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Source code for galaxy.webapps.tool_shed.api.tools

import json
import logging
from collections import namedtuple

from galaxy import (
from galaxy.exceptions import (
from galaxy.tools.parameters import params_to_strings
from galaxy.tools.repositories import ValidationContext
from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless
from galaxy.web.base.controller import BaseAPIController
from galaxy.webapps.tool_shed.search.tool_search import ToolSearch
from tool_shed.dependencies.repository import relation_builder
from tool_shed.tools import tool_validator
from tool_shed.util import (
    shed_util_common as suc
from tool_shed.utility_containers import ToolShedUtilityContainerManager

log = logging.getLogger(__name__)

[docs]class ToolsController(BaseAPIController): """RESTful controller for interactions with tools in the Tool Shed."""
[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 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 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('%s(%s);' % (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 ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.') if not conf.whoosh_index_dir: raise ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.') search_term = q.strip() if len(search_term) < 3: raise RequestParameterInvalidException('The search term has to be at least 3 characters 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
[docs] @expose_api_raw_anonymous_and_sessionless def json(self, trans, **kwd): """ GET /api/tools/json Get the tool form JSON for a tool in a repository. :param guid: the GUID of the tool :param guid: str :param tsr_id: the ID of the repository :param tsr_id: str :param changeset: the changeset at which to load the tool json :param changeset: str """ guid = kwd.get('guid', None) tsr_id = kwd.get('tsr_id', None) changeset = kwd.get('changeset', None) if None in [changeset, tsr_id, guid]: message = 'Changeset, repository ID, and tool GUID are all required parameters.' trans.response.status = 400 return {'status': 'error', 'message': message} tsucm = ToolShedUtilityContainerManager(trans.app) repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(repository.user, repository) repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, tsr_id, changeset) toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/') rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url) repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() containers_dict = tsucm.build_repository_containers(repository, changeset, repository_dependencies, repository_metadata) found_tool = None for folder in containers_dict['valid_tools'].folders: if hasattr(folder, 'valid_tools'): for tool in folder.valid_tools: tool.id = tool.tool_id tool_guid = suc.generate_tool_guid(repository_clone_url, tool) if tool_guid == guid: found_tool = tool break if found_tool is None: message = 'Unable to find tool with guid %s in repository %s.' % (guid, repository.name) trans.response.status = 404 return {'status': 'error', 'message': message} with ValidationContext.from_app(trans.app) as validation_context: tv = tool_validator.ToolValidator(validation_context) repository, tool, message = tv.load_tool_from_changeset_revision(tsr_id, changeset, found_tool.tool_config) if message: status = 'error' return dict(message=message, status=status) tool_help = '' if tool.help: tool_help = tool.help.render(static_path=web.url_for('/static'), host_url=web.url_for('/', qualified=True)) tool_help = util.unicodify(tool_help, 'utf-8') tool_dict = tool.to_dict(trans) tool_dict['inputs'] = {} tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs']) tool_dict.update({ 'help' : tool_help, 'citations' : bool(tool.citations), 'biostar_url' : trans.app.config.biostar_url, 'requirements' : [{'name' : r.name, 'version' : r.version} for r in tool.requirements], 'state_inputs' : params_to_strings(tool.inputs, {}, trans.app), 'display' : tool.display_interface, 'action' : web.url_for(tool.action), 'method' : tool.method, 'enctype' : tool.enctype }) return json.dumps(tool_dict)