mhd-model 0.1.40__tar.gz → 0.1.42__tar.gz

{mhd_model-0.1.40 → mhd_model-0.1.42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mhd-model
-Version: 0.1.40
+Version: 0.1.42
 Summary: MetabolomicsHub Common Data Model
 Author-email: MetabolomicsHub Team <help@metabolomicshub.org>
 License-Expression: Apache-2.0

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/__init__.py

@@ -1,7 +1,7 @@
 import pathlib
 import sys
 
-__version__ = "v0.1.40"
+__version__ = "v0.1.42"
 
 application_root_path = pathlib.Path(__file__).parent.parent
 

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/legacy/mhd2announce.py

@@ -339,9 +339,9 @@ def create_announcement_file(
     characteristic_values = get_characteristic_values(all_nodes_map, relationships_map)
 
     if not mhd_file_url:
-        ftp = [str(x) for x in study.dataset_url_list if str(x).startswith("ftp://")]
-        if ftp:
-            mhd_file_url = f"{ftp[0]}/{study.repository_identifier}.mhd.json"
+        http = [str(x) for x in study.dataset_url_list if str(x).startswith("http://")]
+        if http:
+            mhd_file_url = f"{http[0]}/{study.repository_identifier}.mhd.json"
 
     announcement = AnnouncementLegacyProfile(
         repository_name=mhd_dataset.repository_name,
@@ -349,6 +349,8 @@ def create_announcement_file(
         repository_identifier=study.repository_identifier,
         schema_name=announcement_schema_name,
         profile_uri=announcement_profile_uri,
+        revision=mhd_dataset.repository_revision,
+        revision_datetime=mhd_dataset.repository_revision_datetime,
         mhd_metadata_file_url=AnyUrl(mhd_file_url),
         dataset_url_list=dataset_url_list,
         license=study.license,

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/ms/mhd2announce.py

@@ -261,8 +261,12 @@ def create_announcement_file(
     announcement_profile_uri=ANNOUNCEMENT_FILE_V0_1_LEGACY_PROFILE_NAME,
 ):
     mhd_dataset = MhDatasetMsProfile.model_validate(mhd_file)
-    nodes_map = {x.id_: x for x in mhd_dataset.graph.nodes}
-    relationships_map = {x.id_: x for x in mhd_dataset.graph.relationships}
+    nodes_map: dict[str, IdentifiableMhdModel] = {
+        x.id_: x for x in mhd_dataset.graph.nodes
+    }
+    relationships_map: dict[str, BaseMhdRelationship] = {
+        x.id_: x for x in mhd_dataset.graph.relationships
+    }
 
     all_nodes_map: dict[str, BaseMhdModel] = {}
     type_map: dict[str, dict[str, BaseMhdModel]] = {}
@@ -279,7 +283,7 @@ def create_announcement_file(
         relationship_name_map[rel.relationship_name][rel.id_] = rel
 
     if "study" not in type_map:
-        logger.info("Study not found for in input file")
+        logger.error("Study not found for in the input file")
         return
     study: graph_nodes.Study = list(type_map["study"].values())[0]
 
@@ -293,6 +297,7 @@ def create_announcement_file(
             type_map["publication"].values()
         )
         for node in graph_publications:
+            relationships_map.get()
             item = AnnouncementPublication.model_validate(
                 node.model_dump(by_alias=True)
             )

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/graph_nodes.py

@@ -32,6 +32,7 @@ class Person(BaseLabeledMhdModel):
             description="The value of this property MUST be 'person'",
         ),
     ] = "person"
+    repository_identifier: Annotated[None | str, Field()] = None
     full_name: Annotated[
         None | str, Field(min_length=2, description="Full name of person")
     ] = None
@@ -91,6 +92,7 @@ class Project(BaseLabeledMhdModel):
         ),
     ] = "project"
     title: Annotated[None | str, Field(min_length=2)] = None
+    repository_identifier: Annotated[None | str, Field()] = None
     description: Annotated[None | str, Field()] = None
     grant_identifier_list: Annotated[None | list[GrantId], Field()] = None
     doi: Annotated[None | DOI, Field()] = None

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/graph_validation.py

@@ -339,6 +339,14 @@ MHD_BASE_VALIDATION_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="metadata-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -376,6 +384,30 @@ MHD_BASE_VALIDATION_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=1,
             ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="metadata-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="result-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="measured-in",
+                reverse_relationship_name="measures",
+                target="raw-data-file",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -777,6 +809,14 @@ MHD_BASE_VALIDATION_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="raw-data-file",
+                relationship_name="measures",
+                reverse_relationship_name="measured-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -819,6 +859,14 @@ MHD_BASE_VALIDATION_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="result-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/legacy/graph_validation.py

@@ -333,6 +333,14 @@ MHD_LEGACY_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="metadata-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -370,6 +378,30 @@ MHD_LEGACY_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=1,
             ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="metadata-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="result-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="measured-in",
+                reverse_relationship_name="measures",
+                target="raw-data-file",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -771,6 +803,14 @@ MHD_LEGACY_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="raw-data-file",
+                relationship_name="measures",
+                reverse_relationship_name="measured-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -818,6 +858,14 @@ MHD_LEGACY_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="result-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/ms/graph_validation.py

@@ -337,6 +337,14 @@ MHD_MS_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="metadata-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -374,6 +382,30 @@ MHD_MS_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=1,
             ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="metadata-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="reported-in",
+                reverse_relationship_name="reports",
+                target="result-file",
+                min=0,
+                min_for_each_source=0,
+            ),
+            RelationshipValidation(
+                source="metabolite",
+                relationship_name="measured-in",
+                reverse_relationship_name="measures",
+                target="raw-data-file",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -780,6 +812,14 @@ MHD_MS_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="raw-data-file",
+                relationship_name="measures",
+                reverse_relationship_name="measured-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(
@@ -827,6 +867,14 @@ MHD_MS_PROFILE_V0_1.mhd_nodes = [
                 min=0,
                 min_for_each_source=0,
             ),
+            RelationshipValidation(
+                source="result-file",
+                relationship_name="reports",
+                reverse_relationship_name="reported-in",
+                target="metabolite",
+                min=0,
+                min_for_each_source=0,
+            ),
         ],
     ),
     NodeValidation(

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.legacy-profile.json

@@ -1287,4 +1287,4 @@
   ],
   "title": "AnnouncementLegacyProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json

@@ -1921,4 +1921,4 @@
   ],
   "title": "AnnouncementMsProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.schema.json

@@ -1266,4 +1266,4 @@
   ],
   "title": "AnnouncementBaseProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.legacy-profile.json

@@ -1650,6 +1650,18 @@
           "default": null,
           "title": "Label"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "full_name": {
           "anyOf": [
             {
@@ -1861,6 +1873,18 @@
           "default": null,
           "title": "Title"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "description": {
           "anyOf": [
             {
@@ -4349,4 +4373,4 @@
   ],
   "title": "MhDatasetLegacyProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.ms-profile.json

@@ -1650,6 +1650,18 @@
           "default": null,
           "title": "Label"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "full_name": {
           "anyOf": [
             {
@@ -1861,6 +1873,18 @@
           "default": null,
           "title": "Title"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "description": {
           "anyOf": [
             {
@@ -4349,4 +4373,4 @@
   ],
   "title": "MhDatasetMsProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.schema.json

@@ -1650,6 +1650,18 @@
           "default": null,
           "title": "Label"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "full_name": {
           "anyOf": [
             {
@@ -1861,6 +1873,18 @@
           "default": null,
           "title": "Title"
         },
+        "repository_identifier": {
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "title": "Repository Identifier"
+        },
         "description": {
           "anyOf": [
             {
@@ -4349,4 +4373,4 @@
   ],
   "title": "MhDatasetBaseProfile",
   "type": "object"
-}
+}

{mhd_model-0.1.40 → mhd_model-0.1.42}/mhd_model.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mhd-model
-Version: 0.1.40
+Version: 0.1.42
 Summary: MetabolomicsHub Common Data Model
 Author-email: MetabolomicsHub Team <help@metabolomicshub.org>
 License-Expression: Apache-2.0

{mhd_model-0.1.40 → mhd_model-0.1.42}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mhd-model"
-version = "0.1.40"
+version = "0.1.42"
 description = "MetabolomicsHub Common Data Model"
 authors = [{"name"="MetabolomicsHub Team", "email"="help@metabolomicshub.org"}]
 license = "Apache-2.0"
@@ -62,7 +62,7 @@ test = [
 [tool.commitizen]
 name = "cz_conventional_commits"
 version_provider = "uv"
-version = "0.1.40"
+version = "0.1.42"
 tag_format = "v$major.$minor.$patch"
 version_files = [
     "pyproject.toml:version",