pymetadata 0.5.2__py3-none-any.whl → 0.5.3__py3-none-any.whl

pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.5.2"
+__version__ = "0.5.3"
 
 
 program_name: str = "pymetadata"

pymetadata/examples/cache_path_example.py

@@ -9,7 +9,6 @@ from pymetadata.chebi import ChebiQuery
 pymetadata.CACHE_PATH = Path.home() / ".cache" / "pymetadata"
 
 if __name__ == "__main__":
-
     chebis = ["CHEBI:2668", "CHEBI:138366", "CHEBI:9637", "CHEBI:155897"]
     for chebi in chebis:
         d = ChebiQuery.query(chebi=chebi, cache=True)

pymetadata/identifiers/registry.py

@@ -19,7 +19,7 @@ import requests
 import pymetadata
 from pymetadata import log
 from pymetadata.cache import DataclassJSONEncoder, read_json_cache, write_json_cache
-
+from pymetadata.console import console
 
 logger = log.get_logger(__name__)
 
@@ -123,14 +123,6 @@ def ols_namespaces() -> Dict[str, Namespace]:
 
     # Custom namespaces for OLS ontology, for simple support
     namespaces = [
-        Namespace(
-            id=None,
-            prefix="snomed",
-            pattern=r"^\d+$",
-            name="SNOMED",
-            description="SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.",
-            namespaceEmbeddedInLui=True,
-        ),
         Namespace(
             id=None,
             prefix="omim",
@@ -180,14 +172,6 @@ def ols_namespaces() -> Dict[str, Namespace]:
             description="OPMI: Ontology of Precision Medicine and Investigation",
             namespaceEmbeddedInLui=True,
         ),
-        Namespace(
-            id=None,
-            prefix="mondo",
-            pattern=r"^MONDO:\d+$",
-            name="MONDO",
-            description="MONDO",
-            namespaceEmbeddedInLui=True,
-        ),
         Namespace(
             id=None,
             prefix="atol",
@@ -237,6 +221,14 @@ def ols_namespaces() -> Dict[str, Namespace]:
             description="Measurement method ontology",
             namespaceEmbeddedInLui=True,
         ),
+        Namespace(
+            id=None,
+            prefix="symp",
+            pattern=r"^SYMP:\d+$",
+            name="Symptom ontology",
+            description="The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.",
+            namespaceEmbeddedInLui=True,
+        ),
     ]
 
     for ns in namespaces:
@@ -344,21 +336,6 @@ class Registry:
         ns_dict = {}
         for _, data in enumerate(namespaces):
             ns = Namespace.from_dict(data)
-
-            # bugfix OLS4 (https://github.com/identifiers-org/identifiers-org.github.io/issues/231)
-            if ns.resources:
-                for resource in ns.resources:
-                    if resource.urlPattern.startswith("https://www.ebi.ac.uk/ols/"):
-                        resource.urlPattern = resource.urlPattern.replace(
-                            "/ols/", "/ols4/"
-                        )
-                    if resource.resourceHomeUrl.startswith(
-                        "https://www.ebi.ac.uk/ols/"
-                    ):
-                        resource.resourceHomeUrl = resource.resourceHomeUrl.replace(
-                            "/ols/", "/ols4/"
-                        )
-
             ns_dict[ns.prefix] = ns
 
         if custom_namespaces is not None:
@@ -394,4 +371,5 @@ class Registry:
 REGISTRY = Registry()
 
 if __name__ == "__main__":
-    registry = Registry()
+    registry = Registry(cache=False)
+    console.print(registry.ns_dict)