merge main

.github/workflows/main.yaml

@@ -45,12 +45,6 @@ jobs:
       - name: Install library
         run: poetry install --no-interaction
 
-      #----------------------------------------------
-      #              run test suite   
-      #----------------------------------------------
-      - name: Run tests
-        run: poetry run python -m unittest discover
-
       #----------------------------------------------
       #              coverage report   
       #----------------------------------------------

linkml_runtime/__init__.py

@@ -25,6 +25,25 @@
 
 MAIN_SCHEMA_PATH = SCHEMA_DIRECTORY / "meta.yaml"
 
+LINKML_ANNOTATIONS = SCHEMA_DIRECTORY / "annotations.yaml"
+LINKML_ARRAY = SCHEMA_DIRECTORY / "array.yaml"
+LINKML_EXTENSIONS = SCHEMA_DIRECTORY / "extensions.yaml"
+LINKML_MAPPINGS = SCHEMA_DIRECTORY / "mappings.yaml"
+LINKML_TYPES = SCHEMA_DIRECTORY / "types.yaml"
+LINKML_UNITS = SCHEMA_DIRECTORY / "units.yaml"
+LINKML_VALIDATION = SCHEMA_DIRECTORY / "validation.yaml"
+
+
+URI_TO_LOCAL = {
+    'https://w3id.org/linkml/annotations.yaml': str(LINKML_ANNOTATIONS),
+    'https://w3id.org/linkml/array.yaml': str(LINKML_ARRAY),
+    'https://w3id.org/linkml/extensions.yaml': str(LINKML_EXTENSIONS),
+    'https://w3id.org/linkml/mappings.yaml': str(LINKML_MAPPINGS),
+    'https://w3id.org/linkml/meta.yaml': str(MAIN_SCHEMA_PATH),
+    'https://w3id.org/linkml/types.yaml': str(LINKML_TYPES),
+    'https://w3id.org/linkml/units.yaml': str(LINKML_UNITS),
+    'https://w3id.org/linkml/validation.yaml': str(LINKML_VALIDATION),
+}
 
 class MappingError(ValueError):
     """

linkml_runtime/exceptions.py

@@ -0,0 +1,2 @@
+class OrderingError(RuntimeError):
+    """Exception raised when there is a problem with SchemaView ordering"""

linkml_runtime/loaders/loader_root.py

@@ -1,11 +1,16 @@
 from abc import ABC, abstractmethod
 from typing import Iterator, TextIO, Union, Optional, Callable, Dict, Type, Any, List
+from logging import getLogger
 
 from pydantic import BaseModel
 from hbreader import FileInfo, hbread
 from jsonasobj2 import as_dict, JsonObj
 
 from linkml_runtime.utils.yamlutils import YAMLRoot
+from linkml_runtime import URI_TO_LOCAL
+
+CACHE_SIZE = 1024
+
 
 
 class Loader(ABC):
@@ -128,7 +133,7 @@ def iter_instances(self) -> Iterator[Any]:
         pass
 
 
-    def _construct_target_class(self, 
+    def _construct_target_class(self,
                                 data_as_dict: Union[dict, List[dict]],
                                 target_class: Union[Type[YAMLRoot], Type[BaseModel]]) -> Optional[Union[BaseModel, YAMLRoot, List[BaseModel], List[YAMLRoot]]]:
         if data_as_dict:
@@ -151,6 +156,7 @@ def _construct_target_class(self,
         else:
             return None
 
+
     def _read_source(self,
                      source: Union[str, dict, TextIO], 
                      *, 
@@ -163,8 +169,17 @@ def _read_source(self,
             metadata.base_path = base_dir
 
         if not isinstance(source, dict):
-            data = hbread(source, metadata, metadata.base_path, accept_header)
+            # Try to get local version of schema, if one is known to exist
+            try:
+                if str(source) in URI_TO_LOCAL.keys():
+                    source = str(URI_TO_LOCAL[str(source)])
+            except (TypeError, KeyError) as e:
+                # Fine, use original `source` value
+                logger = getLogger('linkml_runtime.loaders.Loader')
+                logger.debug(f"Error converting stringlike source to local linkml file: {source}, got: {e}")
+
+            data = hbread(source, metadata, base_dir, accept_header)
         else:
             data = source
 
-        return data
+        return data

linkml_runtime/utils/eval_utils.py

@@ -17,7 +17,12 @@
 
 def eval_conditional(*conds: List[Tuple[bool, Any]]) -> Any:
     """
-    >>> cond(x < 25 : 'low', x > 25 : 'high', True: 'low')
+    Evaluate a collection of expression,value tuples, returing the first value whose expression is true
+
+    >>> x= 40
+    >>> eval_conditional((x < 25, 'low'),  (x > 25, 'high'), (True, 'low'))
+    'high'
+
     :param subj:
     :return:
     """
@@ -58,10 +63,9 @@ def eval_expr(expr: str, **kwargs) -> Any:
 
     Nulls:
 
-    - If a variable is enclosed in {}s then entire expression will eval to None if variable is unset
+    - If a variable is enclosed in {}s then entire expression will eval to None if any variable is unset
 
-    >>> eval_expr('{x} + {y}', x=None, y=2)
-    None
+    >>> assert eval_expr('{x} + {y}', x=None, y=2) is None
 
     Functions:
 
@@ -92,9 +96,6 @@ def eval_expr(expr: str, **kwargs) -> Any:
 
 
 
-
-
-
 def eval_(node, bindings={}):
     if isinstance(node, ast.Num):
         return node.n

linkml_runtime/utils/namespaces.py

@@ -137,7 +137,9 @@ def _base(self) -> None:
     def curie_for(self, uri: Any, default_ok: bool = True, pythonform: bool = False) -> Optional[str]:
         """
         Return the most appropriate CURIE for URI.  The first longest matching prefix used, if any.  If no CURIE is
-        present, None is returned
+        present, None is returned.
+
+        Please see https://www.w3.org/TR/curie/ for more details about CURIEs.
 
         @param uri: URI to create the CURIE for
         @param default_ok: True means the default prefix is ok. Otherwise, we have to have a real prefix
@@ -191,7 +193,7 @@ def prefix_for(self, uri_or_curie: Any, case_shift: bool = True) -> Optional[str
 
     def prefix_suffix(self, uri_or_curie: Any, case_shift: bool = True) -> Tuple[Optional[str], Optional[str]]:
         uri_or_curie = str(uri_or_curie)
-        if ':/' in uri_or_curie:
+        if '://' in uri_or_curie:
             uri_or_curie = self.curie_for(uri_or_curie)
             if not uri_or_curie:
                 return None, None