mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
189 lines
8.4 KiB
Python
189 lines
8.4 KiB
Python
import json
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import logging
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from collections import namedtuple
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from galaxy import (
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exceptions,
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util,
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web
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)
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from galaxy.tools.parameters import params_to_strings
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from galaxy.tools.repositories import ValidationContext
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from galaxy.web import expose_api_raw_anonymous_and_sessionless
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from galaxy.webapps.base.controller import BaseAPIController
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from tool_shed.dependencies.repository import relation_builder
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from tool_shed.tools import tool_validator
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from tool_shed.util import (
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common_util,
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metadata_util,
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repository_util,
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shed_util_common as suc
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)
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from tool_shed.utility_containers import ToolShedUtilityContainerManager
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from tool_shed.webapp.search.tool_search import ToolSearch
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log = logging.getLogger(__name__)
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class ToolsController(BaseAPIController):
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"""RESTful controller for interactions with tools in the Tool Shed."""
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@expose_api_raw_anonymous_and_sessionless
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def index(self, trans, **kwd):
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"""
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GET /api/tools
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Displays a collection of tools with optional criteria.
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:param q: (optional)if present search on the given query will be performed
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:type q: str
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:param page: (optional)requested page of the search
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:type page: int
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:param page_size: (optional)requested page_size of the search
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:type page_size: int
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:param jsonp: (optional)flag whether to use jsonp format response, defaults to False
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:type jsonp: bool
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:param callback: (optional)name of the function to wrap callback in
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used only when jsonp is true, defaults to 'callback'
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:type callback: str
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:returns dict: object containing list of results and metadata
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Examples:
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GET http://localhost:9009/api/tools
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GET http://localhost:9009/api/tools?q=fastq
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"""
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q = kwd.get('q', '')
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if not q:
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raise exceptions.NotImplemented('Listing of all the tools is not implemented. Provide parameter "q" to search instead.')
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else:
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page = kwd.get('page', 1)
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page_size = kwd.get('page_size', 10)
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try:
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page = int(page)
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page_size = int(page_size)
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except ValueError:
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raise exceptions.RequestParameterInvalidException('The "page" and "page_size" have to be integers.')
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return_jsonp = util.asbool(kwd.get('jsonp', False))
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callback = kwd.get('callback', 'callback')
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search_results = self._search(trans, q, page, page_size)
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if return_jsonp:
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response = str('{}({});'.format(callback, json.dumps(search_results)))
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else:
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response = json.dumps(search_results)
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return response
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def _search(self, trans, q, page=1, page_size=10):
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"""
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Perform the search over TS tools index.
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Note that search works over the Whoosh index which you have
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to pre-create with scripts/tool_shed/build_ts_whoosh_index.sh manually.
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Also TS config option toolshed_search_on has to be True and
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whoosh_index_dir has to be specified.
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"""
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conf = self.app.config
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if not conf.toolshed_search_on:
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raise exceptions.ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
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if not conf.whoosh_index_dir:
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raise exceptions.ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
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search_term = q.strip()
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if len(search_term) < 1:
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raise exceptions.RequestParameterInvalidException('The search term has to be at least one character long.')
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tool_search = ToolSearch()
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Boosts = namedtuple('Boosts', ['tool_name_boost',
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'tool_description_boost',
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'tool_help_boost',
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'tool_repo_owner_username_boost'])
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boosts = Boosts(float(conf.get('tool_name_boost', 1.2)),
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float(conf.get('tool_description_boost', 0.6)),
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float(conf.get('tool_help_boost', 0.4)),
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float(conf.get('tool_repo_owner_username_boost', 0.3)))
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results = tool_search.search(trans,
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search_term,
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page,
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page_size,
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boosts)
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results['hostname'] = web.url_for('/', qualified=True)
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return results
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@expose_api_raw_anonymous_and_sessionless
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def json(self, trans, **kwd):
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"""
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GET /api/tools/json
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Get the tool form JSON for a tool in a repository.
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:param guid: the GUID of the tool
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:param guid: str
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:param tsr_id: the ID of the repository
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:param tsr_id: str
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:param changeset: the changeset at which to load the tool json
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:param changeset: str
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"""
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guid = kwd.get('guid', None)
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tsr_id = kwd.get('tsr_id', None)
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changeset = kwd.get('changeset', None)
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if None in [changeset, tsr_id, guid]:
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message = 'Changeset, repository ID, and tool GUID are all required parameters.'
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trans.response.status = 400
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return {'status': 'error', 'message': message}
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tsucm = ToolShedUtilityContainerManager(trans.app)
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repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
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repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(repository.user, repository)
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repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, tsr_id, changeset)
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toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
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rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
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repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
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containers_dict = tsucm.build_repository_containers(repository,
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changeset,
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repository_dependencies,
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repository_metadata)
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found_tool = None
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for folder in containers_dict['valid_tools'].folders:
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if hasattr(folder, 'valid_tools'):
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for tool in folder.valid_tools:
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tool.id = tool.tool_id
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tool_guid = suc.generate_tool_guid(repository_clone_url, tool)
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if tool_guid == guid:
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found_tool = tool
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break
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if found_tool is None:
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message = f'Unable to find tool with guid {guid} in repository {repository.name}.'
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trans.response.status = 404
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return {'status': 'error', 'message': message}
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with ValidationContext.from_app(trans.app) as validation_context:
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tv = tool_validator.ToolValidator(validation_context)
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repository, tool, valid, message = tv.load_tool_from_changeset_revision(tsr_id,
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changeset,
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found_tool.tool_config)
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if message or not valid:
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status = 'error'
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return dict(message=message, status=status)
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tool_help = ''
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if tool.help:
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tool_help = tool.help.render(static_path=web.url_for('/static'), host_url=web.url_for('/', qualified=True))
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tool_help = util.unicodify(tool_help, 'utf-8')
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tool_dict = tool.to_dict(trans)
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tool_dict['inputs'] = {}
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tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
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tool_dict.update({
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'help' : tool_help,
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'citations' : bool(tool.citations),
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'requirements' : [{'name' : r.name, 'version' : r.version} for r in tool.requirements],
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'state_inputs' : params_to_strings(tool.inputs, {}, trans.app),
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'display' : tool.display_interface,
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'action' : web.url_for(tool.action),
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'method' : tool.method,
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'enctype' : tool.enctype
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})
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return json.dumps(tool_dict)
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