ebi-eva-common-pyutils 0.6.9__tar.gz → 0.6.11__tar.gz

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/CHANGELOG.md

@@ -2,6 +2,18 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.11 (2024-11-15)
+----------------------
+
+- Added hikari max-pool-size connection property to the method that generate property for spring jobs
+
+
+## 0.6.10 (2024-08-06)
+----------------------
+
+- Allow text to be returned from biosamples communicators 
+
+
 ## 0.6.9 (2024-07-29)
 ---------------------
 

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.9
+Version: 0.6.11
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,5 +10,13 @@ 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"

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/ebi_eva_common_pyutils/biosamples_communicators.py

@@ -103,9 +103,15 @@ class HALCommunicator(AppLogger):
                 url = re.sub('{(' + k + ')(:.*)?}', v, url)
         if join_url:
             url += '/' + join_url
+        text_only = False
+        if 'text_only' in kwargs and kwargs.get('text_only'):
+            text_only = kwargs.pop('text_only')
         # Now query the url
-        json_response = self._req(method, url, **kwargs).json()
+        response = self._req(method, url, **kwargs)
+        if text_only:
+            return response.text
 
+        json_response = response.json()
         # Depaginate the call if requested
         if all_pages is True:
             # This depagination code will iterate over all the pages available until the pages comes back  without a

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.9
+Version: 0.6.11
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,5 +10,13 @@ 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"

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
+/home/nkumar2/PycharmProjects/eva-common-pyutils/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-0.6.9 → ebi_eva_common_pyutils-0.6.11}/ebi_eva_internal_pyutils/spring_properties.py

@@ -83,7 +83,7 @@ class SpringPropertiesGenerator:
             'eva.count-stats.password': counts_password
         }
 
-    def _common_properties(self, *, read_preference='primary', chunk_size=100):
+    def _common_properties(self, *, read_preference='primary', chunk_size=100, max_pool_size=2):
         """Properties common to all Spring pipelines"""
         props = {
             'spring.datasource.driver-class-name': 'org.postgresql.Driver',
@@ -98,6 +98,7 @@ class SpringPropertiesGenerator:
             'spring.jpa.properties.hibernate.temp.use_jdbc_metadata_defaults': 'false',
             'spring.jpa.database-platform': 'org.hibernate.dialect.PostgreSQL9Dialect',
             'parameters.chunkSize': chunk_size,
+            'spring.datasource.hikari.maximum-pool-size': max_pool_size
         }
         merge = {**self._mongo_properties(), **self._count_stats_properties(), **props}
         return merge

{ebi_eva_common_pyutils-0.6.9 → ebi_eva_common_pyutils-0.6.11}/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='0.6.9',
+    version='0.6.11',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.11/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']])