January 2015 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3af74bfc026/ Changeset: c3af74bfc026 User: dannon Date: 2015-01-22 23:05:11+00:00 Summary: Import cleanup in history controller. Affected #: 1 file diff -r ef878dcd878a7a59189a36a29c61e23ac8b571aa -r c3af74bfc02696f59b160c1f43fc31653105710a lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -1,31 +1,26 @@ import logging -from cgi import escape -from traceback import format_exc import urllib import galaxy.util -from galaxy import model -from galaxy import web from galaxy import exceptions from galaxy import managers +from galaxy import model +from galaxy import util +from galaxy import web from galaxy.datatypes.data import nice_size +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.orm import and_, eagerload_all, func -from galaxy import util from galaxy.util import Params from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html -from galaxy.web import error, url_for - +from galaxy.web import url_for from galaxy.web.base.controller import BaseUIController -from galaxy.web.base.controller import SharableMixin +from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin -from galaxy.model.item_attrs import UsesAnnotations -from galaxy.model.item_attrs import UsesItemRatings - -from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING - -from galaxy.web.framework.helpers import grids, iff, time_ago, escape +from galaxy.web.base.controller import SharableMixin +from galaxy.web.framework.helpers import escape, grids, iff, time_ago log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/8ad307615510/ Changeset: 8ad307615510 User: dannon Date: 2015-01-22 23:07:19+00:00 Summary: Remove cruft in history controller. Affected #: 1 file diff -r c3af74bfc02696f59b160c1f43fc31653105710a -r 8ad3076155100bbc841efca1b4e4c91376e11568 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -265,7 +265,6 @@ history_ids = galaxy.util.listify( kwargs.get( 'id', [] ) ) # Display no message by default status, message = None, None - refresh_history = False # Load the histories and ensure they all belong to the current user histories = [] for history_id in history_ids: @@ -425,7 +424,6 @@ @web.require_login( "work with shared histories" ) def list_shared( self, trans, **kwargs ): """List histories shared with current user by others""" - msg = galaxy.util.restore_text( kwargs.get( 'msg', '' ) ) status = message = None if 'operation' in kwargs: ids = galaxy.util.listify( kwargs.get( 'id', [] ) ) @@ -999,10 +997,6 @@ # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] } histories = histories or {} msg = "" - sent_to_emails = [] - for send_to_user in histories.keys(): - sent_to_emails.append( send_to_user.email ) - emails = ",".join( e for e in sent_to_emails ) if not histories: send_to_err += "No users have been specified or no histories can be sent without changing permissions or associating a sharing role. " else: @@ -1149,7 +1143,7 @@ if not history: return trans.show_error_message( "The specified history does not exist." ) # Rate history. - history_rating = self.rate_item( trans.sa_session, trans.get_user(), history, rating ) + self.rate_item( trans.sa_session, trans.get_user(), history, rating ) return self.get_ave_item_rating_data( trans.sa_session, history ) #TODO: used in display_base.mako @@ -1271,7 +1265,6 @@ @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" - msg = "" user = trans.get_user() user_history = trans.get_history() # Set referer message 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 22 Jan '15

22 Jan '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04fe1f826e1c/ Changeset: 04fe1f826e1c User: dannon Date: 2015-01-22 22:46:00+00:00 Summary: Import cleanup in visualizations manager. Affected #: 1 file diff -r 7ae2d8430ffc05c779ebbac8c416dbdd47ebcc74 -r 04fe1f826e1c072a577baf44c50df633de6ee3e9 lib/galaxy/managers/visualizations.py --- a/lib/galaxy/managers/visualizations.py +++ b/lib/galaxy/managers/visualizations.py @@ -5,11 +5,7 @@ reproduce a specific view in a Galaxy visualization. """ -from galaxy import exceptions from galaxy import model -import galaxy.web - -from galaxy.managers import base from galaxy.managers import sharable import logging @@ -39,10 +35,10 @@ """ pass - #TODO: revisions + # TODO: revisions -## ============================================================================= +# ============================================================================= class VisualizationSerializer( sharable.SharableModelSerializer ): """ Interface/service object for serializing visualizations into dictionaries. https://bitbucket.org/galaxy/galaxy-central/commits/710c9ff4629c/ Changeset: 710c9ff4629c User: dannon Date: 2015-01-22 22:57:04+00:00 Summary: Cleanup/pep8 in imp_exp. Affected #: 1 file diff -r 04fe1f826e1c072a577baf44c50df633de6ee3e9 -r 710c9ff4629c603f3eb451bfb371fe6fbf9ac523 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -111,7 +111,7 @@ history_attrs = loads( history_attr_str ) # Create history. - new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \ + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=user ) new_history.importing = True new_history.hid_counter = history_attrs['hid_counter'] @@ -170,7 +170,7 @@ sa_session=self.sa_session ) if 'uuid' in dataset_attrs: hda.dataset.uuid = dataset_attrs["uuid"] - if dataset_attrs.get('exported', True) == False: + if dataset_attrs.get('exported', True) is False: hda.state = hda.states.DISCARDED hda.deleted = True hda.purged = True @@ -181,10 +181,10 @@ new_history.add_dataset( hda, genome_build=None ) hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. # TODO: Is there a way to recover permissions? Is this needed? - #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) - #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + # permissions = trans.app.security_agent.history_get_default_permissions( new_history ) + # trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) self.sa_session.flush() - if dataset_attrs.get('exported', True) == True: + if dataset_attrs.get('exported', True) is True: # Do security check and move/copy dataset data. temp_dataset_file_name = \ os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) @@ -195,7 +195,7 @@ else: datasets_usage_counts[ temp_dataset_file_name ] -= 1 shutil.copyfile( temp_dataset_file_name, hda.file_name ) - hda.dataset.set_total_size() #update the filesize record in the database + hda.dataset.set_total_size() # update the filesize record in the database # Set tags, annotations. if user: @@ -227,8 +227,8 @@ """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by the encoded object. This only works because HDAs are created above. """ if obj_dct.get( '__HistoryDatasetAssociation__', False ): - return self.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=obj_dct['hid'] ).first() + return self.sa_session.query( model.HistoryDatasetAssociation + ).filter_by( history=new_history, hid=obj_dct['hid'] ).first() return obj_dct jobs_attrs = loads( jobs_attr_str, object_hook=as_hda ) @@ -278,14 +278,14 @@ input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=value.hid ).first() value = input_hda.id - #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) + # print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) imported_job.add_parameter( name, dumps( value, cls=HistoryDatasetAssociationIDEncoder ) ) # TODO: Connect jobs to input datasets. # Connect jobs to output datasets. for output_hid in job_attrs[ 'output_datasets' ]: - #print "%s job has output dataset %i" % (imported_job.id, output_hid) + # print "%s job has output dataset %i" % (imported_job.id, output_hid) output_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=output_hid ).first() if output_hda: @@ -294,13 +294,11 @@ # Connect jobs to input datasets. if 'input_mapping' in job_attrs: for input_name, input_hid in job_attrs[ 'input_mapping' ].items(): - #print "%s job has input dataset %i" % (imported_job.id, input_hid) input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=input_hid ).first() if input_hda: imported_job.add_input_dataset( input_name, input_hda ) - self.sa_session.flush() # Done importing. @@ -328,13 +326,13 @@ Returns history's datasets. """ query = ( trans.sa_session.query( trans.model.HistoryDatasetAssociation ) - .filter( trans.model.HistoryDatasetAssociation.history == history ) - .options( eagerload( "children" ) ) - .join( "dataset" ) - .options( eagerload_all( "dataset.actions" ) ) - .order_by( trans.model.HistoryDatasetAssociation.hid ) - .filter( trans.model.HistoryDatasetAssociation.deleted == False ) - .filter( trans.model.Dataset.purged == False ) ) + .filter( trans.model.HistoryDatasetAssociation.history == history ) + .options( eagerload( "children" ) ) + .join( "dataset" ) + .options( eagerload_all( "dataset.actions" ) ) + .order_by( trans.model.HistoryDatasetAssociation.hid ) + .filter( trans.model.HistoryDatasetAssociation.deleted == False ) #noqa + .filter( trans.model.Dataset.purged == False ) ) return query.all() # TODO: should use db_session rather than trans in this method. @@ -388,7 +386,7 @@ "deleted": obj.deleted, "visible": obj.visible, "file_name": obj.file_name, - "uuid" : ( lambda uuid: str( uuid ) if uuid else None )( obj.dataset.uuid ), + "uuid": ( lambda uuid: str( uuid ) if uuid else None )( obj.dataset.uuid ), "annotation": to_unicode( getattr( obj, 'annotation', '' ) ), "tags": get_item_tag_dict( obj ), } @@ -492,7 +490,6 @@ job_attrs[ 'create_time' ] = job.create_time.isoformat() job_attrs[ 'update_time' ] = job.update_time.isoformat() - # Get the job's parameters try: params_objects = job.get_param_values( trans.app ) @@ -533,9 +530,11 @@ options = "" if jeha.compressed: options = "-G" - return "python %s %s %s %s %s" % ( - os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \ - options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename ) + return "python %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), + "lib/galaxy/tools/imp_exp/export_history.py" ), + options, history_attrs_filename, + datasets_attrs_filename, + jobs_attrs_filename ) def cleanup_after_job( self, db_session ): """ Remove temporary directory and attribute files generated during setup for this job. """ https://bitbucket.org/galaxy/galaxy-central/commits/ef878dcd878a/ Changeset: ef878dcd878a User: dannon Date: 2015-01-22 22:57:15+00:00 Summary: Merge. Affected #: 1 file diff -r 710c9ff4629c603f3eb451bfb371fe6fbf9ac523 -r ef878dcd878a7a59189a36a29c61e23ac8b571aa lib/galaxy/managers/annotatable.py --- a/lib/galaxy/managers/annotatable.py +++ b/lib/galaxy/managers/annotatable.py @@ -28,7 +28,6 @@ user = trans.user sa_session = self.app.model.context returned = item.get_item_annotation_str( sa_session, user, item ) - print 'annotation:', returned, type( returned ) return returned 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: carlfeberhard: Fix: remove debugging statement
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2915d9600c2/ Changeset: e2915d9600c2 User: carlfeberhard Date: 2015-01-22 22:55:14+00:00 Summary: Fix: remove debugging statement Affected #: 1 file diff -r 7ae2d8430ffc05c779ebbac8c416dbdd47ebcc74 -r e2915d9600c2f461702177f08ab597ce2a7d88ab lib/galaxy/managers/annotatable.py --- a/lib/galaxy/managers/annotatable.py +++ b/lib/galaxy/managers/annotatable.py @@ -28,7 +28,6 @@ user = trans.user sa_session = self.app.model.context returned = item.get_item_annotation_str( sa_session, user, item ) - print 'annotation:', returned, type( returned ) return returned 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: Fix set_slug method in sharable manager / scope issues.
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ae2d8430ffc/ Changeset: 7ae2d8430ffc User: dannon Date: 2015-01-22 22:34:40+00:00 Summary: Fix set_slug method in sharable manager / scope issues. Affected #: 1 file diff -r 62d257911db2b0d3ee1a8c36b50270b66b3c4003 -r 7ae2d8430ffc05c779ebbac8c416dbdd47ebcc74 lib/galaxy/managers/sharable.py --- a/lib/galaxy/managers/sharable.py +++ b/lib/galaxy/managers/sharable.py @@ -248,7 +248,7 @@ raise exceptions.RequestParameterInvalidException( "Invalid slug", slug=new_slug ) # error if slug is already in use - if self._slug_exists( trans, user, slug ): + if self._slug_exists( trans, trans.user, new_slug ): raise exceptions.Conflict( "Slug already exists", slug=new_slug ) item.slug = new_slug 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: carlfeberhard: Sharable managers: Generate slug on user share only if needed
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/62d257911db2/ Changeset: 62d257911db2 User: carlfeberhard Date: 2015-01-22 22:33:02+00:00 Summary: Sharable managers: Generate slug on user share only if needed Affected #: 2 files diff -r 67b17274944c9897620b63e62c3ce5c8ab6a5b9b -r 62d257911db2b0d3ee1a8c36b50270b66b3c4003 lib/galaxy/managers/sharable.py --- a/lib/galaxy/managers/sharable.py +++ b/lib/galaxy/managers/sharable.py @@ -203,8 +203,9 @@ self.associate( trans, user_share_assoc, item ) user_share_assoc.user = user - # waat? - self.create_unique_slug( trans, item ) + # ensure an item slug so shared users can access + if not item.slug: + self.create_unique_slug( trans, item ) if flush: self.app.model.context.flush() diff -r 67b17274944c9897620b63e62c3ce5c8ab6a5b9b -r 62d257911db2b0d3ee1a8c36b50270b66b3c4003 test/unit/managers/test_HistoryManager.py --- a/test/unit/managers/test_HistoryManager.py +++ b/test/unit/managers/test_HistoryManager.py @@ -223,6 +223,7 @@ self.log( "should be unshared by default" ) self.assertEqual( self.history_mgr.get_share_assocs( self.trans, item1 ), [] ) + self.assertEqual( item1.slug, None ) self.log( "should be able to share with specific users" ) share_assoc = self.history_mgr.share_with( self.trans, item1, non_owner ) @@ -232,6 +233,7 @@ len( self.history_mgr.get_share_assocs( self.trans, item1 ) ), 1 ) self.assertEqual( len( self.history_mgr.get_share_assocs( self.trans, item1, user=non_owner ) ), 1 ) + self.assertIsInstance( item1.slug, basestring ) self.log( "should be able to unshare with specific users" ) share_assoc = self.history_mgr.unshare_with( self.trans, item1, non_owner ) 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: 2 new changesets
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d23190cc523/ Changeset: 0d23190cc523 User: dannon Date: 2015-01-22 22:28:43+00:00 Summary: Remove unused imports from pages manager, minor formatting. Affected #: 1 file diff -r bf6e1d84a8dfa0ba732c73de03cd472264583854 -r 0d23190cc5239c837f1c6934bb22a3e38c1637e0 lib/galaxy/managers/pages.py --- a/lib/galaxy/managers/pages.py +++ b/lib/galaxy/managers/pages.py @@ -6,11 +6,7 @@ from within Galaxy. """ -from galaxy import exceptions from galaxy import model -import galaxy.web - -from galaxy.managers import base from galaxy.managers import sharable import logging @@ -41,7 +37,7 @@ pass -## ============================================================================= +# ============================================================================= class PageSerializer( sharable.SharableModelSerializer ): """ Interface/service object for serializing pages into dictionaries. @@ -59,8 +55,8 @@ ] self.serializable_keys = detailed_view + [] self.views = { - 'summary' : summary_view, - 'detailed' : detailed_view + 'summary': summary_view, + 'detailed': detailed_view } self.default_view = 'summary' https://bitbucket.org/galaxy/galaxy-central/commits/67b17274944c/ Changeset: 67b17274944c User: dannon Date: 2015-01-22 22:31:20+00:00 Summary: pep8 lddamanager Affected #: 1 file diff -r 0d23190cc5239c837f1c6934bb22a3e38c1637e0 -r 67b17274944c9897620b63e62c3ce5c8ab6a5b9b lib/galaxy/managers/lddas.py --- a/lib/galaxy/managers/lddas.py +++ b/lib/galaxy/managers/lddas.py @@ -13,5 +13,7 @@ pass def get( self, trans, id, check_accessible=True ): - return manager_base.get_object( trans, id, 'LibraryDatasetDatasetAssociation', - check_ownership=False, check_accessible=check_accessible ) + return manager_base.get_object( trans, id, + 'LibraryDatasetDatasetAssociation', + check_ownership=False, + check_accessible=check_accessible ) 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: Fix missing required import in ldda manager.
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf6e1d84a8df/ Changeset: bf6e1d84a8df User: dannon Date: 2015-01-22 22:22:39+00:00 Summary: Fix missing required import in ldda manager. Affected #: 1 file diff -r eb1b47ff04531023d4e9f19a99c762fb5b16fad6 -r bf6e1d84a8dfa0ba732c73de03cd472264583854 lib/galaxy/managers/lddas.py --- a/lib/galaxy/managers/lddas.py +++ b/lib/galaxy/managers/lddas.py @@ -1,4 +1,4 @@ -#from galaxy.managers import base as manager_base +from galaxy.managers import base as manager_base class LDDAManager( object ): 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: Fix several bugs in histories manager.
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb1b47ff0453/ Changeset: eb1b47ff0453 User: dannon Date: 2015-01-22 22:14:20+00:00 Summary: Fix several bugs in histories manager. Affected #: 1 file diff -r d671e182d2e0ea0d4ccb486efabe32c8353db022 -r eb1b47ff04531023d4e9f19a99c762fb5b16fad6 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -5,15 +5,12 @@ created (or copied) by users over the course of an analysis. """ -from galaxy import exceptions +import galaxy.web from galaxy import model - -import galaxy.web - from galaxy.managers import base +from galaxy.managers import hdas from galaxy.managers import sharable -from galaxy.managers import hdas -from galaxy.managers import collections_util +from galaxy.managers.collections_util import dictify_dataset_collection_instance import logging @@ -125,8 +122,6 @@ #TODO: instantiate here? really? history_serializer = HistorySerializer( self.app ) hda_serializer = hdas.HDASerializer( self.app ) - collection_dictifier = collections_util.dictify_dataset_collection_instance - history_dictionary = {} contents_dictionaries = [] try: @@ -147,7 +142,7 @@ instance_type='history', id=self.app.security.encode_id( content.id ), ) - contents_dict = collection_dictifier( dataset_collection_instance, + contents_dict = dictify_dataset_collection_instance( dataset_collection_instance, security=self.app.security, parent=dataset_collection_instance.history, view="element" ) except Exception, exc: @@ -321,13 +316,15 @@ }) def serialize_contents( self, trans, history, key ): + contents_dictionaries = [] for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ): contents_dict = {} if isinstance( content, model.HistoryDatasetAssociation ): - contents_dict = self.hda_serializer.serialize_to_view( trans, hda, view='detailed' ) + contents_dict = self.hda_serializer.serialize_to_view( trans, content, view='detailed' ) elif isinstance( content, model.HistoryDatasetCollectionAssociation ): - contents_dict = self.serialize_collection( trans, collection ) + contents_dict = self.serialize_collection( trans, content ) contents_dictionaries.append( contents_dict ) + return contents_dictionaries def serialize_collection( self, trans, collection ): service = self.app.dataset_collections_service @@ -336,7 +333,7 @@ instance_type='history', id=self.security.encode_id( collection.id ), ) - return collection_dictifier( dataset_collection_instance, + return dictify_dataset_collection_instance( dataset_collection_instance, security=self.app.security, parent=dataset_collection_instance.history, view="element" ) 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: Fix import error of collections_util in histories manager.
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d671e182d2e0/ Changeset: d671e182d2e0 User: dannon Date: 2015-01-22 22:03:06+00:00 Summary: Fix import error of collections_util in histories manager. Affected #: 1 file diff -r 171ddb2fd2f8cdf3ef2e949f977ae01f9bff57e8 -r d671e182d2e0ea0d4ccb486efabe32c8353db022 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -13,6 +13,8 @@ from galaxy.managers import base from galaxy.managers import sharable from galaxy.managers import hdas +from galaxy.managers import collections_util + import logging log = logging.getLogger( __name__ ) @@ -91,7 +93,7 @@ super( HistoryManager, self ).purge( trans, history, flush=flush, **kwargs ) # ......................................................................... contents - + # ......................................................................... current def get_current( self, trans ): @@ -123,7 +125,7 @@ #TODO: instantiate here? really? history_serializer = HistorySerializer( self.app ) hda_serializer = hdas.HDASerializer( self.app ) - collection_dictifier = managers.collections_util.dictify_dataset_collection_instance + collection_dictifier = collections_util.dictify_dataset_collection_instance history_dictionary = {} contents_dictionaries = [] 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: Prevent redefinition of role in datasets manager. Harmless now, but dangerous laterhg st
by commits-noreply＠bitbucket.org 22 Jan '15

22 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/171ddb2fd2f8/ Changeset: 171ddb2fd2f8 User: dannon Date: 2015-01-22 21:57:45+00:00 Summary: Prevent redefinition of role in datasets manager. Harmless now, but dangerous laterhg st Affected #: 1 file diff -r 68bd633548b2cd8fa32a918a2f59d293a820baca -r 171ddb2fd2f8cdf3ef2e949f977ae01f9bff57e8 lib/galaxy/managers/datasets.py --- a/lib/galaxy/managers/datasets.py +++ b/lib/galaxy/managers/datasets.py @@ -115,7 +115,7 @@ # get a list of role ids to check access for (defaulting to all_roles) user_roles = [ role ] if role else user.all_roles() - user_role_ids = [ role.id for role in user_roles ] + user_role_ids = [ r.id for r in user_roles ] query = ( self.app.model.context.query( model.DatasetPermissions ) .filter( model.DatasetPermissions.action == access_action ) .filter( model.DatasetPermissions.dataset == dataset ) 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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