mtbls-mhd-integration 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.5"
+__version__ = "v0.0.7"
 
 import pathlib
 import sys

mtbls2mhd/v0_1/legacy/builder.py

@@ -1840,7 +1840,7 @@ class MhdLegacyDatasetBuilder:
 
     def build(
         self,
-        mhd_id: str,
+        mhd_id: None | str,
         mhd_output_folder_path: Path,
         mtbls_study_id: str,
         mtbls_study_path: Path,
@@ -1894,8 +1894,8 @@ class MhdLegacyDatasetBuilder:
             error = f"{data.investigation_file_path} file does not have any study. Skipping..."
             logger.warning(error)
             return False, error
+        db_metadata = data.study_db_metadata
         if not revision:
-            db_metadata = data.study_db_metadata
             revision_date = (
                 datetime.datetime.strptime(db_metadata.revision_date, "%Y-%m-%d")
                 if db_metadata and db_metadata.revision_date
@@ -1942,7 +1942,7 @@ class MhdLegacyDatasetBuilder:
         # TODO get revision, dataset_licence from study
         mhd_builder = MhDatasetBuilder(
             repository_name=repository_name,
-            mhd_identifier=mhd_id,
+            mhd_identifier=None,
             repository_identifier=study.identifier,
             schema_name=target_mhd_model_schema_uri,
             profile_uri=target_mhd_model_profile_uri,
@@ -1970,6 +1970,16 @@ class MhdLegacyDatasetBuilder:
                 study.public_release_date,
                 data.study_db_metadata.release_date,
             )
+        public_release_date = (
+            datetime.datetime.strptime(db_metadata.first_public_date, "%Y-%m-%d")
+            if db_metadata and db_metadata.revision_date
+            else None
+        )
+        submission_date = (
+            datetime.datetime.strptime(db_metadata.first_public_date, "%Y-%m-%d")
+            if db_metadata and db_metadata.first_private_date
+            else None
+        )
 
         mhd_study = mhd_domain.Study(
             repository_identifier=study.identifier,
@@ -1977,8 +1987,8 @@ class MhdLegacyDatasetBuilder:
             mhd_identifier=mhd_id,
             title=study.title,
             description=study.description,
-            submission_date=data.study_db_metadata.submission_date,
-            public_release_date=data.study_db_metadata.release_date,
+            submission_date=submission_date,
+            public_release_date=public_release_date,
             dataset_url_list=[mtbls_study_repository_url],
         )
 

mtbls2mhd/v0_1/legacy/convertor.py

@@ -36,14 +36,6 @@ class LegacyProfileV01Convertor(BaseMhdConvertor):
         mtbls_study_path = Path(config.mtbls_studies_root_path) / Path(
             repository_identifier
         )
-        # cached_mtbls_model_files_root_path = Path("/tmp/mtbls2mhd") / Path(
-        #     ".mtbls_model_cache"
-        # )
-        # cached_mtbls_model_files_root_path.mkdir(parents=True, exist_ok=True)
-        # cache_file_name = mhd_identifier or repository_identifier
-        # cached_mtbls_model_file_path = cached_mtbls_model_files_root_path / Path(
-        #     cache_file_name
-        # )
         try:
             success, message = mhd_dataset_builder.build(
                 mhd_id=mhd_identifier,

{mtbls_mhd_integration-0.0.5.dist-info → mtbls_mhd_integration-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.5
+Version: 0.0.7
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0

{mtbls_mhd_integration-0.0.5.dist-info → mtbls_mhd_integration-0.0.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mtbls2mhd/__init__.py,sha256=3byMWcFYU6S6BKe-liUPRtmlSwQrjbuEljIatokiM3s,157
+mtbls2mhd/__init__.py,sha256=6olT1Yu2MjF4fiYjEEUo6rlu5zdyZoIfu0GwJFhKXvA,157
 mtbls2mhd/config.py,sha256=BjOqAyfDhp9byoFjJz70xh4HRR8pu1yrm_5jweqygSI,2310
 mtbls2mhd/convertor_factory.py,sha256=4loatqIRIvIhcaeIS0cSonJNYJu47o56ZllX6593ypk,1133
 mtbls2mhd/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -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=Kz4bHoGIUFTaj3nJaHs5OFG095sgbHmOxd5r-rlCeL0,85414
-mtbls2mhd/v0_1/legacy/convertor.py,sha256=gewPleS8FH3TS63dALqtIUuX26dAkIFo701UMlKiOE8,2607
+mtbls2mhd/v0_1/legacy/builder.py,sha256=XySknfa0W40H4x1b9XrLD_fBf7zCWrZx__54nQCAp2g,85783
+mtbls2mhd/v0_1/legacy/convertor.py,sha256=M4-3NB56C0DN8H5vmM0yC0J_qW87ZImjjL1vzDEBc5s,2208
 mtbls2mhd/v0_1/legacy/db_metadata_collector.py,sha256=4OyA_KD2X2zr7AHn8pQZJ0Y2_bW5r2_2wgTtQ93LM6A,13193
 mtbls2mhd/v0_1/legacy/folder_metadata_collector.py,sha256=1lELGwTsr12nBGwTog_Z8qi9dLt4awma56vBYoI678k,7439
 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-0.0.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mtbls_mhd_integration-0.0.5.dist-info/METADATA,sha256=2BQEjtVChMbUMm737D2dUGEWB2kJoh0oUvmM0Dl57Hs,682
-mtbls_mhd_integration-0.0.5.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-mtbls_mhd_integration-0.0.5.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
-mtbls_mhd_integration-0.0.5.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
-mtbls_mhd_integration-0.0.5.dist-info/RECORD,,
+mtbls_mhd_integration-0.0.7.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mtbls_mhd_integration-0.0.7.dist-info/METADATA,sha256=G6riSBg2kLRmDrW6yDeXFCTULOvQCJ3HeofdF9LGzjg,682
+mtbls_mhd_integration-0.0.7.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mtbls_mhd_integration-0.0.7.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
+mtbls_mhd_integration-0.0.7.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
+mtbls_mhd_integration-0.0.7.dist-info/RECORD,,

{mtbls_mhd_integration-0.0.5.dist-info → mtbls_mhd_integration-0.0.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.10.1)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any