Merge branch 'master' into dev

.github/workflows/doc.yml

@@ -41,6 +41,21 @@ jobs:
         docs-folder: "sphinx/"
         pre-build-command: "apt-get update -y; apt-get install -y pandoc"
 
+    - name: Create context file from ttl
+      run: python sphinx/ttl_to_context.py
+
+    - name: Check if HTML context directory exists
+      run: |
+        if [ ! -d "sphinx/_build/html/context/" ]; then
+          echo "Creating HTML context directory"
+          sudo mkdir -p sphinx/_build/html/context/
+        else
+          echo "HTML context directory already exists"
+        fi
+    
+    - name: Copy context file to HTML directory
+      run: sudo cp context/context.json sphinx/_build/html/context/
+
     - name: Upload artifacts
       uses: actions/upload-artifact@v4
       with:

catalog-v001.xml

@@ -9,7 +9,7 @@
         <uri name="https://w3id.org/emmo/domain/battery/0.1.0-beta/batteryproducts"    		uri="./batteryproducts.ttl"/>
 
         <uri name="https://w3id.org/emmo/domain/chemicalsubstance/0.4.0-beta/chemicalsubstance" uri="https://raw.githubusercontent.com/emmo-repo/domain-chemicalsubstance/main/chemicalsubstance.ttl"/>
-        <uri name="https://w3id.org/emmo/domain/chameo/1.0.0-beta3/chameo" uri="https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/version-update-emmo-1.0.0-beta7/chameo.ttl"/>
+        <uri name="https://w3id.org/emmo/domain/chameo/1.0.0-beta3/chameo" uri="https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/main/chameo.ttl"/>
 
         <uri name="https://w3id.org/emmo/1.0.0-beta7/mereocausality"                  uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta7/mereocausality/mereocausality.ttl"/>
 
@@ -58,4 +58,4 @@
         <uri name="https://w3id.org/emmo/1.0.0-beta7/disciplines/prefixedunits"       uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta7/disciplines/units/prefixedunits.ttl"/>
         <uri name="https://w3id.org/emmo/1.0.0-beta7/disciplines/deprecated"          uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta7/disciplines/units/deprecated.ttl"/>
     </group>
-</catalog>
+</catalog>

docs/scripts/ttl_to_context.py

@@ -21,6 +21,9 @@ def generate_jsonld_context(ttl_file, predicate_uri, label_uri='http://www.w3.or
     """
     g = rdflib.Graph()
     g.parse(ttl_file, format='ttl')
+
+    CHAMEO = rdflib.Namespace("https://w3id.org/emmo/domain/chameo#")
+    g.bind('chameo', CHAMEO)
 
     context = {}
     object_properties  = {}
@@ -44,21 +47,34 @@ def generate_jsonld_context(ttl_file, predicate_uri, label_uri='http://www.w3.or
         elif p == predicate:
             # Normal context entry
             # Use the label as key if it exists
-            label_value = g.value(s, label) if g.value(s, label) else str(s)
+            #label_value = g.value(s, label) if g.value(s, label) else str(s)
+            label_value = str(s)
             other_entries[str(o)] = str(label_value)
 
 
     # Add namespace prefixes to the context
     for prefix, uri in g.namespace_manager.namespaces():
-        namespace_prefixes[prefix] = str(uri)
+        if len(prefix) >= 2:
+            namespace_prefixes[prefix] = str(uri)
 
     # Sort the entries alphabetically
     sorted_object_properties = dict(sorted(object_properties.items()))
     sorted_other_entries = dict(sorted(other_entries.items()))
     sorted_namespace_prefixes = dict(sorted(namespace_prefixes.items()))
 
     # Merge the sorted entries
-    context = {**sorted_namespace_prefixes, **sorted_object_properties, **sorted_other_entries}
+    context = {
+        "@context": {
+            **sorted_namespace_prefixes,
+            **sorted_object_properties,
+            **sorted_other_entries
+        }
+    }
+
+    print("Namespaces:")
+    for prefix, uri in g.namespace_manager.namespaces():
+        print(f"{prefix}: {uri}")
+
 
     return context
 

sphinx/index.rst

@@ -60,7 +60,7 @@ Check out these resources to get started!
         Let's go! Here is some information to help you get started
 
     .. grid-item-card::
-        :link: electrochemistry.html
+        :link: battery.html
 
         :octicon:`book;1em;sd-text-info`  Class Index
         ^^^^^^^^^^^

sphinx/ttl_to_context.py

@@ -0,0 +1,98 @@
+import rdflib
+from rdflib.namespace import RDF, OWL, SKOS
+import json
+import os
+from urllib.parse import urljoin
+from urllib.request import pathname2url
+import warnings
+
+
+def generate_jsonld_context(ttl_file, predicate_uri, label_uri='http://www.w3.org/2000/01/rdf-schema#label'):
+    """
+    Generate a JSON-LD context file from a Turtle file.
+
+    Args:
+    - ttl_file: Path to the Turtle (.ttl) file.
+    - predicate_uri: The URI of the predicate to map to JSON-LD.
+    - label_uri: The URI for the label (default is rdfs:label).
+
+    Returns:
+    - A Python dictionary representing the JSON-LD context.
+    """
+    g = rdflib.Graph()
+    g.parse(ttl_file, format='ttl')
+
+    CHAMEO = rdflib.Namespace("https://w3id.org/emmo/domain/chameo#")
+    g.bind('chameo', CHAMEO)
+
+    context = {}
+    object_properties  = {}
+    other_entries = {}
+    namespace_prefixes= {}
+    predicate = rdflib.URIRef(predicate_uri)
+    label = rdflib.URIRef(label_uri)
+    existing_keys = set()
+
+    for s, p, o in g:
+        if (s, RDF.type, OWL.ObjectProperty) in g:
+            # If the subject is an OWL.ObjectProperty
+            label_value = g.value(s, SKOS.prefLabel)
+            if label_value:
+                object_properties[str(label_value)] = {
+                    "@id": str(s),
+                    "@type": "@id"
+                }
+
+
+        elif p == predicate:
+            # Normal context entry
+            # Use the label as key if it exists
+            #label_value = g.value(s, label) if g.value(s, label) else str(s)
+            label_value = str(s)
+            other_entries[str(o)] = str(label_value)
+
+
+    # Add namespace prefixes to the context
+    for prefix, uri in g.namespace_manager.namespaces():
+        if len(prefix) >= 2:
+            namespace_prefixes[prefix] = str(uri)
+
+    # Sort the entries alphabetically
+    sorted_object_properties = dict(sorted(object_properties.items()))
+    sorted_other_entries = dict(sorted(other_entries.items()))
+    sorted_namespace_prefixes = dict(sorted(namespace_prefixes.items()))
+
+    # Merge the sorted entries
+    context = {
+        "@context": {
+            **sorted_namespace_prefixes,
+            **sorted_object_properties,
+            **sorted_other_entries
+        }
+    }
+
+    print("Namespaces:")
+    for prefix, uri in g.namespace_manager.namespaces():
+        print(f"{prefix}: {uri}")
+
+
+    return context
+
+
+# Example usage
+filename = 'battery-inferred.ttl'
+parent_dir = os.path.dirname(os.path.abspath(__file__))
+file_path = os.path.join(parent_dir, '..', filename)
+
+# Convert the file path to a file URI
+file_uri = urljoin('file:', pathname2url(file_path))
+
+predicate_uri = 'http://www.w3.org/2004/02/skos/core#prefLabel'
+context = generate_jsonld_context(file_uri, predicate_uri)
+
+# Determine the path for saving the context file in the same directory as the HTML docs
+context_file_path = os.path.join(os.path.dirname(parent_dir), 'context/context.json')
+
+# Save to JSON file
+with open(context_file_path, 'w') as f:
+    json.dump(context, f, indent=4)

sphinx/ttl_to_rst.py

@@ -21,7 +21,7 @@ def extract_terms_info_sparql(g: Graph)-> list:
 
     # SPARQL QUERY #
     PREFIXES = """
-        PREFIX emmo: <http://emmo.info/emmo#>
+        PREFIX emmo: <https://w3id.org/emmo#>
         PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
         """