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Source code for galaxy.tool_util.toolbox.base

import errno
import logging
import os
import string
import time
from collections import namedtuple
from errno import ENOENT
from typing import (
from urllib.parse import urlparse

from markupsafe import escape

from galaxy.exceptions import (
from galaxy.tool_util.deps import (
from galaxy.tool_util.loader_directory import looks_like_a_tool
from galaxy.util import (
from galaxy.util.bunch import Bunch
from galaxy.util.dictifiable import Dictifiable
from .filters import FilterFactory
from .integrated_panel import ManagesIntegratedToolPanelMixin
from .lineages import LineageMap
from .panel import (
from .parser import (
from .tags import tool_tag_manager
from .views.edam import (
from .views.interface import (
from .views.static import StaticToolPanelView

log = logging.getLogger(__name__)

SHED_TOOL_CONF_XML = """<?xml version="1.0"?>
<toolbox tool_path="{shed_tools_dir}">

# A fake ToolShedRepository constructed from a shed tool conf
_ToolConfRepository = namedtuple(

[docs]class ToolConfRepository(_ToolConfRepository):
[docs] def get_tool_relative_path(self, *args, **kwargs): # This is a somewhat public function, used by data_manager_manual for instance return self.tool_path, self.repository_path
[docs]class ToolBoxRegistryImpl(ToolBoxRegistry): """View of ToolBox provided to ToolPanelView to reason about tools loaded."""
[docs] def __init__(self, toolbox: "AbstractToolBox"): self.__toolbox = toolbox
[docs] def has_tool(self, tool_id: str) -> bool: return tool_id in self.__toolbox._tools_by_id
[docs] def get_tool(self, tool_id: str): return self.__toolbox.get_tool(tool_id)
[docs] def get_workflow(self, id: str): return self.__toolbox._workflows_by_id[id]
[docs] def add_tool_to_tool_panel_view(self, tool, tool_panel_component) -> None: self.__toolbox.add_tool_to_tool_panel_view(tool, tool_panel_component)
[docs]class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin): """ Abstract container for managing a ToolPanel - containing tools and workflows optionally in labelled sections. """
[docs] def __init__( self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view="default", save_integrated_tool_panel=True, ): """ Create a toolbox from the config files named by `config_filenames`, using `tool_root_dir` as the base directory for finding individual tool config files. """ self._default_panel_view = default_panel_view # The _dynamic_tool_confs list contains dictionaries storing # information about the tools defined in each shed-related # shed_tool_conf.xml file. self._dynamic_tool_confs = [] self._tools_by_id = {} self._tools_by_uuid = {} # Tool lineages can contain chains of related tools with different ids # so each will be present once in the above dictionary. The following # dictionary can instead hold multiple tools with different versions. self._tool_versions_by_id = {} self._workflows_by_id = {} # Cache for tool's to_dict calls specific to toolbox. Invalidates on toolbox reload. self._tool_to_dict_cache = {} self._tool_to_dict_cache_admin = {} # In-memory dictionary that defines the layout of the tool panel. self._tool_panel = ToolPanelElements() self._index = 0 self.data_manager_tools = {} self._lineage_map = LineageMap(app) # Sets self._integrated_tool_panel and self._integrated_tool_panel_config_has_contents self._init_integrated_tool_panel(app.config) # The following refers to the tool_path config setting for backward compatibility. The shed-related # (e.g., shed_tool_conf.xml) files include the tool_path attribute within the <toolbox> tag. self._tool_root_dir = tool_root_dir self.app = app self._tool_watcher = self.app.watchers.tool_watcher self._tool_config_watcher = self.app.watchers.tool_config_watcher self._filter_factory = FilterFactory(self) self._tool_tag_manager = tool_tag_manager(app) self._init_tools_from_configs(config_filenames) if self.app.name == "galaxy" and self._integrated_tool_panel_config_has_contents: self._load_tool_panel() toolbox = self class DefaultToolPanelView(ToolPanelView): def apply_view( self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry ) -> ToolPanelElements: return toolbox._tool_panel def to_model(self) -> ToolPanelViewModel: model_id = "default" name = "Full Tool Panel" description = ( "Galaxy's fully configured toolbox panel with all sections, tools, and configured workflows loaded." ) view_type = ToolPanelViewModelType.default_type model_class = DefaultToolPanelView.__class__.__name__ return ToolPanelViewModel( id=model_id, name=name, description=description, model_class=model_class, view_type=view_type, searchable=True, ) tool_panel_views_list = [ DefaultToolPanelView(), ] for edam_view in listify(self.app.config.edam_panel_views): mode = EdamPanelMode[edam_view] tool_panel_views_list.append(EdamToolPanelView(self.app.config.edam_toolbox_ontology_path, mode=mode)) if view_sources is not None: for definition in view_sources.get_definitions(): tool_panel_views_list.append(StaticToolPanelView(definition)) self._tool_panel_views = {} for tool_panel_view in tool_panel_views_list: self._tool_panel_views[tool_panel_view.to_model().id] = tool_panel_view if self.app.name == "galaxy": self._load_tool_panel_views() if save_integrated_tool_panel: self._save_integrated_tool_panel()
[docs] def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds): raise NotImplementedError()
[docs] def create_dynamic_tool(self, dynamic_tool): raise NotImplementedError()
[docs] def can_load_config_file(self, config_filename): return True
def _init_tools_from_configs(self, config_filenames): """Read through all tool config files and initialize tools in each with init_tools_from_config below. """ execution_timer = ExecutionTimer() self._tool_tag_manager.reset_tags() config_filenames = listify(config_filenames) for config_filename in config_filenames: if os.path.isdir(config_filename): directory_contents = sorted(os.listdir(config_filename)) directory_config_files = [ config_file for config_file in directory_contents if config_file.endswith(".xml") ] config_filenames.remove(config_filename) config_filenames.extend(directory_config_files) for config_filename in config_filenames: if not self.can_load_config_file(config_filename): continue try: self._init_tools_from_config(config_filename) except etree.ParseError: # Occasionally we experience "Missing required parameter 'shed_tool_conf'." # This happens if parsing the shed_tool_conf fails, so we just sleep a second and try again. # TODO: figure out why this fails occasionally (try installing hundreds of tools in batch ...). time.sleep(1) try: self._init_tools_from_config(config_filename) except Exception: raise except Exception: log.exception("Error loading tools defined in config %s", config_filename) log.debug("Reading tools from config files finished %s", execution_timer) def _init_tools_from_config(self, config_filename): """ Read the configuration file and load each tool. The following tags are currently supported: .. raw:: xml <toolbox> <tool file="data_source/upload.xml"/> # tools outside sections <label text="Basic Tools" id="basic_tools" /> # labels outside sections <workflow id="529fd61ab1c6cc36" /> # workflows outside sections <section name="Get Data" id="getext"> # sections <tool file="data_source/biomart.xml" /> # tools inside sections <label text="In Section" id="in_section" /> # labels inside sections <workflow id="adb5f5c93f827949" /> # workflows inside sections <tool file="data_source/foo.xml" labels="beta" /> # label for a single tool </section> </toolbox> """ log.info(f"Parsing the tool configuration {config_filename}") try: tool_conf_source = get_toolbox_parser(config_filename) except OSError as exc: dynamic_confs = (self.app.config.shed_tool_config_file, self.app.config.migrated_tools_config) if config_filename in dynamic_confs and exc.errno == errno.ENOENT: log.info( "Shed-enabled tool configuration file does not exist, but will be created on demand: %s", config_filename, ) stcd = dict( config_filename=config_filename, tool_path=self.app.config.shed_tools_dir, config_elems=[], create=SHED_TOOL_CONF_XML.format(shed_tools_dir=self.app.config.shed_tools_dir), ) self._dynamic_tool_confs.append(stcd) return raise tool_path = tool_conf_source.parse_tool_path() tool_cache_data_dir = tool_conf_source.parse_tool_cache_data_dir() parsing_shed_tool_conf = tool_conf_source.is_shed_tool_conf() if parsing_shed_tool_conf: # Keep an in-memory list of xml elements to enable persistence of the changing tool config. config_elems = [] tool_conf_type = "shed tool" if parsing_shed_tool_conf else "tool" log.debug("Tool path for %s configuration %s is %s", tool_conf_type, config_filename, tool_path) tool_path = self.__resolve_tool_path(tool_path, config_filename) # Only load the panel_dict under certain conditions. load_panel_dict = not self._integrated_tool_panel_config_has_contents for item in tool_conf_source.parse_items(): index = self._index self._index += 1 if parsing_shed_tool_conf: config_elems.append(item.elem) self.load_item( item, tool_path=tool_path, tool_cache_data_dir=tool_cache_data_dir, load_panel_dict=load_panel_dict, guid=item.get("guid"), index=index, ) if parsing_shed_tool_conf: # if read_only mode, (CVMFS consumer) don't add to dynamic_confs if os.access(config_filename, os.W_OK): 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) def _get_tool_by_uuid(self, tool_uuid): if tool_uuid in self._tools_by_uuid: return self._tools_by_uuid[tool_uuid] dynamic_tool = self.app.dynamic_tool_manager.get_tool_by_uuid(tool_uuid) if dynamic_tool: return self.load_dynamic_tool(dynamic_tool) return None
[docs] def panel_views(self) -> List[ToolPanelViewModel]: return [v.to_model() for v in self._tool_panel_views.values()]
[docs] def panel_view_dicts(self) -> Dict[str, Dict]: return {m.id: m.dict() for m in self.panel_views()}
[docs] def panel_has_tool(self, tool, panel_view_id): panel_view_rendered = self._tool_panel_view_rendered[panel_view_id] return panel_view_rendered.has_item_recursive(tool)
[docs] def load_dynamic_tool(self, dynamic_tool): if not dynamic_tool.active: return None tool = self.create_dynamic_tool(dynamic_tool) self.register_tool(tool) self._tools_by_uuid[dynamic_tool.uuid] = tool return tool
[docs] def load_item( self, item, tool_path, panel_dict=None, integrated_panel_dict=None, load_panel_dict=True, guid=None, index=None, tool_cache_data_dir=None, ): with self.app._toolbox_lock: item = ensure_tool_conf_item(item) item_type = item.type if panel_dict is None: panel_dict = self._tool_panel if integrated_panel_dict is None: integrated_panel_dict = self._integrated_tool_panel if item_type == "tool": self._load_tool_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, tool_path=tool_path, load_panel_dict=load_panel_dict, guid=guid, index=index, tool_cache_data_dir=tool_cache_data_dir, ) elif item_type == "workflow": self._load_workflow_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, load_panel_dict=load_panel_dict, index=index, ) elif item_type == "section": self._load_section_tag_set( item, tool_path=tool_path, load_panel_dict=load_panel_dict, index=index, tool_cache_data_dir=tool_cache_data_dir, ) elif item_type == "label": self._load_label_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, load_panel_dict=load_panel_dict, index=index, ) elif item_type == "tool_dir": self._load_tooldir_tag_set( item, panel_dict, tool_path, integrated_panel_dict, load_panel_dict=load_panel_dict, tool_cache_data_dir=tool_cache_data_dir, )
[docs] def get_shed_config_dict_by_filename(self, filename): filename = os.path.abspath(filename) dynamic_tool_conf_paths = [] for shed_config_dict in self._dynamic_tool_confs: dynamic_tool_conf_path = os.path.abspath(shed_config_dict["config_filename"]) dynamic_tool_conf_paths.append(dynamic_tool_conf_path) if dynamic_tool_conf_path == filename: return shed_config_dict log.warning(f"'{filename}' not among installable tool config files ({', '.join(dynamic_tool_conf_paths)})") return None
[docs] def update_shed_config(self, shed_conf): """Update the in-memory descriptions of tools and write out the changes to integrated tool panel unless we are just deactivating a tool (since that doesn't affect that file). """ for index, my_shed_tool_conf in enumerate(self._dynamic_tool_confs): if shed_conf["config_filename"] == my_shed_tool_conf["config_filename"]: self._dynamic_tool_confs[index] = shed_conf self._save_integrated_tool_panel()
[docs] def get_section(self, section_id, new_label=None, create_if_needed=False): tool_panel_section_key = str(section_id) if tool_panel_section_key in self._tool_panel: # Appending a tool to an existing section in toolbox._tool_panel tool_section = self._tool_panel[tool_panel_section_key] log.debug(f"Appending to tool panel section: {str(tool_section.name)}") elif new_label and self._tool_panel.get_label(new_label): tool_section = self._tool_panel.get_label(new_label) tool_panel_section_key = tool_section.id elif create_if_needed: # Appending a new section to toolbox._tool_panel if new_label is None: # This might add an ugly section label to the tool panel, but, oh well... new_label = section_id section_dict = { "name": new_label, "id": section_id, "version": "", } self.create_section(section_dict) tool_section = self._tool_panel[tool_panel_section_key] self._save_integrated_tool_panel() else: tool_section = None return tool_panel_section_key, tool_section
[docs] def create_section(self, section_dict): tool_section = ToolSection(section_dict) self._tool_panel.append_section(tool_section.id, tool_section) log.debug(f"Loading new tool panel section: {str(tool_section.name)}") return tool_section
[docs] def get_section_for_tool(self, tool): tool_id = tool.id return self._tool_panel.get_section_for_tool_id(tool_id)
def __resolve_tool_path(self, tool_path, config_filename): if not tool_path: # Default to backward compatible config setting. tool_path = self._tool_root_dir else: # Allow use of __tool_conf_dir__ in toolbox config files. tool_conf_dir = os.path.dirname(config_filename) tool_path_vars = {"tool_conf_dir": tool_conf_dir} tool_path = string.Template(tool_path).safe_substitute(tool_path_vars) return tool_path
[docs] def add_tool_to_tool_panel_view(self, tool, view_panel_component): self.__add_tool_to_tool_panel(tool, view_panel_component)
def __add_tool_to_tool_panel(self, tool, panel_component, section=None): if section is None: section = isinstance(panel_component, ToolSection) # See if a version of this tool is already loaded into the tool panel. # The value of panel_component will be a ToolSection (if the value of # section=True) or self._tool_panel (if section=False). if tool.hidden: log.debug("Skipping tool panel addition of hidden tool: %s, version: %s", tool.id, tool.version) return tool_id = str(tool.id) tool = self._tools_by_id[tool_id] log_msg = "" if section: panel_dict = panel_component.elems else: panel_dict = panel_component related_tool = self._lineage_in_panel(panel_dict, tool=tool) if related_tool: if self._newer_tool(tool, related_tool): panel_dict.replace_tool( previous_tool_id=related_tool.id, new_tool_id=tool_id, tool=tool, ) log_msg = f"Loaded tool id: {tool.id}, version: {tool.version} into tool panel." else: inserted = False index = self._integrated_tool_panel.index_of_tool_id(tool_id) if index: panel_dict.insert_tool(index, tool) inserted = True if not inserted: # Check the tool's installed versions. if tool.lineage is not None: versions = tool.lineage.get_versions() for tool_lineage_version in versions: lineage_id = tool_lineage_version.id index = self._integrated_tool_panel.index_of_tool_id(lineage_id) if index: panel_dict.insert_tool(index, tool) inserted = True else: log.warning("Could not find lineage for tool '%s'", tool.id) if not inserted: if ( tool.guid is None or tool.tool_shed is None or tool.repository_name is None or tool.repository_owner is None or tool.installed_changeset_revision is None ): # We have a tool that was not installed from the Tool # Shed, but is also not yet defined in # integrated_tool_panel.xml, so append it to the tool # panel. panel_dict.append_tool(tool) log_msg = f"Loaded tool id: {tool.id}, version: {tool.version} into tool panel.." else: # We are in the process of installing the tool or we are reloading the whole toolbox. tool_lineage = self._lineage_map.get(tool_id) already_loaded = self._lineage_in_panel(panel_dict, tool_lineage=tool_lineage) is not None if not already_loaded: # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. panel_dict.append_tool(tool) log_msg = f"Loaded tool id: {tool.id}, version: {tool.version} into tool panel...." if log_msg and (not hasattr(self.app, "tool_cache") or tool_id in self.app.tool_cache._new_tool_ids): log.debug(log_msg) def _load_tool_panel_views(self): self._tool_panel_view_rendered = {} registry = ToolBoxRegistryImpl(self) for key, view in self._tool_panel_views.items(): self._tool_panel_view_rendered[key] = view.apply_view(self._integrated_tool_panel, registry) def _load_tool_panel(self): execution_timer = ExecutionTimer() for key, item_type, val in self._integrated_tool_panel.panel_items_iter(): if item_type == panel_item_types.TOOL: tool_id = key.replace("tool_", "", 1) if tool_id in self._tools_by_id: self.__add_tool_to_tool_panel(val, self._tool_panel, section=False) self._tool_panel.record_section_for_tool_id(tool_id, "", "") elif item_type == panel_item_types.WORKFLOW: workflow_id = key.replace("workflow_", "", 1) if workflow_id in self._workflows_by_id: workflow = self._workflows_by_id[workflow_id] self._tool_panel[key] = workflow log.debug(f"Loaded workflow: {workflow_id} {workflow.name}") elif item_type == panel_item_types.LABEL: self._tool_panel[key] = val elif item_type == panel_item_types.SECTION: section_dict = { "id": val.id or "", "name": val.name or "", "version": val.version or "", } section = ToolSection(section_dict) log.debug(f"Loading section: {section_dict.get('name')}") for section_key, section_item_type, section_val in val.panel_items_iter(): if section_item_type == panel_item_types.TOOL: tool_id = section_key.replace("tool_", "", 1) if tool_id in self._tools_by_id: self.__add_tool_to_tool_panel(section_val, section, section=True) self._tool_panel.record_section_for_tool_id(tool_id, key, val.name) elif section_item_type == panel_item_types.WORKFLOW: workflow_id = section_key.replace("workflow_", "", 1) if workflow_id in self._workflows_by_id: workflow = self._workflows_by_id[workflow_id] section.elems[section_key] = workflow log.debug(f"Loaded workflow: {workflow_id} {workflow.name}") elif section_item_type == panel_item_types.LABEL: if section_val: section.elems[section_key] = section_val log.debug(f"Loaded label: {section_val.text}") self._tool_panel[key] = section log.debug("Loading tool panel finished %s", execution_timer) def _load_integrated_tool_panel_keys(self): """ Load the integrated tool panel keys, setting values for tools and workflows to None. The values will be reset when the various tool panel config files are parsed, at which time the tools and workflows are loaded. """ tree = parse_xml(self._integrated_tool_panel_config) root = tree.getroot() for elem in root: key = elem.get("id") if elem.tag == "tool": self._integrated_tool_panel.stub_tool(key) elif elem.tag == "workflow": self._integrated_tool_panel.stub_workflow(key) elif elem.tag == "section": section = ToolSection(elem) for section_elem in elem: section_id = section_elem.get("id") if section_elem.tag == "tool": section.elems.stub_tool(section_id) elif section_elem.tag == "workflow": section.elems.stub_workflow(section_id) elif section_elem.tag == "label": section.elems.stub_label(section_id) self._integrated_tool_panel.append_section(key, section) elif elem.tag == "label": self._integrated_tool_panel.stub_label(key)
[docs] def get_tool(self, tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None): """Attempt to locate a tool in the tool box. Note that `exact` only refers to the `tool_id`, not the `tool_version`.""" if tool_version: tool_version = str(tool_version) if get_all_versions and exact: raise AssertionError("Cannot specify get_tool with both get_all_versions and exact as True") if tool_id is None: if tool_uuid is not None: tool_from_uuid = self._get_tool_by_uuid(tool_uuid) if tool_from_uuid is None: raise ObjectNotFound(f"Failed to find a tool with uuid [{tool_uuid}]") tool_id = tool_from_uuid.id if tool_id is None: raise AssertionError("get_tool called with tool_id as None") if "/repos/" in tool_id: # test if tool came from a toolshed tool_id_without_tool_shed = tool_id.split("/repos/")[1] available_tool_sheds = [urlparse(_) for _ in self.app.tool_shed_registry.tool_sheds.values()] available_tool_sheds = [url.geturl().replace(f"{url.scheme}://", "", 1) for url in available_tool_sheds] tool_ids = [f"{tool_shed}repos/{tool_id_without_tool_shed}" for tool_shed in available_tool_sheds] if tool_id in tool_ids: # move original tool_id to the top of tool_ids tool_ids.remove(tool_id) tool_ids.insert(0, tool_id) else: tool_ids = [tool_id] for tool_id in tool_ids: if tool_id in self._tools_by_id and not get_all_versions: # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid) if not tool_version: return self._tools_by_id[tool_id] elif tool_version in self._tool_versions_by_id[tool_id]: return self._tool_versions_by_id[tool_id][tool_version] # should be if exact=True not elif? Otherwise we can end up doing non-exact searches even # if exact=True. Anyway, changing it breaks a lot of tests involving built-in tools elif exact: # We're looking for an exact match, so we skip lineage and # versionless mapping, though we may want to check duplicate # toolsheds continue # exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions rval = [] tool_lineage = self._lineage_map.get(tool_id) if tool_lineage: lineage_tool_versions = tool_lineage.get_versions() for lineage_tool_version in lineage_tool_versions: lineage_tool = self._tool_from_lineage_version(lineage_tool_version) if lineage_tool: rval.append(lineage_tool) if not rval: # still no tool, do a deeper search and try to match by old ids for tool in self._tools_by_id.values(): if tool.old_id == tool_id: rval.append(tool) if get_all_versions and tool_id in self._tool_versions_by_id: for tool in self._tool_versions_by_id[tool_id].values(): if tool not in rval: rval.append(tool) # if we don't have a lineage_map for this tool we need to sort by version, # so that the last tool in rval is the newest tool. rval.sort(key=lambda t: t.version) if rval: if get_all_versions: return rval else: if tool_version: # return first tool with matching version for tool in rval: if tool.version == tool_version: return tool # No tool matches by version, simply return the newest matching tool return rval[-1] # We now likely have a Toolshed guid passed in, but no supporting database entries # If the tool exists by exact id and is loaded then provide exact match within a list if tool_id in self._tools_by_id: if get_all_versions: return [self._tools_by_id[tool_id]] else: return self._tools_by_id[tool_id] return None
[docs] def has_tool(self, tool_id, tool_version=None, exact=False): return self.get_tool(tool_id, tool_version=tool_version, exact=exact) is not None
[docs] def is_missing_shed_tool(self, tool_id): """Confirm that the tool ID does reference a shed tool and is not installed.""" if tool_id is None: # This is not a tool ID. return False if "repos" not in tool_id: # This is not a shed tool. return False # This is a valid tool, and it is from a toolshed. Check if it's # missing from the toolbox. if tool_id not in self._tools_by_id: return True return False
[docs] def get_loaded_tools_by_lineage(self, tool_id): """Get all loaded tools associated by lineage to the tool whose id is tool_id.""" tool_lineage = self._lineage_map.get(tool_id) if tool_lineage: lineage_tool_versions = tool_lineage.get_versions() available_tool_versions = [] for lineage_tool_version in lineage_tool_versions: tool = self._tool_from_lineage_version(lineage_tool_version) if tool: available_tool_versions.append(tool) return available_tool_versions else: if tool_id in self._tools_by_id: tool = self._tools_by_id[tool_id] return [tool] return []
[docs] def tools(self): return self._tools_by_id.copy().items()
[docs] def dynamic_confs(self, include_migrated_tool_conf=False): confs = [] for dynamic_tool_conf_dict in self._dynamic_tool_confs: dynamic_tool_conf_filename = dynamic_tool_conf_dict["config_filename"] if include_migrated_tool_conf or (dynamic_tool_conf_filename != self.app.config.migrated_tools_config): confs.append(dynamic_tool_conf_dict) return confs
[docs] def default_shed_tool_conf_dict(self): """If set, returns the first shed_tool_conf_dict corresponding to shed_tool_config_file, else the first dynamic conf.""" dynamic_confs = self.dynamic_confs(include_migrated_tool_conf=False) # Pick the first tool config that doesn't set `is_shed_conf="false"` and that is not a migrated_tool_conf try: shed_config_dict = dynamic_confs[0] except IndexError: raise ConfigurationError("No shed_tool_conf file active") if self.app.config.shed_tool_config_file in self.app.config.tool_configs: # Use shed_tool_config_file if loaded for shed_config_dict in dynamic_confs: if shed_config_dict.get("config_filename") == self.app.config.shed_tool_config_file: break return shed_config_dict
[docs] def dynamic_conf_filenames(self): """Return list of dynamic tool configuration filenames (shed_tools). These must be used with various dynamic tool configuration update operations (e.g. with update_shed_config). """ for dynamic_tool_conf_dict in self.dynamic_confs(): yield dynamic_tool_conf_dict["config_filename"]
def _path_template_kwds(self): return {} def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None, tool_cache_data_dir=None, ): try: path_template = item.get("file") template_kwds = self._path_template_kwds() path = string.Template(path_template).safe_substitute(**template_kwds) concrete_path = os.path.join(tool_path, path) if not os.path.exists(concrete_path): # This is a lot faster than attempting to load a non-existing tool raise OSError(ENOENT, os.strerror(ENOENT)) tool_shed_repository = None can_load_into_panel_dict = True tool = self.load_tool_from_cache(concrete_path) from_cache = tool if from_cache: if guid and tool.id != guid: # In rare cases a tool shed tool is loaded into the cache without guid. # In that case recreating the tool will correct the cached version. from_cache = False if guid and not from_cache: # tool was not in cache and is a tool shed tool tool_shed_repository = self.get_tool_repository_from_xml_item(item.elem, concrete_path) if tool_shed_repository: if hasattr(tool_shed_repository, "deleted"): # The shed tool is in the install database # Only load tools if the repository is not deactivated or uninstalled. can_load_into_panel_dict = not tool_shed_repository.deleted tool = self.load_tool( concrete_path, guid=guid, tool_shed_repository=tool_shed_repository, use_cached=False, tool_cache_data_dir=tool_cache_data_dir, ) if not tool: # tool was not in cache and is not a tool shed tool. tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) if string_as_bool(item.get("hidden", False)): tool.hidden = True key = f"tool_{str(tool.id)}" if can_load_into_panel_dict: if guid and not from_cache: tool.tool_shed = tool_shed_repository.tool_shed tool.repository_name = tool_shed_repository.name tool.repository_owner = tool_shed_repository.owner tool.installed_changeset_revision = tool_shed_repository.installed_changeset_revision tool.guid = guid tool.version = item.elem.find("version").text if item.has_elem: self._tool_tag_manager.handle_tags(tool.id, item.elem) self.__add_tool(tool, load_panel_dict, panel_dict) # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. integrated_panel_dict.update_or_append(index, key, tool) # If labels were specified in the toolbox config, attach them to # the tool. labels = item.labels if labels is not None: tool.labels = labels except OSError as exc: msg = "Error reading tool configuration file from path '%s': %s", path, unicodify(exc) if exc.errno == ENOENT: log.error(msg) else: log.exception(msg) except Exception: log.exception("Error reading tool from path: %s", path)
[docs] def get_tool_repository_from_xml_item(self, elem, path): tool_shed = elem.find("tool_shed").text repository_name = elem.find("repository_name").text repository_owner = elem.find("repository_owner").text # The definition of `installed_changeset_revision` for a repository is that it has been cloned at <tool_path/toolshed/repos/owner/name/installed_changeset_revision> # so if we load a tool it needs to be at a path that contains `installed_changeset_revision`. path_to_installed_changeset_revision = os.path.join(tool_shed, "repos", repository_owner, repository_name) if path_to_installed_changeset_revision in path: installed_changeset_revision = path[ path.index(path_to_installed_changeset_revision) + len(path_to_installed_changeset_revision) : ].split(os.path.sep)[1] else: installed_changeset_revision_elem = elem.find("installed_changeset_revision") if installed_changeset_revision_elem is None: # Backward compatibility issue - the tag used to be named 'changeset_revision'. installed_changeset_revision_elem = elem.find("changeset_revision") installed_changeset_revision = installed_changeset_revision_elem.text repository = self._get_tool_shed_repository( tool_shed=tool_shed, name=repository_name, owner=repository_owner, installed_changeset_revision=installed_changeset_revision, ) if not repository: msg = ( "Attempted to load tool shed tool, but the repository with name '%s' from owner '%s' was not found " "in database. Tool will be loaded without install database." ) log.warning(msg, repository_name, repository_owner) # Figure out path to repository on disk given the tool shed info and the path to the tool contained in the repo repository_path = os.path.join( tool_shed, "repos", repository_owner, repository_name, installed_changeset_revision ) tool_path = path[: path.index(repository_path)] repository = ToolConfRepository( tool_shed, repository_name, repository_owner, installed_changeset_revision, installed_changeset_revision, None, repository_path, tool_path, ) tsr_cache = self.app.tool_shed_repository_cache if tsr_cache: tsr_cache.add_local_repository(repository) return repository
def _get_tool_shed_repository(self, tool_shed, name, owner, installed_changeset_revision): # Abstract class doesn't have a dependency on the database, for full Tool Shed # support the actual Galaxy ToolBox implements this method and returns a Tool Shed repository. return None def __add_tool(self, tool, load_panel_dict, panel_dict): # Allow for the same tool to be loaded into multiple places in the # tool panel. We have to handle the case where the tool is contained # in a repository installed from the tool shed, and the Galaxy # administrator has retrieved updates to the installed repository. In # this case, the tool may have been updated, but the version was not # changed, so the tool should always be reloaded here. We used to # only load the tool if it was not found in self._tools_by_id, but # performing that check did not enable this scenario. tool._lineage = self._lineage_map.register(tool) self.register_tool(tool) if load_panel_dict: self.__add_tool_to_tool_panel(tool, panel_dict) def _load_workflow_tag_set(self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None): try: # TODO: should id be encoded? workflow_id = item.get("id") workflow = self._load_workflow(workflow_id) self._workflows_by_id[workflow_id] = workflow key = f"workflow_{workflow_id}" if load_panel_dict: panel_dict[key] = workflow # Always load workflows into the integrated_panel_dict. integrated_panel_dict.update_or_append(index, key, workflow) except Exception: log.exception("Error loading workflow: %s", workflow_id) def _load_label_tag_set(self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None): label = ToolSectionLabel(item) key = f"label_{label.id}" if load_panel_dict: panel_dict[key] = label integrated_panel_dict.update_or_append(index, key, label) def _load_section_tag_set(self, item, tool_path, load_panel_dict, index=None, tool_cache_data_dir=None): key = item.get("id") if key in self._tool_panel: section = self._tool_panel[key] elems = section.elems else: section = ToolSection(item) elems = section.elems if key in self._integrated_tool_panel: integrated_section = self._integrated_tool_panel[key] integrated_elems = integrated_section.elems else: integrated_section = ToolSection(item) integrated_elems = integrated_section.elems for sub_index, sub_item in enumerate(item.items): self.load_item( sub_item, tool_path=tool_path, panel_dict=elems, integrated_panel_dict=integrated_elems, load_panel_dict=load_panel_dict, guid=sub_item.get("guid"), index=sub_index, tool_cache_data_dir=tool_cache_data_dir, ) # Ensure each tool's section is stored for section_key, section_item_type, section_item in integrated_elems.panel_items_iter(): if section_item_type == panel_item_types.TOOL: if section_item: tool_id = section_key.replace("tool_", "", 1) self._tool_panel.record_section_for_tool_id(tool_id, integrated_section.id, integrated_section.name) if load_panel_dict: self._tool_panel[key] = section # Always load sections into the integrated_tool_panel. self._integrated_tool_panel.update_or_append(index, key, integrated_section) def _load_tooldir_tag_set( self, item, elems, tool_path, integrated_elems, load_panel_dict, tool_cache_data_dir=None ): directory = os.path.join(tool_path, item.get("dir")) recursive = string_as_bool(item.get("recursive", True)) self.__watch_directory( directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=True, tool_cache_data_dir=tool_cache_data_dir, ) def __watch_directory( self, directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=False, tool_cache_data_dir=None, ): def quick_load(tool_file, async_load=True): try: tool = self.load_tool(tool_file, tool_cache_data_dir) self.__add_tool(tool, load_panel_dict, elems) # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. key = f"tool_{str(tool.id)}" integrated_elems[key] = tool if async_load: self._load_tool_panel() self._load_tool_panel_views() self._save_integrated_tool_panel() return tool.id except Exception: log.exception("Failed to load potential tool %s.", tool_file) return None tool_loaded = False if not os.path.isdir(directory): log.error("Failed to read tool directory %s.", directory) return for name in os.listdir(directory): if name.startswith((".", "_")): # Very unlikely that we want to load tools from a hidden or private folder continue child_path = os.path.join(directory, name) if os.path.isdir(child_path) and recursive: self.__watch_directory(child_path, elems, integrated_elems, load_panel_dict, recursive) elif self._looks_like_a_tool(child_path): tool_id = quick_load(child_path, async_load=False) tool_loaded = bool(tool_id) if (tool_loaded or force_watch) and self._tool_watcher: self._tool_watcher.watch_directory(directory, quick_load)
[docs] def load_tool( self, config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element tool = None if use_cached: tool = self.load_tool_from_cache(config_file) if not tool or guid and guid != tool.guid: try: tool = self.create_tool( config_file=config_file, tool_shed_repository=tool_shed_repository, guid=guid, tool_cache_data_dir=tool_cache_data_dir, **kwds, ) except Exception: # If the tool is broken but still exists we can load it from the cache tool = self.load_tool_from_cache(config_file, recover_tool=True) if tool: log.exception(f"Tool '{config_file}' is not valid:") tool.tool_errors = "Current on-disk tool is not valid" else: raise if tool.tool_shed_repository or not guid: self.add_tool_to_cache(tool, config_file) self.watch_tool(tool) return tool
[docs] def watch_tool(self, tool): if not tool.id.startswith("__"): # do not monitor special tools written to tmp directory - no reason # to monitor such a large directory. if self._tool_config_watcher: [self._tool_config_watcher.watch_file(macro_path) for macro_path in tool._macro_paths]
[docs] def add_tool_to_cache(self, tool, config_file): tool_cache = getattr(self.app, "tool_cache", None) if tool_cache: self.app.tool_cache.cache_tool(config_file, tool)
[docs] def load_tool_from_cache(self, config_file, recover_tool=False): tool_cache = getattr(self.app, "tool_cache", None) tool = None if tool_cache: if recover_tool: tool = tool_cache.get_removed_tool(config_file) else: tool = tool_cache.get_tool(config_file) return tool
[docs] def load_hidden_lib_tool(self, path): tool_xml = os.path.join(os.getcwd(), "lib", path) return self.load_hidden_tool(tool_xml)
[docs] def load_hidden_tool(self, config_file, **kwds): """Load a hidden tool (in this context meaning one that does not appear in the tool panel) and register it in _tools_by_id. """ tool = self.load_tool(config_file, **kwds) self.register_tool(tool) return tool
[docs] def register_tool(self, tool): tool_id = tool.id version = tool.version or None if tool_id not in self._tool_versions_by_id: self._tool_versions_by_id[tool_id] = {version: tool} else: self._tool_versions_by_id[tool_id][version] = tool if tool_id in self._tools_by_id: related_tool = self._tools_by_id[tool_id] # This one becomes the default un-versioned tool # if newer. if self._newer_tool(tool, related_tool): self._tools_by_id[tool_id] = tool else: self._tools_by_id[tool_id] = tool
[docs] def package_tool(self, trans, tool_id): """ Create a tarball with the tool's xml, help images, and test data. :param trans: the web transaction :param tool_id: the tool ID from app.toolbox :returns: tuple of tarball filename, success True/False, message/None """ # Make sure the tool is actually loaded. if tool_id not in self._tools_by_id: raise ObjectNotFound(f"No tool found with id '{escape(tool_id)}'.") else: tool = self._tools_by_id[tool_id] return tool.to_archive()
[docs] def reload_tool_by_id(self, tool_id): """ Attempt to reload the tool identified by 'tool_id', if successful replace the old tool. """ if tool_id not in self._tools_by_id: message = f"No tool with id '{escape(tool_id)}'." status = "error" else: old_tool = self._tools_by_id[tool_id] new_tool = self.load_tool(old_tool.config_file, use_cached=False) # The tool may have been installed from a tool shed, so set the tool shed attributes. # Since the tool version may have changed, we don't override it here. new_tool.id = old_tool.id new_tool.guid = old_tool.guid new_tool.tool_shed = old_tool.tool_shed new_tool.repository_name = old_tool.repository_name new_tool.repository_owner = old_tool.repository_owner new_tool.installed_changeset_revision = old_tool.installed_changeset_revision new_tool.old_id = old_tool.old_id # Replace old_tool with new_tool in self._tool_panel self._tool_panel.replace_tool_for_id(tool_id, new_tool) # (Re-)Register the reloaded tool, this will handle # _tools_by_id and _tool_versions_by_id self.register_tool(new_tool) message = {"name": old_tool.name, "id": old_tool.id, "version": old_tool.version} status = "done" return message, status
[docs] def remove_tool_by_id(self, tool_id, remove_from_panel=True): """ Attempt to remove the tool identified by 'tool_id'. Ignores tool lineage - so to remove a tool with potentially multiple versions send remove_from_panel=False and handle the logic of promoting the next newest version of the tool into the panel if needed. """ if tool_id not in self._tools_by_id: message = f"No tool with id {escape(tool_id)}" status = "error" else: tool = self._tools_by_id[tool_id] del self._tools_by_id[tool_id] tool_cache = getattr(self.app, "tool_cache", None) if tool_cache: tool_cache.expire_tool(tool_id) if remove_from_panel: self._tool_panel.remove_tool(tool_id) if tool_id in self.data_manager_tools: del self.data_manager_tools[tool_id] # TODO: do we need to manually remove from the integrated panel here? message = "Removed the tool:<br/>" message += f"<b>name:</b> {escape(tool.name)}<br/>" message += f"<b>id:</b> {escape(tool.id)}<br/>" message += f"<b>version:</b> {escape(tool.version)}" status = "done" return message, status
[docs] def get_sections(self): """Return section id and name pairs. Only used by build_tool_panel_section_select_field in tool shed client code. """ for v in self._tool_panel.values(): if isinstance(v, ToolSection): yield (v.id, v.name)
[docs] def find_section_id(self, tool_panel_section_id): """ Find the section ID referenced by the key or return '' indicating no such section id. """ if not tool_panel_section_id: tool_panel_section_id = "" else: if tool_panel_section_id not in self._tool_panel: # Hack introduced without comment in a29d54619813d5da992b897557162a360b8d610c- # not sure why it is needed. fixed_tool_panel_section_id = f"section_{tool_panel_section_id}" if fixed_tool_panel_section_id in self._tool_panel: tool_panel_section_id = fixed_tool_panel_section_id else: tool_panel_section_id = "" return tool_panel_section_id
def _load_workflow(self, workflow_id): """ Return an instance of 'Workflow' identified by `id`, which is encoded in the tool panel. """ id = self.app.security.decode_id(workflow_id) stored = self.app.model.context.query(self.app.model.StoredWorkflow).get(id) return stored.latest_workflow
[docs] def tool_panel_contents(self, trans, view=None, **kwds): """Filter tool_panel contents for displaying for user.""" if view is None: view = self._default_panel_view if view not in self._tool_panel_view_rendered: raise RequestParameterInvalidException(f"No panel view {view} found.") filter_method = self._build_filter_method(trans) tool_panel_view = self._tool_panel_view_rendered[view] for _, item_type, elt in tool_panel_view.panel_items_iter(): elt = filter_method(elt, item_type) if elt: yield elt
[docs] def get_tool_to_dict(self, trans, tool, tool_help=False): """Return tool's to_dict. Use cache if present, store to cache otherwise. Note: The cached tool's to_dict is specific to the calls from toolbox. """ to_dict = None if not trans.user_is_admin: if not tool_help: to_dict = self._tool_to_dict_cache.get(tool.id, None) if not to_dict: to_dict = tool.to_dict(trans, link_details=True, tool_help=tool_help) if not tool_help: self._tool_to_dict_cache[tool.id] = to_dict else: if not tool_help: to_dict = self._tool_to_dict_cache_admin.get(tool.id, None) if not to_dict: to_dict = tool.to_dict(trans, link_details=True, tool_help=tool_help) if not tool_help: self._tool_to_dict_cache_admin[tool.id] = to_dict return to_dict
[docs] def to_dict(self, trans, in_panel=True, tool_help=False, view=None, **kwds): """ Create a dictionary representation of the toolbox. Uses primitive cache for toolbox-specific tool 'to_dict's. """ rval = [] if in_panel: panel_elts = list(self.tool_panel_contents(trans, view=view, **kwds)) for elt in panel_elts: # Only use cache for objects that are Tools. if hasattr(elt, "tool_type"): rval.append(self.get_tool_to_dict(trans, elt, tool_help=tool_help)) else: kwargs = dict(trans=trans, link_details=True, tool_help=tool_help, toolbox=self) rval.append(elt.to_dict(**kwargs)) else: filter_method = self._build_filter_method(trans) for tool in self._tools_by_id.values(): tool = filter_method(tool, panel_item_types.TOOL) if not tool: continue rval.append(self.get_tool_to_dict(trans, tool, tool_help=tool_help)) return rval
def _lineage_in_panel(self, panel_dict, tool=None, tool_lineage=None): """If tool with same lineage already in panel (or section) - find and return it. Otherwise return None. """ if tool_lineage is None: assert tool is not None tool_lineage = tool.lineage if tool_lineage is not None: for lineage_tool_version in reversed(tool_lineage.get_versions()): lineage_tool = self._tool_from_lineage_version(lineage_tool_version) if lineage_tool: lineage_id = lineage_tool.id if panel_dict.has_tool_with_id(lineage_id): return panel_dict.get_tool_with_id(lineage_id) else: log.warning("Could not find lineage for tool '%s'", tool.id) return None def _newer_tool(self, tool1, tool2): """Return True if tool1 is considered "newer" given its own lineage description. """ return tool1.version_object > tool2.version_object def _tool_from_lineage_version(self, lineage_tool_version): if lineage_tool_version.id_based: return self._tools_by_id.get(lineage_tool_version.id, None) else: return self._tool_versions_by_id.get(lineage_tool_version.id, {}).get(lineage_tool_version.version, None) def _build_filter_method(self, trans): context = Bunch(toolbox=self, trans=trans) filters = self._filter_factory.build_filters(trans) return lambda element, item_type: _filter_for_panel(element, item_type, filters, context)
def _filter_for_panel(item, item_type, filters, context): """ Filters tool panel elements so that only those that are compatible with provided filters are kept. """ def _apply_filter(filter_item, filter_list): for filter_method in filter_list: try: if not filter_method(context, filter_item): return False except Exception as e: raise MessageException(f"Toolbox filter exception from '{filter_method.__name__}': {unicodify(e)}.") return True if item_type == panel_item_types.TOOL: if _apply_filter(item, filters["tool"]): return item elif item_type == panel_item_types.LABEL: if _apply_filter(item, filters["label"]): return item elif item_type == panel_item_types.SECTION: # Filter section item-by-item. Only show a label if there are # non-filtered tools below it. if _apply_filter(item, filters["section"]): cur_label_key = None tools_under_label = False filtered_elems = item.elems.copy() for key, section_item_type, section_item in item.panel_items_iter(): if section_item_type == panel_item_types.TOOL: # Filter tool. if _apply_filter(section_item, filters["tool"]): tools_under_label = True else: del filtered_elems[key] elif section_item_type == panel_item_types.LABEL: # If there is a label and it does not have tools, # remove it. if cur_label_key and (not tools_under_label or not _apply_filter(section_item, filters["label"])): del filtered_elems[cur_label_key] # Reset attributes for new label. cur_label_key = key tools_under_label = False # Handle last label. if cur_label_key and not tools_under_label: del filtered_elems[cur_label_key] # Only return section if there are elements. if len(filtered_elems) != 0: copy = item.copy() copy.elems = filtered_elems return copy return None
[docs]class BaseGalaxyToolBox(AbstractToolBox): """ Extend the AbstractToolBox with more Galaxy tooling-specific functionality. Adds dependencies on dependency resolution and tool loading modules, that an abstract description of panels shouldn't really depend on. """
[docs] def __init__( self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view=None, save_integrated_tool_panel=True, ): super().__init__( config_filenames, tool_root_dir, app, view_sources, default_panel_view, save_integrated_tool_panel ) old_toolbox = getattr(app, "toolbox", None) if old_toolbox: self.dependency_manager = old_toolbox.dependency_manager else: self._init_dependency_manager()
@property def sa_session(self): """ Returns a SQLAlchemy session """ return self.app.model.context def _looks_like_a_tool(self, path): return looks_like_a_tool(path, enable_beta_formats=getattr(self.app.config, "enable_beta_tool_formats", False)) def _init_dependency_manager(self): use_tool_dependency_resolution = getattr(self.app, "use_tool_dependency_resolution", True) if not use_tool_dependency_resolution: self.dependency_manager = NullDependencyManager() return app_config_dict = self.app.config.config_dict conf_file = app_config_dict.get("dependency_resolvers_config_file") default_tool_dependency_dir = os.path.join( self.app.config.data_dir, self.app.config.schema.defaults["tool_dependency_dir"] ) self.dependency_manager = build_dependency_manager( app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir=default_tool_dependency_dir, )
[docs] def reload_dependency_manager(self): self._init_dependency_manager()
[docs] def load_builtin_converters(self): id = "builtin_converters" section = ToolSection({"name": "Built-in Converters", "id": id}) self._tool_panel[id] = section converters = self.app.datatypes_registry.datatype_converters for source, targets in converters.items(): for target, tool in targets.items(): tool.name = f"{source}-to-{target}" tool.description = "converter" tool.hidden = False section.elems.append_tool(tool)