ebi-eva-common-pyutils 0.7.2__py3-none-any.whl → 0.7.4__py3-none-any.whl

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/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.dist-info/METADATA

@@ -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-0.7.2.dist-info → ebi_eva_common_pyutils-0.7.4.dist-info}/RECORD

@@ -1,9 +1,9 @@
 ebi_eva_common_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_common_pyutils/assembly_utils.py,sha256=CklyCGlCjlFp0e9pugg6kSsh5L0xfCe2qPvA2eLVtn0,4187
-ebi_eva_common_pyutils/biosamples_communicators.py,sha256=VdOVFJeNcPHGXTMiQGrMCGytKPW1RnAJ41-s6ui3eY4,7410
+ebi_eva_common_pyutils/biosamples_communicators.py,sha256=ZkemchAYGrHwqbGviJN5X80nYFizDNVTwUX3c_5PZcM,7799
 ebi_eva_common_pyutils/command_utils.py,sha256=PtelWWqcC0eOwIVesjwBw3F9KaXRzEE_uAUJhQFZ4l8,2340
 ebi_eva_common_pyutils/common_utils.py,sha256=ty_glvfRa3VGhnpAht4qtVkNNmv-IYfVtO958mY-BaA,1192
-ebi_eva_common_pyutils/config.py,sha256=j0lD0mpZiQfvGemrF2PSCJuzV-5SmNdLauFssYvF6t4,5107
+ebi_eva_common_pyutils/config.py,sha256=evkOyPub8dXg44sNiZJR-nHq2C8XTVSVk92M37C5eR4,5124
 ebi_eva_common_pyutils/ena_utils.py,sha256=S2MmnWQ_9MJjlkaQY_by1-GGbTyi8SKp8XRcpjWnpZs,1465
 ebi_eva_common_pyutils/file_utils.py,sha256=eIlQKSVKkEjMNX7emrDzaQyQdGvQdb64gnfEhb6uYsE,1375
 ebi_eva_common_pyutils/logger.py,sha256=2BXA-dQFkVAyLrF1kC24GcLGxRMaQhJpt41NQv7jpks,5941
@@ -22,7 +22,7 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=aXmRQ3NAaJotwmmOA2-u2XtcUT6iih-0_e-3QOxynoA,2578
 ebi_eva_common_pyutils/variation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_common_pyutils/variation/contig_utils.py,sha256=kMNEW_P2yPnd8Xx1tep19hy5ee7ojxz6ZOO1grTQsRQ,5230
-ebi_eva_common_pyutils-0.7.2.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.7.4.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
 ebi_eva_internal_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_internal_pyutils/archive_directory.py,sha256=IxVEfh_gaCiT652k0Q_-58fonRusy1yzXu7BCO8yVLo,4989
 ebi_eva_internal_pyutils/config_utils.py,sha256=EGRC5rsmU_ug7OY9-t1UW1XZXRsauSyZB9xPcBux8ts,7909
@@ -34,8 +34,8 @@ ebi_eva_internal_pyutils/mongodb/__init__.py,sha256=0oyTlkYZCV7udlPl09Zl-sDyE3c9
 ebi_eva_internal_pyutils/mongodb/mongo_database.py,sha256=kesaJaaxYFeF_uYZBgL8tbufGKUXll7bXb4WlOS9vKM,9596
 ebi_eva_internal_pyutils/nextflow/__init__.py,sha256=OOiJS8jZOz98q0t77NNog7aI_fFrVxi4kGmiSskuAqM,122
 ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py,sha256=ew623hhK8jmFLQjJwLZbgBmW9RTiJBEULVqHfIUv_dc,10114
-ebi_eva_common_pyutils-0.7.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.7.2.dist-info/METADATA,sha256=x87lMqM27okxZ4fQD4aLKR5yUhvRKZcA_mBPdIwJzkI,903
-ebi_eva_common_pyutils-0.7.2.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-ebi_eva_common_pyutils-0.7.2.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.7.2.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.7.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.7.4.dist-info/METADATA,sha256=-dqz8UYrpmrdcGIKdkgV4m8slivOqND7OM-__q9Fs0s,1022
+ebi_eva_common_pyutils-0.7.4.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+ebi_eva_common_pyutils-0.7.4.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.7.4.dist-info/RECORD,,

{ebi_eva_common_pyutils-0.7.2.dist-info → ebi_eva_common_pyutils-0.7.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ebi_eva_common_pyutils-0.7.2.dist-info/METADATA

@@ -1,24 +0,0 @@
-Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.7.2
-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 ; extra == 'eva-internal'
-Requires-Dist: networkx (<=2.5) ; extra == 'eva-internal'
-