Merge pull request #162 from linkml/hsolbrig/parse_import_map

Enhance import_map functionality to support namespace as well as indi…

Author: cmungall

linkml_runtime/utils/context_utils.py

@@ -1,7 +1,7 @@
 import json
 import os
 from io import TextIOWrapper
-from typing import Optional, Union, List, Any, Dict
+from typing import Optional, Union, List, Any, Dict, Callable
 
 import yaml
 from jsonasobj2 import JsonObj, loads
@@ -50,6 +50,17 @@ def to_file_uri(fname: str) -> str:
         JsonObj(**{"@context": context_list[0] if len(context_list) == 1 else context_list})
 
 
+def map_import(importmap: Dict[str, str], namespaces: Callable[[None], "Namespaces"], imp: Any) -> str:
+    sname = str(imp)
+    if ':' in sname:
+        prefix, lname = sname.split(':', 1)
+        prefix += ':'
+        sname = importmap.get(prefix, prefix) + lname
+    sname = importmap.get(sname, sname)  # Import map may use CURIE
+    sname = str(namespaces().uri_for(sname)) if ':' in sname else sname
+    return importmap.get(sname, sname)  # It may also use URI or other forms
+
+
 def parse_import_map(map_: Optional[Union[str, Dict[str, str], TextIOWrapper]],
                      base: Optional[str] = None) -> Dict[str, str]:
     """

linkml_runtime/utils/schemaview.py

@@ -8,7 +8,7 @@
 from typing import Mapping, Tuple, Type
 from linkml_runtime.utils.namespaces import Namespaces
 from deprecated.classic import deprecated
-from linkml_runtime.utils.context_utils import parse_import_map
+from linkml_runtime.utils.context_utils import parse_import_map, map_import
 from linkml_runtime.linkml_model.meta import *
 from enum import Enum
 logger = logging.getLogger(__name__)
@@ -140,10 +140,7 @@ def namespaces(self) -> Namespaces:
     def load_import(self, imp: str, from_schema: SchemaDefinition = None):
         if from_schema is None:
             from_schema = self.schema
-        # TODO: this code is copied from linkml.utils.schemaloader; put this somewhere reusable
-        sname = self.importmap.get(str(imp), imp)               # Import map may use CURIE
-        sname = self.namespaces().uri_for(sname) if ':' in sname else sname
-        sname = self.importmap.get(str(sname), sname)               # It may also use URI or other forms
+        sname = map_import(self.importmap, self.namespaces, imp)
         logging.info(f'Loading schema {sname} from {from_schema.source_file}')
         schema = load_schema_wrap(sname + '.yaml',
                                   base_dir=os.path.dirname(from_schema.source_file) if from_schema.source_file else None)

tests/test_utils/input/core.yaml

@@ -1,7 +1,7 @@
 id: https://w3id.org/linkml/tests/core
 name: core
 description: |-
-  core schema imported by kitchen_sink    
+  core schema imported by kitchen_sink
 default_curi_maps:
   - semweb_context
 imports:
@@ -33,7 +33,7 @@ classes:
       - description
     exact_mappings:
       - prov:Activity
-      
+
   agent:
     description: "a provence-generating agent"
     slots:
@@ -43,7 +43,7 @@ classes:
     class_uri: prov:Agent
 
   TestClass:
-      
+
 slots:
 
   id:
@@ -54,7 +54,7 @@ slots:
 
   description:
     range: NarrativeText
-  
+
   started at time:
     slot_uri: prov:startedAtTime
     range: date