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

import logging
import os
from json import dumps, loads

from galaxy import exceptions, managers, util, web
from galaxy.managers.collections_util import dictify_dataset_collection_instance
from galaxy.tools import global_tool_errors
from galaxy.web import (
from galaxy.webapps.base.controller import BaseAPIController
from galaxy.webapps.base.controller import UsesVisualizationMixin
from ._fetch_util import validate_and_normalize_targets

log = logging.getLogger(__name__)

# Do not allow these tools to be called directly - they (it) enforces extra security and
# provides access via a different API endpoint.
# Tool search bypasses the fulltext for the following list of terms
SEARCH_RESERVED_TERMS_FAVORITES = ['#favs', '#favorites', '#favourites']

[docs]class ToolsController(BaseAPIController, UsesVisualizationMixin): """ RESTful controller for interactions with tools. """
[docs] def __init__(self, app): super().__init__(app) self.history_manager = managers.histories.HistoryManager(app) self.hda_manager = managers.hdas.HDAManager(app)
[docs] @expose_api_anonymous_and_sessionless def index(self, trans, **kwds): """ GET /api/tools: returns a list of tools defined by parameters:: parameters: in_panel - if true, tools are returned in panel structure, including sections and labels trackster - if true, only tools that are compatible with Trackster are returned q - if present search on the given query will be performed tool_id - if present the given tool_id will be searched for all installed versions """ # Read params. in_panel = util.string_as_bool(kwds.get('in_panel', 'True')) trackster = util.string_as_bool(kwds.get('trackster', 'False')) q = kwds.get('q', '') tool_id = kwds.get('tool_id', '') tool_help = util.string_as_bool(kwds.get('tool_help', 'False')) # Find whether to search. if q: if trans.user and q in SEARCH_RESERVED_TERMS_FAVORITES: if 'favorites' in trans.user.preferences: favorites = loads(trans.user.preferences['favorites']) hits = favorites['tools'] else: hits = None else: hits = self._search(q) results = [] if hits: for hit in hits: try: tool = self._get_tool(hit, user=trans.user) if tool: results.append(tool.id) except exceptions.AuthenticationFailed: pass except exceptions.ObjectNotFound: pass return results # Find whether to detect. if tool_id: detected_versions = self._detect(trans, tool_id) return detected_versions # Return everything. try: return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help) except Exception: raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
[docs] @expose_api_anonymous_and_sessionless def show(self, trans, id, **kwd): """ GET /api/tools/{tool_id} Returns tool information parameters: io_details - if true, parameters and inputs are returned link_details - if true, hyperlink to the tool is returned tool_version - if provided return this tool version """ io_details = util.string_as_bool(kwd.get('io_details', False)) link_details = util.string_as_bool(kwd.get('link_details', False)) tool_version = kwd.get('tool_version') tool = self._get_tool(id, user=trans.user, tool_version=tool_version) return tool.to_dict(trans, io_details=io_details, link_details=link_details)
[docs] @expose_api_anonymous def build(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/build Returns a tool model including dynamic parameters and updated values, repeats block etc. """ if 'payload' in kwd: kwd = kwd.get('payload') tool_version = kwd.get('tool_version', None) tool = self._get_tool(id, tool_version=tool_version, user=trans.user) return tool.to_json(trans, kwd.get('inputs', kwd))
[docs] @web.require_admin @expose_api def test_data_path(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version} """ # TODO: eliminate copy and paste with above code. if 'payload' in kwd: kwd = kwd.get('payload') tool_version = kwd.get('tool_version', None) tool = self._get_tool(id, tool_version=tool_version, user=trans.user) path = tool.test_data_path(kwd.get("filename")) if path: return path else: raise exceptions.ObjectNotFound("Specified test data path not found.")
[docs] @expose_api_raw_anonymous_and_sessionless def test_data_download(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename} """ tool_version = kwd.get('tool_version', None) tool = self._get_tool(id, tool_version=tool_version, user=trans.user) filename = kwd.get("filename") if filename is None: raise exceptions.ObjectNotFound("Test data filename not specified.") path = tool.test_data_path(filename) if path: if os.path.isfile(path): trans.response.headers["Content-Disposition"] = 'attachment; filename="%s"' % filename return open(path, mode='rb') elif os.path.isdir(path): return util.streamball.stream_archive(trans=trans, path=path, upstream_gzip=self.app.config.upstream_gzip) raise exceptions.ObjectNotFound("Specified test data path not found.")
[docs] @expose_api_anonymous_and_sessionless def tests_summary(self, trans, **kwd): """ GET /api/tools/tests_summary Fetch summary information for each tool and version combination with tool tests defined. This summary information currently includes tool name and a count of the tests. Fetch complete test data for each tool with /api/tools/{tool_id}/test_data?tool_version=<tool_version> """ test_counts_by_tool = {} for id, tool in self.app.toolbox.tools(): if not tool.is_datatype_converter: tests = tool.tests if tests: if tool.id not in test_counts_by_tool: test_counts_by_tool[tool.id] = {} available_versions = test_counts_by_tool[tool.id] available_versions[tool.version] = { "tool_name": tool.name, "count": len(tests), } return test_counts_by_tool
[docs] @expose_api_anonymous_and_sessionless def test_data(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/test_data?tool_version={tool_version} This API endpoint is unstable and experimental. In particular the format of the response has not been entirely nailed down (it exposes too many Galaxy internals/Pythonisms in a rough way). If this endpoint is being used from outside of scripts shipped with Galaxy let us know and please be prepared for the response from this API to change its format in some ways. """ # TODO: eliminate copy and paste with above code. if 'payload' in kwd: kwd = kwd.get('payload') tool_version = kwd.get('tool_version', None) tool = self._get_tool(id, tool_version=tool_version, user=trans.user) return [t.to_dict() for t in tool.tests]
[docs] @web.require_admin @expose_api def reload(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/reload Reload specified tool. """ trans.app.queue_worker.send_control_task('reload_tool', noop_self=True, kwargs={'tool_id': id}) message, status = trans.app.toolbox.reload_tool_by_id(id) if status == 'error': raise exceptions.MessageException(message) return {'message': message}
[docs] @web.require_admin @expose_api def all_requirements(self, trans, **kwds): """ GET /api/tools/all_requirements Return list of unique requirements for all tools. """ return trans.app.toolbox.all_requirements
[docs] @web.require_admin @expose_api def requirements(self, trans, id, **kwds): """ GET /api/tools/{tool_id}/requirements Return the resolver status for a specific tool id. [{"status": "installed", "name": "hisat2", "versionless": false, "resolver_type": "conda", "version": "2.0.3", "type": "package"}] """ tool = self._get_tool(id, user=trans.user) return tool.tool_requirements_status
[docs] @web.require_admin @expose_api def install_dependencies(self, trans, id, **kwds): """ POST /api/tools/{tool_id}/dependencies This endpoint is also available through POST /api/tools/{tool_id}/install_dependencies, but will be deprecated in the future. Attempts to install requirements via the dependency resolver parameters: index: index of dependency resolver to use when installing dependency. Defaults to using the highest ranking resolver resolver_type: Use the dependency resolver of this resolver_type to install dependency. build_dependency_cache: If true, attempts to cache dependencies for this tool force_rebuild: If true and cache dir exists, attempts to delete cache dir """ tool = self._get_tool(id, user=trans.user) tool._view.install_dependencies(tool.requirements, **kwds) if kwds.get('build_dependency_cache'): tool.build_dependency_cache(**kwds) # TODO: rework resolver install system to log and report what has been done. # _view.install_dependencies should return a dict with stdout, stderr and success status return tool.tool_requirements_status
[docs] @web.require_admin @expose_api def uninstall_dependencies(self, trans, id, **kwds): """ DELETE /api/tools/{tool_id}/dependencies Attempts to uninstall requirements via the dependency resolver parameters: index: index of dependency resolver to use when installing dependency. Defaults to using the highest ranking resolver resolver_type: Use the dependency resolver of this resolver_type to install dependency """ tool = self._get_tool(id, user=trans.user) tool._view.uninstall_dependencies(requirements=tool.requirements, **kwds) # TODO: rework resolver install system to log and report what has been done. return tool.tool_requirements_status
[docs] @web.require_admin @expose_api def build_dependency_cache(self, trans, id, **kwds): """ POST /api/tools/{tool_id}/build_dependency_cache Attempts to cache installed dependencies. parameters: force_rebuild: If true and chache dir exists, attempts to delete cache dir """ tool = self._get_tool(id) tool.build_dependency_cache(**kwds) # TODO: Should also have a more meaningful return. return tool.tool_requirements_status
[docs] @web.require_admin @expose_api def diagnostics(self, trans, id, **kwd): """ GET /api/tools/{tool_id}/diagnostics Return diagnostic information to help debug panel and dependency related problems. """ # TODO: Move this into tool. def to_dict(x): return x.to_dict() tool = self._get_tool(id, user=trans.user) if hasattr(tool, 'lineage'): lineage_dict = tool.lineage.to_dict() else: lineage_dict = None tool_shed_dependencies = tool.installed_tool_dependencies if tool_shed_dependencies: tool_shed_dependencies_dict = list(map(to_dict, tool_shed_dependencies)) else: tool_shed_dependencies_dict = None return { "tool_id": tool.id, "tool_version": tool.version, "dependency_shell_commands": tool.build_dependency_shell_commands(), "lineage": lineage_dict, "requirements": list(map(to_dict, tool.requirements)), "installed_tool_shed_dependencies": tool_shed_dependencies_dict, "tool_dir": tool.tool_dir, "tool_shed": tool.tool_shed, "repository_name": tool.repository_name, "repository_owner": tool.repository_owner, "installed_changeset_revision": None, "guid": tool.guid, }
def _detect(self, trans, tool_id): """ Detect whether the tool with the given id is installed. :param tool_id: exact id of the tool :type tool_id: str :return: list with available versions "return type: list """ tools = self.app.toolbox.get_tool(tool_id, get_all_versions=True) detected_versions = [] if tools: for tool in tools: if tool and tool.allow_user_access(trans.user): detected_versions.append(tool.version) return detected_versions def _search(self, q): """ Perform the search on the given query. Boosts and numer of results are configurable in galaxy.ini file. :param q: the query to search with :type q: str :return: Dictionary containing the tools' ids of the best hits. :return type: dict """ tool_name_boost = self.app.config.get('tool_name_boost', 9) tool_section_boost = self.app.config.get('tool_section_boost', 3) tool_description_boost = self.app.config.get('tool_description_boost', 2) tool_label_boost = self.app.config.get('tool_label_boost', 1) tool_stub_boost = self.app.config.get('tool_stub_boost', 5) tool_help_boost = self.app.config.get('tool_help_boost', 0.5) tool_search_limit = self.app.config.get('tool_search_limit', 20) tool_enable_ngram_search = self.app.config.get('tool_enable_ngram_search', False) tool_ngram_minsize = self.app.config.get('tool_ngram_minsize', 3) tool_ngram_maxsize = self.app.config.get('tool_ngram_maxsize', 4) results = self.app.toolbox_search.search(q=q, tool_name_boost=tool_name_boost, tool_section_boost=tool_section_boost, tool_description_boost=tool_description_boost, tool_label_boost=tool_label_boost, tool_stub_boost=tool_stub_boost, tool_help_boost=tool_help_boost, tool_search_limit=tool_search_limit, tool_enable_ngram_search=tool_enable_ngram_search, tool_ngram_minsize=tool_ngram_minsize, tool_ngram_maxsize=tool_ngram_maxsize) return results
[docs] @expose_api_anonymous_and_sessionless def citations(self, trans, id, **kwds): tool = self._get_tool(id, user=trans.user) rval = [] for citation in tool.citations: rval.append(citation.to_dict('bibtex')) return rval
[docs] @expose_api_anonymous_and_sessionless def xrefs(self, trans, id, **kwds): tool = self._get_tool(id, user=trans.user) return tool.xrefs
[docs] @web.require_admin @web.legacy_expose_api_raw def download(self, trans, id, **kwds): tool_tarball = trans.app.toolbox.package_tool(trans, id) trans.response.set_content_type('application/x-gzip') download_file = open(tool_tarball, "rb") trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.tgz"' % (id) return download_file
[docs] @expose_api_anonymous def fetch(self, trans, payload, **kwd): """Adapt clean API to tool-constrained API. """ request_version = '1' if "history_id" not in payload: raise exceptions.RequestParameterMissingException("history_id must be specified") history_id = payload.pop("history_id") clean_payload = {} files_payload = {} for key, value in payload.items(): if key == "key": continue if key.startswith('files_') or key.startswith('__files_'): files_payload[key] = value continue clean_payload[key] = value validate_and_normalize_targets(trans, clean_payload) clean_payload["check_content"] = trans.app.config.check_upload_content request = dumps(clean_payload) create_payload = { 'tool_id': "__DATA_FETCH__", 'history_id': history_id, 'inputs': { 'request_version': request_version, 'request_json': request, 'file_count': str(len(files_payload)) }, } create_payload.update(files_payload) return self._create(trans, create_payload, **kwd)
[docs] @web.require_admin @expose_api def error_stack(self, trans, **kwd): """ GET /api/tools/error_stack Returns global tool error stack """ return global_tool_errors.error_stack
[docs] @expose_api_anonymous def create(self, trans, payload, **kwd): """ POST /api/tools Execute tool with a given parameter payload """ tool_id = payload.get("tool_id") tool_uuid = payload.get("tool_uuid") if tool_id in PROTECTED_TOOLS: raise exceptions.RequestParameterInvalidException("Cannot execute tool [%s] directly, must use alternative endpoint." % tool_id) if tool_id is None and tool_uuid is None: raise exceptions.RequestParameterInvalidException("Must specify a valid tool_id to use this endpoint.") return self._create(trans, payload, **kwd)
def _create(self, trans, payload, **kwd): action = payload.get('action', None) if action == 'rerun': raise Exception("'rerun' action has been deprecated") # Get tool. tool_version = payload.get('tool_version', None) tool_id = payload.get('tool_id', None) tool_uuid = payload.get('tool_uuid', None) get_kwds = dict( tool_id=tool_id, tool_uuid=tool_uuid, tool_version=tool_version, ) if tool_id is None and tool_uuid is None: raise exceptions.RequestParameterMissingException("Must specify either a tool_id or a tool_uuid.") tool = trans.app.toolbox.get_tool(**get_kwds) if not tool or not tool.allow_user_access(trans.user): raise exceptions.MessageException('Tool not found or not accessible.') if trans.app.config.user_activation_on: if not trans.user: log.warning("Anonymous user attempts to execute tool, but account activation is turned on.") elif not trans.user.active: log.warning("User \"%s\" attempts to execute tool, but account activation is turned on and user account is not active." % trans.user.email) # Set running history from payload parameters. # History not set correctly as part of this API call for # dataset upload. history_id = payload.get('history_id', None) if history_id: decoded_id = self.decode_id(history_id) target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history) else: target_history = None # Set up inputs. inputs = payload.get('inputs', {}) if not isinstance(inputs, dict): raise exceptions.RequestParameterInvalidException("inputs invalid %s" % inputs) # Find files coming in as multipart file data and add to inputs. for k, v in payload.items(): if k.startswith('files_') or k.startswith('__files_'): inputs[k] = v # for inputs that are coming from the Library, copy them into the history self._patch_library_inputs(trans, inputs, target_history) # TODO: encode data ids and decode ids. # TODO: handle dbkeys params = util.Params(inputs, sanitize=False) incoming = params.__dict__ # use_cached_job can be passed in via the top-level payload or among the tool inputs. # I think it should be a top-level parameter, but because the selector is implemented # as a regular tool parameter we accept both. use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false')) vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job) # TODO: check for errors and ensure that output dataset(s) are available. output_datasets = vars.get('out_data', []) rval = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []} rval['produces_entry_points'] = tool.produces_entry_points job_errors = vars.get('job_errors', []) if job_errors: # If we are here - some jobs were successfully executed but some failed. rval['errors'] = job_errors outputs = rval['outputs'] # TODO:?? poss. only return ids? for output_name, output in output_datasets: output_dict = output.to_dict() # add the output name back into the output data structure # so it's possible to figure out which newly created elements # correspond with which tool file outputs output_dict['output_name'] = output_name outputs.append(trans.security.encode_dict_ids(output_dict, skip_startswith="metadata_")) new_pja_flush = False for job in vars.get('jobs', []): rval['jobs'].append(self.encode_all_ids(trans, job.to_dict(view='collection'), recursive=True)) if inputs.get('send_email_notification', False): # Unless an anonymous user is invoking this via the API it # should never be an option, but check and enforce that here if trans.user is None: raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.") else: job_email_action = trans.model.PostJobAction('EmailAction') job.add_post_job_action(job_email_action) new_pja_flush = True if new_pja_flush: trans.sa_session.flush() for output_name, collection_instance in vars.get('output_collections', []): history = target_history or trans.history output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history) output_dict['output_name'] = output_name rval['output_collections'].append(output_dict) for output_name, collection_instance in vars.get('implicit_collections', {}).items(): history = target_history or trans.history output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history) output_dict['output_name'] = output_name rval['implicit_collections'].append(output_dict) return rval def _patch_library_inputs(self, trans, inputs, target_history): """ Transform inputs from the data libaray to history items. """ for k, v in inputs.items(): new_value = self._patch_library_dataset(trans, v, target_history) if new_value: v = new_value elif isinstance(v, dict) and 'values' in v: for index, value in enumerate(v['values']): patched = self._patch_library_dataset(trans, value, target_history) if patched: v['values'][index] = patched inputs[k] = v def _patch_library_dataset(self, trans, v, target_history): if isinstance(v, dict) and 'id' in v and v.get('src') == 'ldda': ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id'])) if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset): return ldda.to_history_dataset_association(target_history, add_to_history=True) # # -- Helper methods -- # def _get_tool(self, id, tool_version=None, user=None): tool = self.app.toolbox.get_tool(id, tool_version) if not tool: raise exceptions.ObjectNotFound("Could not find tool with id '%s'." % id) if not tool.allow_user_access(user): raise exceptions.AuthenticationFailed("Access denied, please login for tool with id '%s'." % id) return tool