# Buggy code
def guess_shed_config(self, app, default=None):
    tool_ids = []
    for tool in self.metadata.get("tools", []):
        tool_ids.append(tool.get("guid"))
    for shed_tool_conf_dict in app.toolbox.dynamic_confs(
        include_migrated_tool_conf=True
    ):
        name = shed_tool_conf_dict["config_filename"]
        for elem in shed_tool_conf_dict["config_elems"]:
            if elem.tag == "tool":
                for sub_elem in elem.findall("id"):
                    tool_id = sub_elem.text.strip()
                    if tool_id in tool_ids:
                        self.shed_config_filename = name
                        return shed_tool_conf_dict
            elif elem.tag == "section":
                for tool_elem in elem.findall("tool"):
                    for sub_elem in tool_elem.findall("id"):
                        tool_id = sub_elem.text.strip()
                        if tool_id in tool_ids:
                            self.shed_config_filename = name
                            return shed_tool_conf_dict
    if self.includes_datatypes or self.includes_data_managers:
        # We need to search by file paths here, which is less desirable.
        tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(
            self.tool_shed
        )
        for shed_tool_conf_dict in app.toolbox.dynamic_confs(
            include_migrated_tool_conf=True
        ):
            tool_path = shed_tool_conf_dict["tool_path"]
            relative_path = os.path.join(
                tool_path,
                tool_shed,
                "repos",
                self.owner,
                self.name,
                self.installed_changeset_revision,
            )
            if os.path.exists(relative_path):
                self.shed_config_filename = shed_tool_conf_dict["config_filename"]
                return shed_tool_conf_dict
    return default


# 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 guess_shed_config(self, app):
    tool_ids = []
    for tool in self.metadata.get("tools", []):
        tool_ids.append(tool.get("guid"))
    for shed_tool_conf_dict in app.toolbox.dynamic_confs(
        include_migrated_tool_conf=True
    ):
        name = shed_tool_conf_dict["config_filename"]
        for elem in shed_tool_conf_dict["config_elems"]:
            if elem.tag == "tool":
                for sub_elem in elem.findall("id"):
                    tool_id = sub_elem.text.strip()
                    if tool_id in tool_ids:
                        self.shed_config_filename = name
                        return shed_tool_conf_dict
            elif elem.tag == "section":
                for tool_elem in elem.findall("tool"):
                    for sub_elem in tool_elem.findall("id"):
                        tool_id = sub_elem.text.strip()
                        if tool_id in tool_ids:
                            self.shed_config_filename = name
                            return shed_tool_conf_dict
    # We need to search by file paths here, which is less desirable.
    tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
    for shed_tool_conf_dict in app.toolbox.dynamic_confs(
        include_migrated_tool_conf=True
    ):
        tool_path = shed_tool_conf_dict["tool_path"]
        relative_path = os.path.join(
            tool_path, tool_shed, "repos", self.owner, self.name
        )
        if os.path.exists(relative_path):
            self.shed_config_filename = shed_tool_conf_dict["config_filename"]
            return shed_tool_conf_dict
    return {}