mtbls-mhd-integration 0.0.13__py3-none-any.whl → 0.0.15__py3-none-any.whl

mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.13"
+__version__ = "v0.0.15"
 
 import pathlib
 import sys

mtbls2mhd/convertor_factory.py

@@ -6,6 +6,7 @@ from mhd_model.model.definitions import (
 )
 
 from mtbls2mhd.v0_1.legacy.convertor import LegacyProfileV01Convertor
+from mtbls2mhd.v0_1.ms.convertor import MsProfileConvertor
 
 
 class Mtbls2MhdConvertorFactory(BaseMhdConvertorFactory):
@@ -21,7 +22,10 @@ class Mtbls2MhdConvertorFactory(BaseMhdConvertorFactory):
                     target_mhd_model_profile_uri=target_mhd_model_profile_uri,
                 )
             elif target_mhd_model_profile_uri == MHD_MODEL_V0_1_MS_PROFILE_NAME:
-                raise NotImplementedError()
+                return MsProfileConvertor(
+                    target_mhd_model_schema_uri=target_mhd_model_schema_uri,
+                    target_mhd_model_profile_uri=target_mhd_model_profile_uri,
+                )
             raise NotImplementedError()
         else:
             raise NotImplementedError()

mtbls2mhd/v0_1/legacy/builder.py

@@ -361,14 +361,14 @@ class MhdLegacyDatasetBuilder:
                     reverse_relationship_name="affiliates",
                 )
                 for role in contact.roles:
-                    if role.term == "principal investigator":
+                    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",
@@ -449,6 +449,46 @@ 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,
@@ -1808,7 +1848,7 @@ class MhdLegacyDatasetBuilder:
         files_map,
     ) -> dict[str, mhd_domain.Assay]:
         protocol_summaries: OrderedDict[str, ProtocolRunSummary] = OrderedDict()
-        assays = dict[str, mhd_domain.Assay] = OrderedDict()
+        assays: OrderedDict[str, mhd_domain.Assay] = OrderedDict()
         for assay in selected_assays:
             if assay.file_name not in data.assays:
                 continue
@@ -1864,28 +1904,32 @@ 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 +2154,9 @@ 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,

mtbls2mhd/v0_1/ms/convertor.py

@@ -1,3 +1,59 @@
-class Mtbs2MhdMsProfileConvertor:
-    def convert():
-        raise NotImplementedError()
+from pathlib import Path
+
+from mhd_model.convertors.mhd.convertor import BaseMhdConvertor
+from mhd_model.shared.model import Revision
+
+from mtbls2mhd.config import Mtbls2MhdConfiguration, get_default_config
+from mtbls2mhd.v0_1.legacy.builder import BuildType, MhdLegacyDatasetBuilder
+
+
+class MsProfileConvertor(BaseMhdConvertor):
+    def __init__(
+        self,
+        target_mhd_model_schema_uri: str,
+        target_mhd_model_profile_uri: str,
+    ):
+        self.target_mhd_model_schema_uri = target_mhd_model_schema_uri
+        self.target_mhd_model_profile_uri = target_mhd_model_profile_uri
+
+    def convert(
+        self,
+        repository_name: str,
+        repository_identifier: str,
+        mhd_identifier: None | str,
+        repository_revision: None | Revision = None,
+        config: None | Mtbls2MhdConfiguration = None,  # noqa: F821
+        cached_mtbls_model_file_path: None | str = None,
+        **kwargs,
+    ):
+        if not config:
+            config = get_default_config()
+        mhd_dataset_builder = MhdLegacyDatasetBuilder()
+        mtbls_study_repository_url = (
+            f"{config.study_http_base_url}/{repository_identifier}"
+        )
+
+        mtbls_study_path = Path(config.mtbls_studies_root_path) / Path(
+            repository_identifier
+        )
+        try:
+            success, message = mhd_dataset_builder.build(
+                mhd_id=mhd_identifier,
+                mtbls_study_id=repository_identifier,
+                mtbls_study_path=mtbls_study_path,
+                mtbls_study_repository_url=mtbls_study_repository_url,
+                target_mhd_model_schema_uri=self.target_mhd_model_schema_uri,
+                target_mhd_model_profile_uri=self.target_mhd_model_profile_uri,
+                config=config,
+                cached_mtbls_model_file_path=cached_mtbls_model_file_path,
+                revision=repository_revision,
+                repository_name=repository_name,
+                build_type=BuildType.FULL_AND_CUSTOM_NODES,
+                **kwargs,
+            )
+            return success, message
+        except Exception as ex:
+            import traceback
+
+            traceback.print_exc()
+            return False, str(ex)

{mtbls_mhd_integration-0.0.13.dist-info → mtbls_mhd_integration-0.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.13
+Version: 0.0.15
 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>=0.1.44
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.13.dist-info → mtbls_mhd_integration-0.0.15.dist-info}/RECORD

@@ -1,6 +1,6 @@
-mtbls2mhd/__init__.py,sha256=9NntcMjl9WIHQAy6xlxCyDazWlWBRKDTjy517m_kTgc,158
+mtbls2mhd/__init__.py,sha256=sP6P2r3ohpNSNphplpratyl2bhnzH2tDhPYOOAPAmDg,158
 mtbls2mhd/config.py,sha256=BjOqAyfDhp9byoFjJz70xh4HRR8pu1yrm_5jweqygSI,2310
-mtbls2mhd/convertor_factory.py,sha256=4loatqIRIvIhcaeIS0cSonJNYJu47o56ZllX6593ypk,1133
+mtbls2mhd/convertor_factory.py,sha256=WNXgzLFq84whwv0phrB1B2L1YRabO2tD0nPDT9QJ6gQ,1365
 mtbls2mhd/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mtbls2mhd/commands/cli.py,sha256=XhLcqBxmBNX_nSEc4aU9q2D9VoYvqZKeRuYLbt-JwZ8,662
 mtbls2mhd/commands/create.py,sha256=fcZO5Ez5yams95Zpx1vQjjagBiJzfnZrIKfk5Z6qoRw,452
@@ -8,16 +8,16 @@ mtbls2mhd/commands/create_mhd_file.py,sha256=0sDr-Cm0JhhEB5V1g66uoag3rlcaAnGP8Md
 mtbls2mhd/commands/validate.py,sha256=iwIKegviRxdH0r8scRXbDISlwQUzAq5uVoCHinU7x6Q,473
 mtbls2mhd/v0_1/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mtbls2mhd/v0_1/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mtbls2mhd/v0_1/legacy/builder.py,sha256=4V0jxjeXrKRFv9ojC0lg1l8aO1FDVTugrW1zh8L2VL4,90582
+mtbls2mhd/v0_1/legacy/builder.py,sha256=xYPy_qoWIV_c6GGD_2AE-pCVAwxe_7BPq5Cn6tQqRbc,92682
 mtbls2mhd/v0_1/legacy/convertor.py,sha256=Nu6xJvEk8WsRQJQFoxM5eo-y46tVfWV8EkedVoqI9rI,2198
 mtbls2mhd/v0_1/legacy/db_metadata_collector.py,sha256=UGk1AeST1NQ9lWwy_sYZxaaWs0ajgaKELDJtXJ4-Uco,13071
 mtbls2mhd/v0_1/legacy/folder_metadata_collector.py,sha256=QwtXI9rBvdh6pxILQDHymIwYDqzGuMxqdOcqtdAObME,7538
 mtbls2mhd/v0_1/legacy/mtbls_study_schema.py,sha256=gUTbRmI8GfHI5leLiw8dxsmWnV3NnWw5RPX_LQWRFRQ,3162
 mtbls2mhd/v0_1/ms/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mtbls2mhd/v0_1/ms/convertor.py,sha256=kLIUpxOrH6hcs2Y9Bq1D0Mdvypg40pLyEJpHtGj6H_g,89
-mtbls_mhd_integration-0.0.13.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mtbls_mhd_integration-0.0.13.dist-info/METADATA,sha256=pww_KrAeo8l_Ehfxht5GJIGyvPC-5bvJjNEr95sTOU4,688
-mtbls_mhd_integration-0.0.13.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-mtbls_mhd_integration-0.0.13.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
-mtbls_mhd_integration-0.0.13.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
-mtbls_mhd_integration-0.0.13.dist-info/RECORD,,
+mtbls2mhd/v0_1/ms/convertor.py,sha256=axkKDRx00ix6ceqJe9-KruEYEZOgaVtsAgCHiixPo5k,2201
+mtbls_mhd_integration-0.0.15.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mtbls_mhd_integration-0.0.15.dist-info/METADATA,sha256=zBXoZ7dOlmyE9AvtJxz2VyXflWLwqM-xe0JOampcOF0,688
+mtbls_mhd_integration-0.0.15.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mtbls_mhd_integration-0.0.15.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
+mtbls_mhd_integration-0.0.15.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
+mtbls_mhd_integration-0.0.15.dist-info/RECORD,,