ebi-eva-common-pyutils 0.7.0__py3-none-any.whl → 0.7.2__py3-none-any.whl

ebi_eva_common_pyutils/config.py

@@ -2,6 +2,9 @@ import os
 
 import yaml
 
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+
+logger = log_cfg.get_logger(__name__)
 
 class Configuration:
     """
@@ -120,6 +123,9 @@ class WritableConfig(Configuration):
         for p in path[:-1]:
             if p not in top_level:
                 top_level[p] = {}
+            elif not isinstance(top_level[p], dict):
+                logger.warning(f'Overwriting existing config path {".".join(path)}')
+                top_level[p] = {}
             top_level = top_level[p]
         top_level[path[-1]] = value
 

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/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-0.7.0.dist-info → ebi_eva_common_pyutils-0.7.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.7.0
+Version: 0.7.2
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -12,7 +12,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
 License-File: LICENSE
 Requires-Dist: requests (==2.*)
-Requires-Dist: lxml (==4.*,>4.9)
+Requires-Dist: lxml (==5.*)
 Requires-Dist: pyyaml (==6.*)
 Requires-Dist: cached-property (==1.5.*)
 Requires-Dist: retry (==0.*,>0.9)

{ebi_eva_common_pyutils-0.7.0.dist-info → ebi_eva_common_pyutils-0.7.2.dist-info}/RECORD

@@ -3,10 +3,10 @@ ebi_eva_common_pyutils/assembly_utils.py,sha256=CklyCGlCjlFp0e9pugg6kSsh5L0xfCe2
 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
+ebi_eva_common_pyutils/config.py,sha256=j0lD0mpZiQfvGemrF2PSCJuzV-5SmNdLauFssYvF6t4,5107
 ebi_eva_common_pyutils/ena_utils.py,sha256=S2MmnWQ_9MJjlkaQY_by1-GGbTyi8SKp8XRcpjWnpZs,1465
 ebi_eva_common_pyutils/file_utils.py,sha256=eIlQKSVKkEjMNX7emrDzaQyQdGvQdb64gnfEhb6uYsE,1375
-ebi_eva_common_pyutils/logger.py,sha256=hT20ktN_oGeB_5ofVfd_aGXB6xYOe0Y5b3EVRYCuFb8,5093
+ebi_eva_common_pyutils/logger.py,sha256=2BXA-dQFkVAyLrF1kC24GcLGxRMaQhJpt41NQv7jpks,5941
 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
@@ -14,7 +14,7 @@ ebi_eva_common_pyutils/assembly/assembly.py,sha256=Lf-3Gs4E8hReqQA0roGLiT6nEaz67
 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/assembly.py,sha256=FG_APZ8AL_R70t6UEgSft3uN-0IjZwBMt25JtLd6bN0,12417
 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
@@ -22,7 +22,7 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 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-0.7.0.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.7.2.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
@@ -34,8 +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-0.7.0.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,,
+ebi_eva_common_pyutils-0.7.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.7.2.dist-info/METADATA,sha256=x87lMqM27okxZ4fQD4aLKR5yUhvRKZcA_mBPdIwJzkI,903
+ebi_eva_common_pyutils-0.7.2.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.7.2.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.7.2.dist-info/RECORD,,