ebi-eva-common-pyutils 0.6.14__py3-none-any.whl → 0.6.16__py3-none-any.whl

ebi_eva_common_pyutils/taxonomy/taxonomy.py

@@ -16,6 +16,10 @@ import re
 
 from ebi_eva_common_pyutils.ncbi_utils import retrieve_species_scientific_name_from_tax_id_ncbi
 from ebi_eva_common_pyutils.network_utils import json_request
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+
+
+logger = log_cfg.get_logger(__name__)
 
 
 def get_scientific_name_from_ensembl(taxonomy_id: int) -> str:
@@ -41,12 +45,16 @@ def get_normalized_scientific_name_from_ensembl(taxonomy_id: int) -> str:
     return normalise_taxon_scientific_name(get_scientific_name_from_ensembl(taxonomy_id))
 
 
-def get_scientific_name_from_taxonomy(taxonomy_id: int) -> str:
+def get_scientific_name_from_taxonomy(taxonomy_id: int, api_key: str=None) -> str:
     """
     Search for a species scientific name based on the taxonomy id.
     Will first attempt to retrieve from Ensembl and then NCBI, if not found returns None.
     """
-    species_name = get_scientific_name_from_ensembl(taxonomy_id)
+    try:
+        species_name = get_scientific_name_from_ensembl(taxonomy_id)
+    except Exception:
+        logger.warning("Failed to retrieve scientific name in Ensembl for taxonomy id {0}".format(taxonomy_id))
+        species_name = None
     if not species_name:
-        species_name = retrieve_species_scientific_name_from_tax_id_ncbi(taxonomy_id)
+        species_name = retrieve_species_scientific_name_from_tax_id_ncbi(taxonomy_id, api_key=api_key)
     return species_name

ebi_eva_common_pyutils-0.6.16.dist-info/METADATA

@@ -0,0 +1,24 @@
+Metadata-Version: 2.1
+Name: ebi-eva-common-pyutils
+Version: 0.6.16
+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 (==4.*,>4.9)
+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'
+

{ebi_eva_common_pyutils-0.6.14.dist-info → ebi_eva_common_pyutils-0.6.16.dist-info}/RECORD

@@ -17,10 +17,10 @@ ebi_eva_common_pyutils/reference/__init__.py,sha256=NsDjGCu2H2CZLOPaEL6GCoZo5ND_
 ebi_eva_common_pyutils/reference/assembly.py,sha256=FK4zsvg4_GDeKd9z2z5ZeM9R84TsusgQYdMOGuggQU0,12162
 ebi_eva_common_pyutils/reference/sequence.py,sha256=bg96QcuB-oytQYpaUkV10OzM_RIFhxsy6t3PQOg2Gy0,3911
 ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=p3XV4g3y0hEjyeZ4PwgN7Q3Et9G515ctQkSIo1kdDbU,2259
+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-0.6.14.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.16.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
@@ -32,8 +32,8 @@ 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-0.6.14.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.14.dist-info/METADATA,sha256=13ykCwUwZJ9YSL7MG8vItGSaw-4dvFvLZuJE-U2vVKg,956
-ebi_eva_common_pyutils-0.6.14.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-ebi_eva_common_pyutils-0.6.14.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.14.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.16.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.16.dist-info/METADATA,sha256=63KHAq4SOKke2g7o47PLlud1X_20OMOezWXkrb6afrw,909
+ebi_eva_common_pyutils-0.6.16.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.6.16.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.16.dist-info/RECORD,,

{ebi_eva_common_pyutils-0.6.14.dist-info → ebi_eva_common_pyutils-0.6.16.dist-info}/WHEEL

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

ebi_eva_common_pyutils-0.6.14.dist-info/METADATA

@@ -1,29 +0,0 @@
-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