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Source code for galaxy.webapps.galaxy.api.toolshed

import json
import logging
import re
from six.moves.urllib.parse import quote as urlquote
from six.moves.urllib.parse import unquote as urlunquote

from galaxy import util
from galaxy import web

from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController

from tool_shed.util import common_util
from tool_shed.util import repository_util
from tool_shed.util import tool_util

log = logging.getLogger(__name__)


[docs]class ToolShedController(BaseAPIController): """RESTful controller for interactions with tool sheds.""" def __get_repo_dict_by_id(self, id): tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app, id) if tool_shed_repository is None: log.debug("Unable to locate tool_shed_repository record for id %s." % (str(id))) return {} tool_shed_repository_dict = tool_shed_repository.as_dict(value_mapper=self.__get_value_mapper(tool_shed_repository)) tool_shed_repository_dict['url'] = web.url_for(controller='tool_shed_repositories', action='show', id=self.app.security.encode_id(tool_shed_repository.id)) tool_shed_repository_dict['repository_dependencies'] = self.__flatten_repository_dependency_list(tool_shed_repository) return tool_shed_repository_dict def __get_tool_dependencies(self, metadata, tool_dependencies=None): if tool_dependencies is None: tool_dependencies = [] for key, dependency_dict in metadata['tool_dependencies'].items(): if 'readme' in dependency_dict: del(dependency_dict['readme']) if dependency_dict not in tool_dependencies: tool_dependencies.append(dependency_dict) if metadata['has_repository_dependencies']: for dependency in metadata['repository_dependencies']: tool_dependencies = self.__get_tool_dependencies(dependency, tool_dependencies) return tool_dependencies def __flatten_repository_dependency_list(self, tool_shed_repository): ''' Return a recursive exclusive flattened list of all tool_shed_repository's dependencies. ''' dependencies = [] for dependency in tool_shed_repository.repository_dependencies: if len(dependency.repository_dependencies) > 0: sub_dependencies = self.__flatten_repository_dependency_list(dependency) for sub_dependency in sub_dependencies: if sub_dependency not in dependencies: dependencies.append(sub_dependency) if dependency not in dependencies: dependencies.append(dependency.as_dict(value_mapper=self.__get_value_mapper(tool_shed_repository))) return dependencies def __get_value_mapper(self, tool_shed_repository): value_mapper = {'id': self.app.security.encode_id(tool_shed_repository.id), 'error_message': tool_shed_repository.error_message or ''} return value_mapper def __get_tools(self, metadata, tools=None): if tools is None: tools = [] if metadata['includes_tools_for_display_in_tool_panel']: for key, tool_dict in metadata['tools']: tool_info = dict(clean=re.sub('[^a-zA-Z0-9]+', '_', tool_dict['name']).lower(), name=tool_dict['name'], version=tool_dict['version'], description=tool_dict['description']) if tool_info not in tools: tools.append(tool_info) if metadata['has_repository_dependencies']: for dependency in metadata['repository_dependencies']: tools = self.__get_tools(dependency, tools) return tools
[docs] @expose_api def index(self, trans, **kwd): """ GET /api/tool_shed Interact with this galaxy instance's toolshed registry. """ sheds = [] for name, url in trans.app.tool_shed_registry.tool_sheds.items(): # api_url = web.url_for( controller='api/tool_shed', # action='contents', # tool_shed_url=urlquote( url, '' ), # qualified=True ) sheds.append(dict(name=name, url=urlquote(url, ''))) return sheds
[docs] @expose_api @web.require_admin def status(self, trans, **kwd): """ GET /api/tool_shed_repositories/{id}/status Display a dictionary containing information about a specified repository's installation status and a list of its dependencies and the status of each. :param id: the repository's encoded id """ repository_ids = kwd.get('repositories', None) repositories = [] if repository_ids is not None: for repository_id in repository_ids.split('|'): tool_shed_repository_dict = self.__get_repo_dict_by_id(repository_id) repositories.append(tool_shed_repository_dict) return repositories else: return []
# return tool_shed_repository_dict
[docs] @expose_api @web.require_admin def tool_json(self, trans, **kwd): """ GET /api/tool_shed_repositories/shed_tool_json Get the tool form JSON for a tool in a toolshed 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 :param tool_shed_url: the URL of the toolshed to load from :param tool_shed_url: str """ tool_shed_url = kwd.get('tool_shed_url', None) tsr_id = kwd.get('tsr_id', None) guid = kwd.get('guid', None) changeset = kwd.get('changeset', None) if None in [tool_shed_url, tsr_id, guid, changeset]: message = 'Tool shed URL, changeset, repository ID, and tool GUID are all required parameters.' trans.response.status = 400 return {'status': 'error', 'message': message} response = json.loads(util.url_get(tool_shed_url, params=dict(tsr_id=tsr_id, guid=guid, changeset=changeset.split(':')[-1]), pathspec=['api', 'tools', 'json'])) return response
[docs] @expose_api def show(self, trans, **kwd): """ GET /api/tool_shed/contents Display a list of categories in the selected toolshed. :param tool_shed_url: the url of the toolshed to get categories from """ tool_shed_url = urlunquote(kwd.get('tool_shed_url', '')) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url) url = util.build_url(tool_shed_url, pathspec=['api', 'categories']) categories = [] for category in json.loads(util.url_get(url)): api_url = web.url_for(controller='api/tool_shed', action='category', tool_shed_url=urlquote(tool_shed_url), category_id=category['id'], qualified=True) category['url'] = api_url categories.append(category) return categories
[docs] @expose_api @web.require_admin def category(self, trans, **kwd): """ GET /api/tool_shed/category Display a list of repositories in the selected category. :param tool_shed_url: the url of the toolshed to get repositories from :param category_id: the category to get repositories from """ tool_shed_url = urlunquote(kwd.get('tool_shed_url', '')) category_id = kwd.get('category_id', '') params = dict(installable=True) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url) url = util.build_url(tool_shed_url, pathspec=['api', 'categories', category_id, 'repositories'], params=params) repositories = [] return_json = json.loads(util.url_get(url)) for repository in return_json['repositories']: api_url = web.url_for(controller='api/tool_shed', action='repository', tool_shed_url=urlquote(tool_shed_url), repository_id=repository['id'], qualified=True) repository['url'] = api_url repositories.append(repository) return_json['repositories'] = repositories return return_json
[docs] @expose_api def repository(self, trans, **kwd): """ GET /api/tool_shed/repository Get details about the specified repository from its shed. :param repository_id: the tool_shed_repository_id :param repository_id: str :param tool_shed_url: the URL of the toolshed whence to retrieve repository details :param tool_shed_url: str :param tool_ids: (optional) comma-separated list of tool IDs :param tool_ids: str """ tool_dependencies = dict() tools = dict() tool_shed_url = urlunquote(kwd.get('tool_shed_url', '')) log.debug(tool_shed_url) repository_id = kwd.get('repository_id', None) tool_ids = kwd.get('tool_ids', None) if tool_ids is not None: tool_ids = util.listify(tool_ids) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app) tool_panel_section_dict = {'name': tool_panel_section_select_field.name, 'id': tool_panel_section_select_field.field_id, 'sections': []} for name, id, _ in tool_panel_section_select_field.options: tool_panel_section_dict['sections'].append(dict(id=id, name=name)) repository_data = dict() if tool_ids is not None: if len(tool_shed_url) == 0: # By design, this list should always be from the same toolshed. If # this is ever not the case, this code will need to be updated. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_ids[0].split('/')[0]) found_repository = json.loads(util.url_get(tool_shed_url, params=dict(tool_ids=','.join(tool_ids)), pathspec=['api', 'repositories'])) fr_keys = found_repository.keys() repository_id = found_repository[fr_keys[0]]['repository_id'] repository_data['current_changeset'] = found_repository['current_changeset'] repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id])) del found_repository['current_changeset'] repository_data['tool_shed_url'] = tool_shed_url else: repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id])) repository_data['repository']['metadata'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id, 'metadata'])) repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).get_html().replace('\n', '') repository_data['panel_section_html'] = tool_panel_section_select_field.get_html(extra_attr={'style': 'width: 30em;'}).replace('\n', '') repository_data['panel_section_dict'] = tool_panel_section_dict for changeset, metadata in repository_data['repository']['metadata'].items(): if changeset not in tool_dependencies: tool_dependencies[changeset] = [] if metadata['includes_tools_for_display_in_tool_panel']: if changeset not in tools: tools[changeset] = [] for tool_dict in metadata['tools']: tool_info = dict(clean=re.sub('[^a-zA-Z0-9]+', '_', tool_dict['name']).lower(), guid=tool_dict['guid'], name=tool_dict['name'], version=tool_dict['version'], description=tool_dict['description']) if tool_info not in tools[changeset]: tools[changeset].append(tool_info) if metadata['has_repository_dependencies']: for repository_dependency in metadata['repository_dependencies']: tools[changeset] = self.__get_tools(repository_dependency, tools[changeset]) repository_data['tools'] = tools for key, dependency_dict in metadata['tool_dependencies'].items(): if 'readme' in dependency_dict: del(dependency_dict['readme']) if dependency_dict not in tool_dependencies[changeset]: tool_dependencies[changeset].append(dependency_dict) if metadata['has_repository_dependencies']: for repository_dependency in metadata['repository_dependencies']: tool_dependencies[changeset] = self.__get_tool_dependencies(repository_dependency, tool_dependencies[changeset]) repository_data['tool_dependencies'] = tool_dependencies return repository_data
[docs] @expose_api @web.require_admin def search(self, trans, **kwd): """ GET /api/tool_shed/search Search for a specific repository in the toolshed. :param q: the query string to search for :param q: str :param tool_shed_url: the URL of the toolshed to search :param tool_shed_url: str """ tool_shed_url = kwd.get('tool_shed_url', None) q = kwd.get('term', None) if None in [q, tool_shed_url]: return {} response = json.loads(util.url_get(tool_shed_url, params=dict(q=q), pathspec=['api', 'repositories'])) return response