ebi-eva-common-pyutils 0.7.1__py3-none-any.whl → 0.7.3__py3-none-any.whl

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Files changed (7) hide show
  1. ebi_eva_common_pyutils/config.py +6 -0
  2. {ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/METADATA +2 -2
  3. {ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/RECORD +7 -7
  4. {ebi_eva_common_pyutils-0.7.1.data → ebi_eva_common_pyutils-0.7.3.data}/scripts/archive_directory.py +0 -0
  5. {ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/LICENSE +0 -0
  6. {ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/WHEEL +0 -0
  7. {ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/top_level.txt +0 -0
ebi_eva_common_pyutils/config.py CHANGED
@@ -2,6 +2,9 @@ import os
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  import yaml
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+ from ebi_eva_common_pyutils.logger import logging_config as log_cfg
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+
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+ logger = log_cfg.get_logger(__name__)
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  class Configuration:
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  """
@@ -120,6 +123,9 @@ class WritableConfig(Configuration):
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  for p in path[:-1]:
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  if p not in top_level:
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  top_level[p] = {}
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+ elif not isinstance(top_level[p], dict):
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+ logger.warning(f'Overwriting existing config path {".".join(path)}')
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+ top_level[p] = {}
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  top_level = top_level[p]
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  top_level[path[-1]] = value
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{ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ebi-eva-common-pyutils
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- Version: 0.7.1
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+ Version: 0.7.3
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  Summary: EBI EVA - Common Python Utilities
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  Home-page: https://github.com/EBIVariation/eva-common-pyutils
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  License: Apache
@@ -12,7 +12,7 @@ Classifier: License :: OSI Approved :: Apache Software License
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  Classifier: Programming Language :: Python :: 3
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  License-File: LICENSE
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  Requires-Dist: requests (==2.*)
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- Requires-Dist: lxml (==4.*,>4.9)
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+ Requires-Dist: lxml (==5.*)
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  Requires-Dist: pyyaml (==6.*)
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  Requires-Dist: cached-property (==1.5.*)
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  Requires-Dist: retry (==0.*,>0.9)
{ebi_eva_common_pyutils-0.7.1.dist-info → ebi_eva_common_pyutils-0.7.3.dist-info}/RECORD RENAMED
@@ -3,7 +3,7 @@ ebi_eva_common_pyutils/assembly_utils.py,sha256=CklyCGlCjlFp0e9pugg6kSsh5L0xfCe2
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  ebi_eva_common_pyutils/biosamples_communicators.py,sha256=VdOVFJeNcPHGXTMiQGrMCGytKPW1RnAJ41-s6ui3eY4,7410
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  ebi_eva_common_pyutils/command_utils.py,sha256=PtelWWqcC0eOwIVesjwBw3F9KaXRzEE_uAUJhQFZ4l8,2340
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  ebi_eva_common_pyutils/common_utils.py,sha256=ty_glvfRa3VGhnpAht4qtVkNNmv-IYfVtO958mY-BaA,1192
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- ebi_eva_common_pyutils/config.py,sha256=PtD2SgHf96kk21OA9tVIjEgsDXEFuAU-INy_kfQdoPw,4828
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+ ebi_eva_common_pyutils/config.py,sha256=j0lD0mpZiQfvGemrF2PSCJuzV-5SmNdLauFssYvF6t4,5107
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  ebi_eva_common_pyutils/ena_utils.py,sha256=S2MmnWQ_9MJjlkaQY_by1-GGbTyi8SKp8XRcpjWnpZs,1465
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  ebi_eva_common_pyutils/file_utils.py,sha256=eIlQKSVKkEjMNX7emrDzaQyQdGvQdb64gnfEhb6uYsE,1375
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  ebi_eva_common_pyutils/logger.py,sha256=2BXA-dQFkVAyLrF1kC24GcLGxRMaQhJpt41NQv7jpks,5941
@@ -22,7 +22,7 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
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  ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=aXmRQ3NAaJotwmmOA2-u2XtcUT6iih-0_e-3QOxynoA,2578
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  ebi_eva_common_pyutils/variation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ebi_eva_common_pyutils/variation/contig_utils.py,sha256=kMNEW_P2yPnd8Xx1tep19hy5ee7ojxz6ZOO1grTQsRQ,5230
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- ebi_eva_common_pyutils-0.7.1.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
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+ ebi_eva_common_pyutils-0.7.3.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
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  ebi_eva_internal_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ebi_eva_internal_pyutils/archive_directory.py,sha256=IxVEfh_gaCiT652k0Q_-58fonRusy1yzXu7BCO8yVLo,4989
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  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
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  ebi_eva_internal_pyutils/mongodb/mongo_database.py,sha256=kesaJaaxYFeF_uYZBgL8tbufGKUXll7bXb4WlOS9vKM,9596
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  ebi_eva_internal_pyutils/nextflow/__init__.py,sha256=OOiJS8jZOz98q0t77NNog7aI_fFrVxi4kGmiSskuAqM,122
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  ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py,sha256=ew623hhK8jmFLQjJwLZbgBmW9RTiJBEULVqHfIUv_dc,10114
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- ebi_eva_common_pyutils-0.7.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- ebi_eva_common_pyutils-0.7.1.dist-info/METADATA,sha256=9SaM_mpO_7okgIuMiMWDGNu3Ln4MpBYkYNRUU2xNEdc,908
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- ebi_eva_common_pyutils-0.7.1.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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- ebi_eva_common_pyutils-0.7.1.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
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- ebi_eva_common_pyutils-0.7.1.dist-info/RECORD,,
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+ ebi_eva_common_pyutils-0.7.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ ebi_eva_common_pyutils-0.7.3.dist-info/METADATA,sha256=JxihFuZa8agK_iZyRSjKVFclbPBirTJsUjlW-UixnSY,903
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+ ebi_eva_common_pyutils-0.7.3.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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+ ebi_eva_common_pyutils-0.7.3.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
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+ ebi_eva_common_pyutils-0.7.3.dist-info/RECORD,,