ebi-eva-common-pyutils 0.6.12__tar.gz → 0.6.14__tar.gz

{ebi_eva_common_pyutils-0.6.12 → ebi_eva_common_pyutils-0.6.14}/CHANGELOG.md

@@ -2,6 +2,17 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.14 (2025-03-05)
+----------------------
+
+- Bugfix for connection string
+
+
+## 0.6.13 (2025-03-05)
+----------------------
+
+- Update spring properties to use mongo connection string with retryWrites=true
+
 ## 0.6.12 (2025-01-21)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.12 → ebi_eva_common_pyutils-0.6.14}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: ebi_eva_common_pyutils
-Version: 0.6.12
+Version: 0.6.14
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,5 +10,20 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Provides-Extra: eva-internal
 License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: lxml
+Requires-Dist: pyyaml
+Requires-Dist: cached-property
+Requires-Dist: retry
+Provides-Extra: eva-internal
+Requires-Dist: psycopg2-binary; extra == "eva-internal"
+Requires-Dist: pymongo; extra == "eva-internal"
+Requires-Dist: networkx<=2.5; extra == "eva-internal"
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

ebi_eva_common_pyutils-0.6.14/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.2
+Name: ebi_eva_common_pyutils
+Version: 0.6.14
+Summary: EBI EVA - Common Python Utilities
+Home-page: https://github.com/EBIVariation/eva-common-pyutils
+License: Apache
+Keywords: EBI,EVA,PYTHON,UTILITIES
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: lxml
+Requires-Dist: pyyaml
+Requires-Dist: cached-property
+Requires-Dist: retry
+Provides-Extra: eva-internal
+Requires-Dist: psycopg2-binary; extra == "eva-internal"
+Requires-Dist: pymongo; extra == "eva-internal"
+Requires-Dist: networkx<=2.5; extra == "eva-internal"
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

{ebi_eva_common_pyutils-0.6.12 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
+/tmp/ebi_eva_common_pyutils-v0.6.14-5o4eugy3/gitclone/ebi_eva_internal_pyutils/archive_directory.py
 ebi_eva_common_pyutils/__init__.py
 ebi_eva_common_pyutils/assembly_utils.py
 ebi_eva_common_pyutils/biosamples_communicators.py
@@ -41,4 +42,5 @@ ebi_eva_internal_pyutils/spring_properties.py
 ebi_eva_internal_pyutils/mongodb/__init__.py
 ebi_eva_internal_pyutils/mongodb/mongo_database.py
 ebi_eva_internal_pyutils/nextflow/__init__.py
-ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py
+ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py
+tests/test_common.py

{ebi_eva_common_pyutils-0.6.12 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/spring_properties.py

@@ -12,6 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 from collections import defaultdict
+from urllib.parse import quote_plus
 
 from ebi_eva_internal_pyutils.config_utils import get_mongo_creds_for_profile, get_accession_pg_creds_for_profile, \
     get_count_service_creds_for_profile, get_properties_from_xml_file, get_variant_load_job_tracker_creds_for_profile
@@ -55,14 +56,10 @@ class SpringPropertiesGenerator:
     def _mongo_properties(self):
         mongo_host, mongo_user, mongo_pass = get_mongo_creds_for_profile(
             self.maven_profile, self.private_settings_file)
+        username_with_password = (f'{quote_plus(mongo_user)}:{quote_plus(mongo_pass)}@'
+                                  if mongo_user is not None and mongo_pass is not None else '')
         return {
-            'spring.data.mongodb.host': mongo_host,
-            # Don't specify port if hosts already have the port encoded in them
-            # Also see https://github.com/EBIvariation/variation-commons/blob/329d4fa18da73bdad419ca5456b9897c059e33f0/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/utils/MongoClientURIBuilder.java#L44
-            'spring.data.mongodb.port': '' if ':' in mongo_host else 27017,
-            'spring.data.mongodb.username': '' if mongo_user is None else mongo_user,
-            'spring.data.mongodb.password': '' if mongo_pass is None else mongo_pass,
-            'spring.data.mongodb.authentication-database': 'admin',
+            'spring.data.mongodb.uri': f'mongodb://{username_with_password}{mongo_host}/?retryWrites=true&authSource=admin',
         }
 
     def _variant_load_job_tracker_properties(self):

{ebi_eva_common_pyutils-0.6.12 → ebi_eva_common_pyutils-0.6.14}/setup.py

@@ -7,7 +7,7 @@ setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.6.12',
+    version='0.6.14',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.14/tests/test_common.py

@@ -0,0 +1,22 @@
+import os
+from unittest import TestCase
+
+from ebi_eva_common_pyutils.common_utils import merge_two_dicts, pretty_print
+
+
+class TestCommon(TestCase):
+
+    resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
+
+
+class TestCommonUtils(TestCase):
+
+    def test_merge_two_dicts(self):
+        d1 = {'a': 1, 'b': 2, 'c': 3}
+        d2 = {'d': 4, 'a': 5, 'e': 6}
+        assert merge_two_dicts(d1, d2) == {'a': 5, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
+        assert merge_two_dicts(d2, d1) == {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
+
+    def test_pretty_print(self):
+        pretty_print(['Header 1', 'Long Header 2'],
+                     [['row1 cell 1', 'row1 cell 2'], ['row2 cell 1', 'Super long row2 cell 2']])

ebi_eva_common_pyutils-0.6.12/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,14 +0,0 @@
-Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.6.12
-Summary: EBI EVA - Common Python Utilities
-Home-page: https://github.com/EBIVariation/eva-common-pyutils
-License: Apache
-Keywords: EBI,EVA,PYTHON,UTILITIES
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Developers
-Classifier: Topic :: Software Development :: Build Tools
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3
-Provides-Extra: eva-internal
-License-File: LICENSE