[galaxy-commits] commit/galaxy-central: dannon: Merged in carlfeberhard/galaxy-central-fork0 (pull request #484)

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83e45a9e4cc9/ Changeset: 83e45a9e4cc9 User: dannon Date: 2014-09-04 22:30:50 Summary: Merged in carlfeberhard/galaxy-central-fork0 (pull request #484) Break up web/framework/__init__ into more focused modules Affected #: 20 files diff -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f -r 83e45a9e4cc994daed44e406a334660d9db7ed30 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -6,7 +6,6 @@ import copy import cPickle import json -import logging import os import shutil import sys @@ -15,13 +14,19 @@ from os.path import abspath -import galaxy.model -from galaxy.util import listify, stringify_dictionary_keys, string_as_bool -from galaxy.util.odict import odict -from galaxy.util import in_directory -from galaxy.web import form_builder +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) from sqlalchemy.orm import object_session +import galaxy.model +from galaxy.util import listify +from galaxy.util import stringify_dictionary_keys +from galaxy.util import string_as_bool +from galaxy.util import in_directory +from galaxy.util.odict import odict +from galaxy.web import form_builder + +import logging log = logging.getLogger(__name__) STATEMENTS = "__galaxy_statements__" #this is the name of the property in a Datatype class where new metadata spec element Statements are stored diff -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f -r 83e45a9e4cc994daed44e406a334660d9db7ed30 lib/galaxy/managers/context.py --- /dev/null +++ b/lib/galaxy/managers/context.py @@ -0,0 +1,179 @@ +""" +Mixins for transaction-like objects. +""" + +import os + +from galaxy.util.json import to_json_string +from galaxy.util import bunch + +class ProvidesAppContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + database and event handling. + + Mixed in class must provide `app` property. + """ + + def log_action( self, user=None, action=None, context=None, params=None): + """ + Application-level logging of user actions. + """ + if self.app.config.log_actions: + action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) + try: + if user: + action.user = user + else: + action.user = self.user + except: + action.user = None + try: + action.session_id = self.galaxy_session.id + except: + action.session_id = None + self.sa_session.add( action ) + self.sa_session.flush() + + def log_event( self, message, tool_id=None, **kwargs ): + """ + Application level logging. Still needs fleshing out (log levels and such) + Logging events is a config setting - if False, do not log. + """ + if self.app.config.log_events: + event = self.app.model.Event() + event.tool_id = tool_id + try: + event.message = message % kwargs + except: + event.message = message + try: + event.history = self.get_history() + except: + event.history = None + try: + event.history_id = self.history.id + except: + event.history_id = None + try: + event.user = self.user + except: + event.user = None + try: + event.session_id = self.galaxy_session.id + except: + event.session_id = None + self.sa_session.add( event ) + self.sa_session.flush() + + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.app.model.context.current + + def expunge_all( self ): + app = self.app + context = app.model.context + context.expunge_all() + # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all() + if hasattr(app, 'install_model'): + install_model = app.install_model + if install_model != app.model: + install_model.context.expunge_all() + + def get_toolbox(self): + """Returns the application toolbox""" + return self.app.toolbox + + @property + def model( self ): + return self.app.model + + @property + def install_model( self ): + return self.app.install_model + + def request_types(self): + if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: + return True + return False + + +class ProvidesUserContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + reasoning about users. + + Mixed in class must provide `user`, `api_inherit_admin`, and `app` + properties. + """ + + @property + def anonymous( self ): + return self.user is None and not self.api_inherit_admin + + def get_current_user_roles( self ): + user = self.user + if user: + roles = user.all_roles() + else: + roles = [] + return roles + + def user_is_admin( self ): + if self.api_inherit_admin: + return True + return self.user and self.user.email in self.app.config.admin_users_list + + def user_can_do_run_as( self ): + run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ] + if not run_as_users: + return False + user_in_run_as_users = self.user and self.user.email in run_as_users + # Can do if explicitly in list or master_api_key supplied. + can_do_run_as = user_in_run_as_users or self.api_inherit_admin + return can_do_run_as + + @property + def user_ftp_dir( self ): + identifier = self.app.config.ftp_upload_dir_identifier + return os.path.join( self.app.config.ftp_upload_dir, getattr( self.user, identifier ) ) + + +class ProvidesHistoryContext( object ): + """ For transaction-like objects to provide Galaxy convience layer for + reasoning about histories. + + Mixed in class must provide `user`, `history`, and `app` + properties. + """ + + def db_dataset_for( self, dbkey ): + """ + Returns the db_file dataset associated/needed by `dataset`, or `None`. + """ + # If no history, return None. + if self.history is None: + return None +#TODO: when does this happen? is it Bunch or util.bunch.Bunch? + if isinstance( self.history, bunch.Bunch ): + # The API presents a Bunch for a history. Until the API is + # more fully featured for handling this, also return None. + return None + datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ + .filter_by( deleted=False, history_id=self.history.id, extension="len" ) + for ds in datasets: + if dbkey == ds.dbkey: + return ds + return None + + @property + def db_builds( self ): + """ + Returns the builds defined by galaxy and the builds defined by + the user (chromInfo in history). + """ + # FIXME: This method should be removed + return self.app.genome_builds.get_genome_build_names( trans=self ) diff -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f -r 83e45a9e4cc994daed44e406a334660d9db7ed30 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -1,23 +1,25 @@ """ The Galaxy web application framework """ -from framework import expose -from framework import json -from framework import json_pretty -from framework import require_login -from framework import require_admin from framework import url_for -from framework import error -from framework import form -from framework import FormBuilder -from framework import expose_api -from framework import expose_api_anonymous -from framework import expose_api_raw -from framework import expose_api_raw_anonymous -from framework.base import httpexceptions +from framework.decorators import error +from framework.decorators import expose +from framework.decorators import json +from framework.decorators import json_pretty +from framework.decorators import require_login +from framework.decorators import require_admin +from framework.decorators import expose_api +from framework.decorators import expose_api_anonymous +from framework.decorators import expose_api_raw +from framework.decorators import expose_api_raw_anonymous # TODO: Drop and make these the default. -from framework import _future_expose_api -from framework import _future_expose_api_anonymous -from framework import _future_expose_api_raw -from framework import _future_expose_api_raw_anonymous +from framework.decorators import _future_expose_api +from framework.decorators import _future_expose_api_anonymous +from framework.decorators import _future_expose_api_raw +from framework.decorators import _future_expose_api_raw_anonymous + +from framework.formbuilder import form +from framework.formbuilder import FormBuilder + +from framework.base import httpexceptions diff -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f -r 83e45a9e4cc994daed44e406a334660d9db7ed30 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -579,7 +579,7 @@ """ Pass control over to trans and render ``template_filename``. - :type trans: ``galaxy.web.framework.GalaxyWebTransaction`` + :type trans: ``galaxy.web.framework.webapp.GalaxyWebTransaction`` :param trans: transaction doing the rendering :type plugin: ``util.bunch.Bunch`` :param plugin: the plugin containing the template to render diff -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f -r 83e45a9e4cc994daed44e406a334660d9db7ed30 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -2,1395 +2,9 @@ Galaxy web application framework """ -import hashlib -import inspect -import os -import random -import socket -import string -import time -from traceback import format_exc -from Cookie import CookieError -from functools import wraps - from galaxy import eggs - -eggs.require( "Cheetah" ) -from Cheetah.Template import Template - -from galaxy import util -from galaxy.exceptions import error_codes -from galaxy.exceptions import MessageException -from galaxy.util import asbool -from galaxy.util import safe_str_cmp -from galaxy.util.backports.importlib import import_module -from galaxy.util.json import from_json_string, to_json_string -from galaxy.util.sanitize_html import sanitize_html -from galaxy.web.framework import base, helpers - -import paste.httpexceptions - -eggs.require( "Mako" ) -import mako.template -import mako.lookup -import mako.runtime - -eggs.require( "pytz" ) # Used by Babel. -eggs.require( "Babel" ) -from babel.support import Translations -from babel import Locale - -eggs.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy import and_ -from sqlalchemy.orm.exc import NoResultFound - eggs.require( "pexpect" ) eggs.require( "amqp" ) -import logging -log = logging.getLogger( __name__ ) - +import base url_for = base.routes.url_for - -UCSC_SERVERS = ( - 'hgw1.cse.ucsc.edu', - 'hgw2.cse.ucsc.edu', - 'hgw3.cse.ucsc.edu', - 'hgw4.cse.ucsc.edu', - 'hgw5.cse.ucsc.edu', - 'hgw6.cse.ucsc.edu', - 'hgw7.cse.ucsc.edu', - 'hgw8.cse.ucsc.edu', -) - -JSON_CONTENT_TYPE = "application/json" - - -# ----------------------------------------------------------------------------- web controller decorators -def expose( func ): - """ - Decorator: mark a function as 'exposed' and thus web accessible - """ - func.exposed = True - return func - -def json( func, **json_kwargs ): - """ - Format the response as JSON and set the response content type to - JSON_CONTENT_TYPE. - """ - @wraps(func) - def call_and_format( self, trans, *args, **kwargs ): - trans.response.set_content_type( JSON_CONTENT_TYPE ) - return to_json_string( func( self, trans, *args, **kwargs ), **json_kwargs ) - if not hasattr(func, '_orig'): - call_and_format._orig = func - call_and_format.exposed = True - return call_and_format - -def json_pretty( func ): - """ - Indent and sort returned JSON. - """ - return json( func, indent=4, sort_keys=True ) - -def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): - def argcatcher( func ): - @wraps(func) - def decorator( self, trans, *args, **kwargs ): - if trans.get_user(): - return func( self, trans, *args, **kwargs ) - else: - return trans.show_error_message( - 'You must be <a target="galaxy_main" href="%s">logged in</a> to %s.' - % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) - return decorator - return argcatcher - -def require_admin( func ): - @wraps(func) - def decorator( self, trans, *args, **kwargs ): - if not trans.user_is_admin(): - msg = "You must be an administrator to access this feature." - user = trans.get_user() - if not trans.app.config.admin_users_list: - msg = "You must be logged in as an administrator to access this feature, but no administrators are set in the Galaxy configuration." - elif not user: - msg = "You must be logged in as an administrator to access this feature." - trans.response.status = 403 - if trans.response.get_content_type() == 'application/json': - return msg - else: - return trans.show_error_message( msg ) - return func( self, trans, *args, **kwargs ) - return decorator - - -# ----------------------------------------------------------------------------- (original) api decorators -def expose_api( func, to_json=True, user_required=True ): - """ - Expose this function via the API. - """ - @wraps(func) - def decorator( self, trans, *args, **kwargs ): - def error( environ, start_response ): - start_response( error_status, [('Content-type', 'text/plain')] ) - return error_message - error_status = '403 Forbidden' - if trans.error_message: - return trans.error_message - if user_required and trans.anonymous: - error_message = "API Authentication Required for this request" - return error - if trans.request.body: - try: - kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs) - except ValueError: - error_status = '400 Bad Request' - error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' - return error - trans.response.set_content_type( "application/json" ) - # send 'do not cache' headers to handle IE's caching of ajax get responses - trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" - # Perform api_run_as processing, possibly changing identity - if 'payload' in kwargs and 'run_as' in kwargs['payload']: - if not trans.user_can_do_run_as(): - error_message = 'User does not have permissions to run jobs as another user' - return error - try: - decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] ) - except TypeError: - trans.response.status = 400 - return "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] ) - try: - user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) - trans.api_inherit_admin = trans.user_is_admin() - trans.set_user(user) - except: - trans.response.status = 400 - return "That user does not exist." - try: - rval = func( self, trans, *args, **kwargs) - if to_json and trans.debug: - rval = to_json_string( rval, indent=4, sort_keys=True ) - elif to_json: - rval = to_json_string( rval ) - return rval - except paste.httpexceptions.HTTPException: - raise # handled - except: - log.exception( 'Uncaught exception in exposed API method:' ) - raise paste.httpexceptions.HTTPServerError() - if not hasattr(func, '_orig'): - decorator._orig = func - decorator.exposed = True - return decorator - -def __extract_payload_from_request(trans, func, kwargs): - content_type = trans.request.headers['content-type'] - if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): - # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body - # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which - # are not a part of the request body. This is a problem because it's not possible to differentiate between values - # which are a part of the request body, and therefore should be a part of the payload, and values which should not be - # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from - # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. - payload = kwargs.copy() - named_args, _, _, _ = inspect.getargspec(func) - for arg in named_args: - payload.pop(arg, None) - for k, v in payload.iteritems(): - if isinstance(v, (str, unicode)): - try: - payload[k] = from_json_string(v) - except: - # may not actually be json, just continue - pass - payload = util.recursively_stringify_dictionary_keys( payload ) - else: - # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check - # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding - # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. - payload = util.recursively_stringify_dictionary_keys( from_json_string( trans.request.body ) ) - return payload - -def expose_api_raw( func ): - """ - Expose this function via the API but don't dump the results - to JSON. - """ - return expose_api( func, to_json=False ) - -def expose_api_raw_anonymous( func ): - """ - Expose this function via the API but don't dump the results - to JSON. - """ - return expose_api( func, to_json=False, user_required=False ) - -def expose_api_anonymous( func, to_json=True ): - """ - Expose this function via the API but don't require a set user. - """ - return expose_api( func, to_json=to_json, user_required=False ) - - -# ----------------------------------------------------------------------------- (new) api decorators -# TODO: rename as expose_api and make default. -def _future_expose_api( func, to_json=True, user_required=True ): - """ - Expose this function via the API. - """ - @wraps(func) - def decorator( self, trans, *args, **kwargs ): - if trans.error_message: - # TODO: Document this branch, when can this happen, - # I don't understand it. - return __api_error_response( trans, err_msg=trans.error_message ) - if user_required and trans.anonymous: - error_code = error_codes.USER_NO_API_KEY - # Use error codes default error message. - err_msg = "API authentication required for this request" - return __api_error_response( trans, err_code=error_code, err_msg=err_msg, status_code=403 ) - if trans.request.body: - try: - kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs) - except ValueError: - error_code = error_codes.USER_INVALID_JSON - return __api_error_response( trans, status_code=400, err_code=error_code ) - - trans.response.set_content_type( JSON_CONTENT_TYPE ) - # send 'do not cache' headers to handle IE's caching of ajax get responses - trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" - # TODO: Refactor next block out into a helper procedure. - # Perform api_run_as processing, possibly changing identity - if 'payload' in kwargs and 'run_as' in kwargs['payload']: - if not trans.user_can_do_run_as(): - error_code = error_codes.USER_CANNOT_RUN_AS - return __api_error_response( trans, err_code=error_code, status_code=403 ) - try: - decoded_user_id = trans.security.decode_id( kwargs['payload']['run_as'] ) - except TypeError: - error_message = "Malformed user id ( %s ) specified, unable to decode." % str( kwargs['payload']['run_as'] ) - error_code = error_codes.USER_INVALID_RUN_AS - return __api_error_response( trans, err_code=error_code, err_msg=error_message, status_code=400) - try: - user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) - trans.api_inherit_admin = trans.user_is_admin() - trans.set_user(user) - except: - error_code = error_codes.USER_INVALID_RUN_AS - return __api_error_response( trans, err_code=error_code, status_code=400 ) - try: - rval = func( self, trans, *args, **kwargs) - if to_json and trans.debug: - rval = to_json_string( rval, indent=4, sort_keys=True ) - elif to_json: - rval = to_json_string( rval ) - return rval - except MessageException as e: - traceback_string = format_exc() - return __api_error_response( trans, exception=e, traceback=traceback_string ) - except paste.httpexceptions.HTTPException: - # TODO: Allow to pass or format for the API??? - raise # handled - except Exception as e: - traceback_string = format_exc() - error_message = 'Uncaught exception in exposed API method:' - log.exception( error_message ) - return __api_error_response( - trans, - status_code=500, - exception=e, - traceback=traceback_string, - err_msg=error_message, - err_code=error_codes.UNKNOWN - ) - if not hasattr(func, '_orig'): - decorator._orig = func - decorator.exposed = True - return decorator - -def __api_error_message( trans, **kwds ): - exception = kwds.get( "exception", None ) - if exception: - # If we are passed a MessageException use err_msg. - default_error_code = getattr( exception, "err_code", error_codes.UNKNOWN ) - default_error_message = getattr( exception, "err_msg", default_error_code.default_error_message ) - extra_error_info = getattr( exception, 'extra_error_info', {} ) - if not isinstance( extra_error_info, dict ): - extra_error_info = {} - else: - default_error_message = "Error processing API request." - default_error_code = error_codes.UNKNOWN - extra_error_info = {} - traceback_string = kwds.get( "traceback", "No traceback available." ) - err_msg = kwds.get( "err_msg", default_error_message ) - error_code_object = kwds.get( "err_code", default_error_code ) - try: - error_code = error_code_object.code - except AttributeError: - # Some sort of bad error code sent in, logic failure on part of - # Galaxy developer. - error_code = error_codes.UNKNOWN.code - # Would prefer the terminology of error_code and error_message, but - # err_msg used a good number of places already. Might as well not change - # it? - error_response = dict( err_msg=err_msg, err_code=error_code, **extra_error_info ) - if trans.debug: # TODO: Should admins get to see traceback as well? - error_response[ "traceback" ] = traceback_string - return error_response - -def __api_error_response( trans, **kwds ): - error_dict = __api_error_message( trans, **kwds ) - exception = kwds.get( "exception", None ) - # If we are given an status code directly - use it - otherwise check - # the exception for a status_code attribute. - if "status_code" in kwds: - status_code = int( kwds.get( "status_code" ) ) - elif hasattr( exception, "status_code" ): - status_code = int( exception.status_code ) - else: - status_code = 500 - response = trans.response - if not response.status or str(response.status).startswith("20"): - # Unset status code appears to be string '200 OK', if anything - # non-success (i.e. not 200 or 201) has been set, do not override - # underlying controller. - response.status = status_code - return to_json_string( error_dict ) - - -# TODO: rename as expose_api and make default. -def _future_expose_api_anonymous( func, to_json=True ): - """ - Expose this function via the API but don't require a set user. - """ - return _future_expose_api( func, to_json=to_json, user_required=False ) - - -def _future_expose_api_raw( func ): - return _future_expose_api( func, to_json=False, user_required=True ) - - -def _future_expose_api_raw_anonymous( func ): - return _future_expose_api( func, to_json=False, user_required=False ) - - - -NOT_SET = object() - - -def error( message ): - raise MessageException( message, type='error' ) - - -def form( *args, **kwargs ): - return FormBuilder( *args, **kwargs ) - - -class WebApplication( base.WebApplication ): - - def __init__( self, galaxy_app, session_cookie='galaxysession', name=None ): - self.name = name - base.WebApplication.__init__( self ) - self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) - # Mako support - self.mako_template_lookup = self.create_mako_template_lookup( galaxy_app, name ) - # Security helper - self.security = galaxy_app.security - - def create_mako_template_lookup( self, galaxy_app, name ): - paths = [] - # First look in webapp specific directory - if name is not None: - paths.append( os.path.join( galaxy_app.config.template_path, 'webapps', name ) ) - # Then look in root directory - paths.append( galaxy_app.config.template_path ) - # Create TemplateLookup with a small cache - return mako.lookup.TemplateLookup(directories=paths, - module_directory=galaxy_app.config.template_cache, - collection_size=500, - output_encoding='utf-8' ) - - def handle_controller_exception( self, e, trans, **kwargs ): - if isinstance( e, MessageException ): - # In the case of a controller exception, sanitize to make sure - # unsafe html input isn't reflected back to the user - return trans.show_message( sanitize_html(e.err_msg), e.type ) - - def make_body_iterable( self, trans, body ): - if isinstance( body, FormBuilder ): - body = trans.show_form( body ) - return base.WebApplication.make_body_iterable( self, trans, body ) - - def transaction_chooser( self, environ, galaxy_app, session_cookie ): - return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) - - def add_ui_controllers( self, package_name, app ): - """ - Search for UI controllers in `package_name` and add - them to the webapp. - """ - from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable - package = import_module( package_name ) - controller_dir = package.__path__[0] - for fname in os.listdir( controller_dir ): - if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): - name = fname[:-3] - module_name = package_name + "." + name - try: - module = import_module( module_name ) - except ControllerUnavailable, exc: - log.debug("%s could not be loaded: %s" % (module_name, str(exc))) - continue - # Look for a controller inside the modules - for key in dir( module ): - T = getattr( module, key ) - if inspect.isclass( T ) and T is not BaseUIController and issubclass( T, BaseUIController ): - controller = self._instantiate_controller( T, app ) - self.add_ui_controller( name, controller ) - - def add_api_controllers( self, package_name, app ): - """ - Search for UI controllers in `package_name` and add - them to the webapp. - """ - from galaxy.web.base.controller import BaseAPIController - from galaxy.web.base.controller import ControllerUnavailable - package = import_module( package_name ) - controller_dir = package.__path__[0] - for fname in os.listdir( controller_dir ): - if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): - name = fname[:-3] - module_name = package_name + "." + name - try: - module = import_module( module_name ) - except ControllerUnavailable, exc: - log.debug("%s could not be loaded: %s" % (module_name, str(exc))) - continue - for key in dir( module ): - T = getattr( module, key ) - # Exclude classes such as BaseAPIController and BaseTagItemsController - if inspect.isclass( T ) and not key.startswith("Base") and issubclass( T, BaseAPIController ): - # By default use module_name, but allow controller to override name - controller_name = getattr( T, "controller_name", name ) - controller = self._instantiate_controller( T, app ) - self.add_api_controller( controller_name, controller ) - - def _instantiate_controller( self, T, app ): - """ Extension point, allow apps to contstruct controllers differently, - really just used to stub out actual controllers for routes testing. - """ - return T( app ) - - -class ProvidesAppContext( object ): - """ For transaction-like objects to provide Galaxy convience layer for - database and event handling. - - Mixed in class must provide `app` property. - """ - - def log_action( self, user=None, action=None, context=None, params=None): - """ - Application-level logging of user actions. - """ - if self.app.config.log_actions: - action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) - try: - if user: - action.user = user - else: - action.user = self.user - except: - action.user = None - try: - action.session_id = self.galaxy_session.id - except: - action.session_id = None - self.sa_session.add( action ) - self.sa_session.flush() - - def log_event( self, message, tool_id=None, **kwargs ): - """ - Application level logging. Still needs fleshing out (log levels and such) - Logging events is a config setting - if False, do not log. - """ - if self.app.config.log_events: - event = self.app.model.Event() - event.tool_id = tool_id - try: - event.message = message % kwargs - except: - event.message = message - try: - event.history = self.get_history() - except: - event.history = None - try: - event.history_id = self.history.id - except: - event.history_id = None - try: - event.user = self.user - except: - event.user = None - try: - event.session_id = self.galaxy_session.id - except: - event.session_id = None - self.sa_session.add( event ) - self.sa_session.flush() - - @property - def sa_session( self ): - """ - Returns a SQLAlchemy session -- currently just gets the current - session from the threadlocal session context, but this is provided - to allow migration toward a more SQLAlchemy 0.4 style of use. - """ - return self.app.model.context.current - - def expunge_all( self ): - app = self.app - context = app.model.context - context.expunge_all() - # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all() - if hasattr(app, 'install_model'): - install_model = app.install_model - if install_model != app.model: - install_model.context.expunge_all() - - def get_toolbox(self): - """Returns the application toolbox""" - return self.app.toolbox - - @property - def model( self ): - return self.app.model - - @property - def install_model( self ): - return self.app.install_model - - def request_types(self): - if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: - return True - return False - - -class ProvidesUserContext( object ): - """ For transaction-like objects to provide Galaxy convience layer for - reasoning about users. - - Mixed in class must provide `user`, `api_inherit_admin`, and `app` - properties. - """ - - @property - def anonymous( self ): - return self.user is None and not self.api_inherit_admin - - def get_current_user_roles( self ): - user = self.user - if user: - roles = user.all_roles() - else: - roles = [] - return roles - - def user_is_admin( self ): - if self.api_inherit_admin: - return True - return self.user and self.user.email in self.app.config.admin_users_list - - def user_can_do_run_as( self ): - run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ] - if not run_as_users: - return False - user_in_run_as_users = self.user and self.user.email in run_as_users - # Can do if explicitly in list or master_api_key supplied. - can_do_run_as = user_in_run_as_users or self.api_inherit_admin - return can_do_run_as - - @property - def user_ftp_dir( self ): - identifier = self.app.config.ftp_upload_dir_identifier - return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) - - -class ProvidesHistoryContext( object ): - """ For transaction-like objects to provide Galaxy convience layer for - reasoning about histories. - - Mixed in class must provide `user`, `history`, and `app` - properties. - """ - - def db_dataset_for( self, dbkey ): - """ - Returns the db_file dataset associated/needed by `dataset`, or `None`. - """ - # If no history, return None. - if self.history is None: - return None - if isinstance(self.history, Bunch): - # The API presents a Bunch for a history. Until the API is - # more fully featured for handling this, also return None. - return None - datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ - .filter_by( deleted=False, history_id=self.history.id, extension="len" ) - for ds in datasets: - if dbkey == ds.dbkey: - return ds - return None - - @property - def db_builds( self ): - """ - Returns the builds defined by galaxy and the builds defined by - the user (chromInfo in history). - """ - # FIXME: This method should be removed - return self.app.genome_builds.get_genome_build_names( trans=self ) - - -class GalaxyWebTransaction( base.DefaultWebTransaction, ProvidesAppContext, ProvidesUserContext, ProvidesHistoryContext ): - """ - Encapsulates web transaction specific state for the Galaxy application - (specifically the user's "cookie" session and history) - """ - - def __init__( self, environ, app, webapp, session_cookie=None): - self.app = app - self.webapp = webapp - self.security = webapp.security - base.DefaultWebTransaction.__init__( self, environ ) - self.setup_i18n() - self.expunge_all() - self.debug = asbool( self.app.config.get( 'debug', False ) ) - # Flag indicating whether we are in workflow building mode (means - # that the current history should not be used for parameter values - # and such). - self.workflow_building_mode = False - # Flag indicating whether this is an API call and the API key user is an administrator - self.api_inherit_admin = False - self.__user = None - self.galaxy_session = None - self.error_message = None - - if self.environ.get('is_api_request', False): - # With API requests, if there's a key, use it and associate the - # user with the transaction. - # If not, check for an active session but do not create one. - # If an error message is set here, it's sent back using - # trans.show_error in the response -- in expose_api. - self.error_message = self._authenticate_api( session_cookie ) - elif self.app.name == "reports": - self.galaxy_session = None - else: - # This is a web request, get or create session. - self._ensure_valid_session( session_cookie ) - if self.galaxy_session: - # When we've authenticated by session, we have to check the - # following. - # Prevent deleted users from accessing Galaxy - if self.app.config.use_remote_user and self.galaxy_session.user.deleted: - self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) - if self.app.config.require_login: - self._ensure_logged_in_user( environ, session_cookie ) - - def setup_i18n( self ): - locales = [] - if 'HTTP_ACCEPT_LANGUAGE' in self.environ: - # locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3'] - client_locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' ) - for locale in client_locales: - try: - locales.append( Locale.parse( locale.split( ';' )[0].strip(), sep='-' ).language ) - except Exception, e: - log.debug( "Error parsing locale '%s'. %s: %s", locale, type( e ), e ) - if not locales: - # Default to English - locales = 'en' - t = Translations.load( dirname='locale', locales=locales, domain='ginga' ) - self.template_context.update( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) ) - - def get_user( self ): - """Return the current user if logged in or None.""" - if self.galaxy_session: - return self.galaxy_session.user - else: - return self.__user - - def set_user( self, user ): - """Set the current user.""" - if self.galaxy_session: - self.galaxy_session.user = user - self.sa_session.add( self.galaxy_session ) - self.sa_session.flush() - self.__user = user - - user = property( get_user, set_user ) - - def get_cookie( self, name='galaxysession' ): - """Convenience method for getting a session cookie""" - try: - # If we've changed the cookie during the request return the new value - if name in self.response.cookies: - return self.response.cookies[name].value - else: - return self.request.cookies[name].value - except: - return None - - def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): - """Convenience method for setting a session cookie""" - # The galaxysession cookie value must be a high entropy 128 bit random number encrypted - # using a server secret key. Any other value is invalid and could pose security issues. - self.response.cookies[name] = value - self.response.cookies[name]['path'] = path - self.response.cookies[name]['max-age'] = 3600 * 24 * age # 90 days - tstamp = time.localtime( time.time() + 3600 * 24 * age ) - self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) - self.response.cookies[name]['version'] = version - try: - self.response.cookies[name]['httponly'] = True - except CookieError, e: - log.warning( "Error setting httponly attribute in cookie '%s': %s" % ( name, e ) ) - - def _authenticate_api( self, session_cookie ): - """ - Authenticate for the API via key or session (if available). - """ - api_key = self.request.params.get('key', None) - secure_id = self.get_cookie( name=session_cookie ) - api_key_supplied = self.environ.get('is_api_request', False) and api_key - if api_key_supplied and self._check_master_api_key( api_key ): - self.api_inherit_admin = True - log.info( "Session authenticated using Galaxy master api key" ) - self.user = None - self.galaxy_session = None - elif api_key_supplied: - # Sessionless API transaction, we just need to associate a user. - try: - provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() - except NoResultFound: - return 'Provided API key is not valid.' - if provided_key.user.deleted: - return 'User account is deactivated, please contact an administrator.' - newest_key = provided_key.user.api_keys[0] - if newest_key.key != provided_key.key: - return 'Provided API key has expired.' - self.set_user( provided_key.user ) - elif secure_id: - # API authentication via active session - # Associate user using existing session - self._ensure_valid_session( session_cookie ) - else: - # Anonymous API interaction -- anything but @expose_api_anonymous will fail past here. - self.user = None - self.galaxy_session = None - - def _check_master_api_key( self, api_key ): - master_api_key = getattr( self.app.config, 'master_api_key', None ) - if not master_api_key: - return False - # Hash keys to make them the same size, so we can do safe comparison. - master_hash = hashlib.sha256( master_api_key ).hexdigest() - provided_hash = hashlib.sha256( api_key ).hexdigest() - return safe_str_cmp( master_hash, provided_hash ) - - def _ensure_valid_session( self, session_cookie, create=True): - """ - Ensure that a valid Galaxy session exists and is available as - trans.session (part of initialization) - - Support for universe_session and universe_user cookies has been - removed as of 31 Oct 2008. - """ - # Try to load an existing session - secure_id = self.get_cookie( name=session_cookie ) - galaxy_session = None - prev_galaxy_session = None - user_for_new_session = None - invalidate_existing_session = False - # Track whether the session has changed so we can avoid calling flush - # in the most common case (session exists and is valid). - galaxy_session_requires_flush = False - if secure_id: - # Decode the cookie value to get the session_key - session_key = self.security.decode_guid( secure_id ) - try: - # Make sure we have a valid UTF-8 string - session_key = session_key.encode( 'utf8' ) - except UnicodeDecodeError: - # We'll end up creating a new galaxy_session - session_key = None - if session_key: - # Retrieve the galaxy_session id via the unique session_key - galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ - .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, #noqa - self.app.model.GalaxySession.table.c.is_valid==True ) ).first() #noqa - # If remote user is in use it can invalidate the session and in some - # cases won't have a cookie set above, so we need to to check some - # things now. - if self.app.config.use_remote_user: - # If this is an api request, and they've passed a key, we let this go. - assert self.app.config.remote_user_header in self.environ, \ - "use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header - remote_user_email = self.environ[ self.app.config.remote_user_header ] - if getattr( self.app.config, "normalize_remote_user_email", False ): - remote_user_email = remote_user_email.lower() - if galaxy_session: - # An existing session, make sure correct association exists - if galaxy_session.user is None: - # No user, associate - galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) - galaxy_session_requires_flush = True - elif ((galaxy_session.user.email != remote_user_email) and - ((not self.app.config.allow_user_impersonation) or - (remote_user_email not in self.app.config.admin_users_list))): - # Session exists but is not associated with the correct - # remote user, and the currently set remote_user is not a - # potentially impersonating admin. - invalidate_existing_session = True - user_for_new_session = self.get_or_create_remote_user( remote_user_email ) - log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, galaxy_session.user.email ) - else: - # No session exists, get/create user for new session - user_for_new_session = self.get_or_create_remote_user( remote_user_email ) - else: - if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external: - # Remote user support is not enabled, but there is an existing - # session with an external user, invalidate - invalidate_existing_session = True - log.warning( "User '%s' is an external user with an existing session, invalidating session since external auth is disabled", - galaxy_session.user.email ) - elif galaxy_session is not None and galaxy_session.user is not None and galaxy_session.user.deleted: - invalidate_existing_session = True - log.warning( "User '%s' is marked deleted, invalidating session" % galaxy_session.user.email ) - # Do we need to invalidate the session for some reason? - if invalidate_existing_session: - prev_galaxy_session = galaxy_session - prev_galaxy_session.is_valid = False - galaxy_session = None - # No relevant cookies, or couldn't find, or invalid, so create a new session - if galaxy_session is None: - galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) - galaxy_session_requires_flush = True - self.galaxy_session = galaxy_session - self.__update_session_cookie( name=session_cookie ) - else: - self.galaxy_session = galaxy_session - # Do we need to flush the session? - if galaxy_session_requires_flush: - self.sa_session.add( galaxy_session ) - # FIXME: If prev_session is a proper relation this would not - # be needed. - if prev_galaxy_session: - self.sa_session.add( prev_galaxy_session ) - self.sa_session.flush() - # If the old session was invalid, get a new history with our new session - if invalidate_existing_session: - self.new_history() - - def _ensure_logged_in_user( self, environ, session_cookie ): - # The value of session_cookie can be one of - # 'galaxysession' or 'galaxycommunitysession' - # Currently this method does nothing unless session_cookie is 'galaxysession' - if session_cookie == 'galaxysession' and self.galaxy_session.user is None: - # TODO: re-engineer to eliminate the use of allowed_paths - # as maintenance overhead is far too high. - allowed_paths = ( - url_for( controller='root', action='index' ), - url_for( controller='root', action='tool_menu' ), - url_for( controller='root', action='masthead' ), - url_for( controller='root', action='history' ), - url_for( controller='user', action='api_keys' ), - url_for( controller='user', action='create' ), - url_for( controller='user', action='index' ), - url_for( controller='user', action='login' ), - url_for( controller='user', action='logout' ), - url_for( controller='user', action='manage_user_info' ), - url_for( controller='user', action='set_default_permissions' ), - url_for( controller='user', action='reset_password' ), - url_for( controller='user', action='openid_auth' ), - url_for( controller='user', action='openid_process' ), - url_for( controller='user', action='openid_associate' ), - url_for( controller='library', action='browse' ), - url_for( controller='history', action='list' ), - url_for( controller='dataset', action='list' ) - ) - display_as = url_for( controller='root', action='display_as' ) - if self.app.datatypes_registry.get_display_sites('ucsc') and self.request.path == display_as: - try: - host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0] - except( socket.error, socket.herror, socket.gaierror, socket.timeout ): - host = None - if host in UCSC_SERVERS: - return - external_display_path = url_for( controller='', action='display_application' ) - if self.request.path.startswith( external_display_path ): - request_path_split = self.request.path.split( '/' ) - try: - if (self.app.datatypes_registry.display_applications.get( request_path_split[-5] ) - and request_path_split[-4] in self.app.datatypes_registry.display_applications.get( request_path_split[-5] ).links - and request_path_split[-3] != 'None'): - return - except IndexError: - pass - if self.request.path not in allowed_paths: - self.response.send_redirect( url_for( controller='root', action='index' ) ) - - def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): - """ - Create a new GalaxySession for this request, possibly with a connection - to a previous session (in `prev_galaxy_session`) and an existing user - (in `user_for_new_session`). - - Caller is responsible for flushing the returned session. - """ - session_key = self.security.get_new_guid() - galaxy_session = self.app.model.GalaxySession( - session_key=session_key, - is_valid=True, - remote_host=self.request.remote_host, - remote_addr=self.request.remote_addr, - referer=self.request.headers.get( 'Referer', None ) ) - if prev_galaxy_session: - # Invalidated an existing session for some reason, keep track - galaxy_session.prev_session_id = prev_galaxy_session.id - if user_for_new_session: - # The new session should be associated with the user - galaxy_session.user = user_for_new_session - return galaxy_session - - def get_or_create_remote_user( self, remote_user_email ): - """ - Create a remote user with the email remote_user_email and return it - """ - if not self.app.config.use_remote_user: - return None - if getattr( self.app.config, "normalize_remote_user_email", False ): - remote_user_email = remote_user_email.lower() - user = self.sa_session.query( self.app.model.User - ).filter( self.app.model.User.table.c.email==remote_user_email ).first() #noqa - if user: - # GVK: June 29, 2009 - This is to correct the behavior of a previous bug where a private - # role and default user / history permissions were not set for remote users. When a - # remote user authenticates, we'll look for this information, and if missing, create it. - if not self.app.security_agent.get_private_user_role( user ): - self.app.security_agent.create_private_user_role( user ) - if 'webapp' not in self.environ or self.environ['webapp'] != 'tool_shed': - if not user.default_permissions: - self.app.security_agent.user_set_default_permissions( user ) - self.app.security_agent.user_set_default_permissions( user, history=True, dataset=True ) - elif user is None: - username = remote_user_email.split( '@', 1 )[0].lower() - random.seed() - user = self.app.model.User( email=remote_user_email ) - user.set_password_cleartext( ''.join( random.sample( string.letters + string.digits, 12 ) ) ) - user.external = True - # Replace invalid characters in the username - for char in filter( lambda x: x not in string.ascii_lowercase + string.digits + '-', username ): - username = username.replace( char, '-' ) - # Find a unique username - user can change it later - if ( self.sa_session.query( self.app.model.User ).filter_by( username=username ).first() ): - i = 1 - while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ): - i += 1 - username += '-' + str(i) - user.username = username - self.sa_session.add( user ) - self.sa_session.flush() - self.app.security_agent.create_private_user_role( user ) - # We set default user permissions, before we log in and set the default history permissions - if 'webapp' not in self.environ or self.environ['webapp'] != 'tool_shed': - self.app.security_agent.user_set_default_permissions( user ) - # self.log_event( "Automatically created account '%s'", user.email ) - return user - - def __update_session_cookie( self, name='galaxysession' ): - """ - Update the session cookie to match the current session. - """ - self.set_cookie( self.security.encode_guid(self.galaxy_session.session_key ), - name=name, path=self.app.config.cookie_path ) - - def handle_user_login( self, user ): - """ - Login a new user (possibly newly created) - - - create a new session - - associate new session with user - - if old session had a history and it was not associated with a user, associate it with the new session, - otherwise associate the current session's history with the user - - add the disk usage of the current session to the user's total disk usage - """ - # Set the previous session - prev_galaxy_session = self.galaxy_session - prev_galaxy_session.is_valid = False - # Define a new current_session - self.galaxy_session = self.__create_new_session( prev_galaxy_session, user ) - if self.webapp.name == 'galaxy': - cookie_name = 'galaxysession' - # Associated the current user's last accessed history (if exists) with their new session - history = None - try: - users_last_session = user.galaxy_sessions[0] - last_accessed = True - except: - users_last_session = None - last_accessed = False - if (prev_galaxy_session.current_history and not - prev_galaxy_session.current_history.deleted and - prev_galaxy_session.current_history.datasets): - if prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user: - # If the previous galaxy session had a history, associate it with the new - # session, but only if it didn't belong to a different user. - history = prev_galaxy_session.current_history - if prev_galaxy_session.user is None: - # Increase the user's disk usage by the amount of the previous history's datasets if they didn't already own it. - for hda in history.datasets: - user.total_disk_usage += hda.quota_amount( user ) - elif self.galaxy_session.current_history: - history = self.galaxy_session.current_history - if (not history and users_last_session and - users_last_session.current_history and not - users_last_session.current_history.deleted): - history = users_last_session.current_history - elif not history: - history = self.get_history( create=True ) - if history not in self.galaxy_session.histories: - self.galaxy_session.add_history( history ) - if history.user is None: - history.user = user - self.galaxy_session.current_history = history - if not last_accessed: - # Only set default history permissions if current history is not from a previous session - self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True ) - self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) ) - else: - cookie_name = 'galaxycommunitysession' - self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) - self.sa_session.flush() - # This method is not called from the Galaxy reports, so the cookie will always be galaxysession - self.__update_session_cookie( name=cookie_name ) - - def handle_user_logout( self, logout_all=False ): - """ - Logout the current user: - - invalidate the current session - - create a new session with no user associated - """ - prev_galaxy_session = self.galaxy_session - prev_galaxy_session.is_valid = False - self.galaxy_session = self.__create_new_session( prev_galaxy_session ) - self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) - galaxy_user_id = prev_galaxy_session.user_id - if logout_all and galaxy_user_id is not None: - for other_galaxy_session in self.sa_session.query( self.app.model.GalaxySession - ).filter( and_( self.app.model.GalaxySession.table.c.user_id==galaxy_user_id, #noqa - self.app.model.GalaxySession.table.c.is_valid==True, #noqa - self.app.model.GalaxySession.table.c.id!=prev_galaxy_session.id ) ): #noqa - other_galaxy_session.is_valid = False - self.sa_session.add( other_galaxy_session ) - self.sa_session.flush() - if self.webapp.name == 'galaxy': - # This method is not called from the Galaxy reports, so the cookie will always be galaxysession - self.__update_session_cookie( name='galaxysession' ) - elif self.webapp.name == 'tool_shed': - self.__update_session_cookie( name='galaxycommunitysession' ) - - def get_galaxy_session( self ): - """ - Return the current galaxy session - """ - return self.galaxy_session - - def get_history( self, create=False ): - """ - Load the current history, creating a new one only if there is not - current history and we're told to create. - Transactions will not always have an active history (API requests), so - None is a valid response. - """ - history = None - if self.galaxy_session: - history = self.galaxy_session.current_history - if not history and util.string_as_bool( create ): - history = self.new_history() - return history - - def set_history( self, history ): - if history and not history.deleted: - self.galaxy_session.current_history = history - self.sa_session.add( self.galaxy_session ) - self.sa_session.flush() - - history = property( get_history, set_history ) - - def get_or_create_default_history( self ): - """ - Gets or creates a default history and associates it with the current - session. - """ - - # There must be a user to fetch a default history. - if not self.galaxy_session.user: - return self.new_history() - - # Look for default history that (a) has default name + is not deleted and - # (b) has no datasets. If suitable history found, use it; otherwise, create - # new history. - unnamed_histories = self.sa_session.query( self.app.model.History ).filter_by( - user=self.galaxy_session.user, - name=self.app.model.History.default_name, - deleted=False ) - default_history = None - for history in unnamed_histories: - if len( history.datasets ) == 0: - # Found suitable default history. - default_history = history - break - - # Set or create hsitory. - if default_history: - history = default_history - self.set_history( history ) - else: - history = self.new_history() - - return history - - def new_history( self, name=None ): - """ - Create a new history and associate it with the current session and - its associated user (if set). - """ - # Create new history - history = self.app.model.History() - if name: - history.name = name - # Associate with session - history.add_galaxy_session( self.galaxy_session ) - # Make it the session's current history - self.galaxy_session.current_history = history - # Associate with user - if self.galaxy_session.user: - history.user = self.galaxy_session.user - # Track genome_build with history - history.genome_build = self.app.genome_builds.default_value - # Set the user's default history permissions - self.app.security_agent.history_set_default_permissions( history ) - # Save - self.sa_session.add_all( ( self.galaxy_session, history ) ) - self.sa_session.flush() - return history - - @base.lazy_property - def template_context( self ): - return dict() - - def make_form_data( self, name, **kwargs ): - rval = self.template_context[name] = FormData() - rval.values.update( kwargs ) - return rval - - def set_message( self, message, type=None ): - """ - Convenience method for setting the 'message' and 'message_type' - element of the template context. - """ - self.template_context['message'] = message - if type: - self.template_context['status'] = type - - def get_message( self ): - """ - Convenience method for getting the 'message' element of the template - context. - """ - return self.template_context['message'] - - def show_message( self, message, type='info', refresh_frames=[], cont=None, use_panels=False, active_view="" ): - """ - Convenience method for displaying a simple page with a single message. - - `type`: one of "error", "warning", "info", or "done"; determines the - type of dialog box and icon displayed with the message - - `refresh_frames`: names of frames in the interface that should be - refreshed when the message is displayed - """ - return self.fill_template( "message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) - - def show_error_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): - """ - Convenience method for displaying an error message. See `show_message`. - """ - return self.show_message( message, 'error', refresh_frames, use_panels=use_panels, active_view=active_view ) - - def show_ok_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): - """ - Convenience method for displaying an ok message. See `show_message`. - """ - return self.show_message( message, 'done', refresh_frames, use_panels=use_panels, active_view=active_view ) - - def show_warn_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): - """ - Convenience method for displaying an warn message. See `show_message`. - """ - return self.show_message( message, 'warning', refresh_frames, use_panels=use_panels, active_view=active_view ) - - def show_form( self, form, header=None, template="form.mako", use_panels=False, active_view="" ): - """ - Convenience method for displaying a simple page with a single HTML - form. - """ - return self.fill_template( template, form=form, header=header, - use_panels=( form.use_panels or use_panels ), - active_view=active_view ) - - def fill_template(self, filename, **kwargs): - """ - Fill in a template, putting any keyword arguments on the context. - """ - # call get_user so we can invalidate sessions from external users, - # if external auth has been disabled. - self.get_user() - if filename.endswith( ".mako" ): - return self.fill_template_mako( filename, **kwargs ) - else: - template = Template( file=os.path.join(self.app.config.template_path, filename), - searchList=[kwargs, self.template_context, dict(caller=self, t=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app)] ) - return str( template ) - - def fill_template_mako( self, filename, template_lookup=None, **kwargs ): - template_lookup = template_lookup or self.webapp.mako_template_lookup - template = template_lookup.get_template( filename ) - template.output_encoding = 'utf-8' - - data = dict( caller=self, t=self, trans=self, h=helpers, util=util, - request=self.request, response=self.response, app=self.app ) - data.update( self.template_context ) - data.update( kwargs ) - return template.render( **data ) - - def stream_template_mako( self, filename, **kwargs ): - template = self.webapp.mako_template_lookup.get_template( filename ) - template.output_encoding = 'utf-8' - data = dict( caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app ) - data.update( self.template_context ) - data.update( kwargs ) - - def render( environ, start_response ): - response_write = start_response( self.response.wsgi_status(), self.response.wsgi_headeritems() ) - - class StreamBuffer( object ): - def write( self, d ): - response_write( d.encode( 'utf-8' ) ) - buffer = StreamBuffer() - context = mako.runtime.Context( buffer, **data ) - template.render_context( context ) - return [] - return render - - def fill_template_string(self, template_string, context=None, **kwargs): - """ - Fill in a template, putting any keyword arguments on the context. - """ - template = Template( source=template_string, - searchList=[context or kwargs, dict(caller=self)] ) - return str(template) - - -class FormBuilder( object ): - """ - Simple class describing an HTML form - """ - def __init__( self, action="", title="", name="form", submit_text="submit", use_panels=False ): - self.title = title - self.name = name - self.action = action - self.submit_text = submit_text - self.inputs = [] - self.use_panels = use_panels - - def add_input( self, type, name, label, value=None, error=None, help=None, use_label=True ): - self.inputs.append( FormInput( type, label, name, value, error, help, use_label ) ) - return self - - def add_text( self, name, label, value=None, error=None, help=None ): - return self.add_input( 'text', label, name, value, error, help ) - - def add_password( self, name, label, value=None, error=None, help=None ): - return self.add_input( 'password', label, name, value, error, help ) - - def add_select( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): - self.inputs.append( SelectInput( name, label, value=value, options=options, error=error, help=help, use_label=use_label ) ) - return self - - -class FormInput( object ): - """ - Simple class describing a form input element - """ - def __init__( self, type, name, label, value=None, error=None, help=None, use_label=True, extra_attributes={}, **kwargs ): - self.type = type - self.name = name - self.label = label - self.value = value - self.error = error - self.help = help - self.use_label = use_label - self.extra_attributes = extra_attributes - - -class DatalistInput( FormInput ): - """ Data list input """ - - def __init__( self, name, *args, **kwargs ): - if 'extra_attributes' not in kwargs: - kwargs[ 'extra_attributes' ] = {} - kwargs[ 'extra_attributes' ][ 'list' ] = name - FormInput.__init__( self, None, name, *args, **kwargs ) - self.options = kwargs.get( 'options', {} ) - - def body_html( self ): - options = "".join( [ "<option value='%s'>%s</option>" % ( key, value ) for key, value in self.options.iteritems() ] ) - return """<datalist id="%s">%s</datalist>""" % ( self.name, options ) - - -class SelectInput( FormInput ): - """ A select form input. """ - def __init__( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): - FormInput.__init__( self, "select", name, label, value=value, error=error, help=help, use_label=use_label ) - self.options = options - - -class FormData( object ): - """ - Class for passing data about a form to a template, very rudimentary, could - be combined with the tool form handling to build something more general. - """ - def __init__( self ): - self.values = Bunch() - self.errors = Bunch() - - -class Bunch( dict ): - """ - Bunch based on a dict - """ - def __getattr__( self, key ): - if key not in self: - raise AttributeError(key) - return self[key] - - def __setattr__( self, key, value ): - self[key] = value This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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