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Persist tool_cache_data_dir tag if specified

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We noticed that the tag was getting lost when installing new tools,
this fixes that.
This commit is contained in:
mvdbeek
2020-09-24 15:39:42 +02:00
parent ebcf9e67bd
commit 6a50c67463
2 changed files with 6 additions and 3 deletions
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lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
+5 -3
View File
@@ -34,6 +34,7 @@ class ToolPanelManager:
return
old_toolbox = self.app.toolbox
shed_tool_conf = shed_tool_conf_dict['config_filename']
tool_cache_data_dir = shed_tool_conf_dict.get('tool_cache_data_dir')
tool_path = shed_tool_conf_dict['tool_path']
config_elems = []
# Ideally shed_tool_conf.xml would be created before the repo is cloned and added to the DB, but this is called
@@ -57,7 +58,7 @@ class ToolPanelManager:
for elem_entry in elem_list:
config_elems.append(elem_entry)
# Persist the altered shed_tool_config file.
self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path)
self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path, tool_cache_data_dir)
self.app.wait_for_toolbox_reload(old_toolbox)
else:
log.error(error_message)
@@ -94,13 +95,14 @@ class ToolPanelManager:
self.app.toolbox.update_shed_config(shed_tool_conf_dict)
self.add_to_shed_tool_config(shed_tool_conf_dict, elem_list)
def config_elems_to_xml_file(self, config_elems, config_filename, tool_path):
def config_elems_to_xml_file(self, config_elems, config_filename, tool_path, tool_cache_data_dir=None):
"""
Persist the current in-memory list of config_elems to a file named by the
value of config_filename.
"""
try:
root = parse_xml_string('<?xml version="1.0"?>\n<toolbox tool_path="%s"></toolbox>' % str(tool_path))
tool_cache_data_dir = ' tool_cache_data_dir="{}"'.format(tool_cache_data_dir) if tool_cache_data_dir else ''
root = parse_xml_string('<?xml version="1.0"?>\n<toolbox tool_path="{}"{}></toolbox>'.format(tool_path, tool_cache_data_dir))
for elem in config_elems:
root.append(elem)
with RenamedTemporaryFile(config_filename, mode='w') as fh:
lib/galaxy/tools/toolbox/base.py
+1
View File
@@ -218,6 +218,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
if parsing_shed_tool_conf:
shed_tool_conf_dict = dict(config_filename=config_filename,
tool_path=tool_path,
tool_cache_data_dir=tool_cache_data_dir,
config_elems=config_elems)
self._dynamic_tool_confs.append(shed_tool_conf_dict)