=tmp_path, format="xml")
+        onto = world.get_ontology(f"file://{tmp_path}").load()
+    else:
+        # Assume RDF/XML, OWL/XML, N-Triples, etc.
+        # Prepend file:// for local paths if needed
+        if not path_or_url.startswith(("http://", "https://", "file://")):
+            path_or_url = "file://" + os.path.abspath(path_or_url)
+        onto = world.get_ontology(path_or_url).load()
+    return onto
 
 def parsing_arguments():
     parser = argparse.ArgumentParser()
@@ -12,7 +40,7 @@ def parsing_arguments():
     args = parser.parse_args()
     if len(sys.argv) == 5:
         try:
-            ontology = owlready2.get_ontology("file://" + os.path.abspath(str(args.ontology))).load()
+            ontology = load_ontology(str(args.ontology))
             output_path = str(args.output)
             return ontology, output_path
         except ValueError:
@@ -30,7 +58,6 @@ def write_results():
         output_stream.write(dumped_yaml)
 
 if __name__ == "__main__":
-    # Allow execution via: python -m owl2yarrrml -i ontology.owl -o mapping.yaml
     ontology, output_path = parsing_arguments()
     mapping = translate(ontology)
     write_results()

src/owl2yarrrml/constants.py

@@ -1,7 +1,36 @@
 
 
 
-URL_TEMPLATE = "https://raw.githubusercontent.com/oeg-upm/owl2yarrrml/refs/heads/main/refs/resources/template.yaml"
+YAML_TEMPLATE = """
+prefixes:
+  xsd: http://www.w3.org/2001/XMLSchema#
+  rr: http://www.w3.org/ns/r2rml#
+  rml: http://semweb.mmlab.be/ns/rml#
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  ql: http://semweb.mmlab.be/ns/ql#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  foaf: http://xmlns.com/foaf/0.1/
+  schema: http://schema.org/
+  dc: http://purl.org/dc/elements/1.1/
+  skos: http://www.w3.org/2004/02/skos/core#
+
+
+mappings:
+  triplesmap0:
+    sources:
+      - []
+    s: http://$()
+    po:
+      - [a, class]
+      - p: predicate
+        o:
+          - mapping: triplesmap2
+            condition:
+              function: equal
+              parameters:
+                - [str1, $()]
+                - [str2, $()]
+"""
 
 ##############################################################################
 #############################   YARRRML CONSTANTS  ###########################

src/owl2yarrrml/translate.py

@@ -1,20 +1,11 @@
 import yaml
 import copy
-from urllib.request import urlopen
 from owlready2 import *
 from .constants import *
 
 
-def translate(ontology):
-    template = init_yarrrml()
-    construct_mapping(template, ontology)
-    return template
-
 def init_yarrrml():
-    with urlopen(URL_TEMPLATE) as response:
-        content = response.read().decode('utf-8')
-        template = yaml.load(content, Loader=yaml.FullLoader)
-    return template
+    return yaml.load(YAML_TEMPLATE, Loader=yaml.FullLoader)
 
 
 def construct_mapping(template, onto):
@@ -75,7 +66,7 @@ def generate_prefixes(template, onto):
             prefixes[do.namespace.base_iri] = do.namespace.name
     return prefixes
 
-def find_triplesmap(mapping, range):
+def find_triplesmap(mapping, range, prefixes):
     ref_triples_map = ""
     for triplesMap in dict.keys(mapping['mappings']):
         if mapping['mappings'][triplesMap]['po'][0][1] == range.iri.replace(range.namespace.base_iri,  prefixes[range.namespace.base_iri] + ":"):
@@ -108,7 +99,7 @@ def generate_ref_object_maps(triplesmap, join_template, template, c, onto, prefi
 
 
 def create_join_condition(template, join_template, o, triplesmap, range, prefixes):
-    triples_map_parent = find_triplesmap(template, range)
+    triples_map_parent = find_triplesmap(template, range, prefixes)
     join = copy.deepcopy(join_template)
     join['p'] = o.iri.replace(o.namespace.base_iri, prefixes[o.namespace.base_iri] + ":")
     join['o'][0]['mapping'] = triples_map_parent