galaxy-commits September 2014

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commit/galaxy-central: dannon: Pep8 fixes in galaxy.util.json prior to work there.
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a718b389bf1/ Changeset: 6a718b389bf1 User: dannon Date: 2014-09-04 22:58:57 Summary: Pep8 fixes in galaxy.util.json prior to work there. Affected #: 1 file diff -r 83e45a9e4cc994daed44e406a334660d9db7ed30 -r 6a718b389bf1caa5461c5ff7a7dd644f1279cd69 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -5,7 +5,6 @@ import json import logging import random -import socket import string to_json_string = json.dumps @@ -13,6 +12,7 @@ log = logging.getLogger( __name__ ) + def json_fix( val ): if isinstance( val, list ): return [ json_fix( v ) for v in val ] @@ -25,33 +25,44 @@ # Methods for handling JSON-RPC + def validate_jsonrpc_request( request, regular_methods, notification_methods ): try: request = from_json_string( request ) except Exception, e: - return False, request, jsonrpc_response( id = None, error = dict( code = -32700, message = 'Parse error', data = str( e ) ) ) + return False, request, jsonrpc_response( id=None, + error=dict( code=-32700, + message='Parse error', + data=str( e ) ) ) try: assert 'jsonrpc' in request, \ 'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Request object as per the JSON-RPC 2.0 Specification.' assert request['jsonrpc'] == '2.0', \ - 'Requested JSON-RPC version "%s" != required version "2.0".' % request['jsonrpc'] + 'Requested JSON-RPC version "%s" != required version "2.0".' % request['jsonrpc'] assert 'method' in request, 'No "method" member was sent with the Request object' except AssertionError, e: - return False, request, jsonrpc_response( request = request, error = dict( code = -32600, message = 'Invalid Request', data = str( e ) ) ) + return False, request, jsonrpc_response( request=request, + error=dict( code=-32600, + message='Invalid Request', + data=str( e ) ) ) try: assert request['method'] in ( regular_methods + notification_methods ) except AssertionError, e: - return False, request, jsonrpc_response( request = request, - error = dict( code = -32601, - message = 'Method not found', - data = 'Valid methods are: %s' % ', '.join( regular_methods + notification_methods ) ) ) + return False, request, jsonrpc_response( request=request, + error=dict( code=-32601, + message='Method not found', + data='Valid methods are: %s' % ', '.join( regular_methods + notification_methods ) ) ) try: if request['method'] in regular_methods: assert 'id' in request, 'No "id" member was sent with the Request object and the requested method "%s" is not a notification method' % request['method'] except AssertionError, e: - return False, request, jsonrpc_response( request = request, error = dict( code = -32600, message = 'Invalid Request', data = str( e ) ) ) + return False, request, jsonrpc_response( request=request, + error=dict( code=-32600, + message='Invalid Request', + data=str( e ) ) ) return True, request, None + def validate_jsonrpc_response( response, id=None ): try: response = from_json_string( response ) @@ -81,11 +92,12 @@ return False, response return True, response + def jsonrpc_request( method, params=None, id=None, jsonrpc='2.0' ): if method is None: log.error( 'jsonrpc_request(): "method" parameter cannot be None' ) return None - request = dict( jsonrpc = jsonrpc, method = method ) + request = dict( jsonrpc=jsonrpc, method=method ) if params: request['params'] = params if id is not None and id is True: @@ -94,15 +106,16 @@ request['id'] = id return request + def jsonrpc_response( request=None, id=None, result=None, error=None, jsonrpc='2.0' ): if result: - rval = dict( jsonrpc = jsonrpc, result = result ) + rval = dict( jsonrpc=jsonrpc, result=result ) elif error: - rval = dict( jsonrpc = jsonrpc, error = error ) + rval = dict( jsonrpc=jsonrpc, error=error ) else: msg = 'jsonrpc_response() called with out a "result" or "error" parameter' log.error( msg ) - rval = dict( jsonrpc = jsonrpc, error = msg ) + rval = dict( jsonrpc=jsonrpc, error=msg ) if id is not None: rval['id'] = id elif request is not None and 'id' in request: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Close feature branch
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/901144086f2e/ Changeset: 901144086f2e Branch: venv User: dannon Date: 2014-09-04 22:44:25 Summary: Close feature branch Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in carlfeberhard/galaxy-central-fork0 (pull request #484)
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

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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commit/galaxy-central: 14 new changesets
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

14 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d57655849ac4/ Changeset: d57655849ac4 User: carlfeberhard Date: 2014-09-03 14:57:25 Summary: Empty out web/framework/__init__ into decorator, transaction, webapp, and formbuilder, fix related imports Affected #: 18 files diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 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 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 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 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 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.transaction.GalaxyWebTransaction`` :param trans: transaction doing the rendering :type plugin: ``util.bunch.Bunch`` :param plugin: the plugin containing the template to render diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 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.config.ucsc_display_sites 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 diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 lib/galaxy/web/framework/decorators.py --- /dev/null +++ b/lib/galaxy/web/framework/decorators.py @@ -0,0 +1,334 @@ +import inspect +from traceback import format_exc +from functools import wraps + +from galaxy import eggs +eggs.require( "Paste" ) +import paste.httpexceptions + +from galaxy import util +from galaxy.exceptions import error_codes +from galaxy.exceptions import MessageException +from galaxy.util.json import from_json_string, to_json_string + +import logging +log = logging.getLogger( __name__ ) + + +JSON_CONTENT_TYPE = "application/json" + + +def error( message ): + raise MessageException( message, type='error' ) + + +# ----------------------------------------------------------------------------- web controller decorators +def _save_orig_fn( wrapped, orig ): + if not hasattr( orig, '_orig' ): + wrapped._orig = orig + return wrapped + +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 + return expose( _save_orig_fn( call_and_format, func ) ) + +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() + return expose( _save_orig_fn( decorator, func ) ) + +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 ) diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 lib/galaxy/web/framework/formbuilder.py --- /dev/null +++ b/lib/galaxy/web/framework/formbuilder.py @@ -0,0 +1,93 @@ +from galaxy.util import bunch + +import logging +log = logging.getLogger( __name__ ) + +#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 + +def form( *args, **kwargs ): + return FormBuilder( *args, **kwargs ) + +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 ): +#TODO: galaxy's two Bunchs are defined differently. Is this right? + self.values = bunch.Bunch() + self.errors = bunch.Bunch() diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r d57655849ac41b2b1f90b73e2835d618df45e985 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -5,7 +5,8 @@ from galaxy.util import sanitize_text from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict -from galaxy.web.framework import error, url_for +from galaxy.web.framework import decorators +from galaxy.web.framework import url_for from galaxy.web.framework.helpers import iff from sqlalchemy.sql.expression import and_, func, or_ @@ -317,7 +318,7 @@ try: id = map( int, id ) except: - error( "Invalid id" ) + decorators.error( "Invalid id" ) return id # ---- Override these ---------------------------------------------------- def handle_operation( self, trans, operation, ids, **kwargs ): This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/360d9d7839d7/ Changeset: 360d9d7839d7 User: carlfeberhard Date: 2014-09-03 15:59:59 Summary: merge central Affected #: 3 files diff -r d57655849ac41b2b1f90b73e2835d618df45e985 -r 360d9d7839d74f01a2da5b35fb1be10464956112 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -96,11 +96,9 @@ # Load history import/export tools. load_history_imp_exp_tools( self.toolbox ) # visualizations registry: associates resources with visualizations, controls how to render - self.visualizations_registry = None - if self.config.visualization_plugins_directory: - self.visualizations_registry = VisualizationsRegistry( self, - directories_setting=self.config.visualization_plugins_directory, - template_cache_dir=self.config.template_cache ) + self.visualizations_registry = VisualizationsRegistry( self, + directories_setting=self.config.visualization_plugins_directory, + template_cache_dir=self.config.template_cache ) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) diff -r d57655849ac41b2b1f90b73e2835d618df45e985 -r 360d9d7839d74f01a2da5b35fb1be10464956112 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -376,8 +376,9 @@ self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) ) self.fluent_host = kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) ) - # visualization plugin framework - self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', None ) + # directory where the visualization/registry searches for plugins + self.visualization_plugins_directory = kwargs.get( + 'visualization_plugins_directory', 'config/plugins/visualizations' ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff -r d57655849ac41b2b1f90b73e2835d618df45e985 -r 360d9d7839d74f01a2da5b35fb1be10464956112 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -210,8 +210,8 @@ # Visualizations config directory: where to look for individual visualization plugins. # The path is relative to the Galaxy root dir. To use an absolute path begin the path -# with '/'. -visualization_plugins_directory = config/plugins/visualizations +# with '/'. Defaults to "config/plugins/visualizations". +#visualization_plugins_directory = config/plugins/visualizations # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be https://bitbucket.org/galaxy/galaxy-central/commits/a0c16c8930b7/ Changeset: a0c16c8930b7 User: carlfeberhard Date: 2014-09-03 17:22:15 Summary: Combine transaction into webapp, move trans mixins to managers/context.py Affected #: 3 files diff -r 360d9d7839d74f01a2da5b35fb1be10464956112 -r a0c16c8930b76cfe98574b2e8b3311f7b2504361 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.transaction.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 360d9d7839d74f01a2da5b35fb1be10464956112 -r a0c16c8930b76cfe98574b2e8b3311f7b2504361 lib/galaxy/web/framework/transaction.py --- a/lib/galaxy/web/framework/transaction.py +++ /dev/null @@ -1,868 +0,0 @@ -import hashlib -import os -import random -import socket -import string -import time -from Cookie import CookieError - -from galaxy import eggs -eggs.require( "Cheetah" ) -from Cheetah.Template import Template -eggs.require( "Mako" ) -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 - -from galaxy import util -from galaxy.util import asbool -from galaxy.util import safe_str_cmp -from galaxy.util.json import to_json_string -from galaxy.web.framework import base -from galaxy.web.framework import helpers - -import logging -log = logging.getLogger( __name__ ) - - -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', -) - - -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, util.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 ) - - -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.config.ucsc_display_sites 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) - - diff -r 360d9d7839d74f01a2da5b35fb1be10464956112 -r a0c16c8930b76cfe98574b2e8b3311f7b2504361 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -1,16 +1,40 @@ +""" +""" import inspect import os +import hashlib +import random +import socket +import string +import time +from Cookie import CookieError from galaxy import eggs eggs.require( "Cheetah" ) from Cheetah.Template import Template eggs.require( "Mako" ) +import mako.runtime import mako.lookup +# pytz is used by Babel. +eggs.require( "pytz" ) +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 from galaxy.exceptions import MessageException + +from galaxy import util +from galaxy.util import asbool +from galaxy.util import safe_str_cmp from galaxy.util.backports.importlib import import_module from galaxy.util.sanitize_html import sanitize_html + +from galaxy.managers import context from galaxy.web.framework import base +from galaxy.web.framework import helpers from galaxy.web.framework import transaction from galaxy.web.framework import formbuilder @@ -18,8 +42,27 @@ log = logging.getLogger( __name__ ) +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', +) + + class WebApplication( base.WebApplication ): - + """ + A web application that: + * adds API and UI controllers by scanning given directories and + importing all modules found there. + * has a security object. + * builds mako template lookups. + * generates GalaxyWebTransactions. + """ def __init__( self, galaxy_app, session_cookie='galaxysession', name=None ): self.name = name base.WebApplication.__init__( self ) @@ -54,7 +97,7 @@ return base.WebApplication.make_body_iterable( self, trans, body ) def transaction_chooser( self, environ, galaxy_app, session_cookie ): - return transaction.GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) + return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) def add_ui_controllers( self, package_name, app ): """ @@ -113,3 +156,656 @@ really just used to stub out actual controllers for routes testing. """ return T( app ) + + +class GalaxyWebTransaction( base.DefaultWebTransaction, + context.ProvidesAppContext, context.ProvidesUserContext, context.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.config.ucsc_display_sites 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) https://bitbucket.org/galaxy/galaxy-central/commits/d66fefbc6bd6/ Changeset: d66fefbc6bd6 User: carlfeberhard Date: 2014-09-03 17:22:29 Summary: merge central Affected #: 1 file diff -r a0c16c8930b76cfe98574b2e8b3311f7b2504361 -r d66fefbc6bd67201f8833e7c5d5a881d4830951f lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -83,7 +83,7 @@ Check whether the folder is accessible to current user. By default every folder is accessible (contents have their own permissions). """ - return True + return folder def get_folder_dict( self, trans, folder ): """ @@ -156,6 +156,19 @@ add_library_item_role_list = [ ( add_role.name, trans.security.encode_id( add_role.id ) ) for add_role in add_roles ] return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list ) + def can_add_item( self, trans, folder ): + """ + Return true if the user has permissions to add item to the given folder. + """ + if trans.user_is_admin: + return True + current_user_roles = trans.get_current_user_roles() + add_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) + for role in current_user_roles: + if role in add_roles: + return True + return False + def cut_the_prefix( self, encoded_folder_id ): """ Remove the prefix from the encoded folder id. https://bitbucket.org/galaxy/galaxy-central/commits/5bc83c22c468/ Changeset: 5bc83c22c468 User: carlfeberhard Date: 2014-09-03 17:44:25 Summary: Add managers/context.py, remove import of transaction Affected #: 1 file diff -r d66fefbc6bd67201f8833e7c5d5a881d4830951f -r 5bc83c22c4685bae000f6ff7bd2b43a695138022 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -35,7 +35,6 @@ from galaxy.managers import context from galaxy.web.framework import base from galaxy.web.framework import helpers -from galaxy.web.framework import transaction from galaxy.web.framework import formbuilder import logging https://bitbucket.org/galaxy/galaxy-central/commits/efd4b01d8ae6/ Changeset: efd4b01d8ae6 User: carlfeberhard Date: 2014-09-03 17:46:38 Summary: Fix to 5bc83c2 Affected #: 1 file diff -r 5bc83c22c4685bae000f6ff7bd2b43a695138022 -r efd4b01d8ae64f6a7d25011295a919fea3324f1d 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 ) https://bitbucket.org/galaxy/galaxy-central/commits/35a335db606f/ Changeset: 35a335db606f User: carlfeberhard Date: 2014-09-03 21:18:55 Summary: Fix bunch import; fix unit test imports Affected #: 3 files diff -r efd4b01d8ae64f6a7d25011295a919fea3324f1d -r 35a335db606f3f53e5028ef5463ba78fe6f72000 lib/galaxy/webapps/demo_sequencer/framework/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py +++ b/lib/galaxy/webapps/demo_sequencer/framework/__init__.py @@ -32,7 +32,7 @@ from galaxy.web.framework.formbuilder import FormData import galaxy.web.framework.base -from galaxy.web.util.bunch import Bunch +from galaxy.util.bunch import Bunch from galaxy.exceptions import MessageException from galaxy.util import asbool diff -r efd4b01d8ae64f6a7d25011295a919fea3324f1d -r 35a335db606f3f53e5028ef5463ba78fe6f72000 test/unit/test_galaxy_transactions.py --- a/test/unit/test_galaxy_transactions.py +++ b/test/unit/test_galaxy_transactions.py @@ -1,10 +1,10 @@ from galaxy import model from galaxy.model import mapping from galaxy.util import bunch -from galaxy.web import framework +from galaxy.managers import context -class TestTransaction( framework.ProvidesAppContext ): +class TestTransaction( context.ProvidesAppContext ): def __init__( self ): self.app = TestApp() diff -r efd4b01d8ae64f6a7d25011295a919fea3324f1d -r 35a335db606f3f53e5028ef5463ba78fe6f72000 test/unit/test_routes.py --- a/test/unit/test_routes.py +++ b/test/unit/test_routes.py @@ -1,7 +1,7 @@ #import routes # Unused but adds some stuff to routes.Mapper. -from galaxy.web.framework import WebApplication +from galaxy.web.framework.webapp import WebApplication from galaxy.webapps.galaxy import buildapp as galaxy_buildapp from galaxy.web import url_for https://bitbucket.org/galaxy/galaxy-central/commits/19b109c4caa6/ Changeset: 19b109c4caa6 User: carlfeberhard Date: 2014-09-03 21:19:09 Summary: merge central Affected #: 1 file diff -r 35a335db606f3f53e5028ef5463ba78fe6f72000 -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 test/functional/tools/multi_output_configured.xml --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -10,6 +10,8 @@ echo "3" > subdir2/CUSTOM_3.txt; mkdir subdir3; echo "Foo" > subdir3/Foo; + echo "mapped reads" > split_bam_.MAPPED.bam; + echo "unmapped reads" > split_bam_.UNMAPPED.bam; </command><inputs><param name="num_param" type="integer" value="7" /> @@ -17,9 +19,10 @@ </inputs><outputs><data format="txt" name="report"> - <discover_datasets pattern="__designation_and_ext__" directory="subdir1" /> - <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" /> - <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /> + <discover_datasets pattern="__designation_and_ext__" directory="subdir1" visible="true" /> + <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" visible="true" /> + <discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" /> + <discover_datasets pattern="split_bam_\.(?P<designation>([A-Z-])\w+)\.bam" ext="txt" visible="true" /></data></outputs><tests> @@ -45,6 +48,12 @@ <discovered_dataset designation="Foo" ftype="txt"><assert_contents><has_line line="Foo" /></assert_contents></discovered_dataset> + <discovered_dataset designation="MAPPED" ftype="txt"> + <assert_contents><has_line line="mapped reads" /></assert_contents> + </discovered_dataset> + <discovered_dataset designation="UNMAPPED" ftype="txt"> + <assert_contents><has_line line="unmapped reads" /></assert_contents> + </discovered_dataset></output></test></tests> https://bitbucket.org/galaxy/galaxy-central/commits/520eb21f9a1e/ Changeset: 520eb21f9a1e User: carlfeberhard Date: 2014-09-04 16:09:13 Summary: merge central Affected #: 16 files diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -ea12550fbc34260ae70bde38db59a4024f35f988 latest_2014.08.11 +20f4fdf1735aeff23a6e7ab00389781fe3f3142c latest_2014.08.11 diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -248,6 +248,10 @@ def get_initial_value( self, trans, context, history=None ): return self.value + def to_dict( self, trans, view='collection', value_mapper=None ): + d = super(TextToolParameter, self).to_dict(trans) + d['area'] = self.area + return d class IntegerToolParameter( TextToolParameter ): """ @@ -459,6 +463,13 @@ else: return self.falsevalue + def to_dict( self, trans, view='collection', value_mapper=None ): + d = super(BooleanToolParameter, self).to_dict(trans) + d['value'] = self.checked + d['truevalue'] = self.truevalue + d['falsevalue'] = self.falsevalue + return d + @property def legal_values( self ): return [ self.truevalue, self.falsevalue ] @@ -992,7 +1003,8 @@ value = option[1] d[ 'value' ] = value - d[ 'display' ] = self.display + d['display'] = self.display + d['multiple'] = self.multiple return d @@ -1251,7 +1263,10 @@ d = super( ColumnListParameter, self ).to_dict( trans ) # add data reference - d[ 'data_ref' ] = self.data_ref + d['data_ref'] = self.data_ref + + # add numerical flag + d['numerical'] = self.numerical # return return d @@ -2008,6 +2023,11 @@ ref = ref() return ref + def to_dict( self, trans, view='collection', value_mapper=None ): + d = super( DataToolParameter, self ).to_dict( trans ) + d['extensions'] = self.extensions + d['multiple'] = self.multiple + return d class DataCollectionToolParameter( BaseDataToolParameter ): """ @@ -2110,6 +2130,8 @@ elif isinstance( value, basestring ): if value.startswith( "dce:" ): rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] ) + elif value.startswith( "hdca:" ): + rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] ) else: rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value ) if rval and isinstance( rval, trans.app.model.HistoryDatasetCollectionAssociation ): diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -38,9 +38,6 @@ // reset sequential input definition list this.input_list = {}; - // create data model - this.data = new Backbone.Model(); - // initialize datasets this.datasets = new ToolDatasets({ success: function() { diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -11,12 +11,6 @@ // link inputs this.inputs = options.inputs; - // link datasets - this.datasets = app.datasets; - - // link data model - this.data = app.data; - // add table class for tr tag // this assist in transforming the form into a json structure options.cls_tr = 'section-row'; @@ -38,12 +32,12 @@ // load settings elements into table for (var i in this.inputs) { - this._add(this.inputs[i], this.data); + this._add(this.inputs[i]); } }, // add table row - _add: function(input, data) { + _add: function(input) { // link this var self = this; @@ -61,7 +55,7 @@ switch(type) { // conditional field case 'conditional': - this._addConditional(input_def, data); + this._addConditional(input_def); break; // repeat block case 'repeat': @@ -69,12 +63,12 @@ break; // default single element row default: - this._addRow(type, input_def, data); + this._addRow(type, input_def); } }, // add conditional block - _addConditional: function(input_def, data) { + _addConditional: function(input_def) { // add label to input definition root input_def.label = input_def.test_param.label; @@ -82,7 +76,7 @@ input_def.value = input_def.test_param.value; // build options field - this._addRow('conditional', input_def, data); + this._addRow('conditional', input_def); // add fields for (var i in input_def.cases) { @@ -182,7 +176,7 @@ }, // add table row - _addRow: function(field_type, input_def, data) { + _addRow: function(field_type, input_def) { // get id var id = input_def.id; @@ -193,65 +187,59 @@ switch(field_type) { // text input field case 'text' : - field = this._field_text(input_def, data); + field = this._field_text(input_def); break; // select field case 'select' : - field = this._field_select(input_def, data); + field = this._field_select(input_def); break; - // radiobox field - case 'radiobutton' : - field = this._field_radio(input_def, data); - break; - // dataset case 'data': - field = this._field_data(input_def, data); + field = this._field_data(input_def); break; // dataset column case 'data_column': - field = this._field_column(input_def, data); - break; - - // text area field - case 'textarea' : - field = this._field_textarea(input_def, data); + field = this._field_column(input_def); break; // conditional select field case 'conditional': - field = this._field_conditional(input_def, data); + field = this._field_conditional(input_def); break; // hidden field case 'hidden': - field = this._field_hidden(input_def, data); + field = this._field_hidden(input_def); break; // integer field case 'integer': - field = this._field_integer(input_def, data); + field = this._field_slider(input_def); break; + // float field + case 'float': + field = this._field_slider(input_def); + break; + // boolean field case 'boolean': - field = this._field_radiobutton(input_def, data); + field = this._field_boolean(input_def); break; // default default: - field = this._field_text(input_def, data); + field = this._field_text(input_def); console.debug('tools-form::_addRow() : Unmatched field type (' + field_type + ').'); } - // set value - if (!data.get(id)) { - data.set(id, input_def.value); + // set field value + if (input_def.value !== undefined) { + field.value(input_def.value); } - field.value(data.get(id)); // add to field list this.app.field_list[id] = field; @@ -272,7 +260,7 @@ }, // conditional input field - _field_conditional : function(input_def, data) { + _field_conditional : function(input_def) { // link this var self = this; @@ -287,15 +275,10 @@ } // select field - var id = input_def.id; return new Ui.Select.View({ - id : 'field-' + id, + id : 'field-' + input_def.id, data : options, - value : data.get(id), onchange : function(value) { - // update value - data.set(id, value); - // check value in order to hide/show options for (var i in input_def.cases) { // get case @@ -329,7 +312,7 @@ }, // data input field - _field_data : function(input_def, data) { + _field_data : function(input_def) { // link this var self = this; @@ -337,7 +320,7 @@ var id = input_def.id; // get datasets - var datasets = this.datasets.filterType(); + var datasets = this.app.datasets.filterType(); // configure options fields var options = []; @@ -353,15 +336,19 @@ id : 'field-' + id, data : options, value : options[0].value, + multiple : input_def.multiple, onchange : function(value) { - // update value - data.set(id, value); + // pick the first dataset if multiple might be selected + // TODO: iterate over all datasets and filter common/consistent columns + if (input_def.multiple) { + value = value[0]; + } // get referenced columns - var column_list = self.app.tree.findReferences(id); + var column_list = self.app.tree.findReferences(id, 'data_column'); // find selected dataset - var dataset = self.datasets.filter(value); + var dataset = self.app.datasets.filter(value); // check dataset if (dataset && column_list.length > 0) { @@ -376,19 +363,34 @@ console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.'); } - // load column options - var columns = []; - for (var key in meta) { - // add to selection - columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', - 'value' : key - }); - } - // update referenced columns for (var i in column_list) { - var column_field = self.app.field_list[column_list[i]] + // get column input/field + var column_input = self.app.input_list[column_list[i]]; + var column_field = self.app.field_list[column_list[i]]; + if (!column_input || !column_field) { + console.debug('tool-form::field_data() - FAILED: Column not found.'); + } + + // is numerical? + var numerical = column_input.numerical; + + // identify column options + var columns = []; + for (var key in meta) { + // get column type + var column_type = meta[key]; + + // add to selection + if (column_type == 'int' || column_type == 'float' || !numerical) { + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } + } + + // update field if (column_field) { column_field.update(columns); if (!column_field.exists(column_field.value())) { @@ -404,20 +406,8 @@ }); }, - // column selection field - _field_column : function (input_def, data) { - var id = input_def.id; - return new Ui.Select.View({ - id : 'field-' + id, - value : data.get(id), - onchange : function(value) { - data.set(id, value); - } - }); - }, - // select field - _field_select : function (input_def, data) { + _field_select : function (input_def) { // configure options fields var options = []; for (var i in input_def.options) { @@ -430,95 +420,66 @@ // identify display type var SelectClass = Ui.Select; - if (input_def.display == 'checkboxes') { + switch (input_def.display) { + case 'checkboxes': + SelectClass = Ui.Checkbox; + break; + case 'radio': + SelectClass = Ui.RadioButton; + break; + } + + // force checkboxes if multiple has been selected + if (input_def.multiple) { SelectClass = Ui.Checkbox; } // select field - var id = input_def.id; return new SelectClass.View({ - id : 'field-' + id, - data : options, - value : data.get(id), - onchange : function(value) { - data.set(id, value); - } + id : 'field-' + input_def.id, + data : options }); }, - + + // column selection field + _field_column : function (input_def) { + return new Ui.Select.View({ + id : 'field-' + input_def.id, + multiple: input_def.multiple + }); + }, + // text input field - _field_text : function(input_def, data) { - var id = input_def.id; + _field_text : function(input_def) { return new Ui.Input({ - id : 'field-' + id, - value : data.get(id), - onchange : function(value) { - data.set(id, value); - } + id : 'field-' + input_def.id, + area : input_def.area }); }, // integer field - _field_integer: function(input_def, data) { - var id = input_def.id; + _field_slider: function(input_def) { return new Ui.Slider.View({ - id : 'field-' + id, - value : data.get(id), - onchange : function(value) { - data.set(id, value); - } - }); - }, - - // text area - _field_textarea : function(input_def, data) { - var id = input_def.id; - return new Ui.Textarea({ - id : 'field-' + id, - onchange : function() { - data.set(id, field.value()); - } - }); - }, - - // radio field - _field_radio : function(input_def, data) { - var id = input_def.id; - return new Ui.RadioButton({ - id : 'field-' + id, - data : input_def.data, - value : data.get(id), - onchange : function(value) { - data.set(id, value); - } + id : 'field-' + input_def.id, + min : input_def.min || 0, + max : input_def.max || 1000, + decimal : input_def.type == 'float' }); }, // hidden field - _field_hidden : function(input_def, data) { - var id = input_def.id; + _field_hidden : function(input_def) { return new Ui.Hidden({ - id : 'field-' + id, - value : data.get(id) + id : 'field-' + input_def.id }); }, - // hidden field - _field_radiobutton : function(input_def, data) { - var id = input_def.id; + // boolean field + _field_boolean : function(input_def) { return new Ui.RadioButton.View({ - id : 'field-' + id, - value : data.get(id), - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] + id : 'field-' + input_def.id, + data : [ { label : 'Yes', value : true }, + { label : 'No', value : false }] }); } }); diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -66,7 +66,7 @@ }, // find referenced elements - findReferences: function(identifier) { + findReferences: function(identifier, type) { // referenced elements var referenced = []; @@ -105,7 +105,7 @@ } // check for referenced element - if (input.data_ref == name) { + if (input.data_ref == name && input.type == type) { list.push(id); } } diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -312,7 +312,8 @@ placeholder : '', disabled : false, visible : true, - cls : '' + cls : '', + area : false }, // initialize @@ -352,60 +353,11 @@ // element _template: function(options) { - return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">'; - } -}); - -// plugin -var Textarea = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - type : 'text', - placeholder : '', - disabled : false, - visible : true, - cls : '' - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // disable input field - if (this.options.disabled) { - this.$el.prop('disabled', true); + if (options.area) { + return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '"></textarea>'; + } else { + return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">'; } - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // onchange event handler. fires on user activity. - var self = this; - this.$el.on('input', function() { - if (self.options.onchange) { - self.options.onchange(self.$el.val()); - } - }); - }, - - // value - value : function (new_val) { - if (new_val !== undefined) { - this.$el.val(new_val); - } - return this.$el.val(); - }, - - // element - _template: function(options) { - return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '" rows="5"></textarea>'; } }); @@ -455,7 +407,6 @@ Checkbox : Checkbox, Searchbox : Searchbox, Select : Select, - Textarea : Textarea, Hidden : Hidden, Slider : Slider } diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -7,24 +7,19 @@ var View = Backbone.View.extend({ // options optionsDefault : { - id : '', - cls : '', - empty : 'No data available', - visible : true, - wait : false + id : '', + cls : '', + empty : 'No data available', + visible : true, + wait : false, + multiple : false }, - // value - selected : null, - // initialize initialize : function(options) { // configure options this.options = Utils.merge(options, this.optionsDefault); - // initial value - this.selected = this.options.value; - // create new element this.setElement(this._template(this.options)); @@ -32,21 +27,17 @@ this.$select = this.$el.find('#select'); this.$icon = this.$el.find('#icon'); - // add change event. fires only on user activity - var self = this; - this.$select.on('change', function() { - self.value(self.$select.val()); - }); - - // add change event. fires on trigger - this.on('change', function() { - if (self.options.onchange) { - self.options.onchange(self.value()); - } - }); + // configure multiple + if (this.options.multiple) { + this.$select.prop('multiple', true); + this.$select.addClass('ui-select-multiple'); + this.$icon.remove(); + } else { + this.$el.addClass('ui-select'); + } // refresh - this._refresh(); + this.update(this.options.data); // show/hide if (!this.options.visible) { @@ -59,31 +50,25 @@ } else { this.show(); } + + // add change event. fires only on user activity + var self = this; + this.$select.on('change', function() { + self._change(); + }); + + // add change event. fires on trigger + this.on('change', function() { + self._change(); + }); }, // value value : function (new_value) { - - // get current id/value - var before = this.selected; - - // check if new_value is defined if (new_value !== undefined) { - this.selected = new_value; this.$select.val(new_value); } - - // get current id/value - var after = this.selected; - if (after) { - // fire onchange - if (after != before && this.options.onchange) { - this.options.onchange(after); - } - } - - // return - return after; + return this.$select.val(); }, // first @@ -157,6 +142,9 @@ // render update: function(options) { + // backup current value + var current = this.$select.val(); + // remove all options this.$select.find('option').remove(); @@ -167,6 +155,14 @@ // refresh this._refresh(); + + // set previous value + this.$select.val(current); + + // check if any value was set + if (!this.$select.val()) { + this.$select.val(this.first()); + } }, // set on change event @@ -179,6 +175,13 @@ return this.$select.find('option[value=' + value + ']').length > 0; }, + // change + _change: function() { + if (this.options.onchange) { + this.options.onchange(this.$select.val()); + } + }, + // refresh _refresh: function() { // remove placeholder @@ -196,41 +199,21 @@ // enable select field this.enable(); } - - // update value - if (this.selected) { - this.$select.val(this.selected); - } }, - // option + // template option _templateOption: function(options) { return '<option value="' + options.value + '">' + options.label + '</option>'; }, - // element + // template _template: function(options) { - var tmpl = '<div id="' + options.id + '" class="ui-select">' + - '<div class="button">' + - '<i id="icon"/>' + - '</div>' + - '<select id="select" class="select ' + options.cls + ' ' + options.id + '">'; - for (key in options.data) { - // options - var item = options.data[key]; - - // identify selected value - var tag = ''; - if (item.value == options.value || item.value == '') { - tag = 'selected'; - } - - // add template string - tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>'; - } - tmpl += '</select>' + - '</div>'; - return tmpl; + return '<div id="' + options.id + '">' + + '<div class="button">' + + '<i id="icon"/>' + + '</div>' + + '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' + + '</div>'; } }); diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/mvc/ui/ui-slider.js --- a/static/scripts/mvc/ui/ui-slider.js +++ b/static/scripts/mvc/ui/ui-slider.js @@ -7,7 +7,9 @@ optionsDefault: { value : '', min : 1, - max : 100 + max : 100, + step : 0.1, + decimal : false }, // initialize @@ -27,6 +29,11 @@ // backup integer field this.$text = this.$el.find('#text'); + // set step size + if (!this.options.decimal) { + this.options.step = 1; + } + // load slider plugin this.$slider.slider(this.options); @@ -38,7 +45,8 @@ // add text field event this.$text.on('keydown', function (event) { var v = event.which; - if (!(v == 13 || v == 8 || v == 189 || (v >= 48 && v <= 57))) { + if (!(v == 13 || v == 8 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57) + || (self.options.decimal && $(this).val().indexOf('.') == -1) && v == 190)) { event.preventDefault(); } }); diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.data=new Backbone.Model();this.datasets=new h({success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var l=this;this.model.fetch({error:function(m){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){l.inputs=l.model.get("inputs");l.portlet=new g.View({icon:"fa-wrench",title:"<b>"+l.model.get("name")+"</b> "+l.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){console.log(l.tree.create(l))}})}});l.message=new k.Message();l.portlet.append(l.message.$el);$(l.main_el).append(l.portlet.$el);if(l.options.help!=""){$(l.main_el).append(d.help(l.options.help))}if(l.options.citations){$(l.main_el).append(d.citations());var m=new i.ToolCitationCollection();m.tool_id=l.options.id;var n=new a.CitationListView({collection:m});n.render();m.fetch()}l.setElement(l.portlet.content());l.section=new j.View(l,{inputs:l.model.get("inputs")});l.portlet.append(l.section.$el);l.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.datasets=new h({success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var l=this;this.model.fetch({error:function(m){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){l.inputs=l.model.get("inputs");l.portlet=new g.View({icon:"fa-wrench",title:"<b>"+l.model.get("name")+"</b> "+l.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){console.log(l.tree.create(l))}})}});l.message=new k.Message();l.portlet.append(l.message.$el);$(l.main_el).append(l.portlet.$el);if(l.options.help!=""){$(l.main_el).append(d.help(l.options.help))}if(l.options.citations){$(l.main_el).append(d.citations());var m=new i.ToolCitationCollection();m.tool_id=l.options.id;var n=new a.CitationListView({collection:m});n.render();m.fetch()}l.setElement(l.portlet.content());l.section=new j.View(l,{inputs:l.model.get("inputs")});l.portlet.append(l.section.$el);l.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;this.datasets=g.datasets;this.data=g.data;f.cls_tr="section-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f],this.data)}},_add:function(h,j){var g=this;var f=jQuery.extend(true,{},h);f.id=c.uuid();this.app.input_list[f.id]=f;var i=f.type;switch(i){case"conditional":this._addConditional(f,j);break;case"repeat":this._addRepeat(f);break;default:this._addRow(i,f,j)}},_addConditional:function(f,j){f.label=f.test_param.label;f.value=f.test_param.value;this._addRow("conditional",f,j);for(var h in f.cases){var g=f.id+"-section-"+h;var k=new d(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(k.$el);this.table.append(g)}},_addRepeat:function(f){var g=this;var k=new a.View({title_new:"Add "+f.title,max:f.max,onnew:function(){var i=f.id+"-section-"+c.uuid();var m=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:i,title:f.title,$el:m.$el,ondel:function(){k.del(i);k.retitle(f.title);g.app.refresh()}});k.retitle(f.title);k.show(i);g.app.refresh()}});for(var j=0;j<f.min;j++){var h=f.id+"-section-"+c.uuid();var l=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:h,title:f.title,$el:l.$el})}k.retitle(f.title);this.table.add("");this.table.add(k.$el);this.table.append(f.id)},_addRow:function(i,f,g){var k=f.id;var h=null;switch(i){case"text":h=this._field_text(f,g);break;case"select":h=this._field_select(f,g);break;case"radiobutton":h=this._field_radio(f,g);break;case"data":h=this._field_data(f,g);break;case"data_column":h=this._field_column(f,g);break;case"textarea":h=this._field_textarea(f,g);break;case"conditional":h=this._field_conditional(f,g);break;case"hidden":h=this._field_hidden(f,g);break;case"integer":h=this._field_integer(f,g);break;case"boolean":h=this._field_radiobutton(f,g);break;default:h=this._field_text(f,g);console.debug("tools-form::_addRow() : Unmatched field type ("+i+").")}if(!g.get(k)){g.set(k,f.value)}h.value(g.get(k));this.app.field_list[k]=h;var j=$("<div/>");j.append(h.$el);if(f.help){j.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","20%");this.table.add(j);this.table.append(k)},_field_conditional:function(f,l){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}var m=f.id;return new e.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(u){l.set(m,u);for(var s in f.cases){var o=f.cases[s];var r=f.id+"-section-"+s;var n=g.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(f,l){var g=this;var m=f.id;var k=this.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+m,data:h,value:h[0].value,onchange:function(s){l.set(m,s);var o=g.app.tree.findReferences(m);var u=g.datasets.filter(s);if(u&&o.length>0){console.debug("tool-form::field_data() - Selected dataset "+s+".");var t=u.get("metadata_column_types");if(!t){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+s+".")}var r=[];for(var q in t){r.push({label:"Column: "+(parseInt(q)+1)+" ["+t[q]+"]",value:q})}for(var p in o){var n=g.app.field_list[o[p]];if(n){n.update(r);if(!n.exists(n.value())){n.value(n.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+s+".")}}})},_field_column:function(f,g){var h=f.id;return new e.Select.View({id:"field-"+h,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_select:function(f,l){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;if(f.display=="checkboxes"){k=e.Checkbox}var m=f.id;return new k.View({id:"field-"+m,data:g,value:l.get(m),onchange:function(i){l.set(m,i)}})},_field_text:function(f,g){var h=f.id;return new e.Input({id:"field-"+h,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_integer:function(f,g){var h=f.id;return new e.Slider.View({id:"field-"+h,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_textarea:function(f,g){var h=f.id;return new e.Textarea({id:"field-"+h,onchange:function(){g.set(h,field.value())}})},_field_radio:function(f,g){var h=f.id;return new e.RadioButton({id:"field-"+h,data:f.data,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_hidden:function(f,g){var h=f.id;return new e.Hidden({id:"field-"+h,value:g.get(h)})},_field_radiobutton:function(f,g){var h=f.id;return new e.RadioButton.View({id:"field-"+h,value:g.get(h),data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;f.cls_tr="section-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f])}},_add:function(h){var g=this;var f=jQuery.extend(true,{},h);f.id=c.uuid();this.app.input_list[f.id]=f;var i=f.type;switch(i){case"conditional":this._addConditional(f);break;case"repeat":this._addRepeat(f);break;default:this._addRow(i,f)}},_addConditional:function(f){f.label=f.test_param.label;f.value=f.test_param.value;this._addRow("conditional",f);for(var h in f.cases){var g=f.id+"-section-"+h;var j=new d(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(j.$el);this.table.append(g)}},_addRepeat:function(f){var g=this;var k=new a.View({title_new:"Add "+f.title,max:f.max,onnew:function(){var i=f.id+"-section-"+c.uuid();var m=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:i,title:f.title,$el:m.$el,ondel:function(){k.del(i);k.retitle(f.title);g.app.refresh()}});k.retitle(f.title);k.show(i);g.app.refresh()}});for(var j=0;j<f.min;j++){var h=f.id+"-section-"+c.uuid();var l=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:h,title:f.title,$el:l.$el})}k.retitle(f.title);this.table.add("");this.table.add(k.$el);this.table.append(f.id)},_addRow:function(h,f){var j=f.id;var g=null;switch(h){case"text":g=this._field_text(f);break;case"select":g=this._field_select(f);break;case"data":g=this._field_data(f);break;case"data_column":g=this._field_column(f);break;case"conditional":g=this._field_conditional(f);break;case"hidden":g=this._field_hidden(f);break;case"integer":g=this._field_slider(f);break;case"float":g=this._field_slider(f);break;case"boolean":g=this._field_boolean(f);break;default:g=this._field_text(f);console.debug("tools-form::_addRow() : Unmatched field type ("+h+").")}if(f.value!==undefined){g.value(f.value)}this.app.field_list[j]=g;var i=$("<div/>");i.append(g.$el);if(f.help){i.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","20%");this.table.add(i);this.table.append(j)},_field_conditional:function(f){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}return new e.Select.View({id:"field-"+f.id,data:h,onchange:function(s){for(var q in f.cases){var m=f.cases[q];var p=f.id+"-section-"+q;var l=g.table.get(p);var o=false;for(var n in m.inputs){var r=m.inputs[n].type;if(r&&r!=="hidden"){o=true;break}}if(m.value==s&&o){l.fadeIn("fast")}else{l.hide()}}}})},_field_data:function(f){var g=this;var l=f.id;var k=this.app.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+l,data:h,value:h[0].value,onchange:function(u){var s=g.app.tree.findReferences(l,"data_column");var n=g.app.datasets.filter(u);if(n&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=n.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var p in s){var q=g.app.input_list[s[p]];var r=g.app.field_list[s[p]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var o=q.numerical;var m=[];for(var v in w){var t=w[v];if(t=="int"||t=="float"||!o){m.push({label:"Column: "+(parseInt(v)+1)+" ["+w[v]+"]",value:v})}}if(r){r.update(m);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_field_select:function(f){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;switch(f.display){case"checkboxes":k=e.Checkbox;break;case"radio":k=e.RadioButton;break}if(f.multiple){k=e.Checkbox}return new k.View({id:"field-"+f.id,data:g})},_field_column:function(f){return new e.Select.View({id:"field-"+f.id,multiple:f.multiple})},_field_text:function(f){return new e.Input({id:"field-"+f.id,area:f.area})},_field_slider:function(f){return new e.Slider.View({id:"field-"+f.id,min:f.min||0,max:f.max||1000,decimal:f.type=="float"})},_field_hidden:function(f){return new e.Hidden({id:"field-"+f.id})},_field_boolean:function(f){return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:true},{label:"No",value:false}]})}});return{View:d}}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){if(!this.app.section){return{}}this.dict={};this.xml=$("<div/>");this._iterate(this.app.section.$el,this.dict,this.xml)},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})},findReferences:function(c){var f=[];var b=this;function d(g,i){var h=$(i).children();var k=[];var j=false;h.each(function(){var n=this;var m=$(n).attr("id");if(m!==c){var l=b.app.input_list[m];if(l){if(l.name==g){j=true;return false}if(l.data_ref==g){k.push(m)}}}});if(!j){f=f.concat(k);h.each(function(){d(g,this)})}}var e=this.xml.find("#"+c);if(e.length>0){var a=this.app.input_list[c];if(a){d(a.name,e.parent())}}return f}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){if(!this.app.section){return{}}this.dict={};this.xml=$("<div/>");this._iterate(this.app.section.$el,this.dict,this.xml)},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})},findReferences:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g}})}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,h,k,i,b,r,c){var q=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var l=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var d=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick);$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="ui-button '+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var o=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick);$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="ui-button-icon '+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(!t.persistent){var s=this;window.setTimeout(function(){if(s.$el.is(":visible")){s.$el.fadeOut()}else{s.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(s){return'<div class="ui-message alert alert-'+s.status+'"/>'}});var f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));var s=this;if(this.options.onclick){this.$el.on("submit",function(v){var u=s.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var n=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'" rows="5"></textarea>'}});var m=Backbone.View.extend({optionsDefault:{value:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<hidden id="'+s.id+'" value="'+s.value+'"/>'}});return{Anchor:p,Button:g,ButtonIcon:o,ButtonMenu:r,Icon:d,Image:q,Input:n,Label:l,Message:a,Modal:c,RadioButton:b,Checkbox:i,Searchbox:f,Select:h,Textarea:j,Hidden:m,Slider:k}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,f,e,m,q,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="ui-button '+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var i=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="ui-button-icon '+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var g=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=l.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({optionsDefault:{value:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:g,Button:h,ButtonIcon:i,ButtonMenu:q,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Hidden:p,Slider:f}}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false},selected:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.selected=this.options.value;this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");var c=this;this.$select.on("change",function(){c.value(c.$select.val())});this.on("change",function(){if(c.options.onchange){c.options.onchange(c.value())}});this._refresh();if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}},value:function(c){var d=this.selected;if(c!==undefined){this.selected=c;this.$select.val(c)}var e=this.selected;if(e){if(e!=d&&this.options.onchange){this.options.onchange(e)}}return e},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh()},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}if(this.selected){this.$select.val(this.selected)}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(e){var d='<div id="'+e.id+'" class="ui-select"><div class="button"><i id="icon"/></div><select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var f=e.data[key];var c="";if(f.value==e.value||f.value==""){c="selected"}d+='<option value="'+f.value+'" '+c+">"+f.label+"</option>"}d+="</select></div>";return d}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/scripts/packed/mvc/ui/ui-slider.js --- a/static/scripts/packed/mvc/ui/ui-slider.js +++ b/static/scripts/packed/mvc/ui/ui-slider.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$slider=this.$el.find("#slider");this.$text=this.$el.find("#text");this.$slider.slider(this.options);this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==13||e==8||e==189||(e>=48&&e<=57))){f.preventDefault()}});this.$slider.on("slide",function(e,f){c.value(f.value)})},value:function(c){if(c!==undefined){c=Math.max(Math.min(c,this.options.max),this.options.min);if(this.options.onchange){this.options.onchange(c)}this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" style=""><input id="text" type="text" class="ui-input" style="width: 50px; float: left"/><div id="slider" style="width: calc(100% - 60px); float: left; top: 8px; left: 10px;"/></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:0.1,decimal:false},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$slider=this.$el.find("#slider");this.$text=this.$el.find("#text");if(!this.options.decimal){this.options.step=1}this.$slider.slider(this.options);this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==13||e==8||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.decimal&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}});this.$slider.on("slide",function(e,f){c.value(f.value)})},value:function(c){if(c!==undefined){c=Math.max(Math.min(c,this.options.max),this.options.min);if(this.options.onchange){this.options.onchange(c)}this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" style=""><input id="text" type="text" class="ui-input" style="width: 50px; float: left"/><div id="slider" style="width: calc(100% - 60px); float: left; top: 8px; left: 10px;"/></div>'}});return{View:b}}); \ No newline at end of file diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control,.ui-input{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control,.ui-input,.ui-textarea{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -1282,6 +1282,7 @@ .ui-table tbody{cursor:pointer} .ui-table-plain tbody td{padding:5px 0px 5px 5px !important;border:none !important} .ui-table-plain tbody{cursor:auto !important} +.ui-table-form-info{clear:both !important} .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-label{font-weight:bold} .ui-message{padding:2px 2px 2px 10px} @@ -1289,6 +1290,7 @@ .ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} .ui-button-icon .button{margin-right:5px;margin-left:5px} .ui-button-icon .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} +.ui-textarea{height:100px !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} @@ -1298,8 +1300,9 @@ .ui-portlet .no-scroll{height:calc(100% - 80px)} .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} .ui-popover .popover-title{padding:4px 10px} -.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} +.ui-select,.ui-select-multiple{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} +.ui-select-multiple{height:100% !important;width:100% !important} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff -r 19b109c4caa6b89e5c3e3e7a8f81e4fe1ef21746 -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -32,6 +32,7 @@ .ui-table-form-info { &:extend(.toolParamHelp); + clear: both !important; } .ui-table-form-separator { @@ -76,6 +77,11 @@ &:extend(.form-control); } +.ui-textarea { + &:extend(.form-control); + height: 100px !important; +} + .ui-tabs { .ui-tabs-add { font-size : 0.8em; @@ -203,4 +209,10 @@ border-radius: 0; -webkit-appearance: none; } +} + +.ui-select-multiple { + &:extend(.ui-select); + height: 100% !important; + width: 100% !important; } \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/b50fbeda0365/ Changeset: b50fbeda0365 User: carlfeberhard Date: 2014-09-04 16:33:41 Summary: merge central Affected #: 1 file diff -r 520eb21f9a1ef33eed6b4451bf6022e1750ff932 -r b50fbeda0365140ea4b91f332f52e56cc4b9d25a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2466,6 +2466,7 @@ val = getattr( ldda.datatype, name ) rval['metadata_' + name] = val return rval + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templatesThe get_contents # param is passed by callers that are inheriting a template - these @@ -2492,6 +2493,7 @@ else: return template.get_widgets( trans.user ) return [] + def templates_dict( self, use_name=False ): """ Returns a dict of template info @@ -2510,6 +2512,7 @@ tmp_dict[ name ] = content.get( field[ 'name' ] ) template_data[template.name] = tmp_dict return template_data + def templates_json( self, use_name=False ): return json.dumps( self.templates_dict( use_name=use_name ) ) @@ -2533,6 +2536,7 @@ self.info = info self.inheritable = inheritable + class LibraryFolderInfoAssociation( object ): def __init__( self, folder, form_definition, info, inheritable=False ): self.folder = folder @@ -2540,15 +2544,18 @@ self.info = info self.inheritable = inheritable + class LibraryDatasetDatasetInfoAssociation( object ): def __init__( self, library_dataset_dataset_association, form_definition, info ): # TODO: need to figure out if this should be inheritable to the associated LibraryDataset self.library_dataset_dataset_association = library_dataset_dataset_association self.template = form_definition self.info = info + @property def inheritable( self ): - return True #always allow inheriting, used for replacement + return True # always allow inheriting, used for replacement + class ValidationError( object ): def __init__( self, message=None, err_type=None, attributes=None ): @@ -2556,42 +2563,47 @@ self.err_type = err_type self.attributes = attributes + class DatasetToValidationErrorAssociation( object ): def __init__( self, dataset, validation_error ): self.dataset = dataset self.validation_error = validation_error + class ImplicitlyConvertedDatasetAssociation( object ): - def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ): + + def __init__( self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True ): self.id = id if isinstance(dataset, HistoryDatasetAssociation): self.dataset = dataset elif isinstance(dataset, LibraryDatasetDatasetAssociation): self.dataset_ldda = dataset else: - raise AttributeError, 'Unknown dataset type provided for dataset: %s' % type( dataset ) + raise AttributeError( 'Unknown dataset type provided for dataset: %s' % type( dataset ) ) if isinstance(parent, HistoryDatasetAssociation): self.parent_hda = parent elif isinstance(parent, LibraryDatasetDatasetAssociation): self.parent_ldda = parent else: - raise AttributeError, 'Unknown dataset type provided for parent: %s' % type( parent ) + raise AttributeError( 'Unknown dataset type provided for parent: %s' % type( parent ) ) self.type = file_type self.deleted = deleted self.purged = purged self.metadata_safe = metadata_safe - def clear( self, purge = False, delete_dataset = True ): + def clear( self, purge=False, delete_dataset=True ): self.deleted = True if self.dataset: if delete_dataset: self.dataset.deleted = True if purge: self.dataset.purged = True - if purge and self.dataset.deleted: #do something with purging + if purge and self.dataset.deleted: # do something with purging self.purged = True - try: os.unlink( self.file_name ) - except Exception, e: print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) + try: + os.unlink( self.file_name ) + except Exception, e: + print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) DEFAULT_COLLECTION_NAME = "Unnamed Collection" @@ -2903,6 +2915,7 @@ self.tool_id = None self.message = message + class GalaxySession( object ): def __init__( self, id=None, @@ -2924,24 +2937,29 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id self.histories = [] + def add_history( self, history, association=None ): if association is None: self.histories.append( GalaxySessionToHistoryAssociation( self, history ) ) else: self.histories.append( association ) + def get_disk_usage( self ): if self.disk_usage is None: return 0 return self.disk_usage + def set_disk_usage( self, bytes ): self.disk_usage = bytes total_disk_usage = property( get_disk_usage, set_disk_usage ) + class GalaxySessionToHistoryAssociation( object ): def __init__( self, galaxy_session, history ): self.galaxy_session = galaxy_session self.history = history + class UCI( object ): def __init__( self ): self.id = None @@ -2962,14 +2980,14 @@ self.latest_workflow_id = None self.workflows = [] - def copy_tags_from(self,target_user,source_workflow): + def copy_tags_from(self, target_user, source_workflow): for src_swta in source_workflow.owner_tags: new_swta = src_swta.copy() new_swta.user = target_user self.tags.append(new_swta) - def to_dict( self, view='collection', value_mapper = None ): - rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper = value_mapper ) + def to_dict( self, view='collection', value_mapper=None ): + rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper=value_mapper ) tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -3007,12 +3025,11 @@ return False def to_dict( self, view='collection', value_mapper=None): - rval = super( Workflow, self ).to_dict( view=view, value_mapper = value_mapper ) - rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) + rval = super( Workflow, self ).to_dict( view=view, value_mapper=value_mapper ) + rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) return rval - class WorkflowStep( object ): def __init__( self ): @@ -3061,7 +3078,7 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper ) if view == 'element': steps = {} @@ -3072,12 +3089,12 @@ inputs = {} for step in self.steps: - if step.workflow_step.type =='tool': + if step.workflow_step.type == 'tool': for step_input in step.workflow_step.input_connections: if step_input.output_step.type == 'data_input': for job_input in step.job.input_datasets: if job_input.name == step_input.input_name: - inputs[str(step_input.output_step.order_index)] = { "id" : job_input.dataset_id, "src" : "hda"} + inputs[str(step_input.output_step.order_index)] = { "id": job_input.dataset_id, "src": "hda"} rval['inputs'] = inputs return rval @@ -3086,19 +3103,20 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper ) rval['order_index'] = self.workflow_step.order_index return rval class MetadataFile( object ): - def __init__( self, dataset = None, name = None ): + def __init__( self, dataset=None, name=None ): if isinstance( dataset, HistoryDatasetAssociation ): self.history_dataset = dataset elif isinstance( dataset, LibraryDatasetDatasetAssociation ): self.library_dataset = dataset self.name = name + @property def file_name( self ): assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -3129,14 +3147,15 @@ class FormDefinition( object, Dictifiable ): # The following form_builder classes are supported by the FormDefinition class. supported_field_types = [ AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - types = Bunch( REQUEST = 'Sequencing Request Form', - SAMPLE = 'Sequencing Sample Form', - EXTERNAL_SERVICE = 'External Service Information Form', - RUN_DETAILS_TEMPLATE = 'Sample run details template', - LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) + types = Bunch( REQUEST='Sequencing Request Form', + SAMPLE='Sequencing Sample Form', + EXTERNAL_SERVICE='External Service Information Form', + RUN_DETAILS_TEMPLATE='Sample run details template', + LIBRARY_INFO_TEMPLATE='Library information template', + USER_INFO='User Information' ) dict_collection_visible_keys = ( 'id', 'name' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' ) + def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc @@ -3144,6 +3163,7 @@ self.form_definition_current = form_definition_current self.type = form_type self.layout = layout + def grid_fields( self, grid_index ): # Returns a dictionary whose keys are integers corresponding to field positions # on the grid and whose values are the field. @@ -3152,6 +3172,7 @@ if str( f[ 'layout' ] ) == str( grid_index ): gridfields[i] = f return gridfields + def get_widgets( self, user, contents={}, **kwd ): ''' Return the list of widgets that comprise a form definition, @@ -3213,24 +3234,28 @@ field_widget.params = params elif field_type == 'SelectField': for option in field[ 'selectlist' ]: + if option == value: field_widget.add_option( option, option, selected=True ) else: field_widget.add_option( option, option ) elif field_type == 'CheckboxField': + field_widget.set_checked( value ) if field[ 'required' ] == 'required': req = 'Required' else: req = 'Optional' if field[ 'helptext' ]: - helptext='%s (%s)' % ( field[ 'helptext' ], req ) + helptext = '%s (%s)' % ( field[ 'helptext' ], req ) else: helptext = '(%s)' % req widgets.append( dict( label=field[ 'label' ], + widget=field_widget, helptext=helptext ) ) return widgets + def field_as_html( self, field ): """Generates disabled html for a field""" type = field[ 'type' ] @@ -3245,21 +3270,25 @@ # Return None if unsupported field type return None + class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): self.latest_form = form_definition + class FormValues( object ): def __init__(self, form_def=None, content=None): self.form_definition = form_def self.content = content + class Request( object, Dictifiable ): - states = Bunch( NEW = 'New', - SUBMITTED = 'In Progress', - REJECTED = 'Rejected', - COMPLETE = 'Complete' ) + states = Bunch( NEW='New', + SUBMITTED='In Progress', + REJECTED='Rejected', + COMPLETE='Complete' ) dict_collection_visible_keys = ( 'id', 'name', 'state' ) + def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name self.desc = desc @@ -3268,17 +3297,20 @@ self.user = user self.notification = notification self.samples_list = [] + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def samples_have_common_state( self ): """ @@ -3294,6 +3326,7 @@ if s.state.id != state_for_comparison.id: return False return state_for_comparison + @property def last_comment( self ): latest_event = self.latest_event @@ -3302,26 +3335,34 @@ return latest_event.comment return '' return 'No comment' + def get_sample( self, sample_name ): for sample in self.samples: if sample.name == sample_name: return sample return None + @property def is_unsubmitted( self ): return self.state in [ self.states.REJECTED, self.states.NEW ] + @property def is_rejected( self ): return self.state == self.states.REJECTED + @property def is_submitted( self ): return self.state == self.states.SUBMITTED + @property def is_new( self ): + return self.state == self.states.NEW + @property def is_complete( self ): return self.state == self.states.COMPLETE + @property def samples_without_library_destinations( self ): # Return all samples that are not associated with a library @@ -3330,6 +3371,7 @@ if not sample.library: samples.append( sample ) return samples + @property def samples_with_bar_code( self ): # Return all samples that have associated bar code @@ -3338,6 +3380,7 @@ if sample.bar_code: samples.append( sample ) return samples + def send_email_notification( self, trans, common_state, final_state=False ): # Check if an email notification is configured to be sent when the samples # are in this state @@ -3390,7 +3433,7 @@ try: send_mail( frm, to, subject, body, trans.app.config ) comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' ) - except Exception,e: + except Exception, e: comments = "Email notification failed. (%s)" % str(e) # update the request history with the email notification event elif not trans.app.config.smtp_server: @@ -3401,16 +3444,19 @@ trans.sa_session.flush() return comments + class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): self.request = request self.state = request_state self.comment = comment + class ExternalService( object ): - data_transfer_protocol = Bunch( HTTP = 'http', - HTTPS = 'https', - SCP = 'scp' ) + data_transfer_protocol = Bunch( HTTP='http', + HTTPS='https', + SCP='scp' ) + def __init__( self, name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None ): self.name = name self.description = description @@ -3419,9 +3465,11 @@ self.form_definition_id = form_definition_id self.form_values_id = form_values_id self.deleted = deleted - self.label = None # Used in the request_type controller's __build_external_service_select_field() method + self.label = None # Used in the request_type controller's __build_external_service_select_field() method + def get_external_service_type( self, trans ): return trans.app.external_service_types.all_external_service_types[ self.external_service_type_id ] + def load_data_transfer_settings( self, trans ): trans.app.external_service_types.reload( self.external_service_type_id ) self.data_transfer = {} @@ -3442,33 +3490,39 @@ automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) http_configs[ 'automatic_transfer' ] = galaxy.util.string_as_bool( automatic_transfer ) self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs + def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) + class RequestType( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'name', 'desc' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' ) - rename_dataset_options = Bunch( NO = 'Do not rename', - SAMPLE_NAME = 'Preprend sample name', - EXPERIMENT_NAME = 'Prepend experiment name', - EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') + rename_dataset_options = Bunch( NO='Do not rename', + SAMPLE_NAME='Preprend sample name', + EXPERIMENT_NAME='Prepend experiment name', + EXPERIMENT_AND_SAMPLE_NAME='Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) + def __init__( self, name=None, desc=None, request_form=None, sample_form=None ): self.name = name self.desc = desc self.request_form = request_form self.sample_form = sample_form + @property def external_services( self ): external_services = [] for rtesa in self.external_service_associations: external_services.append( rtesa.external_service ) return external_services + def get_external_service( self, external_service_type_id ): for rtesa in self.external_service_associations: if rtesa.external_service.external_service_type_id == external_service_type_id: return rtesa.external_service return None + def get_external_services_for_manual_data_transfer( self, trans ): '''Returns all external services that use manual data transfer''' external_services = [] @@ -3481,6 +3535,7 @@ if not transfer_type_settings[ 'automatic_transfer' ]: external_services.append( external_service ) return external_services + def delete_external_service_associations( self, trans ): '''Deletes all external service associations.''' flush_needed = False @@ -3489,20 +3544,24 @@ flush_needed = True if flush_needed: trans.sa_session.flush() + def add_external_service_association( self, trans, external_service ): rtesa = trans.model.RequestTypeExternalServiceAssociation( self, external_service ) trans.sa_session.add( rtesa ) trans.sa_session.flush() + @property def final_sample_state( self ): # The states mapper for this object orders ascending return self.states[-1] + @property def run_details( self ): if self.run: # self.run[0] is [RequestTypeRunAssociation] return self.run[0] return None + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templates. The get_contents param # is passed by callers that are inheriting a template - these are @@ -3520,23 +3579,27 @@ return template.get_widgets( trans.user ) return [] + class RequestTypeExternalServiceAssociation( object ): def __init__( self, request_type, external_service ): self.request_type = request_type self.external_service = external_service + class RequestTypePermissions( object ): def __init__( self, action, request_type, role ): self.action = action self.request_type = request_type self.role = role + class Sample( object, Dictifiable ): # The following form_builder classes are supported by the Sample class. supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - bulk_operations = Bunch( CHANGE_STATE = 'Change state', - SELECT_LIBRARY = 'Select data library and folder' ) + bulk_operations = Bunch( CHANGE_STATE='Change state', + SELECT_LIBRARY='Select data library and folder' ) dict_collection_visible_keys = ( 'id', 'name' ) + def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None): self.name = name self.desc = desc @@ -3547,17 +3610,20 @@ self.folder = folder self.history = history self.workflow = workflow + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def adding_to_library_dataset_files( self ): adding_to_library_datasets = [] @@ -3565,6 +3631,7 @@ if dataset.status == SampleDataset.transfer_status.ADD_TO_LIBRARY: adding_to_library_datasets.append( dataset ) return adding_to_library_datasets + @property def inprogress_dataset_files( self ): inprogress_datasets = [] @@ -3572,6 +3639,7 @@ if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]: inprogress_datasets.append( dataset ) return inprogress_datasets + @property def queued_dataset_files( self ): queued_datasets = [] @@ -3579,6 +3647,7 @@ if dataset.status == SampleDataset.transfer_status.IN_QUEUE: queued_datasets.append( dataset ) return queued_datasets + @property def transfer_error_dataset_files( self ): transfer_error_datasets = [] @@ -3586,6 +3655,7 @@ if dataset.status == SampleDataset.transfer_status.ERROR: transfer_error_datasets.append( dataset ) return transfer_error_datasets + @property def transferred_dataset_files( self ): transferred_datasets = [] @@ -3593,6 +3663,7 @@ if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets + @property def transferring_dataset_files( self ): transferring_datasets = [] @@ -3600,6 +3671,7 @@ if dataset.status == SampleDataset.transfer_status.TRANSFERRING: transferring_datasets.append( dataset ) return transferring_datasets + @property def untransferred_dataset_files( self ): untransferred_datasets = [] @@ -3607,6 +3679,7 @@ if dataset.status != SampleDataset.transfer_status.COMPLETE: untransferred_datasets.append( dataset ) return untransferred_datasets + def get_untransferred_dataset_size( self, filepath, scp_configs ): def print_ticks( d ): pass https://bitbucket.org/galaxy/galaxy-central/commits/cebadec812f5/ Changeset: cebadec812f5 User: carlfeberhard Date: 2014-09-04 17:06:08 Summary: merge central Affected #: 2 files diff -r b50fbeda0365140ea4b91f332f52e56cc4b9d25a -r cebadec812f5b1ca10abdebdb60456796e061c56 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -98,6 +98,21 @@ return False +def is_uuid( value ): + """ + This method returns True if value is a UUID, otherwise False. + >>> is_uuid( "123e4567-e89b-12d3-a456-426655440000" ) + True + >>> is_uuid( "0x3242340298902834" ) + False + """ + uuid_re = re.compile( "[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}" ) + if re.match( uuid_re, str( value ) ): + return True + else: + return False + + def get_charset_from_http_headers( headers, default=None ): rval = headers.get('content-type', None ) if rval and 'charset=' in rval: diff -r b50fbeda0365140ea4b91f332f52e56cc4b9d25a -r cebadec812f5b1ca10abdebdb60456796e061c56 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -433,24 +433,19 @@ return stored_workflow def __get_stored_workflow( self, trans, workflow_id ): - try: + if util.is_uuid(workflow_id): + # see if they have passed in the UUID for a workflow that is attached to a stored workflow + workflow_uuid = uuid.UUID(workflow_id) + stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_( + trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id, + trans.app.model.Workflow.uuid == workflow_uuid + )).first() + if stored_workflow is None: + raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id ) + else: workflow_id = self.__decode_id( trans, workflow_id ) query = trans.sa_session.query( trans.app.model.StoredWorkflow ) stored_workflow = query.get( workflow_id ) - except Exception: - try: - #see if they have passed in the UUID for a workflow that is attached to a stored workflow - workflow_uuid = uuid.UUID(workflow_id) - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_( - trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id, - trans.app.model.Workflow.uuid == workflow_uuid - )).first() - if stored_workflow is None: - raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id ) - return stored_workflow - except: - pass #let the outer raise exception happen - raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) if stored_workflow is None: raise exceptions.ObjectNotFound( "No such workflow found." ) return stored_workflow https://bitbucket.org/galaxy/galaxy-central/commits/404c21fa0de7/ Changeset: 404c21fa0de7 User: carlfeberhard Date: 2014-09-04 17:06:39 Summary: Fix doc Affected #: 1 file diff -r cebadec812f5b1ca10abdebdb60456796e061c56 -r 404c21fa0de76e20deba7b63eebc15cca617173c lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -55,6 +55,8 @@ class WebApplication( base.WebApplication ): """ + Base WSGI application instantiated for all Galaxy webapps. + A web application that: * adds API and UI controllers by scanning given directories and importing all modules found there. https://bitbucket.org/galaxy/galaxy-central/commits/e6546f41d7b2/ Changeset: e6546f41d7b2 User: carlfeberhard Date: 2014-09-04 22:28:53 Summary: merge central Affected #: 28 files diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -312,4 +312,22 @@ <sniffer type="galaxy.datatypes.assembly:Amos"/> --></sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites></datatypes> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ensembl/ensembl_bam.xml --- a/display_applications/ensembl/ensembl_bam.xml +++ b/display_applications/ensembl/ensembl_bam.xml @@ -1,7 +1,7 @@ <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ensembl/ensembl_gff.xml --- a/display_applications/ensembl/ensembl_gff.xml +++ b/display_applications/ensembl/ensembl_gff.xml @@ -1,7 +1,7 @@ <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ensembl/ensembl_interval_as_bed.xml --- a/display_applications/ensembl/ensembl_interval_as_bed.xml +++ b/display_applications/ensembl/ensembl_interval_as_bed.xml @@ -1,7 +1,7 @@ <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,6 +1,6 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,6 +1,6 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -2,7 +2,7 @@ <display id="igv_bam" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -2,7 +2,7 @@ <display id="igv_vcf" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/rviewer/bed.xml --- a/display_applications/rviewer/bed.xml +++ b/display_applications/rviewer/bed.xml @@ -2,7 +2,7 @@ <display id="rviewer_interval" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/rviewer/vcf.xml --- a/display_applications/rviewer/vcf.xml +++ b/display_applications/rviewer/vcf.xml @@ -2,7 +2,7 @@ <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -1,6 +1,6 @@ <display id="ucsc_bam" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/interval_as_bed.xml --- a/display_applications/ucsc/interval_as_bed.xml +++ b/display_applications/ucsc/interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/maf_customtrack.xml --- a/display_applications/ucsc/maf_customtrack.xml +++ b/display_applications/ucsc/maf_customtrack.xml @@ -1,6 +1,6 @@ <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 display_applications/ucsc/vcf.xml --- a/display_applications/ucsc/vcf.xml +++ b/display_applications/ucsc/vcf.xml @@ -1,6 +1,6 @@ <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,9 +64,6 @@ # Load dbkey / genome build manager self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True ) - # Load build sites (old-style) - self._configure_build_sites() - # Genomes self.genomes = Genomes( self ) # Data providers registry. diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,7 +16,6 @@ from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds -from galaxy.util.build_sites import BuildSites from galaxy import eggs log = logging.getLogger( __name__ ) @@ -224,10 +223,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) - self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root ) - self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root ) - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. @@ -575,9 +570,6 @@ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style ) - def _configure_build_sites( self ): - self.build_sites = BuildSites( self ) - def _configure_toolbox( self ): # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -81,9 +81,13 @@ class DynamicDisplayApplicationBuilder( object ): @classmethod - def __init__( self, elem, display_application ): + def __init__( self, elem, display_application, build_sites ): rval = [] - filename = elem.get( 'from_file', None ) + filename = None + if elem.get( 'site_type', None ) is not None: + filename = build_sites.get( elem.get( 'site_type' ) ) + else: + filename = elem.get( 'from_file', None ) assert filename is not None, 'Filename and id attributes required for dynamic_links' skip_startswith = elem.get( 'skip_startswith', None ) separator = elem.get( 'separator', '\t' ) @@ -176,7 +180,7 @@ if link: rval.links[ link.id ] = link for dynamic_links in elem.findall( 'dynamic_links' ): - for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ): + for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): rval.links[ link.id ] = link return rval def __init__( self, display_id, name, datatypes_registry, version = None ): diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -83,29 +83,31 @@ ret_val = [] ggtail = 'hgGenome_doSubmitUpload=submit' if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! + dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - internal_url = "%s" % url_for( controller='dataset', - dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) - display_url = urllib.quote_plus( display_url ) - # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) - #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) - sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] - #sl.append("&hgt.customText=%s") - sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) - sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") - sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_doSubmitUpload=submit") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) - s = ''.join(sl) - s = urllib.quote_plus(s) - redirect_url = s - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): + if site_name in datatypes_registry.get_display_sites('ucsc'): + site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, + action='display_at', + filename='ucsc_' + site_name ) + display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) + display_url = urllib.quote_plus( display_url ) + # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] + #sl.append("&hgt.customText=%s") + sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) + sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") + sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") + sl.append("&hgGenome_doSubmitUpload=submit") + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) + s = ''.join(sl) + s = urllib.quote_plus(s) + redirect_url = s + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) return ret_val def make_html_table( self, dataset, skipchars=[] ): diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,8 +234,8 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) - if name in app.config.ucsc_display_sites ] + for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ) + if name in app.datatypes_registry.get_display_sites('ucsc') ] if not valid_sites: return [] # If there are any valid sites, we need to generate the estimated @@ -750,8 +750,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) ) @@ -762,8 +762,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) ) @@ -1091,8 +1091,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) ) @@ -1103,8 +1103,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) @@ -1285,8 +1285,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -69,6 +69,10 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None + # Build sites + self.build_sites = {} + self.display_sites = {} + self.legacy_build_sites = {} def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ @@ -285,6 +289,8 @@ handling_proprietary_datatypes=handling_proprietary_datatypes, override=override ) self.upload_file_formats.sort() + # Load build sites + self.load_build_sites( root ) # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and # set_metadata processing. self.to_xml_file() @@ -303,6 +309,34 @@ self.sniff_order.append( datatype ) append_to_sniff_order() + def load_build_sites( self, root ): + if root.find( 'build_sites' ): + for elem in root.find( 'build_sites' ).findall( 'site' ): + if not (elem.get( 'type' ) and elem.get( 'file' )): + self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) + else: + site_type = elem.get( 'type' ) + file = elem.get( 'file' ) + self.build_sites[site_type] = file + if site_type in ('ucsc', 'gbrowse'): + self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file ) + if elem.get( 'display', None ): + display = elem.get( 'display' ) + self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ] + self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display ) + else: + self.log.debug( "Loaded build site '%s': %s", site_type, file ) + + def get_legacy_sites_by_build( self, site_type, build ): + sites = [] + for site in self.legacy_build_sites.get(site_type, []): + if build in site['builds']: + sites.append((site['name'], site['url'])) + return sites + + def get_display_sites( self, site_type ): + return self.display_sites.get( site_type, [] ) + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): """ Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -844,6 +844,30 @@ return db_names +def read_build_sites( filename, check_builds=True ): + """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ + build_sites = [] + try: + for line in open(filename): + try: + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + site_name = fields[0] + site = fields[1] + if check_builds: + site_builds = fields[2].split(",") + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} + else: + site_dict = {'name': site_name, 'url': site} + build_sites.append( site_dict ) + except: + continue + except: + print "ERROR: Unable to read builds for site file %s" % filename + return build_sites + + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ /dev/null @@ -1,52 +0,0 @@ -""" -Functionality for dealing with build sites for legacy display applications. -""" -import os.path - - -class BuildSites( object ): - - def __init__( self, app ): - self._app = app - self._build_sites = {} - self.load_build_sites() - - def read_build_sites( self, filename, check_builds=True ): - """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ - build_sites = [] - try: - for line in open(filename): - try: - if line[0:1] == "#": - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - site_name = fields[0] - site = fields[1] - if check_builds: - site_builds = fields[2].split(",") - site_dict = {'name': site_name, 'url': site, 'builds': site_builds} - else: - site_dict = {'name': site_name, 'url': site} - build_sites.append( site_dict ) - except: - continue - except: - print "ERROR: Unable to read builds for site file %s" % filename - return build_sites - - def load_build_sites( self ): - self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) - self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - - def _get_site_by_build( self, site_type, build ): - sites = [] - for site in self._build_sites[site_type]: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - def get_ucsc_sites_by_build( self, build ): - return self._get_site_by_build( 'ucsc', build ) - - def get_gbrowse_sites_by_build( self, build ): - return self._get_site_by_build( 'gbrowse', build ) diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -429,7 +429,7 @@ url_for( controller='dataset', action='list' ) ) display_as = url_for( controller='root', action='display_as' ) - if self.app.config.ucsc_display_sites and self.request.path == 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 ): diff -r 404c21fa0de76e20deba7b63eebc15cca617173c -r e6546f41d7b2a11dbf26246662a55c6e86495269 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -364,14 +364,6 @@ # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. -# UCSC browsers: -#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: -#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to 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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commit/galaxy-central: dannon: Merged in lance_parsons/galaxy-central-pull-requests/venv (pull request #486)
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1eedbc8a3a8d/ Changeset: 1eedbc8a3a8d User: dannon Date: 2014-09-04 22:25:37 Summary: Merged in lance_parsons/galaxy-central-pull-requests/venv (pull request #486) Source virtualenv prior to python check and source venv for reports webapp Affected #: 2 files diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f run.sh --- a/run.sh +++ b/run.sh @@ -2,6 +2,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 @@ -11,13 +18,6 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi -# If there is a .venv/ directory, assume it contains a virtualenv that we -# should run this instance in. -if [ -d .venv ]; -then - . .venv/bin/activate -fi - if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` daemon=`echo "$@" | grep -q daemon` diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -11,6 +11,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + ./scripts/common_startup.sh --skip-samples GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 05 Sep '14

05 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/22c4bcbfc20f/ Changeset: 22c4bcbfc20f Branch: venv User: lance_parsons Date: 2014-09-04 21:04:34 Summary: Created new branch venv Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/619a8d213032/ Changeset: 619a8d213032 Branch: venv User: lance_parsons Date: 2014-09-04 21:12:04 Summary: Source virtualenv before python check and for reports app Affected #: 2 files diff -r 22c4bcbfc20f116d45398f93b88666ad8a94a4e7 -r 619a8d213032b726eded009572c2ebfc78c70834 run.sh --- a/run.sh +++ b/run.sh @@ -2,6 +2,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 @@ -11,13 +18,6 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi -# If there is a .venv/ directory, assume it contains a virtualenv that we -# should run this instance in. -if [ -d .venv ]; -then - . .venv/bin/activate -fi - if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` daemon=`echo "$@" | grep -q daemon` diff -r 22c4bcbfc20f116d45398f93b88666ad8a94a4e7 -r 619a8d213032b726eded009572c2ebfc78c70834 run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -11,6 +11,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + ./scripts/common_startup.sh --skip-samples GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} https://bitbucket.org/galaxy/galaxy-central/commits/1eedbc8a3a8d/ Changeset: 1eedbc8a3a8d User: dannon Date: 2014-09-04 22:25:37 Summary: Merged in lance_parsons/galaxy-central-pull-requests/venv (pull request #486) Source virtualenv prior to python check and source venv for reports webapp Affected #: 2 files diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f run.sh --- a/run.sh +++ b/run.sh @@ -2,6 +2,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 @@ -11,13 +18,6 @@ python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi -# If there is a .venv/ directory, assume it contains a virtualenv that we -# should run this instance in. -if [ -d .venv ]; -then - . .venv/bin/activate -fi - if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` daemon=`echo "$@" | grep -q daemon` diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 1eedbc8a3a8d6abcb8da2a7db246cb4f924b763f run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -11,6 +11,13 @@ cd `dirname $0` +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi + ./scripts/common_startup.sh --skip-samples GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Merged in natefoo/galaxy-central (pull request #481)
by commits-noreply＠bitbucket.org 04 Sep '14

04 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b6cccb3af2d/ Changeset: 9b6cccb3af2d User: natefoo Date: 2014-09-04 17:38:26 Summary: Merged in natefoo/galaxy-central (pull request #481) Make build sites files configurable Affected #: 27 files diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -312,4 +312,22 @@ <sniffer type="galaxy.datatypes.assembly:Amos"/> --></sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites></datatypes> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_bam.xml --- a/display_applications/ensembl/ensembl_bam.xml +++ b/display_applications/ensembl/ensembl_bam.xml @@ -1,7 +1,7 @@ <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_gff.xml --- a/display_applications/ensembl/ensembl_gff.xml +++ b/display_applications/ensembl/ensembl_gff.xml @@ -1,7 +1,7 @@ <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_interval_as_bed.xml --- a/display_applications/ensembl/ensembl_interval_as_bed.xml +++ b/display_applications/ensembl/ensembl_interval_as_bed.xml @@ -1,7 +1,7 @@ <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,6 +1,6 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,6 +1,6 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -2,7 +2,7 @@ <display id="igv_bam" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -2,7 +2,7 @@ <display id="igv_vcf" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/bed.xml --- a/display_applications/rviewer/bed.xml +++ b/display_applications/rviewer/bed.xml @@ -2,7 +2,7 @@ <display id="rviewer_interval" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/vcf.xml --- a/display_applications/rviewer/vcf.xml +++ b/display_applications/rviewer/vcf.xml @@ -2,7 +2,7 @@ <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -1,6 +1,6 @@ <display id="ucsc_bam" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/interval_as_bed.xml --- a/display_applications/ucsc/interval_as_bed.xml +++ b/display_applications/ucsc/interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/maf_customtrack.xml --- a/display_applications/ucsc/maf_customtrack.xml +++ b/display_applications/ucsc/maf_customtrack.xml @@ -1,6 +1,6 @@ <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/vcf.xml --- a/display_applications/ucsc/vcf.xml +++ b/display_applications/ucsc/vcf.xml @@ -1,6 +1,6 @@ <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,9 +64,6 @@ # Load dbkey / genome build manager self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True ) - # Load build sites (old-style) - self._configure_build_sites() - # Genomes self.genomes = Genomes( self ) # Data providers registry. diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,7 +16,6 @@ from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds -from galaxy.util.build_sites import BuildSites from galaxy import eggs log = logging.getLogger( __name__ ) @@ -224,10 +223,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) - self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root ) - self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root ) - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. @@ -575,9 +570,6 @@ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style ) - def _configure_build_sites( self ): - self.build_sites = BuildSites( self ) - def _configure_toolbox( self ): # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -81,9 +81,13 @@ class DynamicDisplayApplicationBuilder( object ): @classmethod - def __init__( self, elem, display_application ): + def __init__( self, elem, display_application, build_sites ): rval = [] - filename = elem.get( 'from_file', None ) + filename = None + if elem.get( 'site_type', None ) is not None: + filename = build_sites.get( elem.get( 'site_type' ) ) + else: + filename = elem.get( 'from_file', None ) assert filename is not None, 'Filename and id attributes required for dynamic_links' skip_startswith = elem.get( 'skip_startswith', None ) separator = elem.get( 'separator', '\t' ) @@ -176,7 +180,7 @@ if link: rval.links[ link.id ] = link for dynamic_links in elem.findall( 'dynamic_links' ): - for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ): + for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): rval.links[ link.id ] = link return rval def __init__( self, display_id, name, datatypes_registry, version = None ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -83,29 +83,31 @@ ret_val = [] ggtail = 'hgGenome_doSubmitUpload=submit' if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! + dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - internal_url = "%s" % url_for( controller='dataset', - dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) - display_url = urllib.quote_plus( display_url ) - # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) - #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) - sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] - #sl.append("&hgt.customText=%s") - sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) - sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") - sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_doSubmitUpload=submit") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) - s = ''.join(sl) - s = urllib.quote_plus(s) - redirect_url = s - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): + if site_name in datatypes_registry.get_display_sites('ucsc'): + site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, + action='display_at', + filename='ucsc_' + site_name ) + display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) + display_url = urllib.quote_plus( display_url ) + # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] + #sl.append("&hgt.customText=%s") + sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) + sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") + sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") + sl.append("&hgGenome_doSubmitUpload=submit") + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) + s = ''.join(sl) + s = urllib.quote_plus(s) + redirect_url = s + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) return ret_val def make_html_table( self, dataset, skipchars=[] ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,8 +234,8 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) - if name in app.config.ucsc_display_sites ] + for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ) + if name in app.datatypes_registry.get_display_sites('ucsc') ] if not valid_sites: return [] # If there are any valid sites, we need to generate the estimated @@ -750,8 +750,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) ) @@ -762,8 +762,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) ) @@ -1091,8 +1091,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) ) @@ -1103,8 +1103,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) @@ -1285,8 +1285,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -69,6 +69,10 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None + # Build sites + self.build_sites = {} + self.display_sites = {} + self.legacy_build_sites = {} def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ @@ -285,6 +289,8 @@ handling_proprietary_datatypes=handling_proprietary_datatypes, override=override ) self.upload_file_formats.sort() + # Load build sites + self.load_build_sites( root ) # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and # set_metadata processing. self.to_xml_file() @@ -303,6 +309,34 @@ self.sniff_order.append( datatype ) append_to_sniff_order() + def load_build_sites( self, root ): + if root.find( 'build_sites' ): + for elem in root.find( 'build_sites' ).findall( 'site' ): + if not (elem.get( 'type' ) and elem.get( 'file' )): + self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) + else: + site_type = elem.get( 'type' ) + file = elem.get( 'file' ) + self.build_sites[site_type] = file + if site_type in ('ucsc', 'gbrowse'): + self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file ) + if elem.get( 'display', None ): + display = elem.get( 'display' ) + self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ] + self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display ) + else: + self.log.debug( "Loaded build site '%s': %s", site_type, file ) + + def get_legacy_sites_by_build( self, site_type, build ): + sites = [] + for site in self.legacy_build_sites.get(site_type, []): + if build in site['builds']: + sites.append((site['name'], site['url'])) + return sites + + def get_display_sites( self, site_type ): + return self.display_sites.get( site_type, [] ) + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): """ Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -844,6 +844,30 @@ return db_names +def read_build_sites( filename, check_builds=True ): + """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ + build_sites = [] + try: + for line in open(filename): + try: + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + site_name = fields[0] + site = fields[1] + if check_builds: + site_builds = fields[2].split(",") + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} + else: + site_dict = {'name': site_name, 'url': site} + build_sites.append( site_dict ) + except: + continue + except: + print "ERROR: Unable to read builds for site file %s" % filename + return build_sites + + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ /dev/null @@ -1,52 +0,0 @@ -""" -Functionality for dealing with build sites for legacy display applications. -""" -import os.path - - -class BuildSites( object ): - - def __init__( self, app ): - self._app = app - self._build_sites = {} - self.load_build_sites() - - def read_build_sites( self, filename, check_builds=True ): - """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ - build_sites = [] - try: - for line in open(filename): - try: - if line[0:1] == "#": - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - site_name = fields[0] - site = fields[1] - if check_builds: - site_builds = fields[2].split(",") - site_dict = {'name': site_name, 'url': site, 'builds': site_builds} - else: - site_dict = {'name': site_name, 'url': site} - build_sites.append( site_dict ) - except: - continue - except: - print "ERROR: Unable to read builds for site file %s" % filename - return build_sites - - def load_build_sites( self ): - self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) - self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - - def _get_site_by_build( self, site_type, build ): - sites = [] - for site in self._build_sites[site_type]: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - def get_ucsc_sites_by_build( self, build ): - return self._get_site_by_build( 'ucsc', build ) - - def get_gbrowse_sites_by_build( self, build ): - return self._get_site_by_build( 'gbrowse', build ) diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -926,7 +926,7 @@ url_for( controller='dataset', action='list' ) ) display_as = url_for( controller='root', action='display_as' ) - if self.app.config.ucsc_display_sites and self.request.path == 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 ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -364,14 +364,6 @@ # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. -# UCSC browsers: -#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: -#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 04 Sep '14

04 Sep '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3c5b729592b/ Changeset: a3c5b729592b User: natefoo Date: 2014-09-03 00:20:23 Summary: Remove the BuildSites class I recently created and merge its functionality back into util and the datatypes registry. As a result, the build_sites configuration moves to datatypes_conf.xml and display applications can now use configured build sites so that the path is not hardcoded into the individual committed display application files. `from_file` in the display applications is still supported. Affected #: 25 files diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -312,4 +312,12 @@ <sniffer type="galaxy.datatypes.assembly:Amos"/> --></sniffers> + <build_sites> + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites></datatypes> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_bam.xml --- a/display_applications/ensembl/ensembl_bam.xml +++ b/display_applications/ensembl/ensembl_bam.xml @@ -1,7 +1,7 @@ <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_gff.xml --- a/display_applications/ensembl/ensembl_gff.xml +++ b/display_applications/ensembl/ensembl_gff.xml @@ -1,7 +1,7 @@ <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_interval_as_bed.xml --- a/display_applications/ensembl/ensembl_interval_as_bed.xml +++ b/display_applications/ensembl/ensembl_interval_as_bed.xml @@ -1,7 +1,7 @@ <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,6 +1,6 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,6 +1,6 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -2,7 +2,7 @@ <display id="igv_bam" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -2,7 +2,7 @@ <display id="igv_vcf" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/rviewer/bed.xml --- a/display_applications/rviewer/bed.xml +++ b/display_applications/rviewer/bed.xml @@ -2,7 +2,7 @@ <display id="rviewer_interval" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/rviewer/vcf.xml --- a/display_applications/rviewer/vcf.xml +++ b/display_applications/rviewer/vcf.xml @@ -2,7 +2,7 @@ <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -1,6 +1,6 @@ <display id="ucsc_bam" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/interval_as_bed.xml --- a/display_applications/ucsc/interval_as_bed.xml +++ b/display_applications/ucsc/interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/maf_customtrack.xml --- a/display_applications/ucsc/maf_customtrack.xml +++ b/display_applications/ucsc/maf_customtrack.xml @@ -1,6 +1,6 @@ <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/vcf.xml --- a/display_applications/ucsc/vcf.xml +++ b/display_applications/ucsc/vcf.xml @@ -1,6 +1,6 @@ <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,9 +64,6 @@ # Load dbkey / genome build manager self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True ) - # Load build sites (old-style) - self._configure_build_sites() - # Genomes self.genomes = Genomes( self ) # Data providers registry. diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,7 +16,6 @@ from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds -from galaxy.util.build_sites import BuildSites from galaxy import eggs log = logging.getLogger( __name__ ) @@ -224,9 +223,7 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) - self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root ) self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) @@ -574,9 +571,6 @@ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style ) - def _configure_build_sites( self ): - self.build_sites = BuildSites( self ) - def _configure_toolbox( self ): # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -81,9 +81,13 @@ class DynamicDisplayApplicationBuilder( object ): @classmethod - def __init__( self, elem, display_application ): + def __init__( self, elem, display_application, build_sites ): rval = [] - filename = elem.get( 'from_file', None ) + filename = None + if elem.get( 'site_type', None ) is not None: + filename = build_sites.get( elem.get( 'site_type' ) ) + else: + filename = elem.get( 'from_file', None ) assert filename is not None, 'Filename and id attributes required for dynamic_links' skip_startswith = elem.get( 'skip_startswith', None ) separator = elem.get( 'separator', '\t' ) @@ -176,7 +180,7 @@ if link: rval.links[ link.id ] = link for dynamic_links in elem.findall( 'dynamic_links' ): - for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ): + for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): rval.links[ link.id ] = link return rval def __init__( self, display_id, name, datatypes_registry, version = None ): diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -85,7 +85,7 @@ if not dataset.dbkey: dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): if site_name in app.config.ucsc_display_sites: site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,7 +234,7 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) + for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ) if name in app.config.ucsc_display_sites ] if not valid_sites: return [] @@ -750,7 +750,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % @@ -762,7 +762,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] @@ -1091,7 +1091,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] @@ -1103,7 +1103,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) @@ -1285,7 +1285,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey): if site_name in app.config.ucsc_display_sites: internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -69,6 +69,9 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None + # Build sites + self.build_sites = {} + self.legacy_build_sites = {} def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ @@ -285,6 +288,8 @@ handling_proprietary_datatypes=handling_proprietary_datatypes, override=override ) self.upload_file_formats.sort() + # Load build sites + self.load_build_sites( root ) # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and # set_metadata processing. self.to_xml_file() @@ -303,6 +308,26 @@ self.sniff_order.append( datatype ) append_to_sniff_order() + def load_build_sites( self, root ): + if root.find( 'build_sites' ): + for elem in root.find( 'build_sites' ).findall( 'site' ): + if not (elem.get( 'type' ) and elem.get( 'file' )): + self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) + else: + self.build_sites[elem.get( 'type' )] = elem.get( 'file' ) + self.log.debug( "Loaded build site '%s': %s", elem.get( 'type' ), elem.get( 'file' ) ) + for site, file in self.build_sites.items(): + if site in ( 'ucsc', 'gbrowse' ): + self.legacy_build_sites[site] = galaxy.util.read_build_sites( file ) + self.log.debug( "Loaded legacy build site '%s': %s", site, file ) + + def get_legacy_sites_by_build( self, site_type, build ): + sites = [] + for site in self.legacy_build_sites[site_type]: + if build in site['builds']: + sites.append((site['name'], site['url'])) + return sites + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): """ Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -829,6 +829,30 @@ return db_names +def read_build_sites( filename, check_builds=True ): + """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ + build_sites = [] + try: + for line in open(filename): + try: + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + site_name = fields[0] + site = fields[1] + if check_builds: + site_builds = fields[2].split(",") + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} + else: + site_dict = {'name': site_name, 'url': site} + build_sites.append( site_dict ) + except: + continue + except: + print "ERROR: Unable to read builds for site file %s" % filename + return build_sites + + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ /dev/null @@ -1,52 +0,0 @@ -""" -Functionality for dealing with build sites for legacy display applications. -""" -import os.path - - -class BuildSites( object ): - - def __init__( self, app ): - self._app = app - self._build_sites = {} - self.load_build_sites() - - def read_build_sites( self, filename, check_builds=True ): - """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ - build_sites = [] - try: - for line in open(filename): - try: - if line[0:1] == "#": - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - site_name = fields[0] - site = fields[1] - if check_builds: - site_builds = fields[2].split(",") - site_dict = {'name': site_name, 'url': site, 'builds': site_builds} - else: - site_dict = {'name': site_name, 'url': site} - build_sites.append( site_dict ) - except: - continue - except: - print "ERROR: Unable to read builds for site file %s" % filename - return build_sites - - def load_build_sites( self ): - self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) - self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - - def _get_site_by_build( self, site_type, build ): - sites = [] - for site in self._build_sites[site_type]: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - def get_ucsc_sites_by_build( self, build ): - return self._get_site_by_build( 'ucsc', build ) - - def get_gbrowse_sites_by_build( self, build ): - return self._get_site_by_build( 'gbrowse', build ) https://bitbucket.org/galaxy/galaxy-central/commits/6347caa946d7/ Changeset: 6347caa946d7 User: natefoo Date: 2014-09-03 00:21:50 Summary: Remove config options from sample. Affected #: 1 file diff -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d -r 6347caa946d76480267766122718db064ac3e0a1 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -364,12 +364,10 @@ # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. -# UCSC browsers: -#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt +# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt #ucsc_display_sites = main,test,archaea,ucla -# GBrowse servers: -#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt +# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt #gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 # If use_remote_user = True, display application servers will be denied access https://bitbucket.org/galaxy/galaxy-central/commits/4888400b34d1/ Changeset: 4888400b34d1 User: natefoo Date: 2014-09-03 18:25:22 Summary: Move ucsc_display_sites and gbrowse_display_sites into datatypes_conf.xml's new <build_sites> section, as per the suggestion by @nsoranzo. Affected #: 10 files diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -313,8 +313,18 @@ --></sniffers><build_sites> - <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt"/> - <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt"/> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/><site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/><site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/><site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -223,8 +223,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) - self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -86,7 +86,7 @@ dataset.dbkey = 'hg18' # punt! if dataset.has_data(): for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): - if site_name in app.config.ucsc_display_sites: + if site_name in datatypes_registry.get_display_sites('ucsc'): site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -235,7 +235,7 @@ # enabled. valid_sites = [ ( name, url ) for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ) - if name in app.config.ucsc_display_sites ] + if name in app.datatypes_registry.get_display_sites('ucsc') ] if not valid_sites: return [] # If there are any valid sites, we need to generate the estimated @@ -751,7 +751,7 @@ seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) ) @@ -763,7 +763,7 @@ seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) ) @@ -1092,7 +1092,7 @@ chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) ) @@ -1104,7 +1104,7 @@ chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) @@ -1286,7 +1286,7 @@ chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey): - if site_name in app.config.ucsc_display_sites: + if site_name in app.datatypes_registry.get_display_sites('ucsc'): internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -71,6 +71,7 @@ self.xml_filename = None # Build sites self.build_sites = {} + self.display_sites = {} self.legacy_build_sites = {} def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): @@ -314,20 +315,28 @@ if not (elem.get( 'type' ) and elem.get( 'file' )): self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) else: - self.build_sites[elem.get( 'type' )] = elem.get( 'file' ) - self.log.debug( "Loaded build site '%s': %s", elem.get( 'type' ), elem.get( 'file' ) ) - for site, file in self.build_sites.items(): - if site in ( 'ucsc', 'gbrowse' ): - self.legacy_build_sites[site] = galaxy.util.read_build_sites( file ) - self.log.debug( "Loaded legacy build site '%s': %s", site, file ) + site_type = elem.get( 'type' ) + file = elem.get( 'file' ) + self.build_sites[site_type] = file + if site_type in ('ucsc', 'gbrowse'): + self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file ) + if elem.get( 'display', None ): + display = elem.get( 'display' ) + self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ] + self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display ) + else: + self.log.debug( "Loaded build site '%s': %s", site_type, file ) def get_legacy_sites_by_build( self, site_type, build ): sites = [] - for site in self.legacy_build_sites[site_type]: + for site in self.legacy_build_sites.get(site_type, []): if build in site['builds']: sites.append((site['name'], site['url'])) return sites + def get_display_sites( self, site_type ): + return self.display_sites.get( site_type, [] ) + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): """ Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -926,7 +926,7 @@ url_for( controller='dataset', action='list' ) ) display_as = url_for( controller='root', action='display_as' ) - if self.app.config.ucsc_display_sites and self.request.path == 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 ): diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -364,12 +364,6 @@ # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. -# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to https://bitbucket.org/galaxy/galaxy-central/commits/608391566ac8/ Changeset: 608391566ac8 User: natefoo Date: 2014-09-03 18:27:01 Summary: Fix nonstandard indentation. Affected #: 1 file diff -r 4888400b34d120140d163ea3d92d053ba04e2ffb -r 608391566ac80318f703ddf9b8f9506fc46dc866 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -83,29 +83,31 @@ ret_val = [] ggtail = 'hgGenome_doSubmitUpload=submit' if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! + dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): - if site_name in datatypes_registry.get_display_sites('ucsc'): - site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - internal_url = "%s" % url_for( controller='dataset', - dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) - display_url = urllib.quote_plus( display_url ) - # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) - #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) - sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] - #sl.append("&hgt.customText=%s") - sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) - sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") - sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_doSubmitUpload=submit") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) - s = ''.join(sl) - s = urllib.quote_plus(s) - redirect_url = s - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): + if site_name in datatypes_registry.get_display_sites('ucsc'): + site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, + action='display_at', + filename='ucsc_' + site_name ) + display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) + display_url = urllib.quote_plus( display_url ) + # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] + #sl.append("&hgt.customText=%s") + sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) + sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") + sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") + sl.append("&hgGenome_doSubmitUpload=submit") + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) + s = ''.join(sl) + s = urllib.quote_plus(s) + redirect_url = s + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) return ret_val def make_html_table( self, dataset, skipchars=[] ): https://bitbucket.org/galaxy/galaxy-central/commits/f7e396d29268/ Changeset: f7e396d29268 User: natefoo Date: 2014-09-03 19:13:48 Summary: Fix typo in sample config. Affected #: 1 file diff -r 608391566ac80318f703ddf9b8f9506fc46dc866 -r f7e396d292685cd03145225f40ad7eb6f74b9408 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -320,8 +320,8 @@ The `display` attributes on the `ucsc` and `gbrowse` sites replace the `ucsc_display_sites` and `gbrowse_display_sites` options in universe_wsgi.ini. Because these are used by "old-style" display - applications, their types cannot not change if you want the old-style - display links for these sites to work. + applications, their types cannot change if you want the old-style display + links for these sites to work. --><site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/><site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> https://bitbucket.org/galaxy/galaxy-central/commits/9b6cccb3af2d/ Changeset: 9b6cccb3af2d User: natefoo Date: 2014-09-04 17:38:26 Summary: Merged in natefoo/galaxy-central (pull request #481) Make build sites files configurable Affected #: 27 files diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -312,4 +312,22 @@ <sniffer type="galaxy.datatypes.assembly:Amos"/> --></sniffers> + <build_sites> +  + <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/> + <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/> + <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/> + <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/> + <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/> + <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/> + </build_sites></datatypes> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_bam.xml --- a/display_applications/ensembl/ensembl_bam.xml +++ b/display_applications/ensembl/ensembl_bam.xml @@ -1,7 +1,7 @@ <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_gff.xml --- a/display_applications/ensembl/ensembl_gff.xml +++ b/display_applications/ensembl/ensembl_gff.xml @@ -1,7 +1,7 @@ <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_interval_as_bed.xml --- a/display_applications/ensembl/ensembl_interval_as_bed.xml +++ b/display_applications/ensembl/ensembl_interval_as_bed.xml @@ -1,7 +1,7 @@ <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"> - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -41,7 +41,7 @@  - <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,6 +1,6 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,6 +1,6 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -10,7 +10,7 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> + <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -2,7 +2,7 @@ <display id="igv_bam" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -2,7 +2,7 @@ <display id="igv_vcf" version="1.0.0" name="display with IGV"> - <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> @@ -92,4 +92,4 @@ </display> - \ No newline at end of file + diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/bed.xml --- a/display_applications/rviewer/bed.xml +++ b/display_applications/rviewer/bed.xml @@ -2,7 +2,7 @@ <display id="rviewer_interval" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/vcf.xml --- a/display_applications/rviewer/vcf.xml +++ b/display_applications/rviewer/vcf.xml @@ -2,7 +2,7 @@ <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"> - <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><dynamic_param name="site_id" value="0"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -1,6 +1,6 @@ <display id="ucsc_bam" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -1,6 +1,6 @@ <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/interval_as_bed.xml --- a/display_applications/ucsc/interval_as_bed.xml +++ b/display_applications/ucsc/interval_as_bed.xml @@ -1,6 +1,6 @@ <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/maf_customtrack.xml --- a/display_applications/ucsc/maf_customtrack.xml +++ b/display_applications/ucsc/maf_customtrack.xml @@ -1,6 +1,6 @@ <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/vcf.xml --- a/display_applications/ucsc/vcf.xml +++ b/display_applications/ucsc/vcf.xml @@ -1,6 +1,6 @@ <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> - <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/> diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,9 +64,6 @@ # Load dbkey / genome build manager self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True ) - # Load build sites (old-style) - self._configure_build_sites() - # Genomes self.genomes = Genomes( self ) # Data providers registry. diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,7 +16,6 @@ from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds -from galaxy.util.build_sites import BuildSites from galaxy import eggs log = logging.getLogger( __name__ ) @@ -224,10 +223,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) - self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root ) - self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root ) - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. @@ -575,9 +570,6 @@ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style ) - def _configure_build_sites( self ): - self.build_sites = BuildSites( self ) - def _configure_toolbox( self ): # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -81,9 +81,13 @@ class DynamicDisplayApplicationBuilder( object ): @classmethod - def __init__( self, elem, display_application ): + def __init__( self, elem, display_application, build_sites ): rval = [] - filename = elem.get( 'from_file', None ) + filename = None + if elem.get( 'site_type', None ) is not None: + filename = build_sites.get( elem.get( 'site_type' ) ) + else: + filename = elem.get( 'from_file', None ) assert filename is not None, 'Filename and id attributes required for dynamic_links' skip_startswith = elem.get( 'skip_startswith', None ) separator = elem.get( 'separator', '\t' ) @@ -176,7 +180,7 @@ if link: rval.links[ link.id ] = link for dynamic_links in elem.findall( 'dynamic_links' ): - for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ): + for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): rval.links[ link.id ] = link return rval def __init__( self, display_id, name, datatypes_registry, version = None ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -83,29 +83,31 @@ ret_val = [] ggtail = 'hgGenome_doSubmitUpload=submit' if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! + dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - internal_url = "%s" % url_for( controller='dataset', - dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) - display_url = urllib.quote_plus( display_url ) - # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) - #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) - sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] - #sl.append("&hgt.customText=%s") - sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) - sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") - sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_doSubmitUpload=submit") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) - s = ''.join(sl) - s = urllib.quote_plus(s) - redirect_url = s - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey): + if site_name in datatypes_registry.get_display_sites('ucsc'): + site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, + action='display_at', + filename='ucsc_' + site_name ) + display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) + display_url = urllib.quote_plus( display_url ) + # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] + #sl.append("&hgt.customText=%s") + sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) + sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") + sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") + sl.append("&hgGenome_doSubmitUpload=submit") + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) + s = ''.join(sl) + s = urllib.quote_plus(s) + redirect_url = s + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) return ret_val def make_html_table( self, dataset, skipchars=[] ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,8 +234,8 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) - if name in app.config.ucsc_display_sites ] + for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ) + if name in app.datatypes_registry.get_display_sites('ucsc') ] if not valid_sites: return [] # If there are any valid sites, we need to generate the estimated @@ -750,8 +750,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) ) @@ -762,8 +762,8 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) ) @@ -1091,8 +1091,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('gbrowse'): if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) ) @@ -1103,8 +1103,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) @@ -1285,8 +1285,8 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: + for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey): + if site_name in app.datatypes_registry.get_display_sites('ucsc'): internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -69,6 +69,10 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None + # Build sites + self.build_sites = {} + self.display_sites = {} + self.legacy_build_sites = {} def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ @@ -285,6 +289,8 @@ handling_proprietary_datatypes=handling_proprietary_datatypes, override=override ) self.upload_file_formats.sort() + # Load build sites + self.load_build_sites( root ) # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and # set_metadata processing. self.to_xml_file() @@ -303,6 +309,34 @@ self.sniff_order.append( datatype ) append_to_sniff_order() + def load_build_sites( self, root ): + if root.find( 'build_sites' ): + for elem in root.find( 'build_sites' ).findall( 'site' ): + if not (elem.get( 'type' ) and elem.get( 'file' )): + self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) + else: + site_type = elem.get( 'type' ) + file = elem.get( 'file' ) + self.build_sites[site_type] = file + if site_type in ('ucsc', 'gbrowse'): + self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file ) + if elem.get( 'display', None ): + display = elem.get( 'display' ) + self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ] + self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display ) + else: + self.log.debug( "Loaded build site '%s': %s", site_type, file ) + + def get_legacy_sites_by_build( self, site_type, build ): + sites = [] + for site in self.legacy_build_sites.get(site_type, []): + if build in site['builds']: + sites.append((site['name'], site['url'])) + return sites + + def get_display_sites( self, site_type ): + return self.display_sites.get( site_type, [] ) + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): """ Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -844,6 +844,30 @@ return db_names +def read_build_sites( filename, check_builds=True ): + """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ + build_sites = [] + try: + for line in open(filename): + try: + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + site_name = fields[0] + site = fields[1] + if check_builds: + site_builds = fields[2].split(",") + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} + else: + site_dict = {'name': site_name, 'url': site} + build_sites.append( site_dict ) + except: + continue + except: + print "ERROR: Unable to read builds for site file %s" % filename + return build_sites + + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ /dev/null @@ -1,52 +0,0 @@ -""" -Functionality for dealing with build sites for legacy display applications. -""" -import os.path - - -class BuildSites( object ): - - def __init__( self, app ): - self._app = app - self._build_sites = {} - self.load_build_sites() - - def read_build_sites( self, filename, check_builds=True ): - """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ - build_sites = [] - try: - for line in open(filename): - try: - if line[0:1] == "#": - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - site_name = fields[0] - site = fields[1] - if check_builds: - site_builds = fields[2].split(",") - site_dict = {'name': site_name, 'url': site, 'builds': site_builds} - else: - site_dict = {'name': site_name, 'url': site} - build_sites.append( site_dict ) - except: - continue - except: - print "ERROR: Unable to read builds for site file %s" % filename - return build_sites - - def load_build_sites( self ): - self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) - self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - - def _get_site_by_build( self, site_type, build ): - sites = [] - for site in self._build_sites[site_type]: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - def get_ucsc_sites_by_build( self, build ): - return self._get_site_by_build( 'ucsc', build ) - - def get_gbrowse_sites_by_build( self, build ): - return self._get_site_by_build( 'gbrowse', build ) diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -926,7 +926,7 @@ url_for( controller='dataset', action='list' ) ) display_as = url_for( controller='root', action='display_as' ) - if self.app.config.ucsc_display_sites and self.request.path == 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 ): diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -364,14 +364,6 @@ # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. -# UCSC browsers: -#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: -#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 04 Sep '14

04 Sep '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/edc187004292/ Changeset: edc187004292 User: dannon Date: 2014-09-04 01:38:44 Summary: Add is_uuid to lib/galaxy/util Affected #: 1 file diff -r 6070f4fbb38f88eb98cf65f0477924ffea9bc10c -r edc1870042923f32dfeb9dadcc13e1915edff825 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -98,6 +98,21 @@ return False +def is_uuid( value ): + """ + This method returns True if value is a UUID, otherwise False. + >>> is_uuid( "123e4567-e89b-12d3-a456-426655440000" ) + True + >>> is_uuid( "0x3242340298902834" ) + False + """ + uuid_re = re.compile( "[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}" ) + if re.match( uuid_re, str( value ) ): + return True + else: + return False + + def get_charset_from_http_headers( headers, default=None ): rval = headers.get('content-type', None ) if rval and 'charset=' in rval: https://bitbucket.org/galaxy/galaxy-central/commits/8a93d99fccfa/ Changeset: 8a93d99fccfa User: dannon Date: 2014-09-04 01:49:05 Summary: pep8 prior to modifications / whitespace and comment spacing. Affected #: 1 file diff -r edc1870042923f32dfeb9dadcc13e1915edff825 -r 8a93d99fccfa452786836a568976b5ebb50cddf7 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -439,17 +439,17 @@ stored_workflow = query.get( workflow_id ) except Exception: try: - #see if they have passed in the UUID for a workflow that is attached to a stored workflow + # see if they have passed in the UUID for a workflow that is attached to a stored workflow workflow_uuid = uuid.UUID(workflow_id) stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_( trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id, trans.app.model.Workflow.uuid == workflow_uuid - )).first() + )).first() if stored_workflow is None: raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id ) return stored_workflow except: - pass #let the outer raise exception happen + pass # let the outer raise exception happen raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) if stored_workflow is None: raise exceptions.ObjectNotFound( "No such workflow found." ) https://bitbucket.org/galaxy/galaxy-central/commits/75709a2361b1/ Changeset: 75709a2361b1 User: dannon Date: 2014-09-04 16:59:44 Summary: Adjust __get_stored_workflow (by uuid) logic to detect UUIDs and switch accordingly. Affected #: 1 file diff -r 8a93d99fccfa452786836a568976b5ebb50cddf7 -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -433,24 +433,19 @@ return stored_workflow def __get_stored_workflow( self, trans, workflow_id ): - try: + if util.is_uuid(workflow_id): + # see if they have passed in the UUID for a workflow that is attached to a stored workflow + workflow_uuid = uuid.UUID(workflow_id) + stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_( + trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id, + trans.app.model.Workflow.uuid == workflow_uuid + )).first() + if stored_workflow is None: + raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id ) + else: workflow_id = self.__decode_id( trans, workflow_id ) query = trans.sa_session.query( trans.app.model.StoredWorkflow ) stored_workflow = query.get( workflow_id ) - except Exception: - try: - # see if they have passed in the UUID for a workflow that is attached to a stored workflow - workflow_uuid = uuid.UUID(workflow_id) - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_( - trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id, - trans.app.model.Workflow.uuid == workflow_uuid - )).first() - if stored_workflow is None: - raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id ) - return stored_workflow - except: - pass # let the outer raise exception happen - raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) if stored_workflow is None: raise exceptions.ObjectNotFound( "No such workflow found." ) return stored_workflow https://bitbucket.org/galaxy/galaxy-central/commits/9fdca7477f44/ Changeset: 9fdca7477f44 User: dannon Date: 2014-09-04 16:59:59 Summary: Merge. Affected #: 11 files diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -ea12550fbc34260ae70bde38db59a4024f35f988 latest_2014.08.11 +20f4fdf1735aeff23a6e7ab00389781fe3f3142c latest_2014.08.11 diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2466,6 +2466,7 @@ val = getattr( ldda.datatype, name ) rval['metadata_' + name] = val return rval + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templatesThe get_contents # param is passed by callers that are inheriting a template - these @@ -2492,6 +2493,7 @@ else: return template.get_widgets( trans.user ) return [] + def templates_dict( self, use_name=False ): """ Returns a dict of template info @@ -2510,6 +2512,7 @@ tmp_dict[ name ] = content.get( field[ 'name' ] ) template_data[template.name] = tmp_dict return template_data + def templates_json( self, use_name=False ): return json.dumps( self.templates_dict( use_name=use_name ) ) @@ -2533,6 +2536,7 @@ self.info = info self.inheritable = inheritable + class LibraryFolderInfoAssociation( object ): def __init__( self, folder, form_definition, info, inheritable=False ): self.folder = folder @@ -2540,15 +2544,18 @@ self.info = info self.inheritable = inheritable + class LibraryDatasetDatasetInfoAssociation( object ): def __init__( self, library_dataset_dataset_association, form_definition, info ): # TODO: need to figure out if this should be inheritable to the associated LibraryDataset self.library_dataset_dataset_association = library_dataset_dataset_association self.template = form_definition self.info = info + @property def inheritable( self ): - return True #always allow inheriting, used for replacement + return True # always allow inheriting, used for replacement + class ValidationError( object ): def __init__( self, message=None, err_type=None, attributes=None ): @@ -2556,42 +2563,47 @@ self.err_type = err_type self.attributes = attributes + class DatasetToValidationErrorAssociation( object ): def __init__( self, dataset, validation_error ): self.dataset = dataset self.validation_error = validation_error + class ImplicitlyConvertedDatasetAssociation( object ): - def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ): + + def __init__( self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True ): self.id = id if isinstance(dataset, HistoryDatasetAssociation): self.dataset = dataset elif isinstance(dataset, LibraryDatasetDatasetAssociation): self.dataset_ldda = dataset else: - raise AttributeError, 'Unknown dataset type provided for dataset: %s' % type( dataset ) + raise AttributeError( 'Unknown dataset type provided for dataset: %s' % type( dataset ) ) if isinstance(parent, HistoryDatasetAssociation): self.parent_hda = parent elif isinstance(parent, LibraryDatasetDatasetAssociation): self.parent_ldda = parent else: - raise AttributeError, 'Unknown dataset type provided for parent: %s' % type( parent ) + raise AttributeError( 'Unknown dataset type provided for parent: %s' % type( parent ) ) self.type = file_type self.deleted = deleted self.purged = purged self.metadata_safe = metadata_safe - def clear( self, purge = False, delete_dataset = True ): + def clear( self, purge=False, delete_dataset=True ): self.deleted = True if self.dataset: if delete_dataset: self.dataset.deleted = True if purge: self.dataset.purged = True - if purge and self.dataset.deleted: #do something with purging + if purge and self.dataset.deleted: # do something with purging self.purged = True - try: os.unlink( self.file_name ) - except Exception, e: print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) + try: + os.unlink( self.file_name ) + except Exception, e: + print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) DEFAULT_COLLECTION_NAME = "Unnamed Collection" @@ -2903,6 +2915,7 @@ self.tool_id = None self.message = message + class GalaxySession( object ): def __init__( self, id=None, @@ -2924,24 +2937,29 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id self.histories = [] + def add_history( self, history, association=None ): if association is None: self.histories.append( GalaxySessionToHistoryAssociation( self, history ) ) else: self.histories.append( association ) + def get_disk_usage( self ): if self.disk_usage is None: return 0 return self.disk_usage + def set_disk_usage( self, bytes ): self.disk_usage = bytes total_disk_usage = property( get_disk_usage, set_disk_usage ) + class GalaxySessionToHistoryAssociation( object ): def __init__( self, galaxy_session, history ): self.galaxy_session = galaxy_session self.history = history + class UCI( object ): def __init__( self ): self.id = None @@ -2962,14 +2980,14 @@ self.latest_workflow_id = None self.workflows = [] - def copy_tags_from(self,target_user,source_workflow): + def copy_tags_from(self, target_user, source_workflow): for src_swta in source_workflow.owner_tags: new_swta = src_swta.copy() new_swta.user = target_user self.tags.append(new_swta) - def to_dict( self, view='collection', value_mapper = None ): - rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper = value_mapper ) + def to_dict( self, view='collection', value_mapper=None ): + rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper=value_mapper ) tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -3007,12 +3025,11 @@ return False def to_dict( self, view='collection', value_mapper=None): - rval = super( Workflow, self ).to_dict( view=view, value_mapper = value_mapper ) - rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) + rval = super( Workflow, self ).to_dict( view=view, value_mapper=value_mapper ) + rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) return rval - class WorkflowStep( object ): def __init__( self ): @@ -3061,7 +3078,7 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper ) if view == 'element': steps = {} @@ -3072,12 +3089,12 @@ inputs = {} for step in self.steps: - if step.workflow_step.type =='tool': + if step.workflow_step.type == 'tool': for step_input in step.workflow_step.input_connections: if step_input.output_step.type == 'data_input': for job_input in step.job.input_datasets: if job_input.name == step_input.input_name: - inputs[str(step_input.output_step.order_index)] = { "id" : job_input.dataset_id, "src" : "hda"} + inputs[str(step_input.output_step.order_index)] = { "id": job_input.dataset_id, "src": "hda"} rval['inputs'] = inputs return rval @@ -3086,19 +3103,20 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper ) rval['order_index'] = self.workflow_step.order_index return rval class MetadataFile( object ): - def __init__( self, dataset = None, name = None ): + def __init__( self, dataset=None, name=None ): if isinstance( dataset, HistoryDatasetAssociation ): self.history_dataset = dataset elif isinstance( dataset, LibraryDatasetDatasetAssociation ): self.library_dataset = dataset self.name = name + @property def file_name( self ): assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -3129,14 +3147,15 @@ class FormDefinition( object, Dictifiable ): # The following form_builder classes are supported by the FormDefinition class. supported_field_types = [ AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - types = Bunch( REQUEST = 'Sequencing Request Form', - SAMPLE = 'Sequencing Sample Form', - EXTERNAL_SERVICE = 'External Service Information Form', - RUN_DETAILS_TEMPLATE = 'Sample run details template', - LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) + types = Bunch( REQUEST='Sequencing Request Form', + SAMPLE='Sequencing Sample Form', + EXTERNAL_SERVICE='External Service Information Form', + RUN_DETAILS_TEMPLATE='Sample run details template', + LIBRARY_INFO_TEMPLATE='Library information template', + USER_INFO='User Information' ) dict_collection_visible_keys = ( 'id', 'name' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' ) + def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc @@ -3144,6 +3163,7 @@ self.form_definition_current = form_definition_current self.type = form_type self.layout = layout + def grid_fields( self, grid_index ): # Returns a dictionary whose keys are integers corresponding to field positions # on the grid and whose values are the field. @@ -3152,6 +3172,7 @@ if str( f[ 'layout' ] ) == str( grid_index ): gridfields[i] = f return gridfields + def get_widgets( self, user, contents={}, **kwd ): ''' Return the list of widgets that comprise a form definition, @@ -3213,24 +3234,28 @@ field_widget.params = params elif field_type == 'SelectField': for option in field[ 'selectlist' ]: + if option == value: field_widget.add_option( option, option, selected=True ) else: field_widget.add_option( option, option ) elif field_type == 'CheckboxField': + field_widget.set_checked( value ) if field[ 'required' ] == 'required': req = 'Required' else: req = 'Optional' if field[ 'helptext' ]: - helptext='%s (%s)' % ( field[ 'helptext' ], req ) + helptext = '%s (%s)' % ( field[ 'helptext' ], req ) else: helptext = '(%s)' % req widgets.append( dict( label=field[ 'label' ], + widget=field_widget, helptext=helptext ) ) return widgets + def field_as_html( self, field ): """Generates disabled html for a field""" type = field[ 'type' ] @@ -3245,21 +3270,25 @@ # Return None if unsupported field type return None + class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): self.latest_form = form_definition + class FormValues( object ): def __init__(self, form_def=None, content=None): self.form_definition = form_def self.content = content + class Request( object, Dictifiable ): - states = Bunch( NEW = 'New', - SUBMITTED = 'In Progress', - REJECTED = 'Rejected', - COMPLETE = 'Complete' ) + states = Bunch( NEW='New', + SUBMITTED='In Progress', + REJECTED='Rejected', + COMPLETE='Complete' ) dict_collection_visible_keys = ( 'id', 'name', 'state' ) + def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name self.desc = desc @@ -3268,17 +3297,20 @@ self.user = user self.notification = notification self.samples_list = [] + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def samples_have_common_state( self ): """ @@ -3294,6 +3326,7 @@ if s.state.id != state_for_comparison.id: return False return state_for_comparison + @property def last_comment( self ): latest_event = self.latest_event @@ -3302,26 +3335,34 @@ return latest_event.comment return '' return 'No comment' + def get_sample( self, sample_name ): for sample in self.samples: if sample.name == sample_name: return sample return None + @property def is_unsubmitted( self ): return self.state in [ self.states.REJECTED, self.states.NEW ] + @property def is_rejected( self ): return self.state == self.states.REJECTED + @property def is_submitted( self ): return self.state == self.states.SUBMITTED + @property def is_new( self ): + return self.state == self.states.NEW + @property def is_complete( self ): return self.state == self.states.COMPLETE + @property def samples_without_library_destinations( self ): # Return all samples that are not associated with a library @@ -3330,6 +3371,7 @@ if not sample.library: samples.append( sample ) return samples + @property def samples_with_bar_code( self ): # Return all samples that have associated bar code @@ -3338,6 +3380,7 @@ if sample.bar_code: samples.append( sample ) return samples + def send_email_notification( self, trans, common_state, final_state=False ): # Check if an email notification is configured to be sent when the samples # are in this state @@ -3390,7 +3433,7 @@ try: send_mail( frm, to, subject, body, trans.app.config ) comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' ) - except Exception,e: + except Exception, e: comments = "Email notification failed. (%s)" % str(e) # update the request history with the email notification event elif not trans.app.config.smtp_server: @@ -3401,16 +3444,19 @@ trans.sa_session.flush() return comments + class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): self.request = request self.state = request_state self.comment = comment + class ExternalService( object ): - data_transfer_protocol = Bunch( HTTP = 'http', - HTTPS = 'https', - SCP = 'scp' ) + data_transfer_protocol = Bunch( HTTP='http', + HTTPS='https', + SCP='scp' ) + def __init__( self, name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None ): self.name = name self.description = description @@ -3419,9 +3465,11 @@ self.form_definition_id = form_definition_id self.form_values_id = form_values_id self.deleted = deleted - self.label = None # Used in the request_type controller's __build_external_service_select_field() method + self.label = None # Used in the request_type controller's __build_external_service_select_field() method + def get_external_service_type( self, trans ): return trans.app.external_service_types.all_external_service_types[ self.external_service_type_id ] + def load_data_transfer_settings( self, trans ): trans.app.external_service_types.reload( self.external_service_type_id ) self.data_transfer = {} @@ -3442,33 +3490,39 @@ automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) http_configs[ 'automatic_transfer' ] = galaxy.util.string_as_bool( automatic_transfer ) self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs + def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) + class RequestType( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'name', 'desc' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' ) - rename_dataset_options = Bunch( NO = 'Do not rename', - SAMPLE_NAME = 'Preprend sample name', - EXPERIMENT_NAME = 'Prepend experiment name', - EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') + rename_dataset_options = Bunch( NO='Do not rename', + SAMPLE_NAME='Preprend sample name', + EXPERIMENT_NAME='Prepend experiment name', + EXPERIMENT_AND_SAMPLE_NAME='Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) + def __init__( self, name=None, desc=None, request_form=None, sample_form=None ): self.name = name self.desc = desc self.request_form = request_form self.sample_form = sample_form + @property def external_services( self ): external_services = [] for rtesa in self.external_service_associations: external_services.append( rtesa.external_service ) return external_services + def get_external_service( self, external_service_type_id ): for rtesa in self.external_service_associations: if rtesa.external_service.external_service_type_id == external_service_type_id: return rtesa.external_service return None + def get_external_services_for_manual_data_transfer( self, trans ): '''Returns all external services that use manual data transfer''' external_services = [] @@ -3481,6 +3535,7 @@ if not transfer_type_settings[ 'automatic_transfer' ]: external_services.append( external_service ) return external_services + def delete_external_service_associations( self, trans ): '''Deletes all external service associations.''' flush_needed = False @@ -3489,20 +3544,24 @@ flush_needed = True if flush_needed: trans.sa_session.flush() + def add_external_service_association( self, trans, external_service ): rtesa = trans.model.RequestTypeExternalServiceAssociation( self, external_service ) trans.sa_session.add( rtesa ) trans.sa_session.flush() + @property def final_sample_state( self ): # The states mapper for this object orders ascending return self.states[-1] + @property def run_details( self ): if self.run: # self.run[0] is [RequestTypeRunAssociation] return self.run[0] return None + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templates. The get_contents param # is passed by callers that are inheriting a template - these are @@ -3520,23 +3579,27 @@ return template.get_widgets( trans.user ) return [] + class RequestTypeExternalServiceAssociation( object ): def __init__( self, request_type, external_service ): self.request_type = request_type self.external_service = external_service + class RequestTypePermissions( object ): def __init__( self, action, request_type, role ): self.action = action self.request_type = request_type self.role = role + class Sample( object, Dictifiable ): # The following form_builder classes are supported by the Sample class. supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - bulk_operations = Bunch( CHANGE_STATE = 'Change state', - SELECT_LIBRARY = 'Select data library and folder' ) + bulk_operations = Bunch( CHANGE_STATE='Change state', + SELECT_LIBRARY='Select data library and folder' ) dict_collection_visible_keys = ( 'id', 'name' ) + def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None): self.name = name self.desc = desc @@ -3547,17 +3610,20 @@ self.folder = folder self.history = history self.workflow = workflow + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def adding_to_library_dataset_files( self ): adding_to_library_datasets = [] @@ -3565,6 +3631,7 @@ if dataset.status == SampleDataset.transfer_status.ADD_TO_LIBRARY: adding_to_library_datasets.append( dataset ) return adding_to_library_datasets + @property def inprogress_dataset_files( self ): inprogress_datasets = [] @@ -3572,6 +3639,7 @@ if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]: inprogress_datasets.append( dataset ) return inprogress_datasets + @property def queued_dataset_files( self ): queued_datasets = [] @@ -3579,6 +3647,7 @@ if dataset.status == SampleDataset.transfer_status.IN_QUEUE: queued_datasets.append( dataset ) return queued_datasets + @property def transfer_error_dataset_files( self ): transfer_error_datasets = [] @@ -3586,6 +3655,7 @@ if dataset.status == SampleDataset.transfer_status.ERROR: transfer_error_datasets.append( dataset ) return transfer_error_datasets + @property def transferred_dataset_files( self ): transferred_datasets = [] @@ -3593,6 +3663,7 @@ if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets + @property def transferring_dataset_files( self ): transferring_datasets = [] @@ -3600,6 +3671,7 @@ if dataset.status == SampleDataset.transfer_status.TRANSFERRING: transferring_datasets.append( dataset ) return transferring_datasets + @property def untransferred_dataset_files( self ): untransferred_datasets = [] @@ -3607,6 +3679,7 @@ if dataset.status != SampleDataset.transfer_status.COMPLETE: untransferred_datasets.append( dataset ) return untransferred_datasets + def get_untransferred_dataset_size( self, filepath, scp_configs ): def print_ticks( d ): pass diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2130,6 +2130,8 @@ elif isinstance( value, basestring ): if value.startswith( "dce:" ): rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] ) + elif value.startswith( "hdca:" ): + rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] ) else: rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value ) if rval and isinstance( rval, trans.app.model.HistoryDatasetCollectionAssociation ): diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -336,7 +336,14 @@ id : 'field-' + id, data : options, value : options[0].value, + multiple : input_def.multiple, onchange : function(value) { + // pick the first dataset if multiple might be selected + // TODO: iterate over all datasets and filter common/consistent columns + if (input_def.multiple) { + value = value[0]; + } + // get referenced columns var column_list = self.app.tree.findReferences(id, 'data_column'); @@ -437,18 +444,16 @@ // column selection field _field_column : function (input_def) { return new Ui.Select.View({ - id : 'field-' + input_def.id + id : 'field-' + input_def.id, + multiple: input_def.multiple }); }, // text input field _field_text : function(input_def) { - var TextClass = Ui.Input; - if (input_def.area) { - TextClass = Ui.Textarea; - } - return new TextClass({ - id : 'field-' + input_def.id + return new Ui.Input({ + id : 'field-' + input_def.id, + area : input_def.area }); }, diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -312,7 +312,8 @@ placeholder : '', disabled : false, visible : true, - cls : '' + cls : '', + area : false }, // initialize @@ -352,60 +353,11 @@ // element _template: function(options) { - return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">'; - } -}); - -// plugin -var Textarea = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - type : 'text', - placeholder : '', - disabled : false, - visible : true, - cls : '' - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // disable input field - if (this.options.disabled) { - this.$el.prop('disabled', true); + if (options.area) { + return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '"></textarea>'; + } else { + return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="ui-input ' + options.cls + '">'; } - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // onchange event handler. fires on user activity. - var self = this; - this.$el.on('input', function() { - if (self.options.onchange) { - self.options.onchange(self.$el.val()); - } - }); - }, - - // value - value : function (new_val) { - if (new_val !== undefined) { - this.$el.val(new_val); - } - return this.$el.val(); - }, - - // element - _template: function(options) { - return '<textarea id="' + options.id + '" class="ui-textarea ' + options.cls + '"></textarea>'; } }); @@ -455,7 +407,6 @@ Checkbox : Checkbox, Searchbox : Searchbox, Select : Select, - Textarea : Textarea, Hidden : Hidden, Slider : Slider } diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -7,24 +7,19 @@ var View = Backbone.View.extend({ // options optionsDefault : { - id : '', - cls : '', - empty : 'No data available', - visible : true, - wait : false + id : '', + cls : '', + empty : 'No data available', + visible : true, + wait : false, + multiple : false }, - // value - selected : null, - // initialize initialize : function(options) { // configure options this.options = Utils.merge(options, this.optionsDefault); - // initial value - this.selected = this.options.value; - // create new element this.setElement(this._template(this.options)); @@ -32,21 +27,17 @@ this.$select = this.$el.find('#select'); this.$icon = this.$el.find('#icon'); - // add change event. fires only on user activity - var self = this; - this.$select.on('change', function() { - self.value(self.$select.val()); - }); - - // add change event. fires on trigger - this.on('change', function() { - if (self.options.onchange) { - self.options.onchange(self.value()); - } - }); + // configure multiple + if (this.options.multiple) { + this.$select.prop('multiple', true); + this.$select.addClass('ui-select-multiple'); + this.$icon.remove(); + } else { + this.$el.addClass('ui-select'); + } // refresh - this._refresh(); + this.update(this.options.data); // show/hide if (!this.options.visible) { @@ -59,31 +50,25 @@ } else { this.show(); } + + // add change event. fires only on user activity + var self = this; + this.$select.on('change', function() { + self._change(); + }); + + // add change event. fires on trigger + this.on('change', function() { + self._change(); + }); }, // value value : function (new_value) { - - // get current id/value - var before = this.selected; - - // check if new_value is defined if (new_value !== undefined) { - this.selected = new_value; this.$select.val(new_value); } - - // get current id/value - var after = this.selected; - if (after) { - // fire onchange - if (after != before && this.options.onchange) { - this.options.onchange(after); - } - } - - // return - return after; + return this.$select.val(); }, // first @@ -157,6 +142,9 @@ // render update: function(options) { + // backup current value + var current = this.$select.val(); + // remove all options this.$select.find('option').remove(); @@ -167,6 +155,14 @@ // refresh this._refresh(); + + // set previous value + this.$select.val(current); + + // check if any value was set + if (!this.$select.val()) { + this.$select.val(this.first()); + } }, // set on change event @@ -179,6 +175,13 @@ return this.$select.find('option[value=' + value + ']').length > 0; }, + // change + _change: function() { + if (this.options.onchange) { + this.options.onchange(this.$select.val()); + } + }, + // refresh _refresh: function() { // remove placeholder @@ -196,41 +199,21 @@ // enable select field this.enable(); } - - // update value - if (this.selected) { - this.$select.val(this.selected); - } }, - // option + // template option _templateOption: function(options) { return '<option value="' + options.value + '">' + options.label + '</option>'; }, - // element + // template _template: function(options) { - var tmpl = '<div id="' + options.id + '" class="ui-select">' + - '<div class="button">' + - '<i id="icon"/>' + - '</div>' + - '<select id="select" class="select ' + options.cls + ' ' + options.id + '">'; - for (key in options.data) { - // options - var item = options.data[key]; - - // identify selected value - var tag = ''; - if (item.value == options.value || item.value == '') { - tag = 'selected'; - } - - // add template string - tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>'; - } - tmpl += '</select>' + - '</div>'; - return tmpl; + return '<div id="' + options.id + '">' + + '<div class="button">' + + '<i id="icon"/>' + + '</div>' + + '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' + + '</div>'; } }); diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;f.cls_tr="section-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f])}},_add:function(h){var g=this;var f=jQuery.extend(true,{},h);f.id=c.uuid();this.app.input_list[f.id]=f;var i=f.type;switch(i){case"conditional":this._addConditional(f);break;case"repeat":this._addRepeat(f);break;default:this._addRow(i,f)}},_addConditional:function(f){f.label=f.test_param.label;f.value=f.test_param.value;this._addRow("conditional",f);for(var h in f.cases){var g=f.id+"-section-"+h;var j=new d(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(j.$el);this.table.append(g)}},_addRepeat:function(f){var g=this;var k=new a.View({title_new:"Add "+f.title,max:f.max,onnew:function(){var i=f.id+"-section-"+c.uuid();var m=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:i,title:f.title,$el:m.$el,ondel:function(){k.del(i);k.retitle(f.title);g.app.refresh()}});k.retitle(f.title);k.show(i);g.app.refresh()}});for(var j=0;j<f.min;j++){var h=f.id+"-section-"+c.uuid();var l=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:h,title:f.title,$el:l.$el})}k.retitle(f.title);this.table.add("");this.table.add(k.$el);this.table.append(f.id)},_addRow:function(h,f){var j=f.id;var g=null;switch(h){case"text":g=this._field_text(f);break;case"select":g=this._field_select(f);break;case"data":g=this._field_data(f);break;case"data_column":g=this._field_column(f);break;case"conditional":g=this._field_conditional(f);break;case"hidden":g=this._field_hidden(f);break;case"integer":g=this._field_slider(f);break;case"float":g=this._field_slider(f);break;case"boolean":g=this._field_boolean(f);break;default:g=this._field_text(f);console.debug("tools-form::_addRow() : Unmatched field type ("+h+").")}if(f.value!==undefined){g.value(f.value)}this.app.field_list[j]=g;var i=$("<div/>");i.append(g.$el);if(f.help){i.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","20%");this.table.add(i);this.table.append(j)},_field_conditional:function(f){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}return new e.Select.View({id:"field-"+f.id,data:h,onchange:function(s){for(var q in f.cases){var m=f.cases[q];var p=f.id+"-section-"+q;var l=g.table.get(p);var o=false;for(var n in m.inputs){var r=m.inputs[n].type;if(r&&r!=="hidden"){o=true;break}}if(m.value==s&&o){l.fadeIn("fast")}else{l.hide()}}}})},_field_data:function(f){var g=this;var l=f.id;var k=this.app.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+l,data:h,value:h[0].value,onchange:function(u){var s=g.app.tree.findReferences(l,"data_column");var n=g.app.datasets.filter(u);if(n&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=n.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var p in s){var q=g.app.input_list[s[p]];var r=g.app.field_list[s[p]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var o=q.numerical;var m=[];for(var v in w){var t=w[v];if(t=="int"||t=="float"||!o){m.push({label:"Column: "+(parseInt(v)+1)+" ["+w[v]+"]",value:v})}}if(r){r.update(m);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_field_select:function(f){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;switch(f.display){case"checkboxes":k=e.Checkbox;break;case"radio":k=e.RadioButton;break}if(f.multiple){k=e.Checkbox}return new k.View({id:"field-"+f.id,data:g})},_field_column:function(f){return new e.Select.View({id:"field-"+f.id})},_field_text:function(g){var f=e.Input;if(g.area){f=e.Textarea}return new f({id:"field-"+g.id})},_field_slider:function(f){return new e.Slider.View({id:"field-"+f.id,min:f.min||0,max:f.max||1000,decimal:f.type=="float"})},_field_hidden:function(f){return new e.Hidden({id:"field-"+f.id})},_field_boolean:function(f){return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:true},{label:"No",value:false}]})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;f.cls_tr="section-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f])}},_add:function(h){var g=this;var f=jQuery.extend(true,{},h);f.id=c.uuid();this.app.input_list[f.id]=f;var i=f.type;switch(i){case"conditional":this._addConditional(f);break;case"repeat":this._addRepeat(f);break;default:this._addRow(i,f)}},_addConditional:function(f){f.label=f.test_param.label;f.value=f.test_param.value;this._addRow("conditional",f);for(var h in f.cases){var g=f.id+"-section-"+h;var j=new d(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(j.$el);this.table.append(g)}},_addRepeat:function(f){var g=this;var k=new a.View({title_new:"Add "+f.title,max:f.max,onnew:function(){var i=f.id+"-section-"+c.uuid();var m=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:i,title:f.title,$el:m.$el,ondel:function(){k.del(i);k.retitle(f.title);g.app.refresh()}});k.retitle(f.title);k.show(i);g.app.refresh()}});for(var j=0;j<f.min;j++){var h=f.id+"-section-"+c.uuid();var l=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:h,title:f.title,$el:l.$el})}k.retitle(f.title);this.table.add("");this.table.add(k.$el);this.table.append(f.id)},_addRow:function(h,f){var j=f.id;var g=null;switch(h){case"text":g=this._field_text(f);break;case"select":g=this._field_select(f);break;case"data":g=this._field_data(f);break;case"data_column":g=this._field_column(f);break;case"conditional":g=this._field_conditional(f);break;case"hidden":g=this._field_hidden(f);break;case"integer":g=this._field_slider(f);break;case"float":g=this._field_slider(f);break;case"boolean":g=this._field_boolean(f);break;default:g=this._field_text(f);console.debug("tools-form::_addRow() : Unmatched field type ("+h+").")}if(f.value!==undefined){g.value(f.value)}this.app.field_list[j]=g;var i=$("<div/>");i.append(g.$el);if(f.help){i.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","20%");this.table.add(i);this.table.append(j)},_field_conditional:function(f){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}return new e.Select.View({id:"field-"+f.id,data:h,onchange:function(s){for(var q in f.cases){var m=f.cases[q];var p=f.id+"-section-"+q;var l=g.table.get(p);var o=false;for(var n in m.inputs){var r=m.inputs[n].type;if(r&&r!=="hidden"){o=true;break}}if(m.value==s&&o){l.fadeIn("fast")}else{l.hide()}}}})},_field_data:function(f){var g=this;var l=f.id;var k=this.app.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+l,data:h,value:h[0].value,onchange:function(u){var s=g.app.tree.findReferences(l,"data_column");var n=g.app.datasets.filter(u);if(n&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=n.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var p in s){var q=g.app.input_list[s[p]];var r=g.app.field_list[s[p]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var o=q.numerical;var m=[];for(var v in w){var t=w[v];if(t=="int"||t=="float"||!o){m.push({label:"Column: "+(parseInt(v)+1)+" ["+w[v]+"]",value:v})}}if(r){r.update(m);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_field_select:function(f){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;switch(f.display){case"checkboxes":k=e.Checkbox;break;case"radio":k=e.RadioButton;break}if(f.multiple){k=e.Checkbox}return new k.View({id:"field-"+f.id,data:g})},_field_column:function(f){return new e.Select.View({id:"field-"+f.id,multiple:f.multiple})},_field_text:function(f){return new e.Input({id:"field-"+f.id,area:f.area})},_field_slider:function(f){return new e.Slider.View({id:"field-"+f.id,min:f.min||0,max:f.max||1000,decimal:f.type=="float"})},_field_hidden:function(f){return new e.Hidden({id:"field-"+f.id})},_field_boolean:function(f){return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:true},{label:"No",value:false}]})}});return{View:d}}); \ No newline at end of file diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,h,k,i,b,r,c){var q=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var l=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var d=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick);$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="ui-button '+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var o=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick);$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="ui-button-icon '+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(!t.persistent){var s=this;window.setTimeout(function(){if(s.$el.is(":visible")){s.$el.fadeOut()}else{s.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(s){return'<div class="ui-message alert alert-'+s.status+'"/>'}});var f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));var s=this;if(this.options.onclick){this.$el.on("submit",function(v){var u=s.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var n=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}});var m=Backbone.View.extend({optionsDefault:{value:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){return'<hidden id="'+s.id+'" value="'+s.value+'"/>'}});return{Anchor:p,Button:g,ButtonIcon:o,ButtonMenu:r,Icon:d,Image:q,Input:n,Label:l,Message:a,Modal:c,RadioButton:b,Checkbox:i,Searchbox:f,Select:h,Textarea:j,Hidden:m,Slider:k}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,f,e,m,q,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="ui-button '+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var i=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="ui-button-icon '+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var g=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=l.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({optionsDefault:{value:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:g,Button:h,ButtonIcon:i,ButtonMenu:q,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Hidden:p,Slider:f}}); \ No newline at end of file diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false},selected:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.selected=this.options.value;this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");var c=this;this.$select.on("change",function(){c.value(c.$select.val())});this.on("change",function(){if(c.options.onchange){c.options.onchange(c.value())}});this._refresh();if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}},value:function(c){var d=this.selected;if(c!==undefined){this.selected=c;this.$select.val(c)}var e=this.selected;if(e){if(e!=d&&this.options.onchange){this.options.onchange(e)}}return e},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh()},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}if(this.selected){this.$select.val(this.selected)}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(e){var d='<div id="'+e.id+'" class="ui-select"><div class="button"><i id="icon"/></div><select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var f=e.data[key];var c="";if(f.value==e.value||f.value==""){c="selected"}d+='<option value="'+f.value+'" '+c+">"+f.label+"</option>"}d+="</select></div>";return d}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find("option[value="+c+"]").length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1282,6 +1282,7 @@ .ui-table tbody{cursor:pointer} .ui-table-plain tbody td{padding:5px 0px 5px 5px !important;border:none !important} .ui-table-plain tbody{cursor:auto !important} +.ui-table-form-info{clear:both !important} .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-label{font-weight:bold} .ui-message{padding:2px 2px 2px 10px} @@ -1299,8 +1300,9 @@ .ui-portlet .no-scroll{height:calc(100% - 80px)} .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} .ui-popover .popover-title{padding:4px 10px} -.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} +.ui-select,.ui-select-multiple{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} +.ui-select-multiple{height:100% !important;width:100% !important} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff -r 75709a2361b15ba5fd393b0ff2333a81b6ddff87 -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -32,6 +32,7 @@ .ui-table-form-info { &:extend(.toolParamHelp); + clear: both !important; } .ui-table-form-separator { @@ -208,4 +209,10 @@ border-radius: 0; -webkit-appearance: none; } +} + +.ui-select-multiple { + &:extend(.ui-select); + height: 100% !important; + width: 100% !important; } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Some PEP-8 fixes for lib/galaxy/model/__init__.py.
by commits-noreply＠bitbucket.org 04 Sep '14

04 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a90ec4d4066f/ Changeset: a90ec4d4066f User: jmchilton Date: 2014-09-04 16:31:05 Summary: Some PEP-8 fixes for lib/galaxy/model/__init__.py. Affected #: 1 file diff -r dc5e8d1d7a77f9a87a6a825fd8fa9236c9e9a229 -r a90ec4d4066f67149322f68d2dc5c8b98fe4dbcb lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2466,6 +2466,7 @@ val = getattr( ldda.datatype, name ) rval['metadata_' + name] = val return rval + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templatesThe get_contents # param is passed by callers that are inheriting a template - these @@ -2492,6 +2493,7 @@ else: return template.get_widgets( trans.user ) return [] + def templates_dict( self, use_name=False ): """ Returns a dict of template info @@ -2510,6 +2512,7 @@ tmp_dict[ name ] = content.get( field[ 'name' ] ) template_data[template.name] = tmp_dict return template_data + def templates_json( self, use_name=False ): return json.dumps( self.templates_dict( use_name=use_name ) ) @@ -2533,6 +2536,7 @@ self.info = info self.inheritable = inheritable + class LibraryFolderInfoAssociation( object ): def __init__( self, folder, form_definition, info, inheritable=False ): self.folder = folder @@ -2540,15 +2544,18 @@ self.info = info self.inheritable = inheritable + class LibraryDatasetDatasetInfoAssociation( object ): def __init__( self, library_dataset_dataset_association, form_definition, info ): # TODO: need to figure out if this should be inheritable to the associated LibraryDataset self.library_dataset_dataset_association = library_dataset_dataset_association self.template = form_definition self.info = info + @property def inheritable( self ): - return True #always allow inheriting, used for replacement + return True # always allow inheriting, used for replacement + class ValidationError( object ): def __init__( self, message=None, err_type=None, attributes=None ): @@ -2556,42 +2563,47 @@ self.err_type = err_type self.attributes = attributes + class DatasetToValidationErrorAssociation( object ): def __init__( self, dataset, validation_error ): self.dataset = dataset self.validation_error = validation_error + class ImplicitlyConvertedDatasetAssociation( object ): - def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ): + + def __init__( self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True ): self.id = id if isinstance(dataset, HistoryDatasetAssociation): self.dataset = dataset elif isinstance(dataset, LibraryDatasetDatasetAssociation): self.dataset_ldda = dataset else: - raise AttributeError, 'Unknown dataset type provided for dataset: %s' % type( dataset ) + raise AttributeError( 'Unknown dataset type provided for dataset: %s' % type( dataset ) ) if isinstance(parent, HistoryDatasetAssociation): self.parent_hda = parent elif isinstance(parent, LibraryDatasetDatasetAssociation): self.parent_ldda = parent else: - raise AttributeError, 'Unknown dataset type provided for parent: %s' % type( parent ) + raise AttributeError( 'Unknown dataset type provided for parent: %s' % type( parent ) ) self.type = file_type self.deleted = deleted self.purged = purged self.metadata_safe = metadata_safe - def clear( self, purge = False, delete_dataset = True ): + def clear( self, purge=False, delete_dataset=True ): self.deleted = True if self.dataset: if delete_dataset: self.dataset.deleted = True if purge: self.dataset.purged = True - if purge and self.dataset.deleted: #do something with purging + if purge and self.dataset.deleted: # do something with purging self.purged = True - try: os.unlink( self.file_name ) - except Exception, e: print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) + try: + os.unlink( self.file_name ) + except Exception, e: + print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) DEFAULT_COLLECTION_NAME = "Unnamed Collection" @@ -2903,6 +2915,7 @@ self.tool_id = None self.message = message + class GalaxySession( object ): def __init__( self, id=None, @@ -2924,24 +2937,29 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id self.histories = [] + def add_history( self, history, association=None ): if association is None: self.histories.append( GalaxySessionToHistoryAssociation( self, history ) ) else: self.histories.append( association ) + def get_disk_usage( self ): if self.disk_usage is None: return 0 return self.disk_usage + def set_disk_usage( self, bytes ): self.disk_usage = bytes total_disk_usage = property( get_disk_usage, set_disk_usage ) + class GalaxySessionToHistoryAssociation( object ): def __init__( self, galaxy_session, history ): self.galaxy_session = galaxy_session self.history = history + class UCI( object ): def __init__( self ): self.id = None @@ -2962,14 +2980,14 @@ self.latest_workflow_id = None self.workflows = [] - def copy_tags_from(self,target_user,source_workflow): + def copy_tags_from(self, target_user, source_workflow): for src_swta in source_workflow.owner_tags: new_swta = src_swta.copy() new_swta.user = target_user self.tags.append(new_swta) - def to_dict( self, view='collection', value_mapper = None ): - rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper = value_mapper ) + def to_dict( self, view='collection', value_mapper=None ): + rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper=value_mapper ) tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -3007,12 +3025,11 @@ return False def to_dict( self, view='collection', value_mapper=None): - rval = super( Workflow, self ).to_dict( view=view, value_mapper = value_mapper ) - rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) + rval = super( Workflow, self ).to_dict( view=view, value_mapper=value_mapper ) + rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid ) return rval - class WorkflowStep( object ): def __init__( self ): @@ -3061,7 +3078,7 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper ) if view == 'element': steps = {} @@ -3072,12 +3089,12 @@ inputs = {} for step in self.steps: - if step.workflow_step.type =='tool': + if step.workflow_step.type == 'tool': for step_input in step.workflow_step.input_connections: if step_input.output_step.type == 'data_input': for job_input in step.job.input_datasets: if job_input.name == step_input.input_name: - inputs[str(step_input.output_step.order_index)] = { "id" : job_input.dataset_id, "src" : "hda"} + inputs[str(step_input.output_step.order_index)] = { "id": job_input.dataset_id, "src": "hda"} rval['inputs'] = inputs return rval @@ -3086,19 +3103,20 @@ dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' ) - def to_dict( self, view='collection', value_mapper = None ): + def to_dict( self, view='collection', value_mapper=None ): rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper ) rval['order_index'] = self.workflow_step.order_index return rval class MetadataFile( object ): - def __init__( self, dataset = None, name = None ): + def __init__( self, dataset=None, name=None ): if isinstance( dataset, HistoryDatasetAssociation ): self.history_dataset = dataset elif isinstance( dataset, LibraryDatasetDatasetAssociation ): self.library_dataset = dataset self.name = name + @property def file_name( self ): assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -3129,14 +3147,15 @@ class FormDefinition( object, Dictifiable ): # The following form_builder classes are supported by the FormDefinition class. supported_field_types = [ AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - types = Bunch( REQUEST = 'Sequencing Request Form', - SAMPLE = 'Sequencing Sample Form', - EXTERNAL_SERVICE = 'External Service Information Form', - RUN_DETAILS_TEMPLATE = 'Sample run details template', - LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) + types = Bunch( REQUEST='Sequencing Request Form', + SAMPLE='Sequencing Sample Form', + EXTERNAL_SERVICE='External Service Information Form', + RUN_DETAILS_TEMPLATE='Sample run details template', + LIBRARY_INFO_TEMPLATE='Library information template', + USER_INFO='User Information' ) dict_collection_visible_keys = ( 'id', 'name' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout' ) + def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc @@ -3144,6 +3163,7 @@ self.form_definition_current = form_definition_current self.type = form_type self.layout = layout + def grid_fields( self, grid_index ): # Returns a dictionary whose keys are integers corresponding to field positions # on the grid and whose values are the field. @@ -3152,6 +3172,7 @@ if str( f[ 'layout' ] ) == str( grid_index ): gridfields[i] = f return gridfields + def get_widgets( self, user, contents={}, **kwd ): ''' Return the list of widgets that comprise a form definition, @@ -3213,24 +3234,28 @@ field_widget.params = params elif field_type == 'SelectField': for option in field[ 'selectlist' ]: + if option == value: field_widget.add_option( option, option, selected=True ) else: field_widget.add_option( option, option ) elif field_type == 'CheckboxField': + field_widget.set_checked( value ) if field[ 'required' ] == 'required': req = 'Required' else: req = 'Optional' if field[ 'helptext' ]: - helptext='%s (%s)' % ( field[ 'helptext' ], req ) + helptext = '%s (%s)' % ( field[ 'helptext' ], req ) else: helptext = '(%s)' % req widgets.append( dict( label=field[ 'label' ], + widget=field_widget, helptext=helptext ) ) return widgets + def field_as_html( self, field ): """Generates disabled html for a field""" type = field[ 'type' ] @@ -3245,21 +3270,25 @@ # Return None if unsupported field type return None + class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): self.latest_form = form_definition + class FormValues( object ): def __init__(self, form_def=None, content=None): self.form_definition = form_def self.content = content + class Request( object, Dictifiable ): - states = Bunch( NEW = 'New', - SUBMITTED = 'In Progress', - REJECTED = 'Rejected', - COMPLETE = 'Complete' ) + states = Bunch( NEW='New', + SUBMITTED='In Progress', + REJECTED='Rejected', + COMPLETE='Complete' ) dict_collection_visible_keys = ( 'id', 'name', 'state' ) + def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name self.desc = desc @@ -3268,17 +3297,20 @@ self.user = user self.notification = notification self.samples_list = [] + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def samples_have_common_state( self ): """ @@ -3294,6 +3326,7 @@ if s.state.id != state_for_comparison.id: return False return state_for_comparison + @property def last_comment( self ): latest_event = self.latest_event @@ -3302,26 +3335,34 @@ return latest_event.comment return '' return 'No comment' + def get_sample( self, sample_name ): for sample in self.samples: if sample.name == sample_name: return sample return None + @property def is_unsubmitted( self ): return self.state in [ self.states.REJECTED, self.states.NEW ] + @property def is_rejected( self ): return self.state == self.states.REJECTED + @property def is_submitted( self ): return self.state == self.states.SUBMITTED + @property def is_new( self ): + return self.state == self.states.NEW + @property def is_complete( self ): return self.state == self.states.COMPLETE + @property def samples_without_library_destinations( self ): # Return all samples that are not associated with a library @@ -3330,6 +3371,7 @@ if not sample.library: samples.append( sample ) return samples + @property def samples_with_bar_code( self ): # Return all samples that have associated bar code @@ -3338,6 +3380,7 @@ if sample.bar_code: samples.append( sample ) return samples + def send_email_notification( self, trans, common_state, final_state=False ): # Check if an email notification is configured to be sent when the samples # are in this state @@ -3390,7 +3433,7 @@ try: send_mail( frm, to, subject, body, trans.app.config ) comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' ) - except Exception,e: + except Exception, e: comments = "Email notification failed. (%s)" % str(e) # update the request history with the email notification event elif not trans.app.config.smtp_server: @@ -3401,16 +3444,19 @@ trans.sa_session.flush() return comments + class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): self.request = request self.state = request_state self.comment = comment + class ExternalService( object ): - data_transfer_protocol = Bunch( HTTP = 'http', - HTTPS = 'https', - SCP = 'scp' ) + data_transfer_protocol = Bunch( HTTP='http', + HTTPS='https', + SCP='scp' ) + def __init__( self, name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None ): self.name = name self.description = description @@ -3419,9 +3465,11 @@ self.form_definition_id = form_definition_id self.form_values_id = form_values_id self.deleted = deleted - self.label = None # Used in the request_type controller's __build_external_service_select_field() method + self.label = None # Used in the request_type controller's __build_external_service_select_field() method + def get_external_service_type( self, trans ): return trans.app.external_service_types.all_external_service_types[ self.external_service_type_id ] + def load_data_transfer_settings( self, trans ): trans.app.external_service_types.reload( self.external_service_type_id ) self.data_transfer = {} @@ -3442,33 +3490,39 @@ automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) http_configs[ 'automatic_transfer' ] = galaxy.util.string_as_bool( automatic_transfer ) self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs + def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) + class RequestType( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'name', 'desc' ) dict_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' ) - rename_dataset_options = Bunch( NO = 'Do not rename', - SAMPLE_NAME = 'Preprend sample name', - EXPERIMENT_NAME = 'Prepend experiment name', - EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') + rename_dataset_options = Bunch( NO='Do not rename', + SAMPLE_NAME='Preprend sample name', + EXPERIMENT_NAME='Prepend experiment name', + EXPERIMENT_AND_SAMPLE_NAME='Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) + def __init__( self, name=None, desc=None, request_form=None, sample_form=None ): self.name = name self.desc = desc self.request_form = request_form self.sample_form = sample_form + @property def external_services( self ): external_services = [] for rtesa in self.external_service_associations: external_services.append( rtesa.external_service ) return external_services + def get_external_service( self, external_service_type_id ): for rtesa in self.external_service_associations: if rtesa.external_service.external_service_type_id == external_service_type_id: return rtesa.external_service return None + def get_external_services_for_manual_data_transfer( self, trans ): '''Returns all external services that use manual data transfer''' external_services = [] @@ -3481,6 +3535,7 @@ if not transfer_type_settings[ 'automatic_transfer' ]: external_services.append( external_service ) return external_services + def delete_external_service_associations( self, trans ): '''Deletes all external service associations.''' flush_needed = False @@ -3489,20 +3544,24 @@ flush_needed = True if flush_needed: trans.sa_session.flush() + def add_external_service_association( self, trans, external_service ): rtesa = trans.model.RequestTypeExternalServiceAssociation( self, external_service ) trans.sa_session.add( rtesa ) trans.sa_session.flush() + @property def final_sample_state( self ): # The states mapper for this object orders ascending return self.states[-1] + @property def run_details( self ): if self.run: # self.run[0] is [RequestTypeRunAssociation] return self.run[0] return None + def get_template_widgets( self, trans, get_contents=True ): # See if we have any associated templates. The get_contents param # is passed by callers that are inheriting a template - these are @@ -3520,23 +3579,27 @@ return template.get_widgets( trans.user ) return [] + class RequestTypeExternalServiceAssociation( object ): def __init__( self, request_type, external_service ): self.request_type = request_type self.external_service = external_service + class RequestTypePermissions( object ): def __init__( self, action, request_type, role ): self.action = action self.request_type = request_type self.role = role + class Sample( object, Dictifiable ): # The following form_builder classes are supported by the Sample class. supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - bulk_operations = Bunch( CHANGE_STATE = 'Change state', - SELECT_LIBRARY = 'Select data library and folder' ) + bulk_operations = Bunch( CHANGE_STATE='Change state', + SELECT_LIBRARY='Select data library and folder' ) dict_collection_visible_keys = ( 'id', 'name' ) + def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None): self.name = name self.desc = desc @@ -3547,17 +3610,20 @@ self.folder = folder self.history = history self.workflow = workflow + @property def state( self ): latest_event = self.latest_event if latest_event: return latest_event.state return None + @property def latest_event( self ): if self.events: return self.events[0] return None + @property def adding_to_library_dataset_files( self ): adding_to_library_datasets = [] @@ -3565,6 +3631,7 @@ if dataset.status == SampleDataset.transfer_status.ADD_TO_LIBRARY: adding_to_library_datasets.append( dataset ) return adding_to_library_datasets + @property def inprogress_dataset_files( self ): inprogress_datasets = [] @@ -3572,6 +3639,7 @@ if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]: inprogress_datasets.append( dataset ) return inprogress_datasets + @property def queued_dataset_files( self ): queued_datasets = [] @@ -3579,6 +3647,7 @@ if dataset.status == SampleDataset.transfer_status.IN_QUEUE: queued_datasets.append( dataset ) return queued_datasets + @property def transfer_error_dataset_files( self ): transfer_error_datasets = [] @@ -3586,6 +3655,7 @@ if dataset.status == SampleDataset.transfer_status.ERROR: transfer_error_datasets.append( dataset ) return transfer_error_datasets + @property def transferred_dataset_files( self ): transferred_datasets = [] @@ -3593,6 +3663,7 @@ if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets + @property def transferring_dataset_files( self ): transferring_datasets = [] @@ -3600,6 +3671,7 @@ if dataset.status == SampleDataset.transfer_status.TRANSFERRING: transferring_datasets.append( dataset ) return transferring_datasets + @property def untransferred_dataset_files( self ): untransferred_datasets = [] @@ -3607,6 +3679,7 @@ if dataset.status != SampleDataset.transfer_status.COMPLETE: untransferred_datasets.append( dataset ) return untransferred_datasets + def get_untransferred_dataset_size( self, filepath, scp_configs ): def print_ticks( d ): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits September 2014