ebi-eva-common-pyutils 0.6.17__tar.gz → 0.7.1__tar.gz

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/CHANGELOG.md

@@ -2,6 +2,18 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.7.1 (2025-05-21)
+---------------------
+
+- Make sure all loggers are debug by default
+
+
+## 0.7.0 (2025-04-14)
+----------------------
+
+- Deprecate the AAP Authentication method 
+
+
 ## 0.6.17 (2025-03-28)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.17
+Version: 0.7.1
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/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-0.6.17 → ebi_eva_common_pyutils-0.7.1}/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-0.6.17 → ebi_eva_common_pyutils-0.7.1}/ebi_eva_common_pyutils/logger.py

@@ -17,17 +17,28 @@ import logging.handlers
 from sys import stdout, stderr
 from cached_property import cached_property
 
+# The way Logger/Handler/Formatter works
+#  - Logger create the log message
+#  - Formatter describe what is included in the lo message
+#  - Handler Propagate them to where they should go (file/screen, ...)
+# Logger are part of hierarchy and always have parent up to the root logger.
+# The root logger is usually set to WARNING level
+# When a log is emitted to a logger, the logger checks it own level and propagate to its handler.
+# If it does not have any handlers it propagates to its parent (unless propagate is set to false)
+#
+# SPECIAL CASE: When a logger has a level set to NOTSET (0) it inherit the level from its parent
+
 
 class LoggingConfiguration:
     """
-    This class provides an all in one management of all loggers in the stack. By default it pulls existing loggers,
+    This class provides an all in one management of all loggers in the stack. By default, it pulls existing loggers,
     stores additional ones along with handlers and formatters.
     """
 
     default_fmt = '[%(asctime)s][%(name)s][%(levelname)s] %(message)s'
     default_datefmt = '%Y-%b-%d %H:%M:%S'
 
-    def __init__(self, use_existing_logger=True, log_level=logging.INFO):
+    def __init__(self, use_existing_logger=True, log_level=logging.DEBUG):
         self.blank_formatter = logging.Formatter()
         self.handlers = set()
         if use_existing_logger:
@@ -38,6 +49,8 @@ class LoggingConfiguration:
         else:
             self.loggers = {}
         self._log_level = log_level
+        if log_level is not None:
+            self.set_log_level(log_level)
 
     @cached_property
     def formatter(self):
@@ -61,8 +74,8 @@ class LoggingConfiguration:
         else:
             logger = logging.getLogger(name)
             self.loggers[name] = logger
-
-        logger.setLevel(level or self._log_level)
+        log_level = level if level > self._log_level else self._log_level
+        logger.setLevel(log_level)
         for h in self.handlers:
             logger.addHandler(h)
 
@@ -74,19 +87,20 @@ class LoggingConfiguration:
         :param logging.Handler handler:
         :param int level: Log level to assign to the created handler
         """
-        handler.setLevel(level or self._log_level)
+        log_level = level if level > self._log_level else self._log_level
+        handler.setLevel(log_level)
         handler.setFormatter(self.formatter)
         for name in self.loggers:
             self.loggers[name].addHandler(handler)
         self.handlers.add(handler)
 
-    def add_stdout_handler(self, level=None):
+    def add_stdout_handler(self, level=logging.INFO):
         self.add_handler(logging.StreamHandler(stdout), level=level or self._log_level)
 
-    def add_stderr_handler(self, level=None):
+    def add_stderr_handler(self, level=logging.INFO):
         self.add_handler(logging.StreamHandler(stderr), level=level or self._log_level)
 
-    def add_file_handler(self, filename, level=None):
+    def add_file_handler(self, filename, level=logging.INFO):
         self.add_handler(logging.FileHandler(filename=filename), level=level or self._log_level)
 
     def set_log_level(self, level):

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/ebi_eva_common_pyutils/reference/assembly.py

@@ -236,8 +236,12 @@ class NCBIAssembly(AppLogger):
         urllib.request.urlretrieve(url, output_file)
 
     def download_or_construct(self, genbank_only=False, overwrite=False):
-        """First download the assembly report and fasta from the FTP, then append any missing contig from
-        the assembly report to the assembly fasta."""
+        """
+        First download the assembly report and fasta from the FTP, then append any missing contig from
+        the assembly report to the assembly fasta.
+        Setting genbank_only = True ensure that only contigs that have genbank accession will be added to the assembly fasta.
+        Setting overwrite = True delete any existing fasta file and assembly report. then download them again.
+        """
         self.download_assembly_report(overwrite)
         try:
             self.download_assembly_fasta(overwrite)

ebi_eva_common_pyutils-0.7.1/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-0.6.17 → ebi_eva_common_pyutils-0.7.1}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.17
+Version: 0.7.1
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -27,6 +27,8 @@ ebi_eva_common_pyutils/contig_alias/contig_alias.py
 ebi_eva_common_pyutils/reference/__init__.py
 ebi_eva_common_pyutils/reference/assembly.py
 ebi_eva_common_pyutils/reference/sequence.py
+ebi_eva_common_pyutils/spreadsheet/__init__.py
+ebi_eva_common_pyutils/spreadsheet/metadata_xlsx_utils.py
 ebi_eva_common_pyutils/taxonomy/__init__.py
 ebi_eva_common_pyutils/taxonomy/taxonomy.py
 ebi_eva_common_pyutils/variation/__init__.py

{ebi_eva_common_pyutils-0.6.17 → ebi_eva_common_pyutils-0.7.1}/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='0.6.17',
+    version='0.7.1',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',