V0.0.5 (#25)

* [~] Fix path for properties

* [~] Specify current directory

* [~] Clean and fix external links

* [~] Fix version and path posix

Author: StephaneBranly

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -39,6 +39,6 @@ body:
   - type: input
     attributes:
       label: "ontodoc version:"
-      placeholder: e.g., 0.0.4
+      placeholder: e.g., 0.0.5
     validations:
       required: true

ontodoc/classes/Documentation.py

@@ -58,19 +58,18 @@ def generate(self):
             'version': self.version,
             'editionDate': datetime.date.today().strftime('%Y-%m-%d'),
         }
+
         # Init ontology reader
         ontology = Ontology(self.graph, self.onto, self.templates, metadata)
         path = pathlib.Path(self.output)
 
-
-
         # Generate pages
         if self.model == 'json':
             generate_page(json.dumps(ontology.__dict__, indent=2, cls=JSONOntoDocEncoder), f'{self.output}/ontology.json', add_signature=False)
             for c in ontology.classes:
                 generate_page(json.dumps(c.__dict__, indent=2, cls=JSONOntoDocEncoder), f'{self.output}/class/{c.id}.json', add_signature=False)
             for p in chain(ontology.objectProperties, ontology.annotationProperties, ontology.datatypeProperties, ontology.functionalProperties):
-                generate_page(json.dumps(p.__dict__, indent=2, cls=JSONOntoDocEncoder), f'{self.output}property/{p.id}.json', add_signature=False)
+                generate_page(json.dumps(p.__dict__, indent=2, cls=JSONOntoDocEncoder), f'{self.output}/property/{p.id}.json', add_signature=False)
         elif self.model in ['markdown', 'gh_wiki']:
             if self.concatenate:
                 page = ontology.__str__()
@@ -84,6 +83,7 @@ def generate(self):
                     generate_page(path=path, node=n, footer=footer)
         else:
             raise Exception('Model not supported')
+    
         # Copy ontology file
         with open(f'{self.output}/ontology.ttl', mode='w', encoding='utf-8') as f:
             f.write(self.graph.serialize(format='ttl'))

ontodoc/classes/Generic.py

@@ -24,7 +24,7 @@ def __init__(self, onto: Ontology, node: Node, template: Template, default_prope
             self.pagename = pagename
         else:
             self.pagename = (path / self.id).with_suffix('.md') if not onto.metadata.get('concatenate', False) else onto.pagename
-        self.to_root_path = '../' * (len(self.pagename.parts) - 1)
+        self.to_root_path = './' + '../' * (len(self.pagename.parts) - 1)
 
         if onto.metadata.get('concatenate', False) and onto.onto_node != node:
             self.pagename = f"{self.pagename.as_posix()}#{self.id}"

ontodoc/classes/Ontology.py

@@ -22,10 +22,8 @@ def __init__(self, graph: Graph, onto_node: rdflib.Node, templates: dict[str, Te
         self.onto_prefix = [prefix for prefix, uriref in graph.namespace_manager.namespaces() if uriref.n3(graph.namespace_manager) == onto_node.n3(graph.namespace_manager)]
         self.onto_prefix = self.onto_prefix[0] if len(self.onto_prefix) > 0 else None
 
-        self.objectProperties = [Property(self, s, self.templates['property.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=rdflib.OWL.ObjectProperty) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix]
-        self.datatypeProperties = [Property(self, s, self.templates['property.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=rdflib.OWL.DatatypeProperty) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix]
-        self.annotationProperties = [Property(self, s, self.templates['property.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=rdflib.OWL.AnnotationProperty) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix]
-        self.functionalProperties = [Property(self, s, self.templates['property.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=rdflib.OWL.FunctionalProperty) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix]
+        [self.objectProperties, self.datatypeProperties, self.annotationProperties, self.functionalProperties] = [[Property(self, s, self.templates['property.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=object_type) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix] for object_type in [rdflib.OWL.ObjectProperty, rdflib.OWL.DatatypeProperty, rdflib.OWL.AnnotationProperty, rdflib.OWL.FunctionalProperty]]
+
         self.classes = [Class(self, s, self.templates['class.md']) for s in self.graph.subjects(predicate=rdflib.RDF.type, object=rdflib.OWL.Class) if type(s) == rdflib.URIRef and get_prefix(self.graph, s) == self.onto_prefix]
 
         self.update_internal_links()

ontodoc/classes/Property.py

@@ -12,12 +12,12 @@
 
 class Property(Generic):
     def __init__(self, onto: Ontology, property_node: Node, template: Template):
-        super().__init__(onto, property_node, template, PROPERTY, Path('property') if not onto.metadata.get('concatenate', False) else onto.pagename)
+        super().__init__(onto, property_node, template, PROPERTY, Path('./property/') if not onto.metadata.get('concatenate', False) else onto.pagename)
 
         g = onto.graph
 
-        self.range_link = compute_link(onto, property_node, self.range) if self.range else None
-        self.domain_link = compute_link(onto, property_node, self.domain) if self.domain else None
+        self.range_link = compute_link(onto, self, self.range) if self.range else None
+        self.domain_link = compute_link(onto, self, self.domain) if self.domain else None
 
         self.range_label = generate_clean_id_from_term(g, self.range) if self.range else None
         self.domain_label = generate_clean_id_from_term(g, self.domain) if self.domain else None

ontodoc/generate_page.py

@@ -11,7 +11,7 @@ def generate_page(content: str = None, path: Path = None, node: Generic = None,
     path.parent.mkdir(parents=True, exist_ok=True)
     if content == None:
         content = node.__str__()
-    with open(path, mode='w', encoding='utf-8') as f:
+    with open(path.as_posix(), mode='w', encoding='utf-8') as f:
         f.write(content)
 
         if footer:

ontodoc/templates/class.md

@@ -48,7 +48,7 @@ classDiagram
 {%- endif %} | {{triple.label if triple.label}} | {{triple.comment if triple.comment}} |
 
 {%- if triple.range_link -%}
-<kbd>[{{triple.range_n3}}]({{class.to_root_path}}{{triple.range_link}})</kbd>
+<kbd>[{{triple.range_n3}}]({{triple.range_link}})</kbd>
 {%- else -%}
 <kbd>{{triple.range_n3}}</kbd>
 {%- endif %} |
@@ -58,7 +58,7 @@ classDiagram
 {%- if class.subclassof %}
 {%- for subclassof in class.subclassof %}
   {% if subclassof.triples|length %}
-### Inherited from <kbd>[**{{subclassof.label}}**](../{{subclassof.pagename}}.md)</kbd>
+### Inherited from <kbd>[**{{subclassof.label}}**](../{{subclassof.pagename}})</kbd>
 | Predicate | Label | Comment | Type |
 | -------------------------------- | -------------------------------- | ------------------------------------ | ---- |
 | {%- for triple in subclassof.triples | sort(attribute='n3') %} |
@@ -69,7 +69,7 @@ classDiagram
 {%- endif %} | {{triple.label if triple.label}} | {{triple.comment if triple.comment}} |
 
 {%- if triple.range_link -%}
-<kbd>[{{triple.range_n3}}]({{class.to_root_path}}{{triple.range_link}})</kbd>
+<kbd>[{{triple.range_n3}}]({{triple.range_link}})</kbd>
 {%- else -%}
 <kbd>{{triple.range_n3}}</kbd>
 {%- endif %} |

ontodoc/templates/property.md

@@ -1,4 +1,5 @@
 # [{{onto.label}}]({{property.to_root_path}}{{onto.pagename}}) > {{property.id}}
+
 <a name="{{property.id}}"></a>
 ## {{property.label}}
 
@@ -10,14 +11,14 @@
 
 {% if property.range -%}
 - Range : {%- if property.range_link -%}
-[{{property.range}}]({{property.to_root_path}}{{property.range_link}})
+[{{property.range}}]({{property.range_link}})
 {%- elif property.range%}
 <kbd>{{property.range}}</kbd>
 {%- endif %}{%- endif %}
 
 {% if property.domain -%}
 - Domain : {%- if property.domain_link -%}
-[{{property.domain}}]({{property.to_root_path}}{{property.domain_link}})
+[{{property.domain}}]({{property.domain_link}})
 {%- elif property.domain -%}
 <kbd>{{property.domain}}</kbd>
 {%- endif %}{%- endif %}

ontodoc/utils.py

@@ -8,6 +8,7 @@
 from typing import TYPE_CHECKING
 if TYPE_CHECKING:
     from ontodoc.classes.Ontology import Ontology
+    from ontodoc.classes.Generic import Generic
 from ontodoc.ontology_properties import ONTOLOGY_PROP
 
 def concat_templates_environment(default_env: Environment, custom_env: Environment = None):
@@ -70,7 +71,7 @@ def get_suffix(graph: Graph, n: Node):
 def generate_clean_id_from_term(graph: Graph, n: Node):
     return re.sub(r'[^a-zA-Z\-_0-9]+', '_', n.n3(namespace_manager=graph.namespace_manager).split(':')[-1])
 
-def compute_link(onto: Ontology, current_node: Node, n: Node):
+def compute_link(onto: Ontology, current_node: Generic, n: Node):
     graph = onto.graph
     prefix = onto.onto_prefix
     if n and n.n3(graph.namespace_manager).startswith(prefix+':'):
@@ -79,8 +80,8 @@ def compute_link(onto: Ontology, current_node: Node, n: Node):
         type = get_object(graph, n, RDF.type)
         page_name = n.n3(graph.namespace_manager).split(prefix+':')[1]+'.md'
         if type and type in [RDFS.Class, OWL.Class]:
-            return 'class/' + page_name
-        return 'property/' + page_name
+            return current_node.to_root_path + 'class/' + page_name
+        return current_node.to_root_path + 'property/' + page_name
     return n.n3()
 
 def serialize_subset(graph: Graph, n: Node):

ontodoc/version.py

@@ -1 +1 @@
-__version__ = "0.0.4"
+__version__ = "0.0.5"