feat: added support for namespace aliases

biosimulators · Mar 1, 2022 · 6a6874e · 6a6874e
1 parent 0dca966
commit 6a6874e
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Showing 2 changed files with 26 additions and 1 deletion.
diff --git a/biosimulators_utils/omex_meta/data_model.py b/biosimulators_utils/omex_meta/data_model.py
@@ -19,6 +19,7 @@
     'BIOSIMULATIONS_PREDICATE_TYPES',
     'BIOSIMULATIONS_THUMBNAIL_FORMATS',
     'BIOSIMULATIONS_NAMESPACE_PREFIX_MAP',
+    'BIOSIMULATIONS_NAMESPACE_ALIASES',
     'BIOSIMULATIONS_THUMBNAIL_FORMATS',
 ]
 
@@ -352,6 +353,11 @@ class OmexMetadataSchema(str, enum.Enum):
     'http://xmlns.com/foaf/0.1/': 'foaf',
 }
 
+BIOSIMULATIONS_NAMESPACE_ALIASES = {
+    'http://purl.org/dc/elements/1.1/': 'http://dublincore.org/specifications/dublin-core/dcmi-terms/',
+    'http://sempublishing.sourceforge.net/scoro/': 'http://purl.org/spar/scoro/',
+}
+
 BIOSIMULATIONS_THUMBNAIL_FORMATS = [
     'GIF',
     'JPEG',

diff --git a/biosimulators_utils/omex_meta/io.py b/biosimulators_utils/omex_meta/io.py
@@ -11,7 +11,8 @@
 from .data_model import (Triple, OmexMetadataOutputFormat, OmexMetadataSchema,
                          BIOSIMULATIONS_ROOT_URI_PATTERN,
                          BIOSIMULATIONS_PREDICATE_TYPES,
-                         BIOSIMULATIONS_NAMESPACE_PREFIX_MAP)
+                         BIOSIMULATIONS_NAMESPACE_PREFIX_MAP,
+                         BIOSIMULATIONS_NAMESPACE_ALIASES)
 from .utils import get_local_combine_archive_content_uri, get_global_combine_archive_content_uri
 from .validation import validate_biosimulations_metadata
 from lxml import etree
@@ -570,6 +571,24 @@ def parse_triples_to_schema(cls, triples, combine_archive_uri):
         errors = []
         warnings = []
 
+        for triple in triples:
+            subject = str(triple.subject)
+            predicate = str(triple.predicate)
+            object = str(triple.object)
+
+            for ns, alias in BIOSIMULATIONS_NAMESPACE_ALIASES.items():
+                if isinstance(triple.subject, rdflib.term.URIRef) and subject.startswith(ns):
+                    subject = alias + subject[len(ns):]
+                    triple.subject = rdflib.term.URIRef(subject)
+
+                if isinstance(triple.predicate, rdflib.term.URIRef) and predicate.startswith(ns):
+                    predicate = alias + predicate[len(ns):]
+                    triple.predicate = rdflib.term.URIRef(predicate)
+
+                if isinstance(triple.object, rdflib.term.URIRef) and object.startswith(ns):
+                    object = alias + object[len(ns):]
+                    triple.object = rdflib.term.URIRef(object)
+
         objects = {}
         for triple in triples:
             for node, is_subject in [(triple.subject, True), (triple.object, False)]: