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Merge pull request #8634 from selten/data-manager-fix

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Fix a bug that occurs while installing a data manager.
This commit is contained in:
Marius van den Beek
2019-09-13 15:46:09 +02:00
committed by GitHub
parent 3213f43abf 46155acfeb
commit 511aeb126e
2 changed files with 14 additions and 10 deletions
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lib/galaxy/tools/data/__init__.py
+1 -1
View File
@@ -157,7 +157,7 @@ class ToolDataTableManager(object):
from_shed_config=True)
except Exception as e:
error_message = 'Error attempting to parse file %s: %s' % (str(os.path.split(config_filename)[1]), util.unicodify(e))
log.debug(error_message)
log.debug(error_message, exc_info=True)
table_elems = []
if persist:
# Persist Galaxy's version of the changed tool_data_table_conf.xml file.
lib/tool_shed/metadata/metadata_generator.py
+13 -9
View File
@@ -359,21 +359,25 @@ class MetadataGenerator(object):
metadata_dict['sample_files'] = sample_file_metadata_paths
# Copy all sample files included in the repository to a single directory location so we
# can load tools that depend on them.
data_table_conf_xml_sample_files = []
for sample_file in sample_file_copy_paths:
tool_util.copy_sample_file(self.app, sample_file, dest_path=work_dir)
# If the list of sample files includes a tool_data_table_conf.xml.sample file, load
# its table elements into memory.
relative_path, filename = os.path.split(sample_file)
if filename == 'tool_data_table_conf.xml.sample':
# We create a new ToolDataTableManager to avoid adding entries to the app-wide
# tool data tables. This is only used for checking that the data table is valid.
new_table_elems, error_message = \
validation_context.tool_data_tables.add_new_entries_from_config_file(config_filename=sample_file,
tool_data_path=work_dir,
shed_tool_data_table_config=work_dir,
persist=False)
if error_message:
self.invalid_file_tups.append((filename, error_message))
data_table_conf_xml_sample_files.append(sample_file)
for data_table_conf_xml_sample_file in data_table_conf_xml_sample_files:
# We create a new ToolDataTableManager to avoid adding entries to the app-wide
# tool data tables. This is only used for checking that the data table is valid.
new_table_elems, error_message = \
validation_context.tool_data_tables.add_new_entries_from_config_file(config_filename=data_table_conf_xml_sample_file,
tool_data_path=work_dir,
shed_tool_data_table_config=work_dir,
persist=False)
if error_message:
self.invalid_file_tups.append((filename, error_message))
for root, dirs, files in os.walk(files_dir):
if root.find('.hg') < 0 and root.find('hgrc') < 0:
if '.hg' in dirs: