# Buggy code
def get_repository_tools_tups(self):
    """
    Return a list of tuples of the form (relative_path, guid, tool) for each tool defined
    in the received tool shed repository metadata.
    """
    repository_tools_tups = []
    shed_conf_dict = self.tpm.get_shed_tool_conf_dict(
        self.metadata_dict.get("shed_config_filename")
    )
    if "tools" in self.metadata_dict:
        for tool_dict in self.metadata_dict["tools"]:
            load_relative_path = relative_path = tool_dict.get("tool_config", None)
            if shed_conf_dict.get("tool_path"):
                load_relative_path = os.path.join(
                    shed_conf_dict.get("tool_path"), relative_path
                )
            guid = tool_dict.get("guid", None)
            if relative_path and guid:
                tool = self.app.toolbox.load_tool(
                    os.path.abspath(load_relative_path), guid=guid, use_cached=False
                )
            else:
                tool = None
            if tool:
                repository_tools_tups.append((relative_path, guid, tool))
    return repository_tools_tups


# Traceback (ParseError)
Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov  9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.datatypes.registry DEBUG 2019-11-09 13:22:11,317 [p:119216,w:4,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.tools.special_tools DEBUG 2019-11-09 13:22:11,323 [p:119216,w:4,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.tools.special_tools DEBUG 2019-11-09 13:22:11,327 [p:119216,w:4,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.tools.special_tools DEBUG 2019-11-09 13:22:11,330 [p:119216,w:4,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.queue_worker INFO 2019-11-09 13:22:11,332 [p:119216,w:4,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.4.
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.queue_worker DEBUG 2019-11-09 13:22:11,336 [p:119216,w:4,m:0] [Thread-1] Toolbox reload (29743.348 ms)
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.queue_worker INFO 2019-11-09 13:22:11,338 [p:119216,w:4,m:0] [Thread-1] Instance 'main.web.4' received 'reload_toolbox' task, executing now.
Nov 09 13:22:11 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.queue_worker DEBUG 2019-11-09 13:22:11,338 [p:119216,w:4,m:0] [Thread-1] Executing toolbox reload on 'main.web.4'
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3843198]: 115.146.92.55 - - [09/Nov/2019:13:22:11 +0200] "GET /api/jobs/4d16a9b9d521c9b3?key=59001665ead9d0bfd82dad0c0253dda0 HTTP/1.1" 200 - "-" "python-requests/2.22.0"
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3843198]: [pid: 3882852|app: 0|req: 11155/55634] 115.146.92.55 () {70 vars in 992 bytes} [Sat Nov  9 13:22:11 2019] GET /api/jobs/4d16a9b9d521c9b3?key=59001665ead9d0bfd82dad0c0253dda0 => generated 1118 bytes in 88 msecs (HTTP/1.1 200) 2 headers in 110 bytes (1 switches on core 0)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3843198]: galaxy.tools.search DEBUG 2019-11-09 13:22:12,036 [p:228435,w:4,m:0] [Thread-1] Toolbox index finished (29660.792 ms)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.util ERROR 2019-11-09 13:22:12,537 [p:119216,w:4,m:0] [Thread-1] Error parsing file /opt/galaxy/mutable-config/integrated_tool_panel.xml
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: Traceback (most recent call last):
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/util/__init__.py", line 236, in parse_xml
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 657, in parse
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._root = parser.close()
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1654, in close
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._raiseerror(v)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: raise err
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: ParseError: unclosed token: line 10952, column 8
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: galaxy.queue_worker ERROR 2019-11-09 13:22:12,538 [p:119216,w:4,m:0] [Thread-1] Error running control task type: reload_toolbox
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: Traceback (most recent call last):
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/queue_worker.py", line 372, in process_task
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: result = f(self.app, **body['kwargs'])
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/queue_worker.py", line 171, in reload_toolbox
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: _get_new_toolbox(app)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/queue_worker.py", line 188, in _get_new_toolbox
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/tools/__init__.py", line 253, in __init__
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: app=app,
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/tools/toolbox/base.py", line 1163, in __init__
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/tools/toolbox/base.py", line 100, in __init__
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._init_integrated_tool_panel(app.config)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/tools/toolbox/integrated_panel.py", line 39, in _init_integrated_tool_panel
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._load_integrated_tool_panel_keys()
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/tools/toolbox/base.py", line 445, in _load_integrated_tool_panel_keys
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: tree = parse_xml(self._integrated_tool_panel_config)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "lib/galaxy/util/__init__.py", line 236, in parse_xml
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 657, in parse
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._root = parser.close()
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1654, in close
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: self._raiseerror(v)
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: raise err
Nov 09 13:22:12 sn04.bi.uni-freiburg.de uwsgi[3191341]: ParseError: unclosed token: line 10952, column 8

# Fixed code
def get_repository_tools_tups(self):
    """
    Return a list of tuples of the form (relative_path, guid, tool) for each tool defined
    in the received tool shed repository metadata.
    """
    repository_tools_tups = []
    shed_conf_dict = self.tpm.get_shed_tool_conf_dict(
        self.metadata_dict.get("shed_config_filename")
    )
    if "tools" in self.metadata_dict:
        for tool_dict in self.metadata_dict["tools"]:
            load_relative_path = relative_path = tool_dict.get("tool_config", None)
            if shed_conf_dict.get("tool_path"):
                load_relative_path = os.path.join(
                    shed_conf_dict.get("tool_path"), relative_path
                )
            guid = tool_dict.get("guid", None)
            if relative_path and guid:
                try:
                    tool = self.app.toolbox.load_tool(
                        os.path.abspath(load_relative_path), guid=guid, use_cached=False
                    )
                except Exception:
                    log.exception(
                        "Error while loading tool at path '%s'", load_relative_path
                    )
                    tool = None
            else:
                tool = None
            if tool:
                repository_tools_tups.append((relative_path, guid, tool))
    return repository_tools_tups