def to_xml_file(self,
shed_tool_data_table_config,
new_elems=None,
remove_elems=None):
"""
Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.
remove_elems are removed before new_elems are added.
"""
if not (new_elems or remove_elems):
log.debug(
'ToolDataTableManager.to_xml_file called without any elements to add or remove.'
)
return # no changes provided, no need to persist any changes
if not new_elems:
new_elems = []
if not remove_elems:
remove_elems = []
full_path = os.path.abspath(shed_tool_data_table_config)
# FIXME: we should lock changing this file by other threads / head nodes
try:
try:
tree = util.parse_xml(full_path)
except OSError as e:
if e.errno == errno.ENOENT:
with open(full_path, 'w') as fh:
fh.write(TOOL_DATA_TABLE_CONF_XML)
tree = util.parse_xml(full_path)
else:
raise
root = tree.getroot()
out_elems = [elem for elem in root]
except Exception as e:
out_elems = []
log.debug(
'Could not parse existing tool data table config, assume no existing elements: %s',
e)
for elem in remove_elems:
# handle multiple occurrences of remove elem in existing elems
while elem in out_elems:
remove_elems.remove(elem)
# add new elems
out_elems.extend(new_elems)
out_path_is_new = not os.path.exists(full_path)
root = util.parse_xml_string(
'<?xml version="1.0"?>\n<tables></tables>')
for elem in out_elems:
root.append(elem)
with RenamedTemporaryFile(full_path, mode='w') as out:
out.write(util.xml_to_string(root, pretty=True))
os.chmod(full_path, RW_R__R__)
if out_path_is_new:
self.tool_data_path_files.update_files()
def config_elems_to_xml_file(self, config_elems, config_filename, tool_path):
"""
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))
for elem in config_elems:
root.append(elem)
with RenamedTemporaryFile(config_filename, mode='w') as fh:
fh.write(xml_to_string(root, pretty=True))
except Exception:
log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
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:
tool_cache_data_dir = f' tool_cache_data_dir="{tool_cache_data_dir}"' if tool_cache_data_dir else ''
root = parse_xml_string(f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"{tool_cache_data_dir}></toolbox>')
for elem in config_elems:
root.append(elem)
with RenamedTemporaryFile(config_filename, mode='w') as fh:
fh.write(xml_to_string(root, pretty=True))
except Exception:
log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
def data_manager_config_elems_to_xml_file(self, config_elems, config_filename):
"""
Persist the current in-memory list of config_elems to a file named by the value
of config_filename.
"""
data_managers_path = self.data_managers_path
if data_managers_path:
root_str = '<?xml version="1.0"?><data_managers tool_path="%s"></data_managers>' % data_managers_path
else:
root_str = '<?xml version="1.0"?><data_managers></data_managers>'
root = ElementTree.fromstring(root_str)
for elem in config_elems:
root.append(elem)
try:
with RenamedTemporaryFile(config_filename, mode='w') as fh:
fh.write(xml_to_string(root))
except Exception:
log.exception("Exception in DataManagerHandler.data_manager_config_elems_to_xml_file")
def _write_integrated_tool_panel_config_file(self):
"""
Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators
use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
"""
destination = os.path.abspath(self._integrated_tool_panel_config)
log.debug("Writing integrated tool panel config file to '%s'",
destination)
tracking_directory = self._integrated_tool_panel_tracking_directory
if tracking_directory:
if not os.path.exists(tracking_directory):
os.makedirs(tracking_directory)
name = "integrated_tool_panel_%.10f.xml" % time.time()
filename = os.path.join(tracking_directory, name)
else:
filename = destination
template = string.Template("""<?xml version="1.0"?>
<toolbox>
<!--
$INTEGRATED_TOOL_PANEL_DESCRIPTION
-->
$INTEGRATED_TOOL_PANEL
</toolbox>
""")
integrated_tool_panel = []
for key, item_type, item in self._integrated_tool_panel.panel_items_iter(
):
if item:
if item_type == panel_item_types.TOOL:
integrated_tool_panel.append(' <tool id="%s" />\n' %
item.id)
elif item_type == panel_item_types.WORKFLOW:
integrated_tool_panel.append(' <workflow id="%s" />\n' %
item.id)
elif item_type == panel_item_types.LABEL:
label_id = item.id or ''
label_text = item.text or ''
label_version = item.version or ''
integrated_tool_panel.append(
' <label id="%s" text="%s" version="%s" />\n' %
(label_id, label_text, label_version))
elif item_type == panel_item_types.SECTION:
section_id = item.id or ''
section_name = item.name or ''
section_version = item.version or ''
integrated_tool_panel.append(
' <section id="%s" name="%s" version="%s">\n' %
(escape(section_id), escape(section_name),
section_version))
for section_key, section_item_type, section_item in item.panel_items_iter(
):
if section_item_type == panel_item_types.TOOL:
if section_item:
integrated_tool_panel.append(
' <tool id="%s" />\n' %
section_item.id)
elif section_item_type == panel_item_types.WORKFLOW:
if section_item:
integrated_tool_panel.append(
' <workflow id="%s" />\n' %
section_item.id)
elif section_item_type == panel_item_types.LABEL:
if section_item:
label_id = section_item.id or ''
label_text = section_item.text or ''
label_version = section_item.version or ''
integrated_tool_panel.append(
' <label id="%s" text="%s" version="%s" />\n'
% (label_id, label_text, label_version))
integrated_tool_panel.append(' </section>\n')
tool_panel_description = '\n '.join(
[l for l in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if l])
tp_string = template.substitute(
INTEGRATED_TOOL_PANEL_DESCRIPTION=tool_panel_description,
INTEGRATED_TOOL_PANEL='\n'.join(integrated_tool_panel))
with RenamedTemporaryFile(filename, mode='w') as f:
f.write(tp_string)
if tracking_directory:
with open(filename + ".stack", "w") as f:
f.write(''.join(traceback.format_stack()))
shutil.copy(filename, filename + ".copy")
shutil.move(filename + ".copy", destination)
try:
os.chmod(destination, 0o644)
except OSError:
# That can happen if multiple threads are simultaneously moving/chmod'ing this file
# Should be harmless, though this race condition should be avoided.
pass