ebi-eva-common-pyutils 0.6.16__py3-none-any.whl → 0.7.0__py3-none-any.whl

ebi_eva_common_pyutils/assembly/assembly.py

@@ -47,14 +47,18 @@ def get_taxonomy_to_assembly_mapping_from_ensembl_rapid_release():
         strain = asm_data['strain']
         release_date = datetime.strptime(asm_data['release_date'], '%Y-%m-%d')
 
+        # Skip alternate haplotype assemblies
+        if strain and strain.lower() == 'alternate haplotype':
+            continue
+        # Skip non GCA accession
+        if not asm_accession.startswith('GCA_'):
+            continue
+
         # If we haven't seen this taxonomy before, just use this assembly
         if tax_id not in results:
             results[tax_id] = (asm_accession, release_date)
             continue
 
-        # Skip alternate haplotype assemblies
-        if strain and strain.lower() == 'alternate haplotype':
-            continue
         current_assembly, current_date = results[tax_id]
         # Keep the more recent assembly, or the lexicographically last one if release dates are equal
         if current_date < release_date or (current_date == release_date and asm_accession > current_assembly):

ebi_eva_common_pyutils/biosamples_communicators.py

@@ -50,7 +50,7 @@ class HALCommunicator(AppLogger):
 
     @cached_property
     def token(self):
-        """Retrieve the token from the AAP REST API then cache it for further quering"""
+        """Retrieve the token from the REST API then cache it for further querying"""
         response = requests.get(self.auth_url, auth=(self.username, self.password))
         self._validate_response(response)
         return response.text
@@ -144,19 +144,6 @@ class HALCommunicator(AppLogger):
     def communicator_attributes(self):
         raise NotImplementedError
 
-
-class AAPHALCommunicator(HALCommunicator):
-    """Class to navigate BioSamples API using AAP authentication."""
-
-    def __init__(self, auth_url, bsd_url, username, password, domain=None):
-        super(AAPHALCommunicator, self).__init__(auth_url, bsd_url, username, password)
-        self.domain = domain
-
-    @property
-    def communicator_attributes(self):
-        return {'domain': self.domain}
-
-
 class WebinHALCommunicator(HALCommunicator):
     """Class to navigate BioSamples API using Webin authentication."""
 

ebi_eva_common_pyutils/spreadsheet/metadata_xlsx_utils.py

@@ -0,0 +1,15 @@
+import re
+
+from openpyxl.reader.excel import load_workbook
+
+
+def metadata_xlsx_version(metadata_xlsx):
+    workbook = load_workbook(metadata_xlsx)
+    try:
+        instructions_sheet = workbook['PLEASE READ FIRST']
+        xlsx_sheet_version_value = instructions_sheet[3][0].value
+        match = re.search(r'(\d+\.\d+\.\d+)', '' if xlsx_sheet_version_value is None else xlsx_sheet_version_value)
+        xlsx_version = match.group(1) if match else None
+    except (KeyError, IndexError):
+        xlsx_version = None
+    return xlsx_version

{ebi_eva_common_pyutils-0.6.16.dist-info → ebi_eva_common_pyutils-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.16
+Version: 0.7.0
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.16.dist-info → ebi_eva_common_pyutils-0.7.0.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=nyO0E_YpcAeBwbqOfbqe9RDxONq7Oe3NijSTGw7D01I,7815
+ebi_eva_common_pyutils/biosamples_communicators.py,sha256=VdOVFJeNcPHGXTMiQGrMCGytKPW1RnAJ41-s6ui3eY4,7410
 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
@@ -10,17 +10,19 @@ ebi_eva_common_pyutils/logger.py,sha256=hT20ktN_oGeB_5ofVfd_aGXB6xYOe0Y5b3EVRYCu
 ebi_eva_common_pyutils/ncbi_utils.py,sha256=AKuNKv4ue7l-6rwuDDGubWEHGuscXWfv-Gg6o_x1hT0,5005
 ebi_eva_common_pyutils/network_utils.py,sha256=iJjs5PPzT1V4CceZnCHOTs711AmpwlDo59wb1XHdTak,2648
 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/assembly/assembly.py,sha256=Lf-3Gs4E8hReqQA0roGLiT6nEaz679aKWbwNWoBoJhs,3246
 ebi_eva_common_pyutils/contig_alias/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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
+ebi_eva_common_pyutils/spreadsheet/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ebi_eva_common_pyutils/spreadsheet/metadata_xlsx_utils.py,sha256=0yOoV5rfLc5IWPAShSClaAOmaGfJuGZjJOnREfZBtFQ,540
 ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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-0.6.16.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.7.0.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 +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-0.6.16.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-0.7.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.7.0.dist-info/METADATA,sha256=5VMbdT4gEyEIvgeXhixwWNfJRMsvuLjED4fZrdcY0pc,908
+ebi_eva_common_pyutils-0.7.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.7.0.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.7.0.dist-info/RECORD,,