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Source code for tool_shed.webapp.api.tools

import json
import logging
from collections import namedtuple

from galaxy import (
from galaxy.web import (
from galaxy.webapps.base.controller import BaseAPIController
from tool_shed.util.shed_index import build_index
from tool_shed.webapp.search.tool_search import ToolSearch

log = logging.getLogger(__name__)

[docs]class ToolsController(BaseAPIController): """RESTful controller for interactions with tools in the Tool Shed."""
[docs] @expose_api @require_admin def build_search_index(self, trans, **kwd): """ PUT /api/tools/build_search_index Not part of the stable API, just something to simplify bootstrapping tool sheds, scripting, testing, etc... """ repos_indexed, tools_indexed = build_index( trans.app.config.whoosh_index_dir, trans.app.config.file_path, trans.app.config.hgweb_config_dir, trans.app.config.database_connection, ) return { "repositories_indexed": repos_indexed, "tools_indexed": tools_indexed, }
[docs] @expose_api_raw_anonymous_and_sessionless def index(self, trans, **kwd): """ GET /api/tools Displays a collection of tools with optional criteria. :param q: (optional)if present search on the given query will be performed :type q: str :param page: (optional)requested page of the search :type page: int :param page_size: (optional)requested page_size of the search :type page_size: int :param jsonp: (optional)flag whether to use jsonp format response, defaults to False :type jsonp: bool :param callback: (optional)name of the function to wrap callback in used only when jsonp is true, defaults to 'callback' :type callback: str :returns dict: object containing list of results and metadata Examples: GET http://localhost:9009/api/tools GET http://localhost:9009/api/tools?q=fastq """ q = kwd.get("q", "") if not q: raise exceptions.NotImplemented( 'Listing of all the tools is not implemented. Provide parameter "q" to search instead.' ) else: page = kwd.get("page", 1) page_size = kwd.get("page_size", 10) try: page = int(page) page_size = int(page_size) except ValueError: raise exceptions.RequestParameterInvalidException('The "page" and "page_size" have to be integers.') return_jsonp = util.asbool(kwd.get("jsonp", False)) callback = kwd.get("callback", "callback") search_results = self._search(trans, q, page, page_size) if return_jsonp: response = str(f"{callback}({json.dumps(search_results)});") else: response = json.dumps(search_results) return response
def _search(self, trans, q, page=1, page_size=10): """ Perform the search over TS tools index. Note that search works over the Whoosh index which you have to pre-create with scripts/tool_shed/build_ts_whoosh_index.sh manually. Also TS config option toolshed_search_on has to be True and whoosh_index_dir has to be specified. """ conf = self.app.config if not conf.toolshed_search_on: raise exceptions.ConfigDoesNotAllowException( "Searching the TS through the API is turned off for this instance." ) if not conf.whoosh_index_dir: raise exceptions.ConfigDoesNotAllowException( "There is no directory for the search index specified. Please contact the administrator." ) search_term = q.strip() if len(search_term) < 1: raise exceptions.RequestParameterInvalidException("The search term has to be at least one character long.") tool_search = ToolSearch() Boosts = namedtuple( "Boosts", ["tool_name_boost", "tool_description_boost", "tool_help_boost", "tool_repo_owner_username_boost"] ) boosts = Boosts( float(conf.get("tool_name_boost", 1.2)), float(conf.get("tool_description_boost", 0.6)), float(conf.get("tool_help_boost", 0.4)), float(conf.get("tool_repo_owner_username_boost", 0.3)), ) results = tool_search.search(trans, search_term, page, page_size, boosts) results["hostname"] = web.url_for("/", qualified=True) return results