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Merge pull request #5552 from davebx/18.01

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[18.01] Close tempfile handles.
This commit is contained in:
Dannon Baker
2018-02-16 10:22:12 -05:00
committed by GitHub
parent 6b0e20a7a9 fa93d4e04b
commit 5488cf29ea
1 changed files with 9 additions and 13 deletions
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lib/galaxy/tools/repositories.py
+9 -13
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@@ -27,28 +27,24 @@ class ValidationContext(object):
self.config = Bunch()
self.config.tool_data_path = tool_data_path
self.config.shed_tool_data_path = shed_tool_data_path
_, self.config.tool_data_table_config = tempfile.mkstemp()
_, self.config.shed_tool_data_table_config = tempfile.mkstemp()
self.temporary_path = tempfile.mkdtemp(prefix='tool_validation_')
self.config.tool_data_table_config = os.path.join(self.temporary_path, 'tool_data_table_conf.xml')
self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, 'shed_tool_data_table_conf.xml')
self.tool_data_tables = tool_data_tables
self.datatypes_registry = registry or Registry()
self.hgweb_config_manager = hgweb_config_manager
_, self.config.len_file_path = tempfile.mkstemp()
_, self.config.builds_file_path = tempfile.mkstemp()
self.config.len_file_path = os.path.join(self.temporary_path, 'chromlen.txt')
# If the builds file path is set to None, tools/__init__.py will load the default.
# Otherwise it will attempt to load a nonexistent file and log an error. This does
# not appear to be an issue with the len_file_path config option.
self.config.builds_file_path = None
self.genome_builds = GenomeBuilds(self)
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
cleanup_paths = {self.config.builds_file_path,
self.config.len_file_path,
self.config.tool_data_table_config,
self.config.shed_tool_data_table_config}
for path in cleanup_paths:
try:
os.remove(path)
except Exception:
pass
shutil.rmtree(self.temporary_path)
@staticmethod
@contextmanager