mtbls-mhd-integration 0.0.14__tar.gz → 0.0.16__tar.gz

{mtbls_mhd_integration-0.0.14/mtbls_mhd_integration.egg-info → mtbls_mhd_integration-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.14
+Version: 0.0.16
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -8,8 +8,8 @@ Requires-Python: <4.0,>=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg>=0.30.0
-Requires-Dist: metabolights-utils>=1.4.16
-Requires-Dist: mhd-model>=0.1.43
+Requires-Dist: metabolights-utils>=1.4.18
+Requires-Dist: mhd-model>=0.1.45
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.14 → mtbls_mhd_integration-0.0.16}/mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.14"
+__version__ = "v0.0.16"
 
 import pathlib
 import sys

{mtbls_mhd_integration-0.0.14 → mtbls_mhd_integration-0.0.16}/mtbls2mhd/v0_1/legacy/builder.py

@@ -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.",
@@ -360,15 +366,19 @@ class MhdLegacyDatasetBuilder:
                     organization,
                     reverse_relationship_name="affiliates",
                 )
+                roles = set()
                 for role in contact.roles:
-                    if role.term == "principal investigator":
+                    if role.term.lower() in roles:
+                        continue
+                    roles.add(role.term.lower())
+                    if role.term.lower() == "principal investigator":
                         mhd_builder.link(
                             mhd_contact,
                             "principal-investigator-of",
                             mhd_study,
                             reverse_relationship_name="has-principal-investigator",
                         )
-                    elif role.term == "submitter":
+                    elif role.term.lower() == "submitter":
                         mhd_builder.link(
                             mhd_contact,
                             "submits",
@@ -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(
@@ -449,6 +459,46 @@ class MhdLegacyDatasetBuilder:
 
         return organizations
 
+    def add_funders(
+        self,
+        data: MetabolightsStudyModel,
+        mhd_builder: MhDatasetBuilder,
+        mhd_study: mhd_domain.Study,
+        organizations: dict[str, mhd_domain.Organization],
+        build_type: BuildType = BuildType.FULL,
+    ):
+        if build_type == build_type.MINIMUM:
+            return
+        study: Study = data.investigation.studies[0]
+        comments = {x.name: x for x in study.comments if x and x.name}
+        grant_ids = []
+        if comments.get("Funder") and comments["Funder"].value:
+            if isinstance(comments["Funder"].value, str):
+                funders = comments["Funder"].value.split(";") or []
+            else:
+                funders = comments["Funder"].value[0].split(";") or []
+            for funder in funders:
+                organization = organizations.get(funder)
+                if not organization:
+                    organization = mhd_domain.Organization(name=funder)
+                    mhd_builder.add(organization)
+                    organizations[funder] = organization
+            mhd_builder.link(
+                mhd_study,
+                "funded-by",
+                organization,
+                reverse_relationship_name="funds",
+            )
+        grants = comments.get("Grant Identifier")
+        if grants and grants.value:
+            if isinstance(grants.value, str):
+                identifiers = grants.value.split(";")
+            else:
+                identifiers = grants.value[0].split(";")
+            if identifiers:
+                grant_ids.extend(identifiers)
+        mhd_study.grant_identifier_list = grant_ids
+
     def add_publications(
         self,
         data: MetabolightsStudyModel,
@@ -1447,17 +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",
                 )
@@ -1485,20 +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",
                     )
@@ -1864,28 +1911,32 @@ class MhdLegacyDatasetBuilder:
                 )
                 mhd_builder.add(assay_type)
                 mhd_assay.assay_type_ref = assay_type.id_
+            omics_types: list[mhd_domain.CvTermObject] = []
+            measurement_types: list[mhd_domain.CvTermObject] = []
+            measurement = None
+            if "untargeted" in assay.measurement_type.term.lower():
+                measurement = MTBLS_MEASUREMENT_TYPES["untargeted"]
+            elif "targeted" in assay.measurement_type.term.lower():
+                measurement = MTBLS_MEASUREMENT_TYPES["targeted"]
 
             inv_study = data.investigation.studies[0]
             design_types = inv_study.study_design_descriptors.design_types
 
-            omics_types: list[mhd_domain.CvTermObject] = []
-            measurement_types: list[mhd_domain.CvTermObject] = []
             for descriptor in design_types:
-                measurement = None
-                if "untargeted" in descriptor.term.lower():
-                    measurement = MTBLS_MEASUREMENT_TYPES["untargeted"]
-                elif "targeted" in descriptor.term.lower():
-                    measurement = MTBLS_MEASUREMENT_TYPES["targeted"]
-
-                if measurement:
-                    measurement_type = create_cv_term_object(
-                        type_="descriptor",
-                        source=measurement.source,
-                        accession=measurement.accession,
-                        name=measurement.name,
-                    )
-                    measurement_types.append(measurement_type)
-
+                if not measurement:
+                    if "untargeted" in descriptor.term.lower():
+                        measurement = MTBLS_MEASUREMENT_TYPES["untargeted"]
+                    elif "targeted" in descriptor.term.lower():
+                        measurement = MTBLS_MEASUREMENT_TYPES["targeted"]
+
+                    if measurement:
+                        measurement_type = create_cv_term_object(
+                            type_="descriptor",
+                            source=measurement.source,
+                            accession=measurement.accession,
+                            name=measurement.name,
+                        )
+                        measurement_types.append(measurement_type)
                 for v in COMMON_OMICS_TYPES.values():
                     if descriptor.term.lower() == v.name.lower():
                         omics_type = create_cv_term_object(
@@ -2110,7 +2161,9 @@ class MhdLegacyDatasetBuilder:
             reverse_relationship_name="provided-by",
         )
 
-        self.add_contacts(data, mhd_builder, mhd_study, build_type)
+        organizations = self.add_contacts(data, mhd_builder, mhd_study, build_type)
+        self.add_funders(data, mhd_builder, mhd_study, organizations, build_type)
+
         metadata_files = self.add_metadata_files(
             mhd_builder,
             mhd_study,

{mtbls_mhd_integration-0.0.14 → mtbls_mhd_integration-0.0.16/mtbls_mhd_integration.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.14
+Version: 0.0.16
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -8,8 +8,8 @@ Requires-Python: <4.0,>=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg>=0.30.0
-Requires-Dist: metabolights-utils>=1.4.16
-Requires-Dist: mhd-model>=0.1.43
+Requires-Dist: metabolights-utils>=1.4.18
+Requires-Dist: mhd-model>=0.1.45
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.14 → mtbls_mhd_integration-0.0.16}/mtbls_mhd_integration.egg-info/requires.txt

@@ -1,6 +1,6 @@
 asyncpg>=0.30.0
-metabolights-utils>=1.4.16
-mhd-model>=0.1.43
+metabolights-utils>=1.4.18
+mhd-model>=0.1.45
 psycopg[binary,pool]>=3.3.2
 pydantic>=2.12.4
 pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.14 → mtbls_mhd_integration-0.0.16}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mtbls-mhd-integration"
-version = "0.0.14"
+version = "0.0.16"
 description = "MetaboLights - MetabolomicsHub Integration"
 authors = [{"name" = "MetaboLights Team", "email" = "metabolights-help@ebi.ac.uk"}]
 license = "Apache-2.0"
@@ -8,8 +8,8 @@ readme = "README.md"
 requires-python = ">=3.12,<4.0"
 dependencies = [
     "asyncpg>=0.30.0",
-    "metabolights-utils>=1.4.16",
-    "mhd-model>=0.1.43",
+    "metabolights-utils>=1.4.18",
+    "mhd-model>=0.1.45",
     "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 = "0.0.143"
+version = "0.0.163"
 tag_format = "v$major.$minor.$patch"
 version_files = [
     "pyproject.toml:version",