ebi-eva-common-pyutils 0.6.8__py3-none-any.whl → 0.6.10__py3-none-any.whl

ebi_eva_common_pyutils/biosamples_communicators.py

@@ -103,9 +103,15 @@ class HALCommunicator(AppLogger):
                 url = re.sub('{(' + k + ')(:.*)?}', v, url)
         if join_url:
             url += '/' + join_url
+        text_only = False
+        if 'text_only' in kwargs and kwargs.get('text_only'):
+            text_only = kwargs.pop('text_only')
         # Now query the url
-        json_response = self._req(method, url, **kwargs).json()
+        response = self._req(method, url, **kwargs)
+        if text_only:
+            return response.text
 
+        json_response = response.json()
         # Depaginate the call if requested
         if all_pages is True:
             # This depagination code will iterate over all the pages available until the pages comes back  without a

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.dist-info → ebi_eva_common_pyutils-0.6.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: ebi_eva_common_pyutils
-Version: 0.6.8
+Name: ebi-eva-common-pyutils
+Version: 0.6.10
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -19,5 +19,5 @@ 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'
+Requires-Dist: networkx (<=2.5) ; extra == 'eva-internal'
 

{ebi_eva_common_pyutils-0.6.8.dist-info → ebi_eva_common_pyutils-0.6.10.dist-info}/RECORD

@@ -1,6 +1,6 @@
 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=ngWuSvEYkkttkMnJ9Gjxc5D7ZSi7D3_JX1c8BnEO3os,7596
+ebi_eva_common_pyutils/biosamples_communicators.py,sha256=nyO0E_YpcAeBwbqOfbqe9RDxONq7Oe3NijSTGw7D01I,7815
 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=PtD2SgHf96kk21OA9tVIjEgsDXEFuAU-INy_kfQdoPw,4828
@@ -12,7 +12,7 @@ ebi_eva_common_pyutils/network_utils.py,sha256=iJjs5PPzT1V4CceZnCHOTs711AmpwlDo5
 ebi_eva_common_pyutils/assembly/__init__.py,sha256=KSWPwBY5nZj00odxWFntk8Sqg_rw273xH8S5D6Jo-T4,67
 ebi_eva_common_pyutils/assembly/assembly.py,sha256=IEmleROX4ZchPyhINKCuMmET_Ih1Jg4ok-opAKY6Z9A,3142
 ebi_eva_common_pyutils/contig_alias/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ebi_eva_common_pyutils/contig_alias/contig_alias.py,sha256=8mxcIbOhivqedgDjpzsHEY3UbYwHvk9DGoEiyHLLOBk,3056
+ebi_eva_common_pyutils/contig_alias/contig_alias.py,sha256=7tQXljEJtRCMs_JPrglYvTEZ-fJvzl8txwnCvqRB3Ck,5214
 ebi_eva_common_pyutils/reference/__init__.py,sha256=NsDjGCu2H2CZLOPaEL6GCoZo5ND_EA9RFmbzGfpSXRQ,134
 ebi_eva_common_pyutils/reference/assembly.py,sha256=FK4zsvg4_GDeKd9z2z5ZeM9R84TsusgQYdMOGuggQU0,12162
 ebi_eva_common_pyutils/reference/sequence.py,sha256=bg96QcuB-oytQYpaUkV10OzM_RIFhxsy6t3PQOg2Gy0,3911
@@ -20,7 +20,7 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=p3XV4g3y0hEjyeZ4PwgN7Q3Et9G515ctQkSIo1kdDbU,2259
 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-0.6.8.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.10.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-0.6.8.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.8.dist-info/METADATA,sha256=xL-ZPU8JZ9arUWs_6aAraTEq2Xmi4DPBKCz9mWgL6YU,822
-ebi_eva_common_pyutils-0.6.8.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-ebi_eva_common_pyutils-0.6.8.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.8.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.10.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.10.dist-info/METADATA,sha256=bBaC1wBXTMZ8Sip4qg0Fb9MpapoMsaga7Hh0C8pQBWs,825
+ebi_eva_common_pyutils-0.6.10.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.6.10.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.10.dist-info/RECORD,,

{ebi_eva_common_pyutils-0.6.8.dist-info → ebi_eva_common_pyutils-0.6.10.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py3-none-any