ebi-eva-common-pyutils 0.6.8.dev0__tar.gz → 0.6.9__tar.gz

{ebi_eva_common_pyutils-0.6.8.dev0 → ebi_eva_common_pyutils-0.6.9}/CHANGELOG.md

@@ -2,10 +2,15 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
-## 0.6.8 (unreleased)
+## 0.6.9 (2024-07-29)
 ---------------------
 
-- Nothing changed yet.
+- Add get methods to Contig alias client
+
+## 0.6.8 (2024-07-12)
+---------------------
+
+- Add biosamples communicators 
 
 
 ## 0.6.7 (2024-05-15)

{ebi_eva_common_pyutils-0.6.8.dev0/ebi_eva_common_pyutils.egg-info → ebi_eva_common_pyutils-0.6.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.8.dev0
+Version: 0.6.9
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.8.dev0 → ebi_eva_common_pyutils-0.6.9}/ebi_eva_common_pyutils/contig_alias/contig_alias.py

@@ -22,6 +22,9 @@ class InternalServerError(Exception):
     pass
 
 
+CONTING_ALIAS_URL = 'https://www.ebi.ac.uk/eva/webservices/contig-alias'
+
+
 # TODO add the get methods
 class ContigAliasClient(AppLogger):
     """
@@ -29,8 +32,13 @@ class ContigAliasClient(AppLogger):
     Authentication is required if using admin endpoints.
     """
 
-    def __init__(self, base_url, username=None, password=None):
-        self.base_url = base_url
+    def __init__(self, base_url=None, username=None, password=None, default_page_size=1000):
+        if base_url:
+            self.base_url = base_url
+        else:
+            self.base_url = os.environ.get('CONTING_ALIAS_URL') or CONTING_ALIAS_URL
+        # Used for get method
+        self.default_page_size=default_page_size
         # Only required for admin endpoints
         self.username = username
         self.password = password
@@ -69,3 +77,39 @@ class ContigAliasClient(AppLogger):
             raise InternalServerError
         else:
             self.error(f'Assembly accession {assembly} could not be deleted. Response: {response.text}')
+
+    @retry(tries=3, delay=2, backoff=1.2, jitter=(1, 3))
+    def _get_page_for_contig_alias_url(self, sub_url, page=0):
+        """queries the contig alias to retrieve the page of the provided url"""
+        url = f'{self.base_url}/{sub_url}?page={page}&size={self.default_page_size}'
+        response = requests.get(url, headers={'accept': 'application/json'})
+        response.raise_for_status()
+        response_json = response.json()
+        return response_json
+
+    def _depaginate_iter(self, sub_url, entity_to_retrieve):
+        """Generator that provides the contigs in the assembly requested."""
+        page = 0
+        response_json = self._get_page_for_contig_alias_url(sub_url, page=page)
+        for entity in response_json.get('_embedded', {}).get(entity_to_retrieve, []):
+            yield entity
+        while 'next' in response_json['_links']:
+            page += 1
+            response_json = self._get_page_for_contig_alias_url(sub_url, page=page)
+            for entity in response_json.get('_embedded', {}).get(entity_to_retrieve, []):
+                yield entity
+
+    def assembly_contig_iter(self, assembly_accession):
+        """Generator that provides the contigs in the assembly requested."""
+        sub_url = f'v1/assemblies/{assembly_accession}/chromosomes'
+        return self._depaginate_iter(sub_url, 'chromosomeEntities')
+
+    def assembly(self, assembly_accession):
+        """provides the description of the requested assembly."""
+        sub_url = f'v1/assemblies/{assembly_accession}'
+        response_json = self._get_page_for_contig_alias_url(sub_url)
+        return response_json.get('_embedded', {}).get('assemblyEntities', [])[0]
+
+    def contig_iter(self, insdc_accession):
+        sub_url = f'v1/chromosomes/genbank/{insdc_accession}'
+        return self._depaginate_iter(sub_url, 'chromosomeEntities')

{ebi_eva_common_pyutils-0.6.8.dev0 → ebi_eva_common_pyutils-0.6.9/ebi_eva_common_pyutils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: ebi_eva_common_pyutils
-Version: 0.6.8.dev0
+Name: ebi-eva-common-pyutils
+Version: 0.6.9
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.8.dev0 → ebi_eva_common_pyutils-0.6.9}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,7 +4,6 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
-/home/april/projects/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
@@ -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-0.6.8.dev0 → ebi_eva_common_pyutils-0.6.9}/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='0.6.8.dev0',
+    version='0.6.9',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.8.dev0/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']])