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Source code for galaxy.tool_shed.galaxy_install.tools.tool_panel_manager
import errno
import logging
from typing import (
Any,
Dict,
List,
)
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.model.base import transaction
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
from galaxy.tool_shed.util.basic_util import strip_path
from galaxy.tool_shed.util.repository_util import get_repository_owner
from galaxy.tool_shed.util.shed_util_common import get_tool_panel_config_tool_path_install_dir
from galaxy.util import (
etree,
parse_xml_string,
xml_to_string,
)
from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
from galaxy.util.tool_shed.common_util import remove_protocol_and_user_from_clone_url
from galaxy.util.tool_shed.xml_util import parse_xml
log = logging.getLogger(__name__)
[docs]class ToolPanelManager:
app: InstallationTarget
[docs] def add_to_shed_tool_config(self, shed_tool_conf_dict: Dict[str, Any], elem_list: list) -> None:
"""
"A tool shed repository is being installed so change the shed_tool_conf file. Parse the
config file to generate the entire list of config_elems instead of using the in-memory list
since it will be a subset of the entire list if one or more repositories have been deactivated.
"""
if not elem_list:
# We may have an empty elem_list in case a data manager is being installed.
# In that case we don't want to wait for a toolbox reload that will never happen.
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
# from too many places to make it feasible at this time
try:
tree, error_message = parse_xml(shed_tool_conf, check_exists=False)
except OSError as exc:
if exc.errno == errno.ENOENT and shed_tool_conf_dict.get("create", None) is not None:
log.info("Creating shed tool config with default contents: %s", shed_tool_conf)
with open(shed_tool_conf, "w") as fh:
fh.write(shed_tool_conf_dict["create"])
tree, error_message = parse_xml(shed_tool_conf)
else:
log.error("Unable to load shed tool config: %s", shed_tool_conf)
raise
if tree:
root = tree.getroot()
for elem in root:
config_elems.append(elem)
# Add the new elements to the in-memory list of config_elems.
for elem_entry in elem_list:
if elem_entry.tag == "section":
# Loop through section entries in the in-memory tool panel.
for existing_elem in config_elems:
# Compare the section ID for each one to the section ID for the tool being installed.
if existing_elem.tag == "section" and existing_elem.attrib.get(
"id", None
) == elem_entry.attrib.get("id", None):
# We've found a section, add the incoming tools to it.
for child in elem_entry:
existing_elem.append(child)
# Break out of the config_elems loop back to the elem_list loop.
break
# If we reach this point, no section was found. Create one with contents.
else:
config_elems.append(elem_entry)
# This is not a section, but a tool or label. No need to search for matching sections, just add it.
else:
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, tool_cache_data_dir)
self.app.wait_for_toolbox_reload(old_toolbox)
else:
log.error(error_message)
[docs] def add_to_tool_panel(
self,
repository_name,
repository_clone_url,
changeset_revision,
repository_tools_tups,
owner,
shed_tool_conf,
tool_panel_dict,
new_install=True,
tool_panel_section_mapping=None,
):
"""A tool shed repository is being installed or updated so handle tool panel alterations accordingly."""
tool_panel_section_mapping = tool_panel_section_mapping or {}
# We need to change the in-memory version and the file system version of the shed_tool_conf file.
shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf)
tool_panel_dict = self.update_tool_panel_dict(
tool_panel_dict, tool_panel_section_mapping, repository_tools_tups
)
# Generate the list of ElementTree Element objects for each section or tool.
elem_list = self.generate_tool_panel_elem_list(
repository_name,
repository_clone_url,
changeset_revision,
tool_panel_dict,
repository_tools_tups,
owner=owner,
)
if new_install:
tool_path = shed_tool_conf_dict["tool_path"]
# Add the new elements to the shed_tool_conf file on disk.
config_elems = shed_tool_conf_dict["config_elems"]
for config_elem in elem_list:
# Add the new elements to the in-memory list of config_elems.
config_elems.append(config_elem)
# Load the tools into the in-memory tool panel.
self.app.toolbox.load_item(
config_elem,
tool_path=tool_path,
load_panel_dict=True,
guid=config_elem.get("guid"),
)
# Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict.
shed_tool_conf_dict["config_elems"] = config_elems
self.app.toolbox.update_shed_config(shed_tool_conf_dict)
self.add_to_shed_tool_config(shed_tool_conf_dict, elem_list)
[docs] def config_elems_to_xml_file(self, config_elems, config_filename, tool_path, tool_cache_data_dir=None) -> 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")
[docs] def generate_tool_elem(
self, tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section
):
"""Create and return an ElementTree tool Element."""
if tool_section is not None:
tool_elem = etree.SubElement(tool_section, "tool")
else:
tool_elem = etree.Element("tool")
tool_elem.attrib["file"] = tool_file_path
if not tool.guid:
raise ValueError("tool has no guid")
tool_elem.attrib["guid"] = tool.guid
tool_shed_elem = etree.SubElement(tool_elem, "tool_shed")
tool_shed_elem.text = tool_shed
repository_name_elem = etree.SubElement(tool_elem, "repository_name")
repository_name_elem.text = repository_name
repository_owner_elem = etree.SubElement(tool_elem, "repository_owner")
repository_owner_elem.text = owner
changeset_revision_elem = etree.SubElement(tool_elem, "installed_changeset_revision")
changeset_revision_elem.text = changeset_revision
id_elem = etree.SubElement(tool_elem, "id")
id_elem.text = tool.id
version_elem = etree.SubElement(tool_elem, "version")
version_elem.text = tool.version
return tool_elem
[docs] def generate_tool_panel_dict_for_new_install(self, tool_dicts, tool_section=None):
"""
When installing a repository that contains tools, all tools must
currently be defined within the same tool section in the tool panel or
outside of any sections.
"""
tool_panel_dict: Dict[str, List[Dict[str, Any]]] = {}
if tool_section:
section_id = tool_section.id
section_name = tool_section.name
section_version = tool_section.version or ""
else:
section_id = ""
section_name = ""
section_version = ""
for tool_dict in tool_dicts:
if tool_dict.get("add_to_tool_panel", True):
guid = tool_dict["guid"]
tool_config = tool_dict["tool_config"]
tool_section_dict = dict(
tool_config=tool_config, id=section_id, name=section_name, version=section_version
)
if guid in tool_panel_dict:
tool_panel_dict[guid].append(tool_section_dict)
else:
tool_panel_dict[guid] = [tool_section_dict]
return tool_panel_dict
[docs] def generate_tool_panel_dict_for_tool_config(
self, guid, tool_config, tool_sections=None
) -> Dict[str, List[Dict[str, Any]]]:
"""
Create a dictionary of the following type for a single tool config file name.
The intent is to call this method for every tool config in a repository and
append each of these as entries to a tool panel dictionary for the repository.
This enables each tool to be loaded into a different section in the tool panel.
.. code-block::
{<Tool guid> :
[{ tool_config : <tool_config_file>,
id: <ToolSection id>,
version : <ToolSection version>,
name : <TooSection name>}]}
"""
tool_panel_dict: Dict[str, List[Dict[str, Any]]] = {}
file_name = strip_path(tool_config)
tool_section_dicts = self.generate_tool_section_dicts(tool_config=file_name, tool_sections=tool_sections)
tool_panel_dict[guid] = tool_section_dicts
return tool_panel_dict
[docs] def generate_tool_panel_dict_from_shed_tool_conf_entries(self, repository) -> Dict[str, List[Dict[str, Any]]]:
"""
Keep track of the section in the tool panel in which this repository's
tools will be contained by parsing the shed_tool_conf in which the
repository's tools are defined and storing the tool panel definition
of each tool in the repository. This method is called only when the
repository is being deactivated or un-installed and allows for
activation or re-installation using the original layout.
"""
tool_panel_dict: Dict[str, List[Dict[str, Any]]] = {}
shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir(
self.app, repository
)
metadata = repository.metadata_
# Create a dictionary of tool guid and tool config file name for each tool in the repository.
guids_and_configs = {}
if "tools" in metadata:
for tool_dict in metadata["tools"]:
guid = tool_dict["guid"]
tool_config = tool_dict["tool_config"]
file_name = strip_path(tool_config)
guids_and_configs[guid] = file_name
# Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict.
tree, error_message = parse_xml(shed_tool_conf)
if tree is None:
return tool_panel_dict
root = tree.getroot()
for elem in root:
if elem.tag == "tool":
guid = elem.get("guid")
if guid in guids_and_configs:
# The tool is displayed in the tool panel outside of any tool sections.
tool_section_dict = dict(tool_config=guids_and_configs[guid], id="", name="", version="")
if guid in tool_panel_dict:
tool_panel_dict[guid].append(tool_section_dict)
else:
tool_panel_dict[guid] = [tool_section_dict]
elif elem.tag == "section":
section_id = elem.get("id") or ""
section_name = elem.get("name") or ""
section_version = elem.get("version") or ""
for section_elem in elem:
if section_elem.tag == "tool":
guid = section_elem.get("guid")
if guid in guids_and_configs:
# The tool is displayed in the tool panel inside the current tool section.
tool_section_dict = dict(
tool_config=guids_and_configs[guid],
id=section_id,
name=section_name,
version=section_version,
)
if guid in tool_panel_dict:
tool_panel_dict[guid].append(tool_section_dict)
else:
tool_panel_dict[guid] = [tool_section_dict]
return tool_panel_dict
[docs] def generate_tool_panel_elem_list(
self,
repository_name: str,
repository_clone_url: str,
changeset_revision: str,
tool_panel_dict: dict,
repository_tools_tups: List[tuple],
owner="",
):
"""Generate a list of ElementTree Element objects for each section or tool."""
elem_list: List[etree.Element] = []
tool_elem = None
cleaned_repository_clone_url = remove_protocol_and_user_from_clone_url(repository_clone_url)
if not owner:
owner = get_repository_owner(cleaned_repository_clone_url)
tool_shed = cleaned_repository_clone_url.split("/repos/")[0].rstrip("/")
for guid, tool_section_dicts in tool_panel_dict.items():
for tool_section_dict in tool_section_dicts:
tool_section = None
inside_section = False
section_in_elem_list = None
if tool_section_dict["id"]:
inside_section = True
# Create a new section element only if we haven't already created it.
for index, elem in enumerate(elem_list):
if elem.tag == "section":
section_id = elem.get("id", None)
if section_id == tool_section_dict["id"]:
section_in_elem_list = index
tool_section = elem
break
if tool_section is None:
tool_section = self.generate_tool_section_element_from_dict(tool_section_dict)
# Find the tuple containing the current guid from the list of repository_tools_tups.
for repository_tool_tup in repository_tools_tups:
tool_file_path, tup_guid, tool = repository_tool_tup
if tup_guid == guid:
break
tool_elem = self.generate_tool_elem(
tool_shed,
repository_name,
changeset_revision,
owner,
tool_file_path,
tool,
tool_section if inside_section else None,
)
if inside_section:
if section_in_elem_list is not None:
elem_list[section_in_elem_list] = tool_section
else:
elem_list.append(tool_section)
else:
elem_list.append(tool_elem)
return elem_list
[docs] def generate_tool_section_dicts(self, tool_config=None, tool_sections=None) -> List[Dict[str, Any]]:
tool_section_dicts: List[Dict[str, Any]] = []
if tool_config is None:
tool_config = ""
if tool_sections:
for tool_section in tool_sections:
# The value of tool_section will be None if the tool is displayed outside
# of any sections in the tool panel.
if tool_section:
section_id = tool_section.id or ""
section_version = tool_section.version or ""
section_name = tool_section.name or ""
else:
section_id = ""
section_version = ""
section_name = ""
tool_section_dicts.append(
dict(tool_config=tool_config, id=section_id, version=section_version, name=section_name)
)
else:
tool_section_dicts.append(dict(tool_config=tool_config, id="", version="", name=""))
return tool_section_dicts
[docs] def generate_tool_section_element_from_dict(self, tool_section_dict):
# The value of tool_section_dict looks like the following.
# { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}
if tool_section_dict["id"]:
# Create a new tool section.
tool_section = etree.Element("section")
tool_section.attrib["id"] = tool_section_dict["id"]
tool_section.attrib["name"] = tool_section_dict["name"]
tool_section.attrib["version"] = tool_section_dict["version"]
else:
tool_section = None
return tool_section
[docs] def get_or_create_tool_section(self, toolbox, tool_panel_section_id, new_tool_panel_section_label=None):
return toolbox.get_section(
section_id=tool_panel_section_id, new_label=new_tool_panel_section_label, create_if_needed=True
)
[docs] def get_shed_tool_conf_dict(self, shed_tool_conf):
"""
Return the in-memory version of the shed_tool_conf file, which is stored in
the config_elems entry in the shed_tool_conf_dict associated with the file.
"""
for shed_tool_conf_dict in self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
if shed_tool_conf == shed_tool_conf_dict["config_filename"]:
return shed_tool_conf_dict
else:
file_name = strip_path(shed_tool_conf_dict["config_filename"])
if shed_tool_conf == file_name:
return shed_tool_conf_dict
raise RequestParameterInvalidException(
f"Requested shed_tool_conf '{shed_tool_conf}' is not an active shed_tool_config_file"
)
[docs] def handle_tool_panel_section(self, toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None):
"""Return a ToolSection object retrieved from the current in-memory tool_panel."""
# If tool_panel_section_id is received, the section exists in the tool panel. In this
# case, the value of the received tool_panel_section_id must be the id retrieved from a
# tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label
# is received, a new section will be added to the tool panel.
if new_tool_panel_section_label:
section_id = str(new_tool_panel_section_label.lower().replace(" ", "_"))
tool_panel_section_key, tool_section = self.get_or_create_tool_section(
toolbox, tool_panel_section_id=section_id, new_tool_panel_section_label=new_tool_panel_section_label
)
elif tool_panel_section_id:
tool_panel_section_key, tool_section = toolbox.get_section(tool_panel_section_id)
else:
return None, None
return tool_panel_section_key, tool_section
[docs] def handle_tool_panel_selection(
self, toolbox, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label
):
"""
Handle the selected tool panel location for loading tools included in
tool shed repositories when installing or reinstalling them.
"""
# Get the location in the tool panel in which each tool was originally loaded.
tool_section = None
tool_panel_section_key = None
if "tools" in metadata:
# This forces everything to be loaded into the same section (or no section)
# in the tool panel.
if no_changes_checked:
# Make sure the no_changes check box overrides the new_tool_panel_section_label
# if the user checked the check box and entered something into the field.
new_tool_panel_section_label = None
if "tool_panel_section" in metadata:
tool_panel_dict = metadata["tool_panel_section"]
if not tool_panel_dict:
tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata["tools"])
else:
tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata["tools"])
if tool_panel_dict:
# The tool_panel_dict is empty when tools exist but are not installed into a tool panel section.
tool_section_dicts = tool_panel_dict[next(iter(tool_panel_dict))]
tool_section_dict = tool_section_dicts[0]
original_section_id = tool_section_dict["id"]
if original_section_id:
tool_panel_section_key, tool_section = self.get_or_create_tool_section(
toolbox,
tool_panel_section_id=original_section_id,
new_tool_panel_section_label=new_tool_panel_section_label,
)
else:
# The user elected to change the tool panel section to contain the tools.
tool_panel_section_key, tool_section = self.handle_tool_panel_section(
toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label,
)
return tool_section, tool_panel_section_key
[docs] def remove_from_shed_tool_config(self, shed_tool_conf_dict, metadata):
"""
A tool shed repository is being uninstalled so change the
shed_tool_conf file. Parse the config file to generate the entire list
of config_elems instead of using the in-memory list since it will be a
subset of the entire list if one or more repositories have been
deactivated.
"""
if "tools" not in metadata:
return
# We need to use the tool path to uniquely identify the tools to remove,
# since multiple installable revisions of a repository can provide the
# same version of a tool (i.e. there may be another tool with the same
# guid that we should not remove from shed_tool_conf).
guid_paths_to_remove = [(_["guid"], _["tool_config"]) for _ in metadata["tools"]]
shed_tool_conf = shed_tool_conf_dict["config_filename"]
tool_path = shed_tool_conf_dict["tool_path"]
config_elems = []
tree, error_message = parse_xml(shed_tool_conf)
if tree:
root = tree.getroot()
for elem in root:
config_elems.append(elem)
config_elems_to_remove = []
for config_elem in config_elems:
if config_elem.tag == "section":
tool_elems_to_remove = []
for tool_elem in config_elem:
if (tool_elem.get("guid"), tool_elem.get("file")) in guid_paths_to_remove:
tool_elems_to_remove.append(tool_elem)
for tool_elem in tool_elems_to_remove:
# Remove all of the appropriate tool sub-elements from the section element.
config_elem.remove(tool_elem)
if len(config_elem) < 1:
# Keep a list of all empty section elements so they can be removed.
config_elems_to_remove.append(config_elem)
elif config_elem.tag == "tool":
if (config_elem.get("guid"), config_elem.get("file")) in guid_paths_to_remove:
config_elems_to_remove.append(config_elem)
for config_elem in config_elems_to_remove:
config_elems.remove(config_elem)
# Persist the altered in-memory version of the tool config.
self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path)
[docs] def remove_repository_contents(self, repository, shed_tool_conf, uninstall):
"""
A tool shed repository is being deactivated or uninstalled, so handle
tool panel alterations accordingly.
"""
# Determine where the tools are currently defined in the tool panel and store this
# information so the tools can be displayed in the same way when the repository is
# activated or reinstalled.
tool_panel_dict = self.generate_tool_panel_dict_from_shed_tool_conf_entries(repository)
repository.metadata_["tool_panel_section"] = tool_panel_dict
session = self.app.install_model.context
session.add(repository)
with transaction(session):
session.commit()
# Create a list of guids for all tools that will be removed from the in-memory tool panel
# and config file on disk.
guids_to_remove = list(tool_panel_dict.keys())
toolbox = self.app.toolbox
# Remove the tools from the toolbox's tools_by_id dictionary.
for guid_to_remove in guids_to_remove:
# remove_from_tool_panel to false, will handling that logic below.
toolbox.remove_tool_by_id(guid_to_remove, remove_from_panel=False)
shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf)
if uninstall:
# Remove from the shed_tool_conf file on disk.
self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata_)
[docs] def update_tool_panel_dict(self, tool_panel_dict, tool_panel_section_mapping, repository_tools_tups):
for tool_guid in tool_panel_dict:
if tool_guid not in tool_panel_section_mapping:
continue
for tool in tool_panel_dict[tool_guid]:
section_name = tool_panel_section_mapping[tool_guid]["tool_panel_section"]
section_id = str(tool_panel_section_mapping[tool_guid]["tool_panel_section"].lower().replace(" ", "_"))
tool["name"] = section_name
tool["id"] = section_id
return tool_panel_dict