mtbls-mhd-integration 0.0.15__tar.gz → 0.0.17__tar.gz

{mtbls_mhd_integration-0.0.15/mtbls_mhd_integration.egg-info → mtbls_mhd_integration-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.15
+Version: 0.0.17
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -9,7 +9,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg>=0.30.0
 Requires-Dist: metabolights-utils>=1.4.18
-Requires-Dist: mhd-model>=0.1.44
+Requires-Dist: mhd-model>=0.1.46
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.15 → mtbls_mhd_integration-0.0.17}/mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.15"
+__version__ = "v0.0.17"
 
 import pathlib
 import sys

{mtbls_mhd_integration-0.0.15 → mtbls_mhd_integration-0.0.17}/mtbls2mhd/v0_1/legacy/builder.py

@@ -26,7 +26,7 @@ from mhd_model.model.v0_1.dataset.profiles.legacy.profile import MhDatasetLegacy
 from mhd_model.model.v0_1.rules.managed_cv_terms import (
     COMMON_ASSAY_TYPES,
     COMMON_CHARACTERISTIC_DEFINITIONS,
-    COMMON_MEASUREMENT_TYPES,
+    COMMON_MEASUREMENT_TYPES_MAP,
     COMMON_OMICS_TYPES,
     COMMON_PARAMETER_DEFINITIONS,
     COMMON_PROTOCOLS,
@@ -61,11 +61,11 @@ MTBLS_ASSAY_TYPES = {
     "MS": COMMON_ASSAY_TYPES["OBI:0000470"],
 }
 MTBLS_MEASUREMENT_TYPES = {
-    "targeted": COMMON_MEASUREMENT_TYPES["MSIO:0000100"],
-    "untargeted": COMMON_MEASUREMENT_TYPES["MSIO:0000101"],
+    "targeted": COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000100"],
+    "untargeted": COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000101"],
 }
 
-DEFAULT_MEASUREMENT_TYPE = COMMON_MEASUREMENT_TYPES["MSIO:0000101"]
+DEFAULT_MEASUREMENT_TYPE = COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000101"]
 
 DEFAULT_OMICS_TYPE = COMMON_OMICS_TYPES["EDAM:3172"]
 
@@ -283,6 +283,7 @@ class MhdLegacyDatasetBuilder:
                                 if x
                             ]
                         ),
+                        email_list=[submitter.user_name],
                     )
                     mhd_builder.add(mhd_contact)
                     mhd_builder.link(
@@ -331,6 +332,11 @@ class MhdLegacyDatasetBuilder:
                         idx,
                     )
                     continue
+                if contact.additional_emails:
+                    if mhd_contact.email_list:
+                        mhd_contact.email_list.extend(contact.additional_emails)
+                    else:
+                        mhd_contact.email_list = contact.additional_emails
                 if not mhd_contact.email_list:
                     logger.warning(
                         "%s study %s. contact's ('%s') email is empty. Contact will be ignored.",
@@ -360,7 +366,11 @@ class MhdLegacyDatasetBuilder:
                     organization,
                     reverse_relationship_name="affiliates",
                 )
+                roles = set()
                 for role in contact.roles:
+                    if role.term.lower() in roles:
+                        continue
+                    roles.add(role.term.lower())
                     if role.term.lower() == "principal investigator":
                         mhd_builder.link(
                             mhd_contact,
@@ -429,7 +439,7 @@ class MhdLegacyDatasetBuilder:
                     else:
                         mhd_contact = contacts[submitter.user_name]
                     submitter_roles = [
-                        x for x in contact.roles if x.term == "submitter"
+                        x for x in contact.roles if x.term.lower() == "submitter"
                     ]
                     if not submitter_roles:
                         mhd_builder.link(
@@ -1487,17 +1497,17 @@ class MhdLegacyDatasetBuilder:
             )
             mhd_builder.add_node(keyword)
 
-            if item.source and item.source.lower() in ("data-curation", "workflows"):
+            if not item.source or item.source.lower() in ("submitter",):
                 mhd_builder.link(
                     mhd_study,
-                    "has-repository-keyword",
+                    "has-submitter-keyword",
                     keyword,
                     reverse_relationship_name="keyword-of",
                 )
             else:
                 mhd_builder.link(
                     mhd_study,
-                    "has-submitter-keyword",
+                    "has-repository-keyword",
                     keyword,
                     reverse_relationship_name="keyword-of",
                 )
@@ -1525,20 +1535,17 @@ class MhdLegacyDatasetBuilder:
                 )
                 mhd_builder.add_node(keyword)
 
-                if item.source and item.source.lower() in (
-                    "data-curation",
-                    "workflows",
-                ):
+                if not item.source or item.source.lower() in ("submitter",):
                     mhd_builder.link(
                         mhd_assay,
-                        "has-repository-keyword",
+                        "has-submitter-keyword",
                         keyword,
                         reverse_relationship_name="keyword-of",
                     )
                 else:
                     mhd_builder.link(
                         mhd_assay,
-                        "has-submitter-keyword",
+                        "has-repository-keyword",
                         keyword,
                         reverse_relationship_name="keyword-of",
                     )

{mtbls_mhd_integration-0.0.15 → mtbls_mhd_integration-0.0.17/mtbls_mhd_integration.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.15
+Version: 0.0.17
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -9,7 +9,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg>=0.30.0
 Requires-Dist: metabolights-utils>=1.4.18
-Requires-Dist: mhd-model>=0.1.44
+Requires-Dist: mhd-model>=0.1.46
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.15 → mtbls_mhd_integration-0.0.17}/mtbls_mhd_integration.egg-info/requires.txt

@@ -1,6 +1,6 @@
 asyncpg>=0.30.0
 metabolights-utils>=1.4.18
-mhd-model>=0.1.44
+mhd-model>=0.1.46
 psycopg[binary,pool]>=3.3.2
 pydantic>=2.12.4
 pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.15 → mtbls_mhd_integration-0.0.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mtbls-mhd-integration"
-version = "0.0.15"
+version = "0.0.17"
 description = "MetaboLights - MetabolomicsHub Integration"
 authors = [{"name" = "MetaboLights Team", "email" = "metabolights-help@ebi.ac.uk"}]
 license = "Apache-2.0"
@@ -9,7 +9,7 @@ requires-python = ">=3.12,<4.0"
 dependencies = [
     "asyncpg>=0.30.0",
     "metabolights-utils>=1.4.18",
-    "mhd-model>=0.1.44",
+    "mhd-model>=0.1.46",
     "psycopg[binary,pool]>=3.3.2",
     "pydantic>=2.12.4",
     "pydantic-settings>=2.10.1",
@@ -54,7 +54,7 @@ exclude = ["tests*", "docs*"]
 [tool.commitizen]
 name = "cz_conventional_commits"
 version_provider = "uv"
-version = "0.0.153"
+version = "0.0.173"
 tag_format = "v$major.$minor.$patch"
 version_files = [
     "pyproject.toml:version",