enabled saving onthologies in different formats

toardb/utils/TOARII_ontology.py

@@ -33,7 +33,7 @@ class TOAR_Ontology:
     get_class(title):
         find the onthology class for the given title
 
-    get_class_by_id(self, id):
+    get_class_by_id(id):
         find the onthology class for the given id
 
     show_class_definition(ont_class):
@@ -42,7 +42,7 @@ class TOAR_Ontology:
     show_entries(ont_class):
         show information on given ontology class
 
-    add_entry(self, ont_class, idcount, label, definition):
+    add_entry(ont_class, idcount, label, definition):
         add entry to given ontology class
 
     check_entry(entry, ont_class):
@@ -51,14 +51,24 @@ class TOAR_Ontology:
     print(format=""):
         Prints the onthology in the given format
 
-    save(self, filename):
-        save the onthology in json-ld format to the given file
+    save(filename, format):
+        save the onthology in given format to the given file
     """
 
     def __init__(self, filename):
         """
         initialize the onthology
+
+        Parameters
+        ----------
+        filename: str
+            filename containing the ontology in json-ld format
+
+        Returns
+        -------
+        TOAR_Ontology
         """
+
         self.filename = filename
         g = rdflib.Graph()
         self.graph = g.parse(self.filename,format='json-ld')
@@ -66,6 +76,15 @@ class TOAR_Ontology:
     def get_class(self, title):
         """
         find the onthology class for the given title
+
+        Parameters
+        ----------
+        title: str
+            title of class
+
+        Returns
+        -------
+        OWL.Class
         """
         for s, p, o in self.graph.triples( (None,  RDF.type, OWL.Class) ):
             value = self.graph.value(subject=s,predicate=RDFS.label)
@@ -76,6 +95,15 @@ class TOAR_Ontology:
     def get_class_by_id(self, id):
         """
         find the onthology class for the given id
+
+        Parameters
+        ----------
+        id: str
+            id of class
+
+        Returns
+        -------
+        OWL.Class
         """
         for s, p, o in self.graph.triples( (None,  RDF.type, OWL.Class) ):
             if s.strip() == id.strip():
@@ -85,6 +113,15 @@ class TOAR_Ontology:
     def show_class_definition(self, ont_class):
         """
         show information on given ontology class
+
+        Parameters
+        ----------
+        ont_class: OWL.class
+            onthology class
+
+        Returns
+        -------
+        None
         """
         for s, p, o in self.graph.triples( (ont_class,  SKOS.definition, None) ):
             print(f"definition of {ont_class}: {o}")
@@ -92,6 +129,15 @@ class TOAR_Ontology:
     def show_entries(self, ont_class):
         """
         show information on given ontology class
+
+        Parameters
+        ----------
+        ont_class: OWL.class
+            onthology class
+
+        Returns
+        -------
+        None
         """
         for s, p, o in self.graph.triples( (None,  RDF.type, ont_class ) ):
             label=self.graph.value(subject=s,predicate=RDFS.label)
@@ -102,6 +148,21 @@ class TOAR_Ontology:
     def add_entry(self, ont_class, idcount, label, definition):
         """
         add entry to given ontology class
+
+        Parameters
+        ----------
+        ont_class: OWL.class
+            onthology class
+        id_count: int
+            integer for constructing ID "OWLNamedIndividual_nnnnnn"
+        label: str
+            title of entry to be inserted
+        definition: str
+            definition of entry to be inserted
+
+        Returns
+        -------
+        None
         """
         # still to do:
         # how to get rid of "http://www.fz-juelich.de/ontologies/2020/ToarOntotology"?!
@@ -134,6 +195,17 @@ class TOAR_Ontology:
     def check_entry(self, entry, ont_class):
         """
         check whether entry is a valid value of the ontology
+
+        Parameters
+        ----------
+        entry: str
+            title of entry to be checked
+        ont_class: OWL.class
+            onthology class
+
+        Returns
+        -------
+        None
         """
         found=False
         for s, p, o in self.graph.triples( (None,  RDF.type, ont_class ) ):
@@ -144,15 +216,35 @@ class TOAR_Ontology:
     def print(self, format='json-ld'):
         """
         print the onthology in the given format
+
+        Parameters
+        ----------
+        format: str, optional
+            output format (default: json-ld)
+
+        Returns
+        -------
+        None
         """
         print(self.graph.serialize(format=format).decode("utf-8"))
 
-    def save(self, filename):
+    def save(self, filename, format='json-ld'):
         """
         save the onthology in json-ld format to the given file
+
+        Parameters
+        ----------
+        filename: str
+            output file name
+        format: str, optional
+            output format (default: json-ld)
+
+        Returns
+        -------
+        None
         """
         outfile = open(filename,'w')
-        outfile.write(self.graph.serialize(format='json-ld').decode("utf-8"))
+        outfile.write(self.graph.serialize(format=format).decode("utf-8"))
 
 #       #check_entry would have been nicer, if something like this worked:
 #       subj2 = rdflib.URIRef("http://www.fz-juelich.de/ontologies/2020/ToarOntotology#OWLNamedIndividual_000141")