mtbls-mhd-integration 0.0.13__py3-none-any.whl → 0.0.14__py3-none-any.whl

mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.13"
+__version__ = "v0.0.14"
 
 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

@@ -1808,7 +1808,7 @@ 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

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-0.0.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.13
+Version: 0.0.14
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0

{mtbls_mhd_integration-0.0.13.dist-info → mtbls_mhd_integration-0.0.14.dist-info}/RECORD

@@ -1,6 +1,6 @@
-mtbls2mhd/__init__.py,sha256=9NntcMjl9WIHQAy6xlxCyDazWlWBRKDTjy517m_kTgc,158
+mtbls2mhd/__init__.py,sha256=XpOJ1XATu_r7h8z0RvXDGIZ-JHycpLZFRO5bzsIc6W0,158
 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=EhTDcshxkQTs-vz60TZ6e2ECyn6ZwRaJRxJGKwilS0o,90588
 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-0.0.14.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mtbls_mhd_integration-0.0.14.dist-info/METADATA,sha256=7Y-wIcfSz16osVnn30q1V4xd3I1A6kIsYDfcqHBEu0E,688
+mtbls_mhd_integration-0.0.14.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mtbls_mhd_integration-0.0.14.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
+mtbls_mhd_integration-0.0.14.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
+mtbls_mhd_integration-0.0.14.dist-info/RECORD,,