ebi-eva-common-pyutils 0.6.14__tar.gz → 0.6.16__tar.gz

{ebi_eva_common_pyutils-0.6.14 → ebi_eva_common_pyutils-0.6.16}/CHANGELOG.md

@@ -2,6 +2,18 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.16 (2025-03-28)
+----------------------
+
+- New function to get the version of the EVA metadata template
+
+
+## 0.6.15 (2025-03-26)
+----------------------
+
+- Change the scientific name retrieval to first check in Ensembl then NCBI
+
+
 ## 0.6.14 (2025-03-05)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.14/ebi_eva_common_pyutils.egg-info → ebi_eva_common_pyutils-0.6.16}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.14
+Version: 0.6.16
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,20 +10,5 @@ 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
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.14 → ebi_eva_common_pyutils-0.6.16}/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/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -0,0 +1,14 @@
+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
+Provides-Extra: eva-internal
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.14 → ebi_eva_common_pyutils-0.6.16}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,7 +4,6 @@ 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
@@ -42,5 +41,4 @@ 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
-tests/test_common.py
+ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py

ebi_eva_common_pyutils-0.6.16/ebi_eva_common_pyutils.egg-info/requires.txt

@@ -0,0 +1,11 @@
+requests==2.*
+lxml==4.*,>4.9
+pyyaml==6.*
+cached-property==1.5.*
+retry==0.*,>0.9
+openpyxl==3.*
+
+[eva-internal]
+psycopg2-binary
+pymongo
+networkx<=2.5

{ebi_eva_common_pyutils-0.6.14 → ebi_eva_common_pyutils-0.6.16}/setup.py

@@ -7,12 +7,13 @@ 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='0.6.14',
+    version='0.6.16',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',
     keywords=['EBI', 'EVA', 'PYTHON', 'UTILITIES'],
-    install_requires=['requests', 'lxml', 'pyyaml', 'cached-property', 'retry'],
+    install_requires=['requests==2.*', 'lxml>4.9,==4.*', 'pyyaml==6.*', 'cached-property==1.5.*', 'retry>0.9,==0.*',
+                      'openpyxl==3.*'],
     extras_require={'eva-internal': ['psycopg2-binary', 'pymongo', 'networkx<=2.5']},
     classifiers=[
         'Development Status :: 5 - Production/Stable',

ebi_eva_common_pyutils-0.6.14/PKG-INFO

@@ -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

ebi_eva_common_pyutils-0.6.14/ebi_eva_common_pyutils.egg-info/requires.txt

@@ -1,10 +0,0 @@
-requests
-lxml
-pyyaml
-cached-property
-retry
-
-[eva-internal]
-psycopg2-binary
-pymongo
-networkx<=2.5

ebi_eva_common_pyutils-0.6.14/tests/test_common.py

@@ -1,22 +0,0 @@
-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']])