Source code for galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager

import logging
import os

from sqlalchemy import false

from galaxy import util
from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
from galaxy.tool_shed.metadata.metadata_generator import MetadataGenerator
from galaxy.tool_shed.util.repository_util import (
    get_installed_tool_shed_repository,
    get_repository_owner,
)
from galaxy.tool_shed.util.tool_util import generate_message_for_invalid_tools
from galaxy.util import inflector
from galaxy.util.tool_shed import (
    common_util,
    xml_util,
)
from galaxy.web.form_builder import SelectField

log = logging.getLogger(__name__)


[docs]class InstalledRepositoryMetadataManager(MetadataGenerator):
[docs]    def __init__(
        self,
        app,
        tpm=None,
        repository=None,
        changeset_revision=None,
        repository_clone_url=None,
        shed_config_dict=None,
        relative_install_dir=None,
        repository_files_dir=None,
        resetting_all_metadata_on_repository=False,
        updating_installed_repository=False,
        persist=False,
        metadata_dict=None,
    ):
        super().__init__(
            app,
            repository,
            changeset_revision,
            repository_clone_url,
            shed_config_dict,
            relative_install_dir,
            repository_files_dir,
            resetting_all_metadata_on_repository,
            updating_installed_repository,
            persist,
            metadata_dict=metadata_dict,
            user=None,
        )
        if tpm is None:
            self.tpm = tool_panel_manager.ToolPanelManager(self.app)
        else:
            self.tpm = tpm

[docs]    def build_repository_ids_select_field(self, name="repository_ids", multiple=True, display="checkboxes"):
        """Generate the current list of repositories for resetting metadata."""
        repositories_select_field = SelectField(name=name, multiple=multiple, display=display)
        query = self.get_query_for_setting_metadata_on_repositories(order=True)
        for repository in query:
            owner = str(repository.owner)
            option_label = f"{str(repository.name)} ({owner})"
            option_value = f"{self.app.security.encode_id(repository.id)}"
            repositories_select_field.add_option(option_label, option_value)
        return repositories_select_field

[docs]    def get_query_for_setting_metadata_on_repositories(self, order=True):
        """
        Return a query containing repositories for resetting metadata.  The order parameter
        is used for displaying the list of repositories ordered alphabetically for display on
        a page.  When called from the Galaxy API, order is False.
        """
        if order:
            return (
                self.app.install_model.context.query(self.app.install_model.ToolShedRepository)
                .filter(self.app.install_model.ToolShedRepository.table.c.uninstalled == false())
                .order_by(
                    self.app.install_model.ToolShedRepository.table.c.name,
                    self.app.install_model.ToolShedRepository.table.c.owner,
                )
            )
        else:
            return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).filter(
                self.app.install_model.ToolShedRepository.table.c.uninstalled == false()
            )

[docs]    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

[docs]    def reset_all_metadata_on_installed_repository(self):
        """Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
        if self.relative_install_dir:
            original_metadata_dict = self.repository.metadata_
            self.generate_metadata_for_changeset_revision()
            if self.metadata_dict != original_metadata_dict:
                self.repository.metadata_ = self.metadata_dict
                self.update_in_shed_tool_config()
                self.app.install_model.context.add(self.repository)
                self.app.install_model.context.flush()
                log.debug(f"Metadata has been reset on repository {self.repository.name}.")
            else:
                log.debug(f"Metadata did not need to be reset on repository {self.repository.name}.")
        else:
            log.debug(f"Error locating installation directory for repository {self.repository.name}.")

[docs]    def reset_metadata_on_selected_repositories(self, user, **kwd):
        """
        Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
        This method is called from both Galaxy and the Tool Shed.
        """
        repository_ids = util.listify(kwd.get("repository_ids", None))
        message = ""
        status = "done"
        if repository_ids:
            successful_count = 0
            unsuccessful_count = 0
            for repository_id in repository_ids:
                try:
                    repository = get_installed_tool_shed_repository(self.app, repository_id)
                    self.set_repository(repository)
                    self.reset_all_metadata_on_installed_repository()
                    if self.invalid_file_tups:
                        message = generate_message_for_invalid_tools(
                            self.app, self.invalid_file_tups, repository, None, as_html=False
                        )
                        log.debug(message)
                        unsuccessful_count += 1
                    else:
                        log.debug(
                            "Successfully reset metadata on repository %s owned by %s"
                            % (str(repository.name), str(repository.owner))
                        )
                        successful_count += 1
                except Exception:
                    log.exception("Error attempting to reset metadata on repository %s", str(repository.name))
                    unsuccessful_count += 1
            message = "Successfully reset metadata on %d %s.  " % (
                successful_count,
                inflector.cond_plural(successful_count, "repository"),
            )
            if unsuccessful_count:
                message += "Error setting metadata on %d %s - see the galaxy log for details.  " % (
                    unsuccessful_count,
                    inflector.cond_plural(unsuccessful_count, "repository"),
                )
        else:
            message = "Select at least one repository to on which to reset all metadata."
            status = "error"
        return message, status

[docs]    def set_repository(self, repository):
        super().set_repository(repository)
        self.repository_clone_url = common_util.generate_clone_url_for_installed_repository(self.app, repository)

[docs]    def tool_shed_from_repository_clone_url(self):
        """Given a repository clone URL, return the tool shed that contains the repository."""
        cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url(self.repository_clone_url)
        return (
            common_util.remove_protocol_and_user_from_clone_url(cleaned_repository_clone_url)
            .split("/repos/")[0]
            .rstrip("/")
        )

[docs]    def update_in_shed_tool_config(self):
        """
        A tool shed repository is being updated 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.
        """
        shed_conf_dict = self.shed_config_dict or self.repository.get_shed_config_dict(self.app)
        shed_tool_conf = shed_conf_dict["config_filename"]
        tool_path = shed_conf_dict["tool_path"]
        self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries(self.repository)
        repository_tools_tups = self.get_repository_tools_tups()
        clone_url = common_util.generate_clone_url_for_installed_repository(self.app, self.repository)
        tool_shed = self.tool_shed_from_repository_clone_url()
        owner = self.repository.owner
        if not owner:
            cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url(clone_url)
            owner = get_repository_owner(cleaned_repository_clone_url)
        guid_to_tool_elem_dict = {}
        for tool_config_filename, guid, tool in repository_tools_tups:
            guid_to_tool_elem_dict[guid] = self.tpm.generate_tool_elem(
                tool_shed,
                self.repository.name,
                self.repository.changeset_revision,
                self.repository.owner or "",
                tool_config_filename,
                tool,
                None,
            )
        config_elems = []
        tree, error_message = xml_util.parse_xml(shed_tool_conf)
        if tree:
            root = tree.getroot()
            for elem in root:
                if elem.tag == "section":
                    for i, tool_elem in enumerate(elem):
                        guid = tool_elem.attrib.get("guid")
                        if guid in guid_to_tool_elem_dict:
                            elem[i] = guid_to_tool_elem_dict[guid]
                elif elem.tag == "tool":
                    guid = elem.attrib.get("guid")
                    if guid in guid_to_tool_elem_dict:
                        elem = guid_to_tool_elem_dict[guid]
                config_elems.append(elem)
            self.tpm.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path)