Merge pull request #1 from Raphael-Gazzotti/namespace-change

Namespace changes.

Author: lzehl

build.py

@@ -11,7 +11,7 @@
 import yaml
 
 from pipeline.translator import LinkMLClassBuilder, LinkMLSlotBuilder, LinkMLEnumBuilder
-from pipeline.utils import clone_sources, SchemaLoader, InstanceLoader, get_short_name
+from pipeline.utils import clone_sources, SchemaLoader, InstanceLoader, get_short_name, get_short_namespace
 
 
 terms_as_enums = True
@@ -43,6 +43,7 @@
 
 for schema_version in schema_loader.get_schema_versions():
     imports = []
+    short_namespace = get_short_namespace(schema_loader.get_namespaces_version(schema_version)['props'])
 
     # Step 3 - find all involved schemas for the current version
     schemas_file_paths = schema_loader.find_schemas(schema_version)
@@ -98,15 +99,15 @@
             ).build()
             linkml_classes[module].append(linkml_class)
     enum_schema = {
-        "id": f"https://openminds.ebrains.eu/schemas/latest/enums?format=linkml",
+        "id": f"{short_namespace}/schemas/latest/enums?format=linkml",
         "name": "openMINDS-enums",
         "title": f'OpenMINDS instance library as LinkML enums, version "{schema_version}"',
         "description": f'Enums for the LinkML representation of openMINDS metadata framework, version "{schema_version}"',
         "license": "https://spdx.org/licenses/MIT.html",
         "prefixes": {
             "linkml": "https://w3id.org/linkml/",
             "schema": "http://schema.org/",
-            "omi": "https://openminds.ebrains.eu",
+            "omi": f"{short_namespace}",
         },
         "default_prefix": "omi",
         "imports": ["linkml:types"] + linkml_enum_imports,
@@ -122,7 +123,7 @@
         )
         os.makedirs(os.path.dirname(target_file), exist_ok=True)
         module_schema = {
-            "id": f"https://openminds.ebrains.eu/schemas/latest/{module_name}?format=linkml",
+            "id": f"{short_namespace}/schemas/latest/{module_name}?format=linkml",
             "name": f"openMINDS-{module_name}",
             "title": f'OpenMINDS {module_name} module, version "{schema_version}"',
             "description": f'Schemas for the {module_name} module of the openMINDS metadata framework, version "{schema_version}"',
@@ -131,7 +132,7 @@
             "prefixes": {
                 "linkml": "https://w3id.org/linkml/",
                 "schema": "http://schema.org/",
-                "omi": "https://openminds.ebrains.eu",
+                "omi": f"{short_namespace}",
             },
             "default_prefix": "omi",
             "classes": class_list,
@@ -142,15 +143,15 @@
 
     # Step 6 - write slots file
     slots_schema = {
-        "id": f"https://openminds.ebrains.eu/schemas/latest/slots?format=linkml",
+        "id": f"{short_namespace}/schemas/latest/slots?format=linkml",
         "name": "openMINDS-slots",
         "title": f'OpenMINDS properties as LinkML slots, version "{schema_version}"',
         "description": f'Slots for the LinkML representation of the openMINDS metadata framework, version "{schema_version}"',
         "license": "https://spdx.org/licenses/MIT.html",
         "prefixes": {
             "linkml": "https://w3id.org/linkml/",
             "schema": "http://schema.org/",
-            "omi": "https://openminds.ebrains.eu",
+            "omi": f"{short_namespace}",
         },
         "default_prefix": "omi",
         "imports": ["linkml:types"],
@@ -164,7 +165,7 @@
 
     # Step 7 - write types file
     types_metadata = {
-        "id": f"https://openminds.ebrains.eu/schemas/latest/types/?format=linkml",
+        "id": f"{short_namespace}/schemas/latest/types/?format=linkml",
         "name": "openMINDS-types",
         "title": f'Types for OpenMINDS version "{schema_version}"',
         "description": f'Types for the LinkML representation of the openMINDS metadata framework, version "{schema_version}"',
@@ -173,7 +174,7 @@
         "prefixes": {
             "linkml": "https://w3id.org/linkml/",
             "schema": "http://schema.org/",
-            "omi": "https://openminds.ebrains.eu",
+            "omi": f"{short_namespace}",
         },
         "default_prefix": "omi",
         "types": {
@@ -200,7 +201,7 @@
 
     # Step 7 - create overall schema file
     schema_metadata = {
-        "id": f"https://openminds.ebrains.eu/schemas/latest/?format=linkml",
+        "id": f"{short_namespace}/schemas/latest/?format=linkml",
         "name": "openMINDS",
         "title": f'OpenMINDS version "{schema_version}"',
         "description": f'The complete collection of schemas for all metadata models of the openMINDS metadata framework, version "{schema_version}"',
@@ -209,7 +210,7 @@
         "prefixes": {
             "linkml": "https://w3id.org/linkml/",
             "schema": "http://schema.org/",
-            "omi": "https://openminds.ebrains.eu",
+            "omi": f"{short_namespace}",
         },
         "default_prefix": "omi",
     }

pipeline/translator.py

@@ -3,7 +3,7 @@
 import os.path
 from typing import List, Optional, Dict
 
-from pipeline.utils import get_short_name
+from pipeline.utils import get_short_name, get_short_namespace
 
 
 class LinkMLClassBuilder(object):
@@ -304,18 +304,19 @@ def build(self):
         )
         os.makedirs(os.path.dirname(target_file), exist_ok=True)
         short_type = get_short_name(self._schema_payload["_type"])
+        short_namespace = get_short_namespace(self._schema_payload["_type"])
         self.translate()
 
         enum_schema = {
-            "id": f"https://openminds.ebrains.eu/schemas/latest/enums/{short_type}?format=linkml",
+            "id": f"{short_namespace}/schemas/latest/enums/{short_type}?format=linkml",
             "name": f"openMINDS-enums-{short_type}",
             "title": f"OpenMINDS enum for {short_type}",
             "description": f"OpenMINDS enum for {short_type}",
             "license": "https://spdx.org/licenses/MIT.html",
             "prefixes": {
                 "linkml": "https://w3id.org/linkml/",
                 "schema": "http://schema.org/",
-                "omi": "https://openminds.ebrains.eu",
+                "omi": f"{short_namespace}",
             },
             "default_prefix": "omi",
             "enums": {short_type: self._translated_schema},

pipeline/utils.py

@@ -1,6 +1,7 @@
 import glob
 import json
 import os
+import re
 import shutil
 from typing import List
 
@@ -13,6 +14,14 @@ def clone_sources():
     Repo.clone_from(
         "https://github.com/openMetadataInitiative/openMINDS.git",
         to_path="_sources",
+        depth=1
+    )
+    if os.path.exists("_sources_pipeline"):
+        shutil.rmtree("_sources_pipeline")
+    Repo.clone_from(
+        "https://github.com/openMetadataInitiative/openMINDS.git",
+        to_path="_sources_pipeline",
+        branch="pipeline",
         depth=1,
     )
     if os.path.exists("_instances"):
@@ -27,6 +36,10 @@ def clone_sources():
 def get_short_name(uri):
     return uri.split("/")[-1]
 
+def get_short_namespace(uri):
+    match = re.match(r'^(https?:\/\/[^\/]+)', uri)
+    return match.group(1) if match else None
+
 
 class SchemaLoader(object):
 
@@ -46,6 +59,11 @@ def get_properties(self, version:str):
             all_properties = json.load(fp)
         return {name: p for name, p in all_properties.items() if version in p["usedIn"]}
 
+    def get_namespaces_version(self, version:str):
+        path = os.path.join(self._root_directory, "_sources_pipeline", "versions.json")
+        with open(path) as fp:
+            all_namespaces = json.load(fp)
+        return all_namespaces[version]["namespaces"]
 
 
 class InstanceLoader: