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Source code for galaxy.webapps.galaxy.controllers.root

Contains the main interface in the Universe class

import logging
import os

import requests
from webob.compat import cgi_FieldStorage
from webob.exc import (

from galaxy import (
from galaxy.managers.histories import HistoryManager, HistorySerializer
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.structured_app import StructuredApp
from galaxy.util import (
from galaxy.webapps.base import controller
from ..api import depends

log = logging.getLogger(__name__)

# =============================================================================
[docs]class RootController(controller.JSAppLauncher, UsesAnnotations): """ Controller class that maps to the url root of Galaxy (i.e. '/'). """ history_manager: HistoryManager = depends(HistoryManager) history_serializer: HistorySerializer = depends(HistorySerializer)
[docs] def __init__(self, app: StructuredApp): super().__init__(app)
[docs] @web.expose def default(self, trans, target1=None, target2=None, **kwd): """ Called on any url that does not match a controller method. """ raise HTTPNotFound('This link may not be followed from within Galaxy.')
[docs] @web.expose def index(self, trans, tool_id=None, workflow_id=None, history_id=None, m_c=None, m_a=None, **kwd): """ Root and entry point for client-side web app. :type tool_id: str or None :param tool_id: load center panel with given tool if not None :type workflow_id: encoded id or None :param workflow_id: load center panel with given workflow if not None :type history_id: encoded id or None :param history_id: switch current history to given history if not None :type m_c: str or None :param m_c: controller name (e.g. 'user') :type m_a: str or None :param m_a: controller method/action (e.g. 'dbkeys') If m_c and m_a are present, the center panel will be loaded using the controller and action as a url: (e.g. 'user/dbkeys'). """ self._check_require_login(trans) # if a history_id was sent, attempt to switch to that history history = trans.history if history_id: unencoded_id = trans.security.decode_id(history_id) history = self.history_manager.get_owned(unencoded_id, trans.user) trans.set_history(history) return self._bootstrapped_client(trans)
[docs] @web.expose def login(self, trans, redirect=None, is_logout_redirect=False, **kwd): """ User login path for client-side. """ # directly redirect to oidc provider if 1) enable_oidc is True, 2) # there is only one oidc provider, 3) auth_conf.xml has no authenticators if (trans.app.config.enable_oidc and len(trans.app.config.oidc) == 1 and len(trans.app.auth_manager.authenticators) == 0 and is_logout_redirect is False): provider = next(iter(trans.app.config.oidc.keys())) success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans) if success: return trans.response.send_redirect(redirect_uri) return self.template(trans, 'login', redirect=redirect, # an installation may have it's own welcome_url - show it here if they've set that welcome_url=web.url_for(controller='root', action='welcome'), show_welcome_with_login=trans.app.config.show_welcome_with_login)
# ---- Tool related -----------------------------------------------------
[docs] @web.expose def tool_help(self, trans, id): """Return help page for tool identified by 'id' if available """ toolbox = self.get_toolbox() tool = toolbox.get_tool(id) yield "<html><body>" if not tool: # TODO: arent tool ids strings now? yield "Unknown tool id '%d'" % id elif tool.help: yield tool.help else: yield "No additional help available for tool '%s'" % tool.name yield "</body></html>"
# ---- Dataset display / editing ----------------------------------------
[docs] @web.expose def display(self, trans, id=None, hid=None, tofile=None, toext=".txt", encoded_id=None, **kwd): """Returns data directly into the browser. Sets the mime-type according to the extension. Used by the twill tool test driver - used anywhere else? Would like to drop hid argument and path if unneeded now. Likewise, would like to drop encoded_id=XXX and use assume id is encoded (likely id wouldn't be coming in encoded if this is used anywhere else though.) """ # TODO: unencoded id if hid is not None: try: hid = int(hid) except ValueError: return "hid '%s' is invalid" % str(hid) history = trans.get_history() for dataset in history.datasets: if dataset.hid == hid: data = dataset break else: raise Exception("No dataset with hid '%d'" % hid) else: if encoded_id and not id: id = self.decode_id(encoded_id) try: data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id) except Exception: return "Dataset id '%s' is invalid" % str(id) if data: current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.can_access_dataset(current_user_roles, data.dataset): trans.response.set_content_type(data.get_mime()) if tofile: fStat = os.stat(data.file_name) trans.response.headers['Content-Length'] = str(fStat.st_size) if toext[0:1] != ".": toext = "." + toext fname = data.name fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in fname)[0:150] trans.response.headers["Content-Disposition"] = f'attachment; filename="GalaxyHistoryItem-{data.hid}-[{fname}]{toext}"' trans.log_event("Display dataset id: %s" % str(id)) try: return open(data.file_name, 'rb') except Exception: return "This dataset contains no content" else: return "You are not allowed to access this dataset" else: return "No dataset with id '%s'" % str(id)
[docs] @web.expose def display_as(self, trans, id=None, display_app=None, **kwd): """Returns a file in a format that can successfully be displayed in display_app. """ # TODO: unencoded id data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id) authz_method = 'rbac' if 'authz_method' in kwd: authz_method = kwd['authz_method'] if data: current_user_roles = trans.get_current_user_roles() if authz_method == 'rbac' and trans.app.security_agent.can_access_dataset(current_user_roles, data): trans.response.set_content_type(data.get_mime()) trans.log_event("Formatted dataset id {} for display at {}".format(str(id), display_app)) return data.as_display_type(display_app, **kwd) elif authz_method == 'display_at' and trans.app.host_security_agent.allow_action(trans.request.remote_addr, data.permitted_actions.DATASET_ACCESS, dataset=data): trans.response.set_content_type(data.get_mime()) return data.as_display_type(display_app, **kwd) else: return "You are not allowed to access this dataset." else: return "No data with id=%d" % id
# ---- History management -----------------------------------------------
[docs] @web.expose def history_delete(self, trans, id): """Backward compatibility with check_galaxy script. """ # TODO: unused? return trans.webapp.controllers['history'].list(trans, id, operation='delete')
[docs] @web.expose def clear_history(self, trans): """Clears the history for a user. """ # TODO: unused? (seems to only be used in TwillTestCase) history = trans.get_history() for dataset in history.datasets: dataset.deleted = True dataset.clear_associated_files() trans.sa_session.flush() trans.log_event("History id %s cleared" % (str(history.id))) trans.response.send_redirect(web.url_for("/index"))
[docs] @web.expose def history_import(self, trans, id=None, confirm=False, **kwd): # TODO: unused? # TODO: unencoded id user = trans.get_user() user_history = trans.get_history() if not id: return trans.show_error_message("You must specify a history you want to import.") import_history = trans.sa_session.query(trans.app.model.History).get(id) if not import_history: return trans.show_error_message("The specified history does not exist.") if user: if import_history.user_id == user.id: return trans.show_error_message("You cannot import your own history.") new_history = import_history.copy(target_user=trans.user) new_history.name = "imported: " + new_history.name new_history.user_id = user.id galaxy_session = trans.get_galaxy_session() try: association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \ .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \ .first() except Exception: association = None new_history.add_galaxy_session(galaxy_session, association=association) trans.sa_session.add(new_history) trans.sa_session.flush() if not user_history.datasets: trans.set_history(new_history) trans.log_event("History imported, id: {}, name: '{}': ".format(str(new_history.id), new_history.name)) return trans.show_ok_message(""" History "{}" has been imported. Click <a href="{}">here</a> to begin.""".format(new_history.name, web.url_for('/'))) elif not user_history.datasets or confirm: new_history = import_history.copy() new_history.name = "imported: " + new_history.name new_history.user_id = None galaxy_session = trans.get_galaxy_session() try: association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \ .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \ .first() except Exception: association = None new_history.add_galaxy_session(galaxy_session, association=association) trans.sa_session.add(new_history) trans.sa_session.flush() trans.set_history(new_history) trans.log_event("History imported, id: {}, name: '{}': ".format(str(new_history.id), new_history.name)) return trans.show_ok_message(""" History "{}" has been imported. Click <a href="{}">here</a> to begin.""".format(new_history.name, web.url_for('/'))) return trans.show_warn_message(""" Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for(controller='root', action='history_import', id=id, confirm=True))
[docs] @web.expose def history_new(self, trans, name=None): """Create a new history with the given name and refresh the history panel. """ trans.new_history(name=name) trans.log_event("Created new History, id: %s." % str(trans.history.id)) return trans.show_message("New history created", refresh_frames=['history'])
[docs] @web.expose def history_add_to(self, trans, history_id=None, file_data=None, name="Data Added to History", info=None, ext="txt", dbkey="?", copy_access_from=None, **kwd): """Adds a POSTed file to a History. """ # TODO: unencoded id try: history = trans.sa_session.query(trans.app.model.History).get(history_id) data = trans.app.model.HistoryDatasetAssociation(name=name, info=info, extension=ext, dbkey=dbkey, create_dataset=True, sa_session=trans.sa_session) if copy_access_from: copy_access_from = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(copy_access_from) trans.app.security_agent.copy_dataset_permissions(copy_access_from.dataset, data.dataset) else: permissions = trans.app.security_agent.history_get_default_permissions(history) trans.app.security_agent.set_all_dataset_permissions(data.dataset, permissions) trans.sa_session.add(data) trans.sa_session.flush() data_file = open(data.file_name, "wb") file_data.file.seek(0) data_file.write(file_data.file.read()) data_file.close() data.state = data.states.OK data.set_size() data.init_meta() data.set_meta() trans.sa_session.flush() history.add_dataset(data) trans.sa_session.flush() data.set_peek() trans.sa_session.flush() trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id)) return trans.show_ok_message("Dataset " + str(data.hid) + " added to history " + str(history_id) + ".") except Exception as e: msg = "Failed to add dataset to history: %s" % unicodify(e) log.error(msg) trans.log_event(msg) return trans.show_error_message("Adding File to History has Failed")
[docs] @web.expose def dataset_make_primary(self, trans, id=None): """Copies a dataset and makes primary. """ # TODO: unused? # TODO: unencoded id try: old_data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id) new_data = old_data.copy() # new_data.parent = None history = trans.get_history() history.add_dataset(new_data) trans.sa_session.add(new_data) trans.sa_session.flush() return trans.show_message("<p>Secondary dataset has been made primary.</p>", refresh_frames=['history']) except Exception: return trans.show_error_message("<p>Failed to make secondary dataset primary.</p>")
[docs] @web.expose def welcome(self, trans): welcome_url = trans.app.config.welcome_url return trans.response.send_redirect(web.url_for(welcome_url))
[docs] @web.expose def bucket_proxy(self, trans, bucket=None, **kwd): if bucket: trans.response.set_content_type('text/xml') b_list_xml = requests.get('http://s3.amazonaws.com/%s/' % bucket) return b_list_xml.text raise Exception("You must specify a bucket")
# ---- Debug methods ----------------------------------------------------
[docs] @web.expose def echo(self, trans, **kwd): """Echos parameters (debugging). """ rval = "" for k in trans.request.headers: rval += "{}: {} <br/>".format(k, trans.request.headers[k]) for k in kwd: rval += "{}: {} <br/>".format(k, kwd[k]) if isinstance(kwd[k], cgi_FieldStorage): rval += "-> %s" % kwd[k].file.read() return rval
[docs] @web.json def echo_json(self, trans, **kwd): """Echos parameters as JSON (debugging). Attempts to parse values passed as boolean, float, then int. Defaults to string. Non-recursive (will not parse lists). """ # TODO: use json rval = {} for k in kwd: rval[k] = kwd[k] try: if rval[k] in ['true', 'True', 'false', 'False']: rval[k] = string_as_bool(rval[k]) rval[k] = float(rval[k]) rval[k] = int(rval[k]) except Exception: pass return rval
[docs] @web.expose def generate_error(self, trans, code=500): """Raises an exception (debugging). """ trans.response.status = code raise Exception("Fake error!")
[docs] @web.json def generate_json_error(self, trans, code=500): """Raises an exception (debugging). """ try: code = int(code) except ValueError: code = 500 if code == 502: raise HTTPBadGateway() trans.response.status = code return {'error': 'Fake error!'}