mhd-model 0.1.45__py3-none-any.whl → 0.1.46__py3-none-any.whl

mhd_model/__init__.py

@@ -1,7 +1,7 @@
 import pathlib
 import sys
 
-__version__ = "v0.1.45"
+__version__ = "v0.1.46"
 
 application_root_path = pathlib.Path(__file__).parent.parent
 

mhd_model/model/v0_1/dataset/profiles/legacy/graph_validation.py

@@ -15,8 +15,8 @@ from mhd_model.model.v0_1.dataset.validation.profile.definition import (
 from mhd_model.model.v0_1.rules.managed_cv_terms import (
     COMMON_ASSAY_TYPES,
     COMMON_CHARACTERISTIC_DEFINITIONS,
-    COMMON_MEASUREMENT_TYPES,
-    COMMON_OMICS_TYPES,
+    # COMMON_MEASUREMENT_TYPES,
+    # COMMON_OMICS_TYPES,
     COMMON_PROTOCOLS,
     COMMON_TECHNOLOGY_TYPES,
 )
@@ -1555,20 +1555,20 @@ MHD_LEGACY_PROFILE_V0_1.cv_nodes = [
                     )
                 ],
             ),
-            CvTermValidation(
-                node_type="descriptor",
-                validation=AllowedCvTerms(
-                    cv_terms=list(COMMON_MEASUREMENT_TYPES.values())
-                ),
-                condition=[
-                    FilterCondition(
-                        name="Measurement Type",
-                        relationship_name="[embedded].measurement_type_ref",
-                        start_node_type="assay",
-                        expression="measurement_type_ref",
-                    )
-                ],
-            ),
+            # CvTermValidation(
+            #     node_type="descriptor",
+            #     validation=AllowedCvTerms(
+            #         cv_terms=list(COMMON_MEASUREMENT_TYPES.values())
+            #     ),
+            #     condition=[
+            #         FilterCondition(
+            #             name="Measurement Type",
+            #             relationship_name="[embedded].measurement_type_ref",
+            #             start_node_type="assay",
+            #             expression="measurement_type_ref",
+            #         )
+            #     ],
+            # ),
             CvTermValidation(
                 node_type="descriptor",
                 validation=AllowedCvTerms(
@@ -1583,18 +1583,18 @@ MHD_LEGACY_PROFILE_V0_1.cv_nodes = [
                     )
                 ],
             ),
-            CvTermValidation(
-                node_type="descriptor",
-                validation=AllowedCvTerms(cv_terms=list(COMMON_OMICS_TYPES.values())),
-                condition=[
-                    FilterCondition(
-                        name="Omics Type",
-                        relationship_name="[embedded].omics_type_ref",
-                        start_node_type="assay",
-                        expression="omics_type_ref",
-                    )
-                ],
-            ),
+            # CvTermValidation(
+            #     node_type="descriptor",
+            #     validation=AllowedCvTerms(cv_terms=list(COMMON_OMICS_TYPES.values())),
+            #     condition=[
+            #         FilterCondition(
+            #             name="Omics Type",
+            #             relationship_name="[embedded].omics_type_ref",
+            #             start_node_type="assay",
+            #             expression="omics_type_ref",
+            #         )
+            #     ],
+            # ),
         ],
         relationships=[
             RelationshipValidation(

mhd_model/model/v0_1/dataset/validation/validator.py

@@ -27,7 +27,10 @@ logger = logging.getLogger(__name__)
 
 def validate_mhd_file(file_path: str):
     json_data = load_json(file_path)
+    return validate_mhd_file_json(json_data)
 
+
+def validate_mhd_file_json(json_data: dict[str, Any]):
     mhd_validator = MhdFileValidator()
     errors = mhd_validator.validate(json_data)
 

mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json

@@ -1375,16 +1375,6 @@
             }
           ],
           "cvTerms": [
-            {
-              "accession": "MS:1003905",
-              "name": "targeted analysis",
-              "source": "MS"
-            },
-            {
-              "accession": "MS:1003904",
-              "name": "untargeted analysis",
-              "source": "MS"
-            },
             {
               "accession": "MS:1003904",
               "name": "untargeted analysis",

{mhd_model-0.1.45.dist-info → mhd_model-0.1.46.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mhd-model
-Version: 0.1.45
+Version: 0.1.46
 Summary: MetabolomicsHub Common Data Model
 Author-email: MetabolomicsHub Team <help@metabolomicshub.org>
 License-Expression: Apache-2.0

{mhd_model-0.1.45.dist-info → mhd_model-0.1.46.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mhd_model/__init__.py,sha256=o-sOqPqX5UhwWwn4jvVif7LDCCPPHyoD1xO1ZY1_OPs,286
+mhd_model/__init__.py,sha256=qrVDkugICDUTzB1ybw51jBS3f6-EM8YQEvEW3ngUMcE,286
 mhd_model/domain_utils.py,sha256=DQ3qanzv-Chydrt2HIM_G1jATf0Uv6XMP8-MgeaZFDk,939
 mhd_model/log_utils.py,sha256=U3ZmSebJttjeszkZ3HPZzjkczxoD557albXHjPRV4Ro,880
 mhd_model/mhd_client.py,sha256=LGS3jJ0qjnqSi8xYAY_-8K0vKjUgnrjzdM6yh7Fui9E,6939
@@ -56,7 +56,7 @@ mhd_model/model/v0_1/dataset/profiles/base/graph_validation.py,sha256=B6Wpb7ENWC
 mhd_model/model/v0_1/dataset/profiles/base/profile.py,sha256=AfEFmFamoq1Qmcdk2AHIJkKQNICGRjLpVPDRugWkMuM,4852
 mhd_model/model/v0_1/dataset/profiles/base/relationships.py,sha256=EeXBn1IUuNtSHzlEUqAohP0xx-yhiQ8o5oabQaLMess,463
 mhd_model/model/v0_1/dataset/profiles/legacy/__init__.py,sha256=dZI-_giUCGYVeEUQdbXHtH2yPKWVFowc1mj__2VqkIY,57
-mhd_model/model/v0_1/dataset/profiles/legacy/graph_validation.py,sha256=RtrnwNOIO73FbEB-DaivFUGEfB5zxfnODvFAYhy3Mpk,69742
+mhd_model/model/v0_1/dataset/profiles/legacy/graph_validation.py,sha256=2QPbkhUI281uolLy7mn5IF-sB2-1X1H6JwXACBEaXJ0,69798
 mhd_model/model/v0_1/dataset/profiles/legacy/profile.py,sha256=amBxF1xOZDRy7p9rCEjvk-EsnhtT09W5t0Iuk-eOAog,416
 mhd_model/model/v0_1/dataset/profiles/ms/__init__.py,sha256=8ED9PxVT9VzhA4T6UUtBWNs9e6-E4HW4Ilocc1PPQNA,42
 mhd_model/model/v0_1/dataset/profiles/ms/graph_validation.py,sha256=jIpYTAtViw5YrWPHFoztbuEgVgtQ_6_wgMjtGiisHOU,79044
@@ -64,7 +64,7 @@ mhd_model/model/v0_1/dataset/profiles/ms/profile.py,sha256=Cz9y1cXmC8RivsBAjoS2e
 mhd_model/model/v0_1/dataset/validation/__init__.py,sha256=_juFvBF1ZIiL0LvBFKc9iQJkEau2oq9PRMabaGfgEwo,52
 mhd_model/model/v0_1/dataset/validation/base.py,sha256=5MJ1EPRRYRIGiDdTKD_814japT2wbGOnx-mjVItPtOI,66067
 mhd_model/model/v0_1/dataset/validation/utils.py,sha256=hqcpv7tXZTfG7wheZIuKeHIxVPAXQwHGHbyri1M0cw4,965
-mhd_model/model/v0_1/dataset/validation/validator.py,sha256=je7U6P4mJR5FeGB0vuC0rjghLtWv0jI2IIEzufefTb0,4117
+mhd_model/model/v0_1/dataset/validation/validator.py,sha256=j5Kvyrj-mjE041EmsmCRoOK3eSoUF0yFUT2VqWfjm0g,4218
 mhd_model/model/v0_1/dataset/validation/profile/__init__.py,sha256=_85zooOqf7i70JhIb5ea2ykwGukx7_WdVTwUZ0b4aoU,33
 mhd_model/model/v0_1/dataset/validation/profile/base.py,sha256=R3xz2lOQ8n1ZZh3mVNTQMpm6SlrWgG6F6aUX7mIZOB8,2521
 mhd_model/model/v0_1/dataset/validation/profile/definition.py,sha256=o9j3URm6OklYGQFgIFHWPrF3Oq6Z-3VoN-RHyupiTXw,3053
@@ -77,7 +77,7 @@ mhd_model/model/v0_1/sdrf/model.py,sha256=5_qsF6WuUy8ctcW-fcexiEZcxjzSESCMgOYykt
 mhd_model/schemas/__init__.py,sha256=DrLraaFU_swK6sTXualuQ9TTlEm0FvnjLkFi83F9eaI,18
 mhd_model/schemas/mhd/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mhd_model/schemas/mhd/announcement-v0.1.legacy-profile.json,sha256=DY23rzd0_28IXVt1HA_OAawSNF8cjo07uEr9D2iPZjY,27992
-mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json,sha256=O03zQxhN7koOSgvPreYCTj-sLzVMt5uracZLgvp7zXk,50980
+mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json,sha256=GrjS4nV4ZEAFL6XZpDeY0psC1LhCvLh_Yi_RpCPcI_s,50694
 mhd_model/schemas/mhd/announcement-v0.1.schema.json,sha256=8m2lZQE89V7hsNVxVk1pJcmYfC30EbwTO5wscEquTu4,27079
 mhd_model/schemas/mhd/common-data-model-v0.1.legacy-profile.json,sha256=F_DEYMT_wpFMcXS2gy90p9MMNRRC-ih_U3AqRb-yf38,115271
 mhd_model/schemas/mhd/common-data-model-v0.1.ms-profile.json,sha256=uviJ0R4jghluxzinldMC5idhT-YM5fs-BZvrSvoIy-g,115263
@@ -91,9 +91,9 @@ mhd_model/shared/validation/cv_term_helper.py,sha256=ilDYgh_0cMrRQqmnvAwifCphH4f
 mhd_model/shared/validation/definitions.py,sha256=ZBq8LsgflIOMrmZZJaKOEirSkoA7XOudngXO5jQnx6Y,5428
 mhd_model/shared/validation/registry.py,sha256=G90tSEkuS2CHrOjGdE7XQpUfAXzro1hfjFst_UoAkP0,1192
 mhd_model/shared/validation/validators.py,sha256=IhZe9SNP1x8uLf2Ux1XFp1ugQDO9pHHsZDKhkjQZB9M,29445
-mhd_model-0.1.45.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mhd_model-0.1.45.dist-info/METADATA,sha256=P6jHYrt5WCcLUqCvAkcWf6wlveIACwCMQYgq-y1gzaE,4174
-mhd_model-0.1.45.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-mhd_model-0.1.45.dist-info/entry_points.txt,sha256=-F97t5JZgwWwzi15NZOAPaVvNDXR0KvTE_atG8ZYH4w,55
-mhd_model-0.1.45.dist-info/top_level.txt,sha256=_ZgHv-VuH4mrsT8J7_fZ8q0-iuOL4aAFu7xtzglEynI,10
-mhd_model-0.1.45.dist-info/RECORD,,
+mhd_model-0.1.46.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mhd_model-0.1.46.dist-info/METADATA,sha256=kx8swphS7k1uS07fmILUxTVORdbLOGy86mUSnft6XQ0,4174
+mhd_model-0.1.46.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mhd_model-0.1.46.dist-info/entry_points.txt,sha256=-F97t5JZgwWwzi15NZOAPaVvNDXR0KvTE_atG8ZYH4w,55
+mhd_model-0.1.46.dist-info/top_level.txt,sha256=_ZgHv-VuH4mrsT8J7_fZ8q0-iuOL4aAFu7xtzglEynI,10
+mhd_model-0.1.46.dist-info/RECORD,,