mtbls-mhd-integration 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.4"
+__version__ = "v0.0.6"
 
 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,
@@ -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,

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,

mtbls2mhd/v0_1/legacy/db_metadata_collector.py

@@ -4,7 +4,7 @@ from functools import lru_cache
 from logging import getLogger
 from typing import Any, Dict, List
 
-import psycopg2
+import psycopg
 from metabolights_utils.models.common import ErrorMessage
 from metabolights_utils.models.metabolights.model import (
     CurationRequest,
@@ -16,7 +16,7 @@ from metabolights_utils.models.metabolights.model import (
     UserStatus,
 )
 from metabolights_utils.provider.study_provider import AbstractDbMetadataCollector
-from psycopg2.extras import DictCursor
+from psycopg.rows import dict_row
 from sqlalchemy import or_, select
 from sqlalchemy.ext.asyncio import AsyncSession, create_async_engine
 from sqlalchemy.orm import sessionmaker
@@ -83,15 +83,16 @@ def create_postgresql_connection(mtbls2mhd_config: Mtbls2MhdConfiguration):
     Creates and returns a PostgreSQL connection.
     """
     try:
-        connection = psycopg2.connect(
+        connection = psycopg.connect(
             dbname=mtbls2mhd_config.database_name,
             user=mtbls2mhd_config.database_user,
             password=mtbls2mhd_config.database_user_password,
             host=mtbls2mhd_config.database_host,
             port=mtbls2mhd_config.database_host_port,
+            row_factory=dict_row,
         )
         return connection
-    except psycopg2.Error as e:
+    except psycopg.Error as e:
         logger.exception(e)
         raise e
 
@@ -171,7 +172,7 @@ class DbMetadataCollector(AbstractDbMetadataCollector):
         where_clause = " and ".join(_filter)
         _input = f"select acc from studies where {where_clause};"
         try:
-            cursor = connection.cursor(cursor_factory=DictCursor)
+            cursor = connection.cursor()
             cursor.execute(_input)
             data = cursor.fetchall()
             return data
@@ -196,7 +197,7 @@ class DbMetadataCollector(AbstractDbMetadataCollector):
     def _get_study_from_db(self, study_id: str, connection):
         _input = "select * from studies where acc = %(study_id)s;"
         try:
-            cursor = connection.cursor(cursor_factory=DictCursor)
+            cursor = connection.cursor()
             cursor.execute(_input, {"study_id": study_id})
             data = cursor.fetchone()
             return data
@@ -207,7 +208,7 @@ class DbMetadataCollector(AbstractDbMetadataCollector):
     def _get_study_revision_from_db(self, study_id: str, revision: int, connection):
         _input = "select * from study_revisions where accession_number = %(study_id)s and revision_number = %(revision)s;"
         try:
-            cursor = connection.cursor(cursor_factory=DictCursor)
+            cursor = connection.cursor()
             cursor.execute(_input, {"study_id": study_id, "revision": revision})
             data = cursor.fetchone()
             return data
@@ -221,7 +222,7 @@ class DbMetadataCollector(AbstractDbMetadataCollector):
         _input = f"select {', '.join(submitter_fields)} from studies as s, study_user as su, \
             users as u where su.userid = u.id and su.studyid = s.id and s.acc = %(study_id)s;"
         try:
-            cursor = connection.cursor(cursor_factory=DictCursor)
+            cursor = connection.cursor()
             cursor.execute(_input, {"study_id": study_id})
             data = cursor.fetchall()
             if data:

{mtbls_mhd_integration-0.0.4.dist-info → mtbls_mhd_integration-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.4
+Version: 0.0.6
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -9,8 +9,8 @@ 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>=0.1.38
-Requires-Dist: psycopg2-binary>=2.9.11
+Requires-Dist: mhd-model>=0.1.39
+Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1
 Requires-Dist: pyyaml>=6.0.3

{mtbls_mhd_integration-0.0.4.dist-info → mtbls_mhd_integration-0.0.6.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mtbls2mhd/__init__.py,sha256=0RQ_KvhA4PDOi6RAs0G3nZ29xmHs6Cg1-e0ZdmBfJXA,157
+mtbls2mhd/__init__.py,sha256=Ugss0W5GrH7cDSuWHcVxBfQDgbZ_sh8IZGnYPLe0hm8,157
 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/db_metadata_collector.py,sha256=J3ZqlAVsvGu7aM4XsjL7gQ3HMqethuwyna8Tym8TfI0,13267
+mtbls2mhd/v0_1/legacy/builder.py,sha256=965rf27EjL9TaOsbGfRG50LjOEVbe385v8CBL4qv-ig,85419
+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-0.0.4.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mtbls_mhd_integration-0.0.4.dist-info/METADATA,sha256=oDRVRlVaGTSrh_z3CxiH8l6AqhRp-fhTLe3f6XB7k_k,678
-mtbls_mhd_integration-0.0.4.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-mtbls_mhd_integration-0.0.4.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
-mtbls_mhd_integration-0.0.4.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
-mtbls_mhd_integration-0.0.4.dist-info/RECORD,,
+mtbls_mhd_integration-0.0.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mtbls_mhd_integration-0.0.6.dist-info/METADATA,sha256=WYJyNNlk9e-OcVHoAplc5_iMNOjBPE8ZVaeXHzow1AI,682
+mtbls_mhd_integration-0.0.6.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+mtbls_mhd_integration-0.0.6.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
+mtbls_mhd_integration-0.0.6.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
+mtbls_mhd_integration-0.0.6.dist-info/RECORD,,