Details
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Type:
Story
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Status: Done
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Resolution: Done
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Fix Version/s: None
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Component/s: Third Party Software
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Labels:None
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Story Points:2
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Sprint:Arch 2019-04-01, Arch 2019-04-08
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Team:Architecture
Description
With the merge of DM-18367 we are getting many DeprecationWarnings from sqlalchemy when running the test in daf_butler (about 85 of them). This seems to be down to some new code paths being used from within sqlalchemy.
We are currently running 1.2.16. On this ticket I will see if 1.2.18 gets rid of the warnings and possibly try the new 1.3 series.
The current warning comes during schema creation:
File "/Users/timj/work/lsstsw3/build/daf_butler/python/lsst/daf/butler/core/registry.py", line 177, in fromConfig
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return cls(registryConfig, schemaConfig, dimensionConfig, create=create)
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File "/Users/timj/work/lsstsw3/build/daf_butler/python/lsst/daf/butler/registries/sqliteRegistry.py", line 94, in __init__
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super().__init__(registryConfig, schemaConfig, dimensionConfig, create)
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File "/Users/timj/work/lsstsw3/build/daf_butler/python/lsst/daf/butler/registries/sqlRegistry.py", line 82, in __init__
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self._createTables(self._schema, self._connection)
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File "/Users/timj/work/lsstsw3/build/daf_butler/python/lsst/daf/butler/registries/sqlRegistry.py", line 154, in _createTables
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schema.metadata.create_all(connection)
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 4201, in create_all
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ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/engine/base.py", line 1593, in _run_visitor
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visitorcallable(self.dialect, self, **kwargs).traverse_single(element)
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/visitors.py", line 130, in traverse_single
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return meth(obj, **kw)
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/ddl.py", line 757, in visit_metadata
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[t for t in tables if self._can_create_table(t)]
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/ddl.py", line 1174, in sort_tables_and_constraints
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deterministic_order=True,
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/util/topological.py", line 50, in sort
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for set_ in sort_as_subsets(tuples, allitems, deterministic_order):
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/util/topological.py", line 36, in sort_as_subsets
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_gen_edges(edges),
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/exc.py", line 139, in __init__
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message += " (%s)" % ", ".join(repr(s) for s in cycles)
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/exc.py", line 139, in <genexpr>
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message += " (%s)" % ", ".join(repr(s) for s in cycles)
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 692, in __repr__
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+ ["%s=%s" % (k, repr(getattr(self, k))) for k in ["schema"]]
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 691, in <listcomp>
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+ [repr(x) for x in self.columns]
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 1400, in __repr__
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+ ["%s=%s" % (k, repr(getattr(self, k))) for k in kwarg]
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 1400, in <listcomp>
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+ ["%s=%s" % (k, repr(getattr(self, k))) for k in kwarg]
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/sql/schema.py", line 112, in __repr__
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return util.generic_repr(self, omit_kwarg=["info"])
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/util/langhelpers.py", line 556, in generic_repr
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val = getattr(obj, arg, missing)
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File "<string>", line 2, in quote
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File "/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/util/deprecations.py", line 118, in warned
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warnings.warn(message, wtype, stacklevel=3)
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File "/Users/timj/work/lsstsw3/miniconda/envs/lsst-scipipe/lib/python3.7/warnings.py", line 110, in _showwarnmsg
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msg.file, msg.line)
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File "xxx.py", line 12, in warn_with_traceback
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traceback.print_stack(file=log)
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/Users/timj/work/lsstsw3/stack/DarwinX86/sqlalchemy/1.2.16/lib/python/SQLAlchemy-1.2.16-py3.7-macosx-10.7-x86_64.egg/sqlalchemy/util/langhelpers.py:556: SADeprecationWarning: Use ``<obj>.name.quote``
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val = getattr(obj, arg, missing)
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The deprecation warnings were fixed in DM-18863 – this ticket now relates specifically to updating sqlalchemy.
Jenkins passes with 1.3.8 so I think this is ready for merging. Our conda env is using 1.3.1 so there should be no clash.
This was discussed in the Gen3 meeting today. It passed some tests. Please release eups package with new SQLAlchemy.
In v1.3.1 the deprecation warning is still there but the wording has changed:
SADeprecationWarning: The SchemaItem.quote attribute is deprecated and will be removed in a future release. Use the quoted_name.quote attribute on the ``name`` field of the target schema item to retrievequoted status.