ebi-eva-common-pyutils 0.7.3__tar.gz → 0.7.4__tar.gz

{ebi_eva_common_pyutils-0.7.3 → ebi_eva_common_pyutils-0.7.4}/CHANGELOG.md

@@ -2,6 +2,13 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.7.4 (2025-08-07)
+---------------------
+
+- Prevent multiple configs from sharing the same content
+- Update biosamples communicator to not retry 404s
+
+
 ## 0.7.3 (2025-06-19)
 ---------------------
 

ebi_eva_common_pyutils-0.7.4/PKG-INFO

@@ -0,0 +1,30 @@
+Metadata-Version: 2.2
+Name: ebi_eva_common_pyutils
+Version: 0.7.4
+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==2.*
+Requires-Dist: lxml==5.*
+Requires-Dist: pyyaml==6.*
+Requires-Dist: cached-property==1.5.*
+Requires-Dist: retry==0.*,>0.9
+Requires-Dist: openpyxl==3.*
+Provides-Extra: eva-internal
+Requires-Dist: psycopg2-binary; extra == "eva-internal"
+Requires-Dist: pymongo<=3.12; 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-0.7.3 → ebi_eva_common_pyutils-0.7.4}/ebi_eva_common_pyutils/biosamples_communicators.py

@@ -25,11 +25,18 @@ class HALNotReadyError(Exception):
     pass
 
 
+# Extends ValueError so clients can still expect ValueErrors to be raised on failed requests,
+# but we have a more specific class internally to know when to retry.
+class HttpErrorRetry(ValueError):
+    pass
+
+
 class HALCommunicator(AppLogger):
     """
     This class helps navigate through REST API that uses the HAL standard.
     """
     acceptable_code = [200, 201]
+    no_retry_code = [404]
 
     def __init__(self, auth_url, bsd_url, username, password):
         self.auth_url = auth_url
@@ -43,9 +50,12 @@ class HALCommunicator(AppLogger):
             self.error(response.request.method + ': ' + response.request.url + " with " + str(response.request.body))
             self.error("headers: {}".format(response.request.headers))
             self.error("<{}>: {}".format(response.status_code, response.text))
-            raise ValueError('The HTTP status code ({}) is not one of the acceptable codes ({})'.format(
+            error_msg = 'The HTTP status code ({}) is not one of the acceptable codes ({})'.format(
                 str(response.status_code), str(self.acceptable_code))
-            )
+            if response.status_code in self.no_retry_code:
+                raise ValueError(error_msg)
+            else:
+                raise HttpErrorRetry(error_msg)
         return response
 
     @cached_property
@@ -55,7 +65,7 @@ class HALCommunicator(AppLogger):
         self._validate_response(response)
         return response.text
 
-    @retry(exceptions=(ValueError, requests.RequestException), tries=3, delay=2, backoff=1.2, jitter=(1, 3))
+    @retry(exceptions=(HttpErrorRetry, requests.RequestException), tries=3, delay=2, backoff=1.2, jitter=(1, 3))
     def _req(self, method, url, **kwargs):
         """Private method that sends a request using the specified method. It adds the headers required by bsd"""
         headers = kwargs.pop('headers', {})

{ebi_eva_common_pyutils-0.7.3 → ebi_eva_common_pyutils-0.7.4}/ebi_eva_common_pyutils/config.py

@@ -11,10 +11,9 @@ class Configuration:
     Configuration class that allow to load a yaml file either at construction or later in the execution.
     It can be used like a dict but should be used as readonly.
     """
-    config_file = None
-    content = {}
-
     def __init__(self, *search_path):
+        self.config_file = None
+        self.content = {}
         if search_path:
             self.load_config_file(*search_path)
 

ebi_eva_common_pyutils-0.7.4/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -0,0 +1,30 @@
+Metadata-Version: 2.2
+Name: ebi_eva_common_pyutils
+Version: 0.7.4
+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==2.*
+Requires-Dist: lxml==5.*
+Requires-Dist: pyyaml==6.*
+Requires-Dist: cached-property==1.5.*
+Requires-Dist: retry==0.*,>0.9
+Requires-Dist: openpyxl==3.*
+Provides-Extra: eva-internal
+Requires-Dist: psycopg2-binary; extra == "eva-internal"
+Requires-Dist: pymongo<=3.12; 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-0.7.3 → ebi_eva_common_pyutils-0.7.4}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -5,6 +5,7 @@ README.md
 requirements.txt
 setup.cfg
 setup.py
+/tmp/ebi_eva_common_pyutils-v0.7.4-_d3almln/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
@@ -44,4 +45,5 @@ 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-0.7.3 → ebi_eva_common_pyutils-0.7.4}/ebi_eva_common_pyutils.egg-info/requires.txt

@@ -7,5 +7,5 @@ openpyxl==3.*
 
 [eva-internal]
 psycopg2-binary
-pymongo
+pymongo<=3.12
 networkx<=2.5

{ebi_eva_common_pyutils-0.7.3 → ebi_eva_common_pyutils-0.7.4}/setup.py

@@ -11,13 +11,13 @@ 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='0.7.3',
+    version='0.7.4',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',
     keywords=['EBI', 'EVA', 'PYTHON', 'UTILITIES'],
     install_requires=requirements,
-    extras_require={'eva-internal': ['psycopg2-binary', 'pymongo', 'networkx<=2.5']},
+    extras_require={'eva-internal': ['psycopg2-binary', 'pymongo<=3.12', 'networkx<=2.5']},
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',

ebi_eva_common_pyutils-0.7.4/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-0.7.3/PKG-INFO

@@ -1,14 +0,0 @@
-Metadata-Version: 2.1
-Name: ebi_eva_common_pyutils
-Version: 0.7.3
-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

ebi_eva_common_pyutils-0.7.3/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,14 +0,0 @@
-Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.7.3
-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