mtbls-mhd-integration 0.0.15__py3-none-any.whl → 0.0.17__py3-none-any.whl

mtbls2mhd/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "v0.0.15"
+__version__ = "v0.0.17"
 
 import pathlib
 import sys

mtbls2mhd/v0_1/legacy/builder.py

@@ -26,7 +26,7 @@ from mhd_model.model.v0_1.dataset.profiles.legacy.profile import MhDatasetLegacy
 from mhd_model.model.v0_1.rules.managed_cv_terms import (
     COMMON_ASSAY_TYPES,
     COMMON_CHARACTERISTIC_DEFINITIONS,
-    COMMON_MEASUREMENT_TYPES,
+    COMMON_MEASUREMENT_TYPES_MAP,
     COMMON_OMICS_TYPES,
     COMMON_PARAMETER_DEFINITIONS,
     COMMON_PROTOCOLS,
@@ -61,11 +61,11 @@ MTBLS_ASSAY_TYPES = {
     "MS": COMMON_ASSAY_TYPES["OBI:0000470"],
 }
 MTBLS_MEASUREMENT_TYPES = {
-    "targeted": COMMON_MEASUREMENT_TYPES["MSIO:0000100"],
-    "untargeted": COMMON_MEASUREMENT_TYPES["MSIO:0000101"],
+    "targeted": COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000100"],
+    "untargeted": COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000101"],
 }
 
-DEFAULT_MEASUREMENT_TYPE = COMMON_MEASUREMENT_TYPES["MSIO:0000101"]
+DEFAULT_MEASUREMENT_TYPE = COMMON_MEASUREMENT_TYPES_MAP["MSIO:0000101"]
 
 DEFAULT_OMICS_TYPE = COMMON_OMICS_TYPES["EDAM:3172"]
 
@@ -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.",
@@ -360,7 +366,11 @@ class MhdLegacyDatasetBuilder:
                     organization,
                     reverse_relationship_name="affiliates",
                 )
+                roles = set()
                 for role in contact.roles:
+                    if role.term.lower() in roles:
+                        continue
+                    roles.add(role.term.lower())
                     if role.term.lower() == "principal investigator":
                         mhd_builder.link(
                             mhd_contact,
@@ -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(
@@ -1487,17 +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",
                 )
@@ -1525,20 +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",
                     )

{mtbls_mhd_integration-0.0.15.dist-info → mtbls_mhd_integration-0.0.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mtbls-mhd-integration
-Version: 0.0.15
+Version: 0.0.17
 Summary: MetaboLights - MetabolomicsHub Integration
 Author-email: MetaboLights Team <metabolights-help@ebi.ac.uk>
 License-Expression: Apache-2.0
@@ -9,7 +9,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg>=0.30.0
 Requires-Dist: metabolights-utils>=1.4.18
-Requires-Dist: mhd-model>=0.1.44
+Requires-Dist: mhd-model>=0.1.46
 Requires-Dist: psycopg[binary,pool]>=3.3.2
 Requires-Dist: pydantic>=2.12.4
 Requires-Dist: pydantic-settings>=2.10.1

{mtbls_mhd_integration-0.0.15.dist-info → mtbls_mhd_integration-0.0.17.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mtbls2mhd/__init__.py,sha256=sP6P2r3ohpNSNphplpratyl2bhnzH2tDhPYOOAPAmDg,158
+mtbls2mhd/__init__.py,sha256=lkJhnuTb0LawSiMqaWAugon4vfs7AMhVqkBwwjO7xfg,158
 mtbls2mhd/config.py,sha256=BjOqAyfDhp9byoFjJz70xh4HRR8pu1yrm_5jweqygSI,2310
 mtbls2mhd/convertor_factory.py,sha256=WNXgzLFq84whwv0phrB1B2L1YRabO2tD0nPDT9QJ6gQ,1365
 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=xYPy_qoWIV_c6GGD_2AE-pCVAwxe_7BPq5Cn6tQqRbc,92682
+mtbls2mhd/v0_1/legacy/builder.py,sha256=sG6hc50FFdvarm1406E2z1xrzVvR3zqZMmFA8jOZBSQ,93117
 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=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,,
+mtbls_mhd_integration-0.0.17.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mtbls_mhd_integration-0.0.17.dist-info/METADATA,sha256=WVYl02uLUuCzx-5iqXouy1a5I1u78voiAB1RQrwgml0,688
+mtbls_mhd_integration-0.0.17.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mtbls_mhd_integration-0.0.17.dist-info/entry_points.txt,sha256=WQjM4flaYMyvHyv9zGKjCVk1i1_FGdNlhTmFVGgLgxs,61
+mtbls_mhd_integration-0.0.17.dist-info/top_level.txt,sha256=b7pI95n6HIQMFXDD0yL1NwldiDc-XdeWql4Iw-uYygQ,10
+mtbls_mhd_integration-0.0.17.dist-info/RECORD,,