Merge pull request #221 from elevont/subjectSorting

Implements subject sorting in output with --sort

Author: nicholascar

pylode/cli.py

@@ -34,6 +34,13 @@
     default="true",
 )
 
+parser.add_argument(
+    "-s",
+    "--sort",
+    help="Enables sorting of the subjects in the ontology in the output",
+    action='store_true',
+)
+
 parser.add_argument(
     "-p",
     "--profile",
@@ -50,12 +57,13 @@ def main():
     args = parser.parse_args()
 
     try:
+        sort_subjects = args.sort
         if args.profile == "ontpub":
-            html = OntPub(args.input)
+            html = OntPub(args.input, sort_subjects = sort_subjects)
         elif args.profile == "vocpub":
-            html = VocPub(args.input)
+            html = VocPub(args.input, sort_subjects = sort_subjects)
         elif args.profile == "supermodel":
-            html = Supermodel(args.input)
+            html = Supermodel(args.input, sort_subjects = sort_subjects)
         else:
             raise ValueError(f"Unexpected profile type '{args.profile}'")
     except PylodeError as e:

pylode/profiles/ontpub.py

@@ -56,6 +56,7 @@
         get_ns,
         prop_obj_pair_html,
         section_html,
+        sort_ontology,
         make_pylode_logo,
     )
 
@@ -71,6 +72,7 @@
         get_ns,
         prop_obj_pair_html,
         section_html,
+        sort_ontology,
         make_pylode_logo,
     )
 
@@ -102,8 +104,10 @@ class OntPub:
         od.make_html(destination="some-resulting-html-file.html")
     """
 
-    def __init__(self, ontology: Union[Graph, Path, str]):
+    def __init__(self, ontology: Union[Graph, Path, str], sort_subjects: bool = False):
         self.ont = load_ontology(ontology)
+        if sort_subjects:
+            self.ont = sort_ontology(self.ont)
         self._ontdoc_inference(self.ont)
         self.back_onts = load_background_onts()
         self.back_onts_titles = load_background_onts_titles(self.back_onts)

pylode/profiles/supermodel/html.py

@@ -38,6 +38,7 @@
 from pylode.utils import (
     PylodeError,
     load_ontology,
+    sort_ontology,
 )
 from pylode.profiles.supermodel.query import Query
 from pylode.profiles.supermodel.model import (
@@ -93,9 +94,12 @@ def get_headings(doc: dominate.document) -> list:
 
 class Supermodel:
     def __init__(
-        self, ontology: Graph | Path | str, QueryClass: Type[Query] = Query
+        self, ontology: Graph | Path | str, QueryClass: Type[Query] = Query,
+        sort_subjects: bool = False
     ) -> None:
         self.ont = load_ontology(ontology)
+        if sort_subjects:
+            self.ont = sort_ontology(self.ont)
         self.query = QueryClass(self.ont)
 
         self.toc: dict[str, str] = {}

pylode/profiles/vocpub.py

@@ -55,6 +55,7 @@
         get_ns,
         prop_obj_pair_html,
         section_html,
+        sort_ontology,
         make_pylode_logo,
     )
 
@@ -70,6 +71,7 @@
         get_ns,
         prop_obj_pair_html,
         section_html,
+        sort_ontology,
         make_pylode_logo,
     )
 
@@ -105,8 +107,10 @@ class VocPub:
         od.make_html(destination="some-resulting-html-file.html")
     """
 
-    def __init__(self, ontology: Union[Graph, Path, str]):
+    def __init__(self, ontology: Union[Graph, Path, str], sort_subjects: bool = False):
         self.ont = load_ontology(ontology)
+        if sort_subjects:
+            self.ont = sort_ontology(self.ont)
         self._ontdoc_inference(self.ont)
         self.back_onts = load_background_onts()
         self.back_onts_titles = load_background_onts_titles(self.back_onts)

pylode/utils.py

@@ -288,6 +288,14 @@ def load_ontology(ontology: Union[Graph, Path, str]) -> Graph:
         print(f"{type(e).__name__} Error {e}")
         exit()
 
+def sort_ontology(ont_orig: Graph) -> Graph:
+    """Creates a copy of the supplied ontology, sorted by subjects"""
+    trpls = ont_orig.triples((None, None, None))
+    trpls_srt = sorted(trpls)
+    ont_sorted = Graph()
+    for trpl in trpls_srt:
+        ont_sorted.add(trpl)
+    return ont_sorted
 
 def load_background_onts():
     """Loads background ontology files into an RDFLib graph from either