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Source code for galaxy.webapps.galaxy.controllers.async

Controller to handle communication of tools of type data_source_async

import logging
from urllib.parse import urlencode

import requests

from galaxy import web
from galaxy.model.base import transaction
from galaxy.util import (
from galaxy.util.hash_util import hmac_new
from galaxy.webapps.base.controller import BaseUIController

log = logging.getLogger(__name__)

[docs]class ASync(BaseUIController):
[docs] @web.expose def default(self, trans, tool_id=None, data_id=None, data_secret=None, **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, data_id=data_id, data_secret=data_secret, **kwd)
[docs] @web.expose def index(self, trans, tool_id=None, data_secret=None, **kwd): """Manages ascynchronous connections""" if tool_id is None: return "tool_id argument is required" tool_id = str(tool_id) # redirect to main when getting no parameters if not kwd: return trans.response.send_redirect("/index") params = Params(kwd, sanitize=False) data_id = params.data_id log.debug(f"async dataid -> {data_id}") trans.log_event(f"Async dataid -> {str(data_id)}") # initialize the tool toolbox = self.get_toolbox() tool = toolbox.get_tool(tool_id) if not tool: return f"Tool with id {tool_id} not found" if data_id: # # we have an incoming data_id # data = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(data_id) if not data: return f"Data {data_id} does not exist or has already been deleted" if data.state in data.dataset.terminal_states: log.debug(f"Tool {tool.id}: execution stopped as data {data_id} has entered terminal state prematurely") trans.log_event( f"Tool {tool.id}: execution stopped as data {data_id} has entered terminal state prematurely" ) return f"Data {data_id} has finished processing before job could be completed" # map params from the tool's <request_param_translation> section; # ignore any other params that may have been passed by the remote # server with the exception of STATUS and URL; # if name, info, dbkey and data_type are not handled via incoming params, # use the metadata from the already existing dataset; # preserve original params under nested dict params_dict = dict( STATUS=params.STATUS, URL=params.URL, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext, incoming_request_params=params.__dict__.copy(), ) if tool.input_translator: tool.input_translator.translate(params) tool_declared_params = { translator.galaxy_name for translator in tool.input_translator.param_trans_dict.values() } for param in params: if param in tool_declared_params: params_dict[param] = params.get(param, None) params = params_dict if not params.get("URL"): return f"No URL parameter was submitted for data {data_id}" STATUS = params.get("STATUS") if STATUS == "OK": key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) if key != data_secret: return f"You do not have permission to alter data {data_id}." if not params.get("GALAXY_URL"): # provide a fallback for GALAXY_URL params["GALAXY_URL"] = f"{trans.request.url_path}/async/{tool_id}/{data.id}/{key}" # push the job into the queue data.state = data.blurb = data.states.RUNNING log.debug(f"executing tool {tool.id}") trans.log_event(f"Async executing tool {tool.id}", tool_id=tool.id) # Assume there is exactly one output file possible TOOL_OUTPUT_TYPE = None for key, obj in tool.outputs.items(): try: TOOL_OUTPUT_TYPE = obj.format params[key] = data.id break except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption continue if TOOL_OUTPUT_TYPE is None: raise Exception("Error: ToolOutput object not found") original_history = trans.sa_session.query(trans.app.model.History).get(data.history_id) job, *_ = tool.execute(trans, incoming=params, history=original_history) trans.app.job_manager.enqueue(job, tool=tool) else: log.debug(f"async error -> {STATUS}") trans.log_event(f"Async error -> {STATUS}") data.state = data.blurb = "error" data.info = f"Error -> {STATUS}" with transaction(trans.sa_session): trans.sa_session.commit() return f"Data {data_id} with status {STATUS} received. OK" else: # no data_id must be parameter submission # # create new dataset, put it into running state, # send request for data to remote server and see if the response # ends in ok; # the request that's getting sent goes to the URL found in # params.URL or, in its absence, to the one found as the value of # the "action" attribute of the data source tool's "inputs" tag. # Included in the request are the parameters: # - data_id, which indicates to the remote server that Galaxy is # ready to accept data # - GALAXY_URL, which takes the form: # {base_url}/async/{tool_id}/{data_id}/{data_secret}, and which # when used by the remote server to send a data download link, # will trigger the if branch above. GALAXY_TYPE = None if params.data_type: GALAXY_TYPE = params.data_type elif params.galaxyFileFormat == "wig": # this is an undocumented legacy special case GALAXY_TYPE = "wig" elif params.GALAXY_TYPE: GALAXY_TYPE = params.GALAXY_TYPE else: # Assume there is exactly one output outputs_count = 0 for obj in tool.outputs.values(): try: GALAXY_TYPE = obj.format outputs_count += 1 except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption # a collection object does not have the 'format' attribute, so it will throw an exception continue if outputs_count > 1: raise Exception("Error: the tool should have just one output") if GALAXY_TYPE is None: raise Exception("Error: ToolOutput object not found") GALAXY_NAME = params.name or params.GALAXY_NAME or f"{tool.name} query" GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or "" GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or "?" # data = datatypes.factory(ext=GALAXY_TYPE)() # data.ext = GALAXY_TYPE # data.name = GALAXY_NAME # data.info = GALAXY_INFO # data.dbkey = GALAXY_BUILD # data.state = jobs.JOB_OK # history.datasets.add_dataset( data ) data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE ) trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions(trans.history) ) data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO trans.sa_session.add( data ) # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW trans.history.add_dataset(data, genome_build=GALAXY_BUILD) trans.sa_session.add(trans.history) with transaction(trans.sa_session): trans.sa_session.commit() # Need to explicitly create the file data.dataset.object_store.create(data.dataset) trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id), tool_id=tool_id) try: key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) galaxy_url = f"{trans.request.url_path}/async/{tool_id}/{data.id}/{key}" params.update({"GALAXY_URL": galaxy_url}) params.update({"data_id": data.id}) # Use provided URL or fallback to tool action url = params.URL or tool.action # Does url already have query params? if "?" in url: url_join_char = "&" else: url_join_char = "?" url = f"{url}{url_join_char}{urlencode(params.flatten())}" log.debug(f"connecting to -> {url}") trans.log_event(f"Async connecting to -> {url}") text = requests.get(url, timeout=DEFAULT_SOCKET_TIMEOUT).text.strip() if not text.endswith("OK"): raise Exception(text) data.state = data.blurb = data.states.RUNNING except Exception as e: data.info = unicodify(e) data.state = data.blurb = data.states.ERROR with transaction(trans.sa_session): trans.sa_session.commit() return trans.fill_template("root/tool_runner.mako", out_data={}, num_jobs=1, job_errors=[])