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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80a640cc37c3/ Changeset: 80a640cc37c3 User: dannon Date: 2015-02-22 16:43:09+00:00 Summary: Clean up imports in workflow controller. Affected #: 1 file diff -r 37494bde7c95a6718d6be5313a2f7949cacb71c2 -r 80a640cc37c3b0821fcb5d4e22cfcec405db0db5 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -4,42 +4,31 @@ import os import sgmllib import urllib2 -import copy from sqlalchemy import and_ + from tool_shed.util import common_util from tool_shed.util import encoding_util from galaxy import model from galaxy import util from galaxy import web -from galaxy.datatypes.data import Data +from galaxy.managers import workflows from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc -from galaxy.tools.parameters.basic import DataToolParameter -from galaxy.tools.parameters.basic import DataCollectionToolParameter -from galaxy.tools.parameters import visit_input_values from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape -from galaxy.managers import workflows +from galaxy.web.framework.helpers import escape, grids, time_ago, to_unicode +from galaxy.workflow.extract import extract_workflow +from galaxy.workflow.extract import summarize +from galaxy.workflow.modules import MissingToolException +from galaxy.workflow.modules import module_factory from galaxy.workflow.modules import WorkflowModuleInjector -from galaxy.workflow.modules import MissingToolException -from galaxy.workflow.modules import module_factory, is_tool_module_type +from galaxy.workflow.render import WorkflowCanvas from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig -from galaxy.workflow.extract import summarize -from galaxy.workflow.extract import extract_workflow -from galaxy.workflow.steps import ( - attach_ordered_steps, - order_workflow_steps, - edgelist_for_workflow_steps, - order_workflow_steps_with_levels, -) -from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING -from markupsafe import escape class StoredWorkflowListGrid( grids.Grid ): https://bitbucket.org/galaxy/galaxy-central/commits/8d3323ccb3f8/ Changeset: 8d3323ccb3f8 User: dannon Date: 2015-02-23 14:36:10+00:00 Summary: Cleanup, pep8 in workflow controller. Affected #: 1 file diff -r 80a640cc37c3b0821fcb5d4e22cfcec405db0db5 -r 8d3323ccb3f89ca949ab443b2ea37b8992a4f509 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -45,7 +45,11 @@ default_sort_key = "-update_time" columns = [ grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), + grids.IndividualTagsColumn( "Tags", + "tags", + model_tag_association_class=model.StoredWorkflowTagAssociation, + filterable="advanced", + grid_name="StoredWorkflowListGrid" ), StepsColumn( "Steps" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -78,10 +82,15 @@ use_async = True columns = [ grids.PublicURLColumn( "Name", key="name", filterable="advanced", attach_popup=True ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", + key="annotation", + model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, + filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", + model_tag_association_class=model.StoredWorkflowTagAssociation, + filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -406,16 +415,14 @@ stored.name = san_new_name stored.latest_workflow.name = san_new_name trans.sa_session.flush() - # For current workflows grid: trans.set_message( "Workflow renamed to '%s'." % san_new_name ) return self.list( trans ) - # For new workflows grid: - #message = "Workflow renamed to '%s'." % new_name - #return self.list_grid( trans, message=message, status='done' ) else: return form( url_for(controller='workflow', action='rename', id=trans.security.encode_id(stored.id) ), - "Rename workflow", submit_text="Rename", use_panels=True ) \ - .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) + "Rename workflow", + submit_text="Rename", + use_panels=True + ).add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) @web.expose @web.require_login( "use Galaxy workflows" ) @@ -486,7 +493,11 @@ """ Returns workflow's name and link. """ stored = self.get_stored_workflow( trans, id ) - return_dict = { "name": stored.name, "link": url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } + return_dict = { "name": stored.name, + "link": url_for(controller='workflow', + action="display_by_username_and_slug", + username=stored.user.username, + slug=stored.slug ) } return return_dict @web.expose @@ -559,7 +570,10 @@ else: return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ - .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) + .add_text( "workflow_annotation", + "Workflow Annotation", + value="", + help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @web.expose def delete( self, trans, id=None ): @@ -605,10 +619,8 @@ 'tool_id': tool_id, 'tool_state': tool_state } ) - # update module state module.update_state( incoming ) - if type == 'tool': return { 'tool_state': module.get_state(), @@ -684,7 +696,8 @@ except workflows.MissingToolsException as e: return dict( name=e.workflow.name, - message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", + message="This workflow includes missing or invalid tools. " + "It cannot be saved until the following steps are removed or the missing tools are enabled.", errors=e.errors, ) @@ -797,7 +810,7 @@ # Stream workflow to file. stored_dict = self._workflow_to_dict( trans, stored ) if not stored_dict: - #This workflow has a tool that's missing from the distribution + # This workflow has a tool that's missing from the distribution trans.response.status = 400 return "Workflow cannot be exported due to missing tools." valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -918,7 +931,10 @@ message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/>" for missing_tool_tup in missing_tool_tups: missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup - message += "<b>Tool name</b> %s, <b>id</b> %s, <b>version</b> %s<br/>" % ( escape( missing_tool_name ), escape( missing_tool_id ), escape( missing_tool_version ) ) + message += "<b>Tool name</b> %s, <b>id</b> %s, <b>version</b> %s<br/>" % ( + escape( missing_tool_name ), + escape( missing_tool_id ), + escape( missing_tool_version ) ) message += "<br/>" for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): @@ -998,9 +1014,10 @@ ) # Index page with message workflow_id = trans.security.encode_id( stored_workflow.id ) - return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % - ( escape( workflow_name ), url_for( controller='workflow', action='editor', id=workflow_id ), - url_for( controller='workflow', action='run', id=workflow_id ) ) ) + return trans.show_message( 'Workflow "%s" created from current history. ' + 'You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' + % ( escape( workflow_name ), url_for( controller='workflow', action='editor', id=workflow_id ), + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): @@ -1015,7 +1032,6 @@ # It is possible for a workflow to have 0 steps if len( workflow.steps ) == 0: error( "Workflow cannot be run because it does not have any steps" ) - #workflow = Workflow.from_simple( json.loads( stored.encoded_value ), trans.app ) if workflow.has_cycles: error( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: @@ -1068,7 +1084,8 @@ else: nh_name = "History from %s workflow" % workflow.name instance_inputs = [kwargs[multi_input_key] for multi_input_key in multi_input_keys] - instance_ds_names = [trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( instance_input ).name for instance_input in instance_inputs] + instance_ds_names = [trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( instance_input ).name + for instance_input in instance_inputs] nh_name = '%s%s' % (nh_name, _build_workflow_on_str( instance_ds_names )) new_history = trans.app.model.History( user=trans.user, name=nh_name ) new_history.copy_tags_from(trans.user, trans.get_history()) https://bitbucket.org/galaxy/galaxy-central/commits/67222d8cb3a5/ Changeset: 67222d8cb3a5 User: dannon Date: 2015-02-23 14:46:26+00:00 Summary: Update queries/filters in workflow controller to use sqlalchemy constructs for True, False, testing for None. Affected #: 1 file diff -r 8d3323ccb3f89ca949ab443b2ea37b8992a4f509 -r 67222d8cb3a54c7a3dc28accc8f16ff502fe547b lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -6,6 +6,7 @@ import urllib2 from sqlalchemy import and_ +from sqlalchemy.sql import expression from tool_shed.util import common_util from tool_shed.util import encoding_util @@ -121,7 +122,10 @@ def apply_query_filter( self, trans, query, **kwargs ): # A public workflow is published, has a slug, and is not deleted. - return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) + return query.filter( + self.model_class.published == expression.true() ).filter( + self.model_class.slug.isnot(None)).filter( + self.model_class.deleted == expression.false()) # Simple SGML parser to get all content in a single tag. @@ -182,7 +186,7 @@ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ .join( 'stored_workflow' ) \ - .filter( model.StoredWorkflow.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == expression.false() ) \ .order_by( desc( model.StoredWorkflow.update_time ) ) \ .all() @@ -213,7 +217,7 @@ shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == expression.false() ) \ .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() return trans.fill_template( "workflow/list_for_run.mako", @@ -307,7 +311,7 @@ if email: other = trans.sa_session.query( model.User ) \ .filter( and_( model.User.table.c.email == email, - model.User.table.c.deleted == False ) ) \ + model.User.table.c.deleted == expression.false() ) ) \ .first() if not other: mtype = "error" @@ -1274,7 +1278,7 @@ shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == expression.false() ) \ .all() return trans.fill_template( "workflow/configure_menu.mako", workflows=workflows, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fixes for handling Data Managers that use undeclared data tables.
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98ecd305e3d3/ Changeset: 98ecd305e3d3 Branch: release_15.03 User: dan Date: 2015-02-18 19:39:07+00:00 Summary: Fixes for handling Data Managers that use undeclared data tables. Affected #: 3 files diff -r b3a0812f9129f8e1e8bdad3a273c3410edba4e7a -r 98ecd305e3d3f02af78c9f61297f8299966a5187 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -154,7 +154,7 @@ with open( full_path, 'wb' ) as out: out.write( '<?xml version="1.0"?>\n<tables>\n' ) for elem in out_elems: - out.write( util.xml_to_string( elem ) ) + out.write( util.xml_to_string( elem, pretty=True ) ) out.write( '</tables>\n' ) os.chmod( full_path, 0644 ) @@ -452,19 +452,53 @@ """ Returns table entry associated with a col/val pair. """ + rval = self.get_entries( query_attr, query_val, return_attr, default=default, limit=1 ) + if rval: + return rval[0] + return default + + def get_entries( self, query_attr, query_val, return_attr, default=None, limit=None ): + """ + Returns table entry associated with a col/val pair. + """ query_col = self.columns.get( query_attr, None ) if query_col is None: return default - return_col = self.columns.get( return_attr, None ) - if return_col is None: - return default - rval = default + if return_attr is not None: + return_col = self.columns.get( return_attr, None ) + if return_col is None: + return default + rval = [] # Look for table entry. for fields in self.get_fields(): if fields[ query_col ] == query_val: - rval = fields[ return_col ] + if return_attr is None: + field_dict = {} + for i, col_name in enumerate( self.get_column_name_list() ): + field_dict[ col_name or i ] = fields[i] + rval.append( field_dict ) + else: + rval.append( fields[ return_col ] ) + if limit is not None and len( rval ) == limit: + break + return rval or default + + def get_filename_for_source( self, source, default=None ): + if source: + #if dict, assume is compatible info dict, otherwise call method + if isinstance( source, dict ): + source_repo_info = source + else: + source_repo_info = source.get_tool_shed_repository_info_dict() + else: + source_repo_info = None + filename = default + for name, value in self.filenames.iteritems(): + repo_info = value.get( 'tool_shed_repository', None ) + if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): + filename = name break - return rval + return filename def _add_entry( self, entry, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): #accepts dict or list of columns @@ -493,19 +527,7 @@ filename = None if persist and ( not is_error or persist_on_error ): - if entry_source: - #if dict, assume is compatible info dict, otherwise call method - if isinstance( entry_source, dict ): - source_repo_info = entry_source - else: - source_repo_info = entry_source.get_tool_shed_repository_info_dict() - else: - source_repo_info = None - for name, value in self.filenames.iteritems(): - repo_info = value.get( 'tool_shed_repository', None ) - if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): - filename = name - break + filename = self.get_filename_for_source( entry_source ) if filename is None: #should we default to using any filename here instead? log.error( "Unable to determine filename for persisting data table '%s' values: '%s'.", self.name, fields ) diff -r b3a0812f9129f8e1e8bdad3a273c3410edba4e7a -r 98ecd305e3d3f02af78c9f61297f8299966a5187 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -117,6 +117,7 @@ self.move_by_data_table_column = {} self.value_translation_by_data_table_column = {} self.tool_shed_repository_info_dict = None + self.undeclared_tables = False if elem is not None: self.load_from_element( elem, tool_path or self.data_managers.tool_path ) @@ -175,6 +176,7 @@ tool_shed_repository_id=tool_shed_repository_id ) self.name = elem.get( 'name', self.tool.name ) self.description = elem.get( 'description', self.tool.description ) + self.undeclared_tables = util.asbool( elem.get( 'undeclared_tables', self.undeclared_tables ) ) for data_table_elem in elem.findall( 'data_table' ): data_table_name = data_table_elem.get( "name" ) @@ -299,11 +301,28 @@ moved = self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) data_table_value[ name ] = self.process_value_translation( data_table_name, name, **data_table_value ) data_table.add_entry( data_table_value, persist=True, entry_source=self ) - - for data_table_name, data_table_values in data_tables_dict.iteritems(): - #tool returned extra data table entries, but data table was not declared in data manager - #do not add these values, but do provide messages - log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) + if self.undeclared_tables and data_tables_dict: + # We handle the data move, by just moving all the data out of the extra files path + # moving a directory and the target already exists, we move the contents instead + log.debug( 'Attempting to add entries for undeclared tables: %s.', ', '.join( data_tables_dict.keys() ) ) + for ref_file in out_data.values(): + util.move_merge( ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path ) + path_column_names = [ 'path' ] + for data_table_name, data_table_values in data_tables_dict.iteritems(): + data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None ) + if not isinstance( data_table_values, list ): + data_table_values = [ data_table_values ] + for data_table_row in data_table_values: + data_table_value = dict( **data_table_row ) #keep original values here + for name, value in data_table_row.iteritems(): + if name in path_column_names: + data_table_value[ name ] = os.path.abspath( os.path.join( self.data_managers.app.config.galaxy_data_manager_data_path, value ) ) + data_table.add_entry( data_table_value, persist=True, entry_source=self ) + else: + for data_table_name, data_table_values in data_tables_dict.iteritems(): + # tool returned extra data table entries, but data table was not declared in data manager + # do not add these values, but do provide messages + log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) def process_move( self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd ): if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[ data_table_name ]: diff -r b3a0812f9129f8e1e8bdad3a273c3410edba4e7a -r 98ecd305e3d3f02af78c9f61297f8299966a5187 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -113,16 +113,20 @@ error = True return error, message + def get_target_install_dir( self, tool_shed_repository ): + tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) + # This is where index files will reside on a per repo/installed version basis. + target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) + if not os.path.exists( target_dir ): + os.makedirs( target_dir ) + return target_dir, tool_path, relative_target_dir + def install_tool_data_tables( self, tool_shed_repository, tool_index_sample_files ): TOOL_DATA_TABLE_FILE_NAME = 'tool_data_table_conf.xml' TOOL_DATA_TABLE_FILE_SAMPLE_NAME = '%s.sample' % ( TOOL_DATA_TABLE_FILE_NAME ) SAMPLE_SUFFIX = '.sample' SAMPLE_SUFFIX_OFFSET = -len( SAMPLE_SUFFIX ) - tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) - # This is where index files will reside on a per repo/installed version basis. - target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) - if not os.path.exists( target_dir ): - os.makedirs( target_dir ) + target_dir, tool_path, relative_target_dir = self.get_target_install_dir( tool_shed_repository ) for sample_file in tool_index_sample_files: path, filename = os.path.split ( sample_file ) target_filename = filename Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af072108e340/ Changeset: af072108e340 Branch: next-stable User: natefoo Date: 2015-02-23 14:48:21+00:00 Summary: Close next-stable branch (will be using per-release branches from here on out instead). Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/37494bde7c95/ Changeset: 37494bde7c95 User: natefoo Date: 2015-02-23 14:48:53+00:00 Summary: Merge closed next-stable 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: 4 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e65b4583b7fd/ Changeset: e65b4583b7fd User: dan Date: 2015-02-18 19:39:07+00:00 Summary: Fixes for handling Data Managers that use undeclared data tables. Affected #: 3 files diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e65b4583b7fdee6b1a91c66601de1c2720aaa2a5 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -154,7 +154,7 @@ with open( full_path, 'wb' ) as out: out.write( '<?xml version="1.0"?>\n<tables>\n' ) for elem in out_elems: - out.write( util.xml_to_string( elem ) ) + out.write( util.xml_to_string( elem, pretty=True ) ) out.write( '</tables>\n' ) os.chmod( full_path, 0644 ) @@ -452,19 +452,53 @@ """ Returns table entry associated with a col/val pair. """ + rval = self.get_entries( query_attr, query_val, return_attr, default=default, limit=1 ) + if rval: + return rval[0] + return default + + def get_entries( self, query_attr, query_val, return_attr, default=None, limit=None ): + """ + Returns table entry associated with a col/val pair. + """ query_col = self.columns.get( query_attr, None ) if query_col is None: return default - return_col = self.columns.get( return_attr, None ) - if return_col is None: - return default - rval = default + if return_attr is not None: + return_col = self.columns.get( return_attr, None ) + if return_col is None: + return default + rval = [] # Look for table entry. for fields in self.get_fields(): if fields[ query_col ] == query_val: - rval = fields[ return_col ] + if return_attr is None: + field_dict = {} + for i, col_name in enumerate( self.get_column_name_list() ): + field_dict[ col_name or i ] = fields[i] + rval.append( field_dict ) + else: + rval.append( fields[ return_col ] ) + if limit is not None and len( rval ) == limit: + break + return rval or default + + def get_filename_for_source( self, source, default=None ): + if source: + #if dict, assume is compatible info dict, otherwise call method + if isinstance( source, dict ): + source_repo_info = source + else: + source_repo_info = source.get_tool_shed_repository_info_dict() + else: + source_repo_info = None + filename = default + for name, value in self.filenames.iteritems(): + repo_info = value.get( 'tool_shed_repository', None ) + if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): + filename = name break - return rval + return filename def _add_entry( self, entry, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): #accepts dict or list of columns @@ -493,19 +527,7 @@ filename = None if persist and ( not is_error or persist_on_error ): - if entry_source: - #if dict, assume is compatible info dict, otherwise call method - if isinstance( entry_source, dict ): - source_repo_info = entry_source - else: - source_repo_info = entry_source.get_tool_shed_repository_info_dict() - else: - source_repo_info = None - for name, value in self.filenames.iteritems(): - repo_info = value.get( 'tool_shed_repository', None ) - if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): - filename = name - break + filename = self.get_filename_for_source( entry_source ) if filename is None: #should we default to using any filename here instead? log.error( "Unable to determine filename for persisting data table '%s' values: '%s'.", self.name, fields ) diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e65b4583b7fdee6b1a91c66601de1c2720aaa2a5 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -117,6 +117,7 @@ self.move_by_data_table_column = {} self.value_translation_by_data_table_column = {} self.tool_shed_repository_info_dict = None + self.undeclared_tables = False if elem is not None: self.load_from_element( elem, tool_path or self.data_managers.tool_path ) @@ -175,6 +176,7 @@ tool_shed_repository_id=tool_shed_repository_id ) self.name = elem.get( 'name', self.tool.name ) self.description = elem.get( 'description', self.tool.description ) + self.undeclared_tables = util.asbool( elem.get( 'undeclared_tables', self.undeclared_tables ) ) for data_table_elem in elem.findall( 'data_table' ): data_table_name = data_table_elem.get( "name" ) @@ -299,11 +301,28 @@ moved = self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) data_table_value[ name ] = self.process_value_translation( data_table_name, name, **data_table_value ) data_table.add_entry( data_table_value, persist=True, entry_source=self ) - - for data_table_name, data_table_values in data_tables_dict.iteritems(): - #tool returned extra data table entries, but data table was not declared in data manager - #do not add these values, but do provide messages - log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) + if self.undeclared_tables and data_tables_dict: + # We handle the data move, by just moving all the data out of the extra files path + # moving a directory and the target already exists, we move the contents instead + log.debug( 'Attempting to add entries for undeclared tables: %s.', ', '.join( data_tables_dict.keys() ) ) + for ref_file in out_data.values(): + util.move_merge( ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path ) + path_column_names = [ 'path' ] + for data_table_name, data_table_values in data_tables_dict.iteritems(): + data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None ) + if not isinstance( data_table_values, list ): + data_table_values = [ data_table_values ] + for data_table_row in data_table_values: + data_table_value = dict( **data_table_row ) #keep original values here + for name, value in data_table_row.iteritems(): + if name in path_column_names: + data_table_value[ name ] = os.path.abspath( os.path.join( self.data_managers.app.config.galaxy_data_manager_data_path, value ) ) + data_table.add_entry( data_table_value, persist=True, entry_source=self ) + else: + for data_table_name, data_table_values in data_tables_dict.iteritems(): + # tool returned extra data table entries, but data table was not declared in data manager + # do not add these values, but do provide messages + log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) def process_move( self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd ): if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[ data_table_name ]: diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e65b4583b7fdee6b1a91c66601de1c2720aaa2a5 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -113,16 +113,20 @@ error = True return error, message + def get_target_install_dir( self, tool_shed_repository ): + tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) + # This is where index files will reside on a per repo/installed version basis. + target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) + if not os.path.exists( target_dir ): + os.makedirs( target_dir ) + return target_dir, tool_path, relative_target_dir + def install_tool_data_tables( self, tool_shed_repository, tool_index_sample_files ): TOOL_DATA_TABLE_FILE_NAME = 'tool_data_table_conf.xml' TOOL_DATA_TABLE_FILE_SAMPLE_NAME = '%s.sample' % ( TOOL_DATA_TABLE_FILE_NAME ) SAMPLE_SUFFIX = '.sample' SAMPLE_SUFFIX_OFFSET = -len( SAMPLE_SUFFIX ) - tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) - # This is where index files will reside on a per repo/installed version basis. - target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) - if not os.path.exists( target_dir ): - os.makedirs( target_dir ) + target_dir, tool_path, relative_target_dir = self.get_target_install_dir( tool_shed_repository ) for sample_file in tool_index_sample_files: path, filename = os.path.split ( sample_file ) target_filename = filename https://bitbucket.org/galaxy/galaxy-central/commits/122459ce965a/ Changeset: 122459ce965a User: martenson Date: 2015-02-19 19:37:17+00:00 Summary: fi the missing import Affected #: 1 file diff -r e65b4583b7fdee6b1a91c66601de1c2720aaa2a5 -r 122459ce965a4cdbcb2a99894e42ee74852683aa lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -1,4 +1,5 @@ import sys, os.path, logging +import pkg_resources from galaxy import eggs https://bitbucket.org/galaxy/galaxy-central/commits/a978e7166f1b/ Changeset: a978e7166f1b User: dannon Date: 2015-02-19 19:45:44+00:00 Summary: Slightly adjust aforementioned import, use the standard eggs.require Affected #: 1 file diff -r 122459ce965a4cdbcb2a99894e42ee74852683aa -r a978e7166f1b1f5fd53a072184912d3a467cac92 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -1,5 +1,6 @@ -import sys, os.path, logging -import pkg_resources +import logging +import os.path +import sys from galaxy import eggs @@ -39,7 +40,7 @@ try: egg = dialect_to_egg[dialect] try: - pkg_resources.require( egg ) + eggs.require( egg ) log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) except: # If the module is in the path elsewhere (i.e. non-egg), it'll still load. https://bitbucket.org/galaxy/galaxy-central/commits/82cf6a9e708d/ Changeset: 82cf6a9e708d User: dannon Date: 2015-02-19 22:53:12+00:00 Summary: Per IRC discussion, remove demo_sequencer webapp. Affected #: 19 files diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca config/demo_sequencer_wsgi.ini.sample --- a/config/demo_sequencer_wsgi.ini.sample +++ /dev/null @@ -1,66 +0,0 @@ -# ---- HTTP Server ---------------------------------------------------------- - -[server:main] - -use = egg:Paste#http -port = 9011 -host = 0.0.0.0 -use_threadpool = true -threadpool_workers = 10 - -# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- - -[app:main] - -# Specifies the factory for the universe WSGI application -paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory -log_level = DEBUG - -# Where dataset files are saved -file_path = database/demo_sequencer_files -# Temporary storage for additional datasets, this should be shared through the cluster -new_file_path = database/tmp - -# Sequencer emulator actions -sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml - -# Session support (beaker) -use_beaker_session = True -session_type = memory -session_data_dir = %(here)s/database/beaker_sessions -session_key = galaxysessions -session_secret = changethisinproduction - -# Galaxy session security -id_secret = changethisinproductiontoo - -# Configuration for debugging middleware -debug = true -use_lint = false - -# NEVER enable this on a public site (even test or QA) -# use_interactive = true - -# this should be a comma-separated list of valid Galaxy users -#admin_users = test(a)bx.psu.edu - -# Force everyone to log in (disable anonymous access) -require_login = False - -# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) -## use_heartbeat = True - -# Profiling middleware (cProfile based) -## use_profile = True - -# Use the new iframe / javascript based layout -use_new_layout = true - -# Serving static files (needed if running standalone) -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst +++ /dev/null @@ -1,19 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`common` Module --------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.controllers.common - :members: - :undoc-members: - :show-inheritance: - diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst +++ /dev/null @@ -1,11 +0,0 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.framework - :members: - :undoc-members: - :show-inheritance: - diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca doc/source/lib/galaxy.webapps.demo_sequencer.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.rst +++ /dev/null @@ -1,51 +0,0 @@ -demo_sequencer Package -====================== - -:mod:`demo_sequencer` Package ------------------------------ - -.. automodule:: galaxy.webapps.demo_sequencer - :members: - :undoc-members: - :show-inheritance: - -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.demo_sequencer.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.config - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.registry - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.webapps.demo_sequencer.controllers - galaxy.webapps.demo_sequencer.framework - diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca doc/source/lib/galaxy.webapps.rst --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -15,7 +15,6 @@ .. toctree:: galaxy.webapps.community - galaxy.webapps.demo_sequencer galaxy.webapps.galaxy galaxy.webapps.reports diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -"""The Galaxy Demo Sequencer Emulator application.""" -# This webapp is for demo purposes only! - -from galaxy.web.framework import url_for -from galaxy.web.framework.decorators import expose diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/app.py --- a/lib/galaxy/webapps/demo_sequencer/app.py +++ /dev/null @@ -1,19 +0,0 @@ -import sys, config -from galaxy.web import security -import galaxy.webapps.demo_sequencer.registry - -class UniverseApplication( object ): - """Encapsulates the state of a Universe application""" - def __init__( self, **kwargs ): - print >> sys.stderr, "python path is: " + ", ".join( sys.path ) - self.name = "demo_sequencer" - # Read config file and check for errors - self.config = config.Configuration( **kwargs ) - self.config.check() - config.configure_logging( self.config ) - # Set up sequencer actions registry - self.sequencer_actions_registry = galaxy.webapps.demo_sequencer.registry.Registry( self.config.root, self.config.sequencer_actions_config ) - # Security helper - self.security = security.SecurityHelper( id_secret=self.config.id_secret ) - def shutdown( self ): - pass diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/buildapp.py --- a/lib/galaxy/webapps/demo_sequencer/buildapp.py +++ /dev/null @@ -1,171 +0,0 @@ -""" -Provides factory methods to assemble the Galaxy web application -""" - -import logging, atexit -import os, os.path, sys - -from inspect import isclass - -from paste.request import parse_formvars -from paste.util import import_string -from paste import httpexceptions -from galaxy.util import asbool -import pkg_resources - -log = logging.getLogger( __name__ ) - -import config -import galaxy.webapps.demo_sequencer.framework - -def add_ui_controllers( webapp, app ): - """ - Search for controllers in the 'galaxy.webapps.demo_sequencer.controllers' - directory and add them to the webapp. - """ - from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable - import galaxy.webapps.demo_sequencer.controllers - controller_dir = galaxy.webapps.demo_sequencer.controllers.__path__[0] - for fname in os.listdir( controller_dir ): - if not fname.startswith( "_" ) and fname.endswith( ".py" ): - name = fname[:-3] - module_name = "galaxy.webapps.demo_sequencer.controllers." + name - module = __import__( module_name ) - for comp in module_name.split( "." )[1:]: - module = getattr( module, comp ) - # Look for a controller inside the modules - for key in dir( module ): - T = getattr( module, key ) - if isclass( T ) and T is not BaseUIController and issubclass( T, BaseUIController ): - webapp.add_ui_controller( name, T( app ) ) - -def app_factory( global_conf, **kwargs ): - """Return a wsgi application serving the root object""" - # Create the Galaxy application unless passed in - if 'app' in kwargs: - app = kwargs.pop( 'app' ) - else: - try: - from galaxy.webapps.demo_sequencer.app import UniverseApplication - app = UniverseApplication( global_conf = global_conf, **kwargs ) - except: - import traceback, sys - traceback.print_exc() - sys.exit( 1 ) - atexit.register( app.shutdown ) - # Create the universe WSGI application - webapp = galaxy.webapps.demo_sequencer.framework.WebApplication( app, session_cookie='galaxydemo_sequencersession', name="demo_sequencer" ) - add_ui_controllers( webapp, app ) - # These two routes handle our simple needs at the moment - webapp.add_route( '/:controller/:action', action='index' ) - webapp.add_route( '/:action', controller='common', action='index' ) - webapp.finalize_config() - # Wrap the webapp in some useful middleware - if kwargs.get( 'middleware', True ): - webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if kwargs.get( 'static_enabled', True ): - webapp = wrap_in_static( webapp, global_conf, **kwargs ) - # Return - return webapp - -def wrap_in_middleware( app, global_conf, **local_conf ): - """Based on the configuration wrap `app` in a set of common and useful middleware.""" - # Merge the global and local configurations - conf = global_conf.copy() - conf.update(local_conf) - debug = asbool( conf.get( 'debug', False ) ) - # First put into place httpexceptions, which must be most closely - # wrapped around the application (it can interact poorly with - # other middleware): - app = httpexceptions.make_middleware( app, conf ) - log.debug( "Enabling 'httpexceptions' middleware" ) - # The recursive middleware allows for including requests in other - # requests or forwarding of requests, all on the server side. - if asbool(conf.get('use_recursive', True)): - from paste import recursive - app = recursive.RecursiveMiddleware( app, conf ) - log.debug( "Enabling 'recursive' middleware" ) - # Various debug middleware that can only be turned on if the debug - # flag is set, either because they are insecure or greatly hurt - # performance - if debug: - # Middleware to check for WSGI compliance - if asbool( conf.get( 'use_lint', True ) ): - from paste import lint - app = lint.make_middleware( app, conf ) - log.debug( "Enabling 'lint' middleware" ) - # Middleware to run the python profiler on each request - if asbool( conf.get( 'use_profile', False ) ): - import profile - app = profile.ProfileMiddleware( app, conf ) - log.debug( "Enabling 'profile' middleware" ) - # Middleware that intercepts print statements and shows them on the - # returned page - if asbool( conf.get( 'use_printdebug', True ) ): - from paste.debug import prints - app = prints.PrintDebugMiddleware( app, conf ) - log.debug( "Enabling 'print debug' middleware" ) - if debug and asbool( conf.get( 'use_interactive', False ) ): - # Interactive exception debugging, scary dangerous if publicly - # accessible, if not enabled we'll use the regular error printing - # middleware. - pkg_resources.require( "WebError" ) - from weberror import evalexception - app = evalexception.EvalException( app, conf, - templating_formatters=build_template_error_formatters() ) - log.debug( "Enabling 'eval exceptions' middleware" ) - else: - # Not in interactive debug mode, just use the regular error middleware - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) - log.debug( "Enabling 'error' middleware" ) - # Transaction logging (apache access.log style) - if asbool( conf.get( 'use_translogger', True ) ): - from paste.translogger import TransLogger - app = TransLogger( app ) - log.debug( "Enabling 'trans logger' middleware" ) - # X-Forwarded-Host handling - from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware - app = XForwardedHostMiddleware( app ) - log.debug( "Enabling 'x-forwarded-host' middleware" ) - return app - -def wrap_in_static( app, global_conf, **local_conf ): - from paste.urlmap import URLMap - from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static - urlmap = URLMap() - # Merge the global and local configurations - conf = global_conf.copy() - conf.update(local_conf) - # Get cache time in seconds - cache_time = conf.get( "static_cache_time", None ) - if cache_time is not None: - cache_time = int( cache_time ) - # Send to dynamic app by default - urlmap["/"] = app - # Define static mappings from config - urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time ) - urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time ) - urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time ) - urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time ) - urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time ) - # URL mapper becomes the root webapp - return urlmap - -def build_template_error_formatters(): - """ - Build a list of template error formatters for WebError. When an error - occurs, WebError pass the exception to each function in this list until - one returns a value, which will be displayed on the error page. - """ - formatters = [] - # Formatter for mako - import mako.exceptions - def mako_html_data( exc_value ): - if isinstance( exc_value, ( mako.exceptions.CompileException, mako.exceptions.SyntaxException ) ): - return mako.exceptions.html_error_template().render( full=False, css=False ) - if isinstance( exc_value, AttributeError ) and exc_value.args[0].startswith( "'Undefined' object has no attribute" ): - return mako.exceptions.html_error_template().render( full=False, css=False ) - formatters.append( mako_html_data ) - return formatters diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ /dev/null @@ -1,121 +0,0 @@ -""" -Universe configuration builder. -""" - -import sys, os -import logging, logging.config -from optparse import OptionParser -import ConfigParser -from galaxy.util import string_as_bool - -from galaxy import eggs -import pkg_resources - -log = logging.getLogger( __name__ ) - -def resolve_path( path, root ): - """If 'path' is relative make absolute by prepending 'root'""" - if not( os.path.isabs( path ) ): - path = os.path.join( root, path ) - return path - -class ConfigurationError( Exception ): - pass - -class Configuration( object ): - def __init__( self, **kwargs ): - self.config_dict = kwargs - self.root = kwargs.get( 'root_dir', '.' ) - # Collect the umask and primary gid from the environment - self.umask = os.umask( 077 ) # get the current umask - os.umask( self.umask ) # can't get w/o set, so set it back - # Where dataset files are stored - self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) - self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) - self.cookie_path = kwargs.get( "cookie_path", "/" ) - self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) - self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) - self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) - self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) - self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) - self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) - self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) - self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) - self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) - self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) - self.admin_users = kwargs.get( "admin_users", "" ) - self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") - self.error_email_to = kwargs.get( 'error_email_to', None ) - self.smtp_server = kwargs.get( 'smtp_server', None ) - self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) - self.brand = kwargs.get( 'brand', None ) - self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) - self.blog_url = kwargs.get( 'blog_url', None ) - self.screencasts_url = kwargs.get( 'screencasts_url', None ) - self.log_events = False - self.cloud_controller_instance = False - # Proxy features - self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) - self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) - self.sequencer_actions_config = kwargs.get( 'sequencer_actions_config_file', 'galaxy/webapps/demo_sequencer/sequencer_actions.xml' ) - # Parse global_conf and save the parser - global_conf = kwargs.get( 'global_conf', None ) - global_conf_parser = ConfigParser.ConfigParser() - self.global_conf_parser = global_conf_parser - if global_conf and "__file__" in global_conf: - global_conf_parser.read(global_conf['__file__']) - def get( self, key, default ): - return self.config_dict.get( key, default ) - def get_bool( self, key, default ): - if key in self.config_dict: - return string_as_bool( self.config_dict[key] ) - else: - return default - def check( self ): - # Check that required directories exist - for path in self.root, self.file_path, self.template_path: - if not os.path.isdir( path ): - raise ConfigurationError("Directory does not exist: %s" % path ) - def is_admin_user( self, user ): - """ - Determine if the provided user is listed in `admin_users`. - """ - admin_users = self.get( "admin_users", "" ).split( "," ) - return user is not None and user.email in admin_users - -def configure_logging( config ): - """ - Allow some basic logging configuration to be read from the cherrpy - config. - """ - # PasteScript will have already configured the logger if the appropriate - # sections were found in the config file, so we do nothing if the - # config has a loggers section, otherwise we do some simple setup - # using the 'log_*' values from the config. - if config.global_conf_parser.has_section( "loggers" ): - return - format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) - level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] - destination = config.get( "log_destination", "stdout" ) - log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) - # Get root logger - root = logging.getLogger() - # Set level - root.setLevel( level ) - # Turn down paste httpserver logging - if level <= logging.DEBUG: - logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) - # Remove old handlers - for h in root.handlers[:]: - root.removeHandler(h) - # Create handler - if destination == "stdout": - handler = logging.StreamHandler( sys.stdout ) - else: - handler = logging.FileHandler( destination ) - # Create formatter - formatter = logging.Formatter( format ) - # Hook everything up - handler.setFormatter( formatter ) - root.addHandler( handler ) diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/controllers/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/controllers/__init__.py +++ /dev/null @@ -1,1 +0,0 @@ -"""Galaxy demo sequencer emulator controllers.""" diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/controllers/common.py --- a/lib/galaxy/webapps/demo_sequencer/controllers/common.py +++ /dev/null @@ -1,228 +0,0 @@ -from galaxy.web.base.controller import * -from galaxy.web.framework.helpers import time_ago -from galaxy import util -import time, socket, urllib, urllib2, base64, copy -from galaxy.util.json import * -from urllib import quote_plus, unquote_plus -from markupsafe import escape - -import logging -log = logging.getLogger( __name__ ) - -class CommonController( BaseUIController ): - @web.expose - def index( self, trans, **kwd ): - redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) - titles = util.restore_text( kwd.get( 'titles', '' ) ) - titles = util.listify( titles ) - JobId = util.restore_text( kwd.get( 'JobId', '' ) ) - sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) - message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) - status = kwd.get( 'status', 'done' ) - redirect_delay = trans.app.sequencer_actions_registry.redirect_delay - sequencer_redirects = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_redirects ) - sequencer_requests = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_requests ) - requests = [] - if redirect_action == 'stop': - # Handle any additional requests - for request_tup in sequencer_requests: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - response = self.handle_request( trans, url, http_method, **request_params ) - # Handle response, currently only handles json - if response_type == 'json': - response = loads( response ) - # Handle response that is an error, for example: - # { "Success":false, "Message":"some error string" } - if 'Success' in response and response[ 'Success' ] == 'false': - message = response[ 'Message' ] - return self.handle_failure( trans, url, message ) - if 'JobId' in response: - JobId = str( response[ 'JobId' ] ) - kwd[ 'JobId' ] = JobId - # Handle the final redirect, if any ( should only be 0 or 1 ). - for request_tup in trans.app.sequencer_actions_registry.final_redirect: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) - # Exit if we have no redirection - redirect_action = 'exit' - elif not redirect_action: - # Specially handle the initial request to the demo sequencer by starting with the first defined redirect. - redirect_action, action_dict = sequencer_redirects.items()[0] - titles = [ action_dict[ 'title' ] ] - if 'requests' in action_dict: - requests = action_dict[ 'requests' ] - else: - for index, key in enumerate( sequencer_redirects.iterkeys() ): - if redirect_action == key: - try: - # Move to the next action, if there is one. - redirect_action = sequencer_redirects.keys()[ index + 1 ] - action_dict = sequencer_redirects[ redirect_action ] - titles.append( action_dict[ 'title' ] ) - except: - # If we're done redirecting, stop. - redirect_action = 'stop' - break - if not trans.app.sequencer_actions_registry.authenticated: - # Support various types of authentication - if trans.app.sequencer_actions_registry.browser_login: - # We'll just build the URL here since authentication will be handled in the browser - url = trans.app.sequencer_actions_registry.browser_login[ 'url' ] - params = trans.app.sequencer_actions_registry.browser_login[ 'params' ] - trans.app.sequencer_actions_registry.browser_login = '%s?%s' %( url, urllib.urlencode( params ) ) - if not trans.app.sequencer_actions_registry.final_redirect: - # If we don't have a final_redirect tag, but we want our browser to authenticate, - # do it ow. If we have a final_redirect tag, browser authentication will happen there. - url = web.url_for( controller='common', action='index', **kwd ) - return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) - if trans.app.sequencer_actions_registry.basic_http_authentication: - # Example tag: - # <basic_http_authentication user="administrator" password="galaxy" url="http://127.0.0.1" realm="" /> - user, password, url, realm = trans.app.sequencer_actions_registry.basic_http_authentication - # Create a password manager - password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm() - # Add the username, password and realm. - if not realm: - realm = None - password_mgr.add_password( realm, url, user, password ) - handler = urllib2.HTTPBasicAuthHandler( password_mgr ) - # Create "opener" (OpenerDirector instance) - opener = urllib2.build_opener( handler ) - # Install the opener, now all calls to urllib2.urlopen use our opener. - urllib2.install_opener( opener ) - trans.app.sequencer_actions_registry.authenticated = True - if trans.app.sequencer_actions_registry.http_headers_authorization: - # Example tag: - # <http_headers_authorization credentials="administrator:galaxy" url="http://127.0.0.1" /> - url, credentials = trans.app.sequencer_actions_registry.http_headers_authorization - req = urllib2.Request( url ) - req.add_header( 'Authorization', 'Basic %s' % base64.b64encode( credentials ) ) - trans.app.sequencer_actions_registry.authenticated = True - if trans.app.sequencer_actions_registry.http_cookie_processor_authentication: - # Example tag: - # <http_cookie_processor_authentication url="http://127.0.0.1/login"> - # <param name="user" value="administrator"/> - # <param name="password" value="galaxy"/> - # </http_cookie_processor_authentication> - url = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'url' ] - params = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'params' ] - # Build opener with HTTPCookieProcessor - opener = urllib2.build_opener( urllib2.HTTPCookieProcessor() ) - urllib2.install_opener( opener ) - # Perform login with params - page = opener.open( url, urllib.urlencode( params ) ) - response = page.read() - page.close() - # Any additional requests should automatically pass back any - # cookies received during login, thanks to the HTTPCookieProcessor - trans.app.sequencer_actions_registry.authenticated = True - # Handle requests, if there are any - for request_tup in requests: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - response = self.handle_request( trans, url, http_method, **request_params ) - # Handle response, currently only handles json - if response_type == 'json': - response = loads( response ) - # Handle response that is an error, for example: - # { "Success":false, "Message":"some error string" } - if 'Success' in response and response[ 'Success' ] == 'false': - message = response[ 'Message' ] - return self.handle_failure( trans, url, message ) - if 'JobId' in response: - JobId = str( response[ 'JobId' ] ) - kwd[ 'JobId' ] = JobId - titles = ','.join( titles ) - return trans.fill_template( "webapps/demo_sequencer/index.mako", - redirect_action=redirect_action, - redirect_delay=redirect_delay, - titles=titles, - sample_id=sample_id, - JobId=JobId, - message=message, - status=status ) - def parse_request_tup( self, request_tup, **kwd ): - redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) - titles = util.restore_text( kwd.get( 'titles', '' ) ) - JobId = util.restore_text( kwd.get( 'JobId', '' ) ) - sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) - message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) - status = kwd.get( 'status', 'done' ) - url, http_method, request_params, response_type = request_tup - url = unquote_plus( url ) - # Handle URLs in which we replace param values, which will look something like: - # http://127.0.0.1/getinfo/{id}. - replace_with_param = url.find( '{' ) > 0 - if replace_with_param: - # Handle the special-case {JobId} param. - if url.find( '{JobId}' ) > 0: - if JobId: - url = url.replace( '{JobId}', str( JobId ) ) - for key, value in kwd.items(): - # Don't attempt to replace if there is nothing with which to do it - # or if the value itself should be replaced with something. - if value and not value.startswith( '{' ): - replace_str = '{%s}' % key - if url.find( replace_str ) > 0: - url = url.replace( replace_str, value ) - # Handle request parameters in which we replace param values. - for key, val in request_params.items(): - if val and val.startswith( '{' ): - replace_key = val.lstrip( '{' ).rstrip( '}' ) - if replace_key in kwd: - request_params[ key ] = kwd[ replace_key ] - return url, http_method, request_params, response_type - def handle_request( self, trans, url, http_method=None, **kwd ): - if 'Name' in kwd and not kwd[ 'Name' ]: - # Hack: specially handle parameters named "Name" if no param_value is given - # by providing a date / time string - guarantees uniqueness, if required. - kwd[ 'Name' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) - if 'Comments' in kwd and not kwd[ 'Comments' ]: - # Hack: specially handle parameters named "Comments" if no param_value is given - # by providing a date / time string. - kwd[ 'Comments' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) - socket.setdefaulttimeout( 600 ) - # The following calls to urllib2.urlopen() will use the above default timeout. - try: - if not http_method or http_method == 'get': - page = urllib2.urlopen( url ) - response = page.read() - page.close() - return response - elif http_method == 'post': - page = urllib2.urlopen( url, urllib.urlencode( kwd ) ) - response = page.read() - page.close() - return response - elif http_method == 'put': - url += '/' + str( kwd.pop( 'id' ) ) + '?key=' + kwd.pop( 'key' ) - output = self.put( url, **kwd ) - except Exception, e: - raise - message = 'Problem sending request to the web application: %s. URL: %s. kwd: %s. Http method: %s' % \ - ( str( e ), str( url ), str( kwd ), str( http_method ) ) - return self.handle_failure( trans, url, message ) - def handle_failure( self, trans, url, message ): - message = '%s, URL: %s' % ( message, url ) - params = dict( message = message, - status = 'error', - redirect_action = 'exit', - titles = 'Error' ) - return trans.response.send_redirect( web.url_for( controller='common', - action='index', - **params ) ) - def put( self, url, **kwd ): - opener = urllib2.build_opener( urllib2.HTTPHandler ) - request = urllib2.Request( url, data=dumps( kwd ) ) - request.add_header( 'Content-Type', 'application/json' ) - request.get_method = lambda: 'PUT' - url = opener.open( request ) - output = url.read() - return loads( output ) - @web.expose - def login( self, trans, **kwd ): - trans.app.sequencer_actions_registry.authenticated = True - return trans.fill_template( "webapps/demo_sequencer/login.mako" ) - @web.expose - def empty_page( self, trans, **kwd ): - # Hack to not display responses in the browser - src for a hidden iframe. - return trans.fill_template( "webapps/demo_sequencer/empty.mako" ) diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/framework/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py +++ /dev/null @@ -1,215 +0,0 @@ -""" -Demo sequencer web application framework -""" - -import json -import os -import pkg_resources -import random -import socket -import string -import sys -import time - -pkg_resources.require( "Cheetah" ) -from Cheetah.Template import Template - -from galaxy.web.framework import helpers - -from galaxy import util -from galaxy.util.json import dumps -from galaxy.util.json import loads -from galaxy.web.framework import url_for -from galaxy.web.framework.decorators import expose -from galaxy.web.framework.decorators import json -from galaxy.web.framework.decorators import json_pretty -from galaxy.web.framework.decorators import require_login -from galaxy.web.framework.decorators import expose_api -from galaxy.web.framework.decorators import error -from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.formbuilder import FormBuilder -from galaxy.web.framework.formbuilder import FormInput -from galaxy.web.framework.formbuilder import FormData -import galaxy.web.framework.base - -from galaxy.util.bunch import Bunch -from galaxy.exceptions import MessageException -from galaxy.util import asbool - -pkg_resources.require( "Mako" ) -import mako.template -import mako.lookup -import mako.runtime - -pkg_resources.require( "pexpect" ) -pkg_resources.require( "amqp" ) - -import logging -log = logging.getLogger( __name__ ) - -class WebApplication( galaxy.web.framework.base.WebApplication ): - def __init__( self, demo_app, session_cookie='demosequencersession' ): - galaxy.web.framework.base.WebApplication.__init__( self ) - self.set_transaction_factory( lambda e: self.transaction_chooser( e, demo_app, session_cookie ) ) - # Mako support - self.mako_template_lookup = mako.lookup.TemplateLookup( - directories = [ demo_app.config.template_path ] , - module_directory = demo_app.config.template_cache, - collection_size = 500, - output_encoding = 'utf-8' ) - # Security helper - self.security = demo_app.security - def handle_controller_exception( self, e, trans, **kwargs ): - if isinstance( e, MessageException ): - return trans.show_message( e.err_msg, e.type ) - def make_body_iterable( self, trans, body ): - if isinstance( body, FormBuilder ): - body = trans.show_form( body ) - return galaxy.web.framework.base.WebApplication.make_body_iterable( self, trans, body ) - def transaction_chooser( self, environ, demo_app, session_cookie ): - if 'is_api_request' in environ: - return DemoWebAPITransaction( environ, demo_app, self ) - else: - return DemoWebUITransaction( environ, demo_app, self, session_cookie ) - -class DemoWebTransaction( galaxy.web.framework.base.DefaultWebTransaction ): - """ - Encapsulates web transaction specific state for the Demo application - (specifically the user's "cookie") - """ - def __init__( self, environ, app, webapp ): - self.app = app - self.webapp = webapp - self.security = webapp.security - galaxy.web.framework.base.DefaultWebTransaction.__init__( self, environ ) - self.debug = asbool( self.app.config.get( 'debug', False ) ) - def get_cookie( self, name='demosequencersession' ): - """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='demosequencersession', path='/', age=90, version='1' ): - """Convenience method for setting a session cookie""" - # The demosequencersession 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 - 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 get_galaxy_session( self ): - """ - Return the current galaxy session - """ - return self.galaxy_session - @galaxy.web.framework.base.lazy_property - def template_context( self ): - return dict() - - 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. - """ - 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, **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 ) - 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 ) - ## return template.render( **data ) - 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 DemoWebAPITransaction( DemoWebTransaction ): - def __init__( self, environ, app, webapp ): - DemoWebTransaction.__init__( self, environ, app, webapp ) - -class DemoWebUITransaction( DemoWebTransaction ): - def __init__( self, environ, app, webapp, session_cookie ): - DemoWebTransaction.__init__( self, environ, app, webapp ) diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/registry.py --- a/lib/galaxy/webapps/demo_sequencer/registry.py +++ /dev/null @@ -1,109 +0,0 @@ -import logging -import galaxy.util -from galaxy.util.odict import odict - -class Registry( object ): - def __init__( self, root_dir=None, config=None ): - self.log = logging.getLogger( __name__ ) - self.log.addHandler( logging.NullHandler() ) - self.redirect_delay = 2.0 # Default to 2 seconds - self.final_redirect = [] - self.sequencer_redirects = odict() - self.sequencer_requests = [] - self.authenticated = False - self.browser_login = None - self.http_headers_authorization = None - self.basic_http_authentication = None - self.http_cookie_processor_authentication = None - if root_dir and config: - tree = galaxy.util.parse_xml( config ) - root = tree.getroot() - self.log.debug( 'Loading sequencer actions from %s' % config ) - try: - # Load the redirect delay value, if any ( default is 2 seconds ). - for redirect_delay in root.findall( 'redirect_delay' ): - delay = redirect_delay.get( 'value', self.redirect_delay ) - self.redirect_delay = float( delay ) - # Load http_headers_authorization information, if any. - for authentication_elem in root.findall( 'http_headers_authorization' ): - # Example tag: - # <http_headers_authorization credentials="administrator:galaxy" url="http://127.0.0.1" /> - url = authentication_elem.get( 'url', '' ) - credentials = authentication_elem.get( 'credentials', '' ) - self.http_headers_authorization = ( url, credentials ) - # Load basic_http_authentication information, if any. - for authentication_elem in root.findall( 'basic_http_authentication' ): - # Example tag: - # <basic_http_authentication user="administrator" password="galaxy" url="http://127.0.0.1" realm="" /> - urls = [] - user = authentication_elem.get( 'user', '' ) - password = authentication_elem.get( 'password', '' ) - url = authentication_elem.get( 'url', '' ) - realm = authentication_elem.get( 'realm', '' ) - self.basic_http_authentication.append( ( user, password, url, realm ) ) - # Load http_cookie_processor_authentication information, if any. - for authentication_elem in root.findall( 'http_cookie_processor_authentication' ): - # Example tag: - # <http_cookie_processor_authentication url="http://127.0.0.1/login"> - # <param name="user" value="administrator"/> - # <param name="password" value="galaxy"/> - # </http_cookie_processor_authentication> - url = authentication_elem.get( 'url', None ) - if url: - # Include parameters, if any - params = {} - for param_elem in authentication_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - self.http_cookie_processor_authentication = dict( url=url, params=params ) - # Load browser_login information, if any. - for authentication_elem in root.findall( 'browser_login' ): - url = authentication_elem.get( 'url', None ) - if url: - # Include parameters, if any - params = {} - for param_elem in authentication_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - self.browser_login = dict( url=url, params=params ) - # Load redirects - for redirect_elem in root.findall( 'redirect' ): - requests = [] - action_dict = {} - action_dict[ 'title' ] = redirect_elem.get( 'title', None ) - action = redirect_elem.get( 'action', None ) - # Load the external webapp requests, if any exist for this redirect action - for request_elem in redirect_elem.findall( 'external_webapp' ): - requests.append( self.parse_request_elem( request_elem ) ) - if requests: - action_dict[ 'requests' ] = requests - self.sequencer_redirects[ action ] = action_dict - # Load the external webapp requests, if any exist for the sequencer action - for request_elem in root.findall( 'external_webapp' ): - self.sequencer_requests.append( self.parse_request_elem( request_elem ) ) - # Load the special final redirect, used to redirect the browser to defined URL. - for request_elem in root.findall( 'final_redirect' ): - self.final_redirect.append( self.parse_request_elem( request_elem ) ) - except Exception, e: - self.log.debug( 'Error loading sequencer action: %s' % str( e ) ) - # Default values - if not self.sequencer_redirects: - self.sequencer_redirects[ 'start_run' ] = dict( title = 'Start run' ) - self.sequencer_redirects[ 'run_finished' ] = dict( title = 'Run finished' ) - def parse_request_elem( self, request_elem ): - request = request_elem.get( 'request', None ) - # Get the http method, default is get - http_method = request_elem.get( 'http_method', 'get' ) - # Include request parameters, if any - params = {} - for param_elem in request_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - # Handle response, if any ( there should only be 0 or 1 ). - response_type = None - for response_elem in request_elem.findall( 'response' ): - response_type = response_elem.get( 'type', None ) - return ( request, http_method, params, response_type ) diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml.sample --- a/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml.sample +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<sequencer_actions> - <redirect title="Start run" action="start_run"/> - <redirect title="Run finished" action="run_finished"/> -</sequencer_actions> diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca run_demo_sequencer.sh --- a/run_demo_sequencer.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python ./scripts/paster.py serve demo_sequencer_wsgi.ini --pid-file=demo_sequencer_webapp.pid --log-file=demo_sequencer_webapp.log $@ \ No newline at end of file diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca templates/webapps/demo_sequencer/empty.mako --- a/templates/webapps/demo_sequencer/empty.mako +++ /dev/null @@ -1,4 +0,0 @@ -<html> - <body> - </body> -</html> diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca templates/webapps/demo_sequencer/index.mako --- a/templates/webapps/demo_sequencer/index.mako +++ /dev/null @@ -1,54 +0,0 @@ -<%inherit file="/base.mako"/> - -<% - import galaxy.util - titles_list = util.listify( titles ) -%> - -<%def name="javascripts()"> - ${parent.javascripts()} - %if redirect_action != 'exit': - <script type="text/javascript"> - function redirect(){ - top.location.href = "${h.url_for( controller='common', action='index', redirect_action=redirect_action, titles=titles, JobId=JobId, sample_id=sample_id )}"; - } - function set_redirect(){ - %if redirect_delay: - setTimeout("redirect()", ${int(redirect_delay)*1000}); - %else: - setTimeout("redirect()", 2000); - %endif - } - </script> - %endif -</%def> - -## Render a message - can't import because we don't support language encoding here -<%def name="render_message( message, status='done' )"> - <div class="${status}message">${message}</div> - <br/> -</%def> - -%if message: - ${render_message( message, status )} -%endif - -<body onload="set_redirect()"> - <table border="0" align="center" valign="center" cellpadding="5" cellspacing="5"> - <tr><td><img src='static/images/sequencer.png' alt="Sequencer" /></td></tr> - <tr> - <td align="center"> - %if titles_list: - %for title in titles_list: - <h2>${title}</h2> - %endfor - %else: - <h2> </h2> - %endif - </td> - </tr> - </table> - %if not trans.app.sequencer_actions_registry.authenticated and trans.app.sequencer_actions_registry.browser_login: - <iframe name="login" id="login" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="login" )}"></iframe> - %endif -</body> diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca templates/webapps/demo_sequencer/login.mako --- a/templates/webapps/demo_sequencer/login.mako +++ /dev/null @@ -1,10 +0,0 @@ -<html> - <body> - <iframe name="trash" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="empty_page" )}"></iframe> - <form id="logOnForm" name="logOnForm" method="post" action="${trans.app.sequencer_actions_registry.browser_login}" target="trash"> - </form> - <script type="text/javascript"> - document.logOnForm.submit(); - </script> - </body> -</html> diff -r a978e7166f1b1f5fd53a072184912d3a467cac92 -r 82cf6a9e708d437d61c7ce292e6f56e0147634ca templates/webapps/demo_sequencer/redirect.mako --- a/templates/webapps/demo_sequencer/redirect.mako +++ /dev/null @@ -1,10 +0,0 @@ -<html> - <head> - <meta http-equiv="refresh" content="1;url=${redirect_url}"> - </head> - <body> - %if trans.app.sequencer_actions_registry.browser_login: - <iframe name="login" id="login" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="login" )}"></iframe> - %endif - </body> -</html> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 23 Feb '15

23 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7d7c6fb9e48/ Changeset: e7d7c6fb9e48 User: Daniel Blankenberg Date: 2015-02-18 19:39:07+00:00 Summary: Fixes for handling Data Managers that use undeclared data tables. Affected #: 3 files diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e7d7c6fb9e48d5f737ec6247c208cbadc0ec5e64 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -154,7 +154,7 @@ with open( full_path, 'wb' ) as out: out.write( '<?xml version="1.0"?>\n<tables>\n' ) for elem in out_elems: - out.write( util.xml_to_string( elem ) ) + out.write( util.xml_to_string( elem, pretty=True ) ) out.write( '</tables>\n' ) os.chmod( full_path, 0644 ) @@ -452,19 +452,53 @@ """ Returns table entry associated with a col/val pair. """ + rval = self.get_entries( query_attr, query_val, return_attr, default=default, limit=1 ) + if rval: + return rval[0] + return default + + def get_entries( self, query_attr, query_val, return_attr, default=None, limit=None ): + """ + Returns table entry associated with a col/val pair. + """ query_col = self.columns.get( query_attr, None ) if query_col is None: return default - return_col = self.columns.get( return_attr, None ) - if return_col is None: - return default - rval = default + if return_attr is not None: + return_col = self.columns.get( return_attr, None ) + if return_col is None: + return default + rval = [] # Look for table entry. for fields in self.get_fields(): if fields[ query_col ] == query_val: - rval = fields[ return_col ] + if return_attr is None: + field_dict = {} + for i, col_name in enumerate( self.get_column_name_list() ): + field_dict[ col_name or i ] = fields[i] + rval.append( field_dict ) + else: + rval.append( fields[ return_col ] ) + if limit is not None and len( rval ) == limit: + break + return rval or default + + def get_filename_for_source( self, source, default=None ): + if source: + #if dict, assume is compatible info dict, otherwise call method + if isinstance( source, dict ): + source_repo_info = source + else: + source_repo_info = source.get_tool_shed_repository_info_dict() + else: + source_repo_info = None + filename = default + for name, value in self.filenames.iteritems(): + repo_info = value.get( 'tool_shed_repository', None ) + if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): + filename = name break - return rval + return filename def _add_entry( self, entry, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): #accepts dict or list of columns @@ -493,19 +527,7 @@ filename = None if persist and ( not is_error or persist_on_error ): - if entry_source: - #if dict, assume is compatible info dict, otherwise call method - if isinstance( entry_source, dict ): - source_repo_info = entry_source - else: - source_repo_info = entry_source.get_tool_shed_repository_info_dict() - else: - source_repo_info = None - for name, value in self.filenames.iteritems(): - repo_info = value.get( 'tool_shed_repository', None ) - if ( not source_repo_info and not repo_info ) or ( source_repo_info and repo_info and source_repo_info == repo_info ): - filename = name - break + filename = self.get_filename_for_source( entry_source ) if filename is None: #should we default to using any filename here instead? log.error( "Unable to determine filename for persisting data table '%s' values: '%s'.", self.name, fields ) diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e7d7c6fb9e48d5f737ec6247c208cbadc0ec5e64 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -117,6 +117,7 @@ self.move_by_data_table_column = {} self.value_translation_by_data_table_column = {} self.tool_shed_repository_info_dict = None + self.undeclared_tables = False if elem is not None: self.load_from_element( elem, tool_path or self.data_managers.tool_path ) @@ -175,6 +176,7 @@ tool_shed_repository_id=tool_shed_repository_id ) self.name = elem.get( 'name', self.tool.name ) self.description = elem.get( 'description', self.tool.description ) + self.undeclared_tables = util.asbool( elem.get( 'undeclared_tables', self.undeclared_tables ) ) for data_table_elem in elem.findall( 'data_table' ): data_table_name = data_table_elem.get( "name" ) @@ -299,11 +301,28 @@ moved = self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) data_table_value[ name ] = self.process_value_translation( data_table_name, name, **data_table_value ) data_table.add_entry( data_table_value, persist=True, entry_source=self ) - - for data_table_name, data_table_values in data_tables_dict.iteritems(): - #tool returned extra data table entries, but data table was not declared in data manager - #do not add these values, but do provide messages - log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) + if self.undeclared_tables and data_tables_dict: + # We handle the data move, by just moving all the data out of the extra files path + # moving a directory and the target already exists, we move the contents instead + log.debug( 'Attempting to add entries for undeclared tables: %s.', ', '.join( data_tables_dict.keys() ) ) + for ref_file in out_data.values(): + util.move_merge( ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path ) + path_column_names = [ 'path' ] + for data_table_name, data_table_values in data_tables_dict.iteritems(): + data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None ) + if not isinstance( data_table_values, list ): + data_table_values = [ data_table_values ] + for data_table_row in data_table_values: + data_table_value = dict( **data_table_row ) #keep original values here + for name, value in data_table_row.iteritems(): + if name in path_column_names: + data_table_value[ name ] = os.path.abspath( os.path.join( self.data_managers.app.config.galaxy_data_manager_data_path, value ) ) + data_table.add_entry( data_table_value, persist=True, entry_source=self ) + else: + for data_table_name, data_table_values in data_tables_dict.iteritems(): + # tool returned extra data table entries, but data table was not declared in data manager + # do not add these values, but do provide messages + log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) ) def process_move( self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd ): if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[ data_table_name ]: diff -r 503b95e63d0a5268c16a0a87016449bfe969e382 -r e7d7c6fb9e48d5f737ec6247c208cbadc0ec5e64 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -113,16 +113,20 @@ error = True return error, message + def get_target_install_dir( self, tool_shed_repository ): + tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) + # This is where index files will reside on a per repo/installed version basis. + target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) + if not os.path.exists( target_dir ): + os.makedirs( target_dir ) + return target_dir, tool_path, relative_target_dir + def install_tool_data_tables( self, tool_shed_repository, tool_index_sample_files ): TOOL_DATA_TABLE_FILE_NAME = 'tool_data_table_conf.xml' TOOL_DATA_TABLE_FILE_SAMPLE_NAME = '%s.sample' % ( TOOL_DATA_TABLE_FILE_NAME ) SAMPLE_SUFFIX = '.sample' SAMPLE_SUFFIX_OFFSET = -len( SAMPLE_SUFFIX ) - tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path( self.app ) - # This is where index files will reside on a per repo/installed version basis. - target_dir = os.path.join( self.app.config.shed_tool_data_path, relative_target_dir ) - if not os.path.exists( target_dir ): - os.makedirs( target_dir ) + target_dir, tool_path, relative_target_dir = self.get_target_install_dir( tool_shed_repository ) for sample_file in tool_index_sample_files: path, filename = os.path.split ( sample_file ) target_filename = filename https://bitbucket.org/galaxy/galaxy-central/commits/103d62154004/ Changeset: 103d62154004 User: lepsiobec Date: 2015-02-19 19:37:17+00:00 Summary: fi the missing import Affected #: 1 file diff -r e7d7c6fb9e48d5f737ec6247c208cbadc0ec5e64 -r 103d621540041522781a086bff4ac322255aeb49 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -1,4 +1,5 @@ import sys, os.path, logging +import pkg_resources from galaxy import eggs https://bitbucket.org/galaxy/galaxy-central/commits/4b4eee11c31b/ Changeset: 4b4eee11c31b User: dannon Date: 2015-02-19 19:45:44+00:00 Summary: Slightly adjust aforementioned import, use the standard eggs.require Affected #: 1 file diff -r 103d621540041522781a086bff4ac322255aeb49 -r 4b4eee11c31b90eae05db88047a5a675ec645f1b lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -1,5 +1,6 @@ -import sys, os.path, logging -import pkg_resources +import logging +import os.path +import sys from galaxy import eggs @@ -39,7 +40,7 @@ try: egg = dialect_to_egg[dialect] try: - pkg_resources.require( egg ) + eggs.require( egg ) log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) except: # If the module is in the path elsewhere (i.e. non-egg), it'll still load. https://bitbucket.org/galaxy/galaxy-central/commits/d99406f5b690/ Changeset: d99406f5b690 User: dannon Date: 2015-02-19 22:53:12+00:00 Summary: Per IRC discussion, remove demo_sequencer webapp. Affected #: 19 files diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 config/demo_sequencer_wsgi.ini.sample --- a/config/demo_sequencer_wsgi.ini.sample +++ /dev/null @@ -1,66 +0,0 @@ -# ---- HTTP Server ---------------------------------------------------------- - -[server:main] - -use = egg:Paste#http -port = 9011 -host = 0.0.0.0 -use_threadpool = true -threadpool_workers = 10 - -# ---- Galaxy Demo Sequencer Emulator Interface ------------------------------------------------- - -[app:main] - -# Specifies the factory for the universe WSGI application -paste.app_factory = galaxy.webapps.demo_sequencer.buildapp:app_factory -log_level = DEBUG - -# Where dataset files are saved -file_path = database/demo_sequencer_files -# Temporary storage for additional datasets, this should be shared through the cluster -new_file_path = database/tmp - -# Sequencer emulator actions -sequencer_actions_config_file = %(here)s/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml - -# Session support (beaker) -use_beaker_session = True -session_type = memory -session_data_dir = %(here)s/database/beaker_sessions -session_key = galaxysessions -session_secret = changethisinproduction - -# Galaxy session security -id_secret = changethisinproductiontoo - -# Configuration for debugging middleware -debug = true -use_lint = false - -# NEVER enable this on a public site (even test or QA) -# use_interactive = true - -# this should be a comma-separated list of valid Galaxy users -#admin_users = test(a)bx.psu.edu - -# Force everyone to log in (disable anonymous access) -require_login = False - -# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) -## use_heartbeat = True - -# Profiling middleware (cProfile based) -## use_profile = True - -# Use the new iframe / javascript based layout -use_new_layout = true - -# Serving static files (needed if running standalone) -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst +++ /dev/null @@ -1,19 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`common` Module --------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.controllers.common - :members: - :undoc-members: - :show-inheritance: - diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst +++ /dev/null @@ -1,11 +0,0 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.framework - :members: - :undoc-members: - :show-inheritance: - diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 doc/source/lib/galaxy.webapps.demo_sequencer.rst --- a/doc/source/lib/galaxy.webapps.demo_sequencer.rst +++ /dev/null @@ -1,51 +0,0 @@ -demo_sequencer Package -====================== - -:mod:`demo_sequencer` Package ------------------------------ - -.. automodule:: galaxy.webapps.demo_sequencer - :members: - :undoc-members: - :show-inheritance: - -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.demo_sequencer.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.config - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.webapps.demo_sequencer.registry - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.webapps.demo_sequencer.controllers - galaxy.webapps.demo_sequencer.framework - diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 doc/source/lib/galaxy.webapps.rst --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -15,7 +15,6 @@ .. toctree:: galaxy.webapps.community - galaxy.webapps.demo_sequencer galaxy.webapps.galaxy galaxy.webapps.reports diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -"""The Galaxy Demo Sequencer Emulator application.""" -# This webapp is for demo purposes only! - -from galaxy.web.framework import url_for -from galaxy.web.framework.decorators import expose diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/app.py --- a/lib/galaxy/webapps/demo_sequencer/app.py +++ /dev/null @@ -1,19 +0,0 @@ -import sys, config -from galaxy.web import security -import galaxy.webapps.demo_sequencer.registry - -class UniverseApplication( object ): - """Encapsulates the state of a Universe application""" - def __init__( self, **kwargs ): - print >> sys.stderr, "python path is: " + ", ".join( sys.path ) - self.name = "demo_sequencer" - # Read config file and check for errors - self.config = config.Configuration( **kwargs ) - self.config.check() - config.configure_logging( self.config ) - # Set up sequencer actions registry - self.sequencer_actions_registry = galaxy.webapps.demo_sequencer.registry.Registry( self.config.root, self.config.sequencer_actions_config ) - # Security helper - self.security = security.SecurityHelper( id_secret=self.config.id_secret ) - def shutdown( self ): - pass diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/buildapp.py --- a/lib/galaxy/webapps/demo_sequencer/buildapp.py +++ /dev/null @@ -1,171 +0,0 @@ -""" -Provides factory methods to assemble the Galaxy web application -""" - -import logging, atexit -import os, os.path, sys - -from inspect import isclass - -from paste.request import parse_formvars -from paste.util import import_string -from paste import httpexceptions -from galaxy.util import asbool -import pkg_resources - -log = logging.getLogger( __name__ ) - -import config -import galaxy.webapps.demo_sequencer.framework - -def add_ui_controllers( webapp, app ): - """ - Search for controllers in the 'galaxy.webapps.demo_sequencer.controllers' - directory and add them to the webapp. - """ - from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable - import galaxy.webapps.demo_sequencer.controllers - controller_dir = galaxy.webapps.demo_sequencer.controllers.__path__[0] - for fname in os.listdir( controller_dir ): - if not fname.startswith( "_" ) and fname.endswith( ".py" ): - name = fname[:-3] - module_name = "galaxy.webapps.demo_sequencer.controllers." + name - module = __import__( module_name ) - for comp in module_name.split( "." )[1:]: - module = getattr( module, comp ) - # Look for a controller inside the modules - for key in dir( module ): - T = getattr( module, key ) - if isclass( T ) and T is not BaseUIController and issubclass( T, BaseUIController ): - webapp.add_ui_controller( name, T( app ) ) - -def app_factory( global_conf, **kwargs ): - """Return a wsgi application serving the root object""" - # Create the Galaxy application unless passed in - if 'app' in kwargs: - app = kwargs.pop( 'app' ) - else: - try: - from galaxy.webapps.demo_sequencer.app import UniverseApplication - app = UniverseApplication( global_conf = global_conf, **kwargs ) - except: - import traceback, sys - traceback.print_exc() - sys.exit( 1 ) - atexit.register( app.shutdown ) - # Create the universe WSGI application - webapp = galaxy.webapps.demo_sequencer.framework.WebApplication( app, session_cookie='galaxydemo_sequencersession', name="demo_sequencer" ) - add_ui_controllers( webapp, app ) - # These two routes handle our simple needs at the moment - webapp.add_route( '/:controller/:action', action='index' ) - webapp.add_route( '/:action', controller='common', action='index' ) - webapp.finalize_config() - # Wrap the webapp in some useful middleware - if kwargs.get( 'middleware', True ): - webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if kwargs.get( 'static_enabled', True ): - webapp = wrap_in_static( webapp, global_conf, **kwargs ) - # Return - return webapp - -def wrap_in_middleware( app, global_conf, **local_conf ): - """Based on the configuration wrap `app` in a set of common and useful middleware.""" - # Merge the global and local configurations - conf = global_conf.copy() - conf.update(local_conf) - debug = asbool( conf.get( 'debug', False ) ) - # First put into place httpexceptions, which must be most closely - # wrapped around the application (it can interact poorly with - # other middleware): - app = httpexceptions.make_middleware( app, conf ) - log.debug( "Enabling 'httpexceptions' middleware" ) - # The recursive middleware allows for including requests in other - # requests or forwarding of requests, all on the server side. - if asbool(conf.get('use_recursive', True)): - from paste import recursive - app = recursive.RecursiveMiddleware( app, conf ) - log.debug( "Enabling 'recursive' middleware" ) - # Various debug middleware that can only be turned on if the debug - # flag is set, either because they are insecure or greatly hurt - # performance - if debug: - # Middleware to check for WSGI compliance - if asbool( conf.get( 'use_lint', True ) ): - from paste import lint - app = lint.make_middleware( app, conf ) - log.debug( "Enabling 'lint' middleware" ) - # Middleware to run the python profiler on each request - if asbool( conf.get( 'use_profile', False ) ): - import profile - app = profile.ProfileMiddleware( app, conf ) - log.debug( "Enabling 'profile' middleware" ) - # Middleware that intercepts print statements and shows them on the - # returned page - if asbool( conf.get( 'use_printdebug', True ) ): - from paste.debug import prints - app = prints.PrintDebugMiddleware( app, conf ) - log.debug( "Enabling 'print debug' middleware" ) - if debug and asbool( conf.get( 'use_interactive', False ) ): - # Interactive exception debugging, scary dangerous if publicly - # accessible, if not enabled we'll use the regular error printing - # middleware. - pkg_resources.require( "WebError" ) - from weberror import evalexception - app = evalexception.EvalException( app, conf, - templating_formatters=build_template_error_formatters() ) - log.debug( "Enabling 'eval exceptions' middleware" ) - else: - # Not in interactive debug mode, just use the regular error middleware - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) - log.debug( "Enabling 'error' middleware" ) - # Transaction logging (apache access.log style) - if asbool( conf.get( 'use_translogger', True ) ): - from paste.translogger import TransLogger - app = TransLogger( app ) - log.debug( "Enabling 'trans logger' middleware" ) - # X-Forwarded-Host handling - from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware - app = XForwardedHostMiddleware( app ) - log.debug( "Enabling 'x-forwarded-host' middleware" ) - return app - -def wrap_in_static( app, global_conf, **local_conf ): - from paste.urlmap import URLMap - from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static - urlmap = URLMap() - # Merge the global and local configurations - conf = global_conf.copy() - conf.update(local_conf) - # Get cache time in seconds - cache_time = conf.get( "static_cache_time", None ) - if cache_time is not None: - cache_time = int( cache_time ) - # Send to dynamic app by default - urlmap["/"] = app - # Define static mappings from config - urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time ) - urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time ) - urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time ) - urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time ) - urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time ) - # URL mapper becomes the root webapp - return urlmap - -def build_template_error_formatters(): - """ - Build a list of template error formatters for WebError. When an error - occurs, WebError pass the exception to each function in this list until - one returns a value, which will be displayed on the error page. - """ - formatters = [] - # Formatter for mako - import mako.exceptions - def mako_html_data( exc_value ): - if isinstance( exc_value, ( mako.exceptions.CompileException, mako.exceptions.SyntaxException ) ): - return mako.exceptions.html_error_template().render( full=False, css=False ) - if isinstance( exc_value, AttributeError ) and exc_value.args[0].startswith( "'Undefined' object has no attribute" ): - return mako.exceptions.html_error_template().render( full=False, css=False ) - formatters.append( mako_html_data ) - return formatters diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ /dev/null @@ -1,121 +0,0 @@ -""" -Universe configuration builder. -""" - -import sys, os -import logging, logging.config -from optparse import OptionParser -import ConfigParser -from galaxy.util import string_as_bool - -from galaxy import eggs -import pkg_resources - -log = logging.getLogger( __name__ ) - -def resolve_path( path, root ): - """If 'path' is relative make absolute by prepending 'root'""" - if not( os.path.isabs( path ) ): - path = os.path.join( root, path ) - return path - -class ConfigurationError( Exception ): - pass - -class Configuration( object ): - def __init__( self, **kwargs ): - self.config_dict = kwargs - self.root = kwargs.get( 'root_dir', '.' ) - # Collect the umask and primary gid from the environment - self.umask = os.umask( 077 ) # get the current umask - os.umask( self.umask ) # can't get w/o set, so set it back - # Where dataset files are stored - self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) - self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) - self.cookie_path = kwargs.get( "cookie_path", "/" ) - self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) - self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) - self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) - self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) - self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) - self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) - self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) - self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) - self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) - self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) - self.admin_users = kwargs.get( "admin_users", "" ) - self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") - self.error_email_to = kwargs.get( 'error_email_to', None ) - self.smtp_server = kwargs.get( 'smtp_server', None ) - self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) - self.brand = kwargs.get( 'brand', None ) - self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) - self.blog_url = kwargs.get( 'blog_url', None ) - self.screencasts_url = kwargs.get( 'screencasts_url', None ) - self.log_events = False - self.cloud_controller_instance = False - # Proxy features - self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) - self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) - self.sequencer_actions_config = kwargs.get( 'sequencer_actions_config_file', 'galaxy/webapps/demo_sequencer/sequencer_actions.xml' ) - # Parse global_conf and save the parser - global_conf = kwargs.get( 'global_conf', None ) - global_conf_parser = ConfigParser.ConfigParser() - self.global_conf_parser = global_conf_parser - if global_conf and "__file__" in global_conf: - global_conf_parser.read(global_conf['__file__']) - def get( self, key, default ): - return self.config_dict.get( key, default ) - def get_bool( self, key, default ): - if key in self.config_dict: - return string_as_bool( self.config_dict[key] ) - else: - return default - def check( self ): - # Check that required directories exist - for path in self.root, self.file_path, self.template_path: - if not os.path.isdir( path ): - raise ConfigurationError("Directory does not exist: %s" % path ) - def is_admin_user( self, user ): - """ - Determine if the provided user is listed in `admin_users`. - """ - admin_users = self.get( "admin_users", "" ).split( "," ) - return user is not None and user.email in admin_users - -def configure_logging( config ): - """ - Allow some basic logging configuration to be read from the cherrpy - config. - """ - # PasteScript will have already configured the logger if the appropriate - # sections were found in the config file, so we do nothing if the - # config has a loggers section, otherwise we do some simple setup - # using the 'log_*' values from the config. - if config.global_conf_parser.has_section( "loggers" ): - return - format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) - level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] - destination = config.get( "log_destination", "stdout" ) - log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) - # Get root logger - root = logging.getLogger() - # Set level - root.setLevel( level ) - # Turn down paste httpserver logging - if level <= logging.DEBUG: - logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) - # Remove old handlers - for h in root.handlers[:]: - root.removeHandler(h) - # Create handler - if destination == "stdout": - handler = logging.StreamHandler( sys.stdout ) - else: - handler = logging.FileHandler( destination ) - # Create formatter - formatter = logging.Formatter( format ) - # Hook everything up - handler.setFormatter( formatter ) - root.addHandler( handler ) diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/controllers/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/controllers/__init__.py +++ /dev/null @@ -1,1 +0,0 @@ -"""Galaxy demo sequencer emulator controllers.""" diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/controllers/common.py --- a/lib/galaxy/webapps/demo_sequencer/controllers/common.py +++ /dev/null @@ -1,228 +0,0 @@ -from galaxy.web.base.controller import * -from galaxy.web.framework.helpers import time_ago -from galaxy import util -import time, socket, urllib, urllib2, base64, copy -from galaxy.util.json import * -from urllib import quote_plus, unquote_plus -from markupsafe import escape - -import logging -log = logging.getLogger( __name__ ) - -class CommonController( BaseUIController ): - @web.expose - def index( self, trans, **kwd ): - redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) - titles = util.restore_text( kwd.get( 'titles', '' ) ) - titles = util.listify( titles ) - JobId = util.restore_text( kwd.get( 'JobId', '' ) ) - sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) - message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) - status = kwd.get( 'status', 'done' ) - redirect_delay = trans.app.sequencer_actions_registry.redirect_delay - sequencer_redirects = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_redirects ) - sequencer_requests = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_requests ) - requests = [] - if redirect_action == 'stop': - # Handle any additional requests - for request_tup in sequencer_requests: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - response = self.handle_request( trans, url, http_method, **request_params ) - # Handle response, currently only handles json - if response_type == 'json': - response = loads( response ) - # Handle response that is an error, for example: - # { "Success":false, "Message":"some error string" } - if 'Success' in response and response[ 'Success' ] == 'false': - message = response[ 'Message' ] - return self.handle_failure( trans, url, message ) - if 'JobId' in response: - JobId = str( response[ 'JobId' ] ) - kwd[ 'JobId' ] = JobId - # Handle the final redirect, if any ( should only be 0 or 1 ). - for request_tup in trans.app.sequencer_actions_registry.final_redirect: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) - # Exit if we have no redirection - redirect_action = 'exit' - elif not redirect_action: - # Specially handle the initial request to the demo sequencer by starting with the first defined redirect. - redirect_action, action_dict = sequencer_redirects.items()[0] - titles = [ action_dict[ 'title' ] ] - if 'requests' in action_dict: - requests = action_dict[ 'requests' ] - else: - for index, key in enumerate( sequencer_redirects.iterkeys() ): - if redirect_action == key: - try: - # Move to the next action, if there is one. - redirect_action = sequencer_redirects.keys()[ index + 1 ] - action_dict = sequencer_redirects[ redirect_action ] - titles.append( action_dict[ 'title' ] ) - except: - # If we're done redirecting, stop. - redirect_action = 'stop' - break - if not trans.app.sequencer_actions_registry.authenticated: - # Support various types of authentication - if trans.app.sequencer_actions_registry.browser_login: - # We'll just build the URL here since authentication will be handled in the browser - url = trans.app.sequencer_actions_registry.browser_login[ 'url' ] - params = trans.app.sequencer_actions_registry.browser_login[ 'params' ] - trans.app.sequencer_actions_registry.browser_login = '%s?%s' %( url, urllib.urlencode( params ) ) - if not trans.app.sequencer_actions_registry.final_redirect: - # If we don't have a final_redirect tag, but we want our browser to authenticate, - # do it ow. If we have a final_redirect tag, browser authentication will happen there. - url = web.url_for( controller='common', action='index', **kwd ) - return trans.fill_template( 'webapps/demo_sequencer/redirect.mako', redirect_url=url ) - if trans.app.sequencer_actions_registry.basic_http_authentication: - # Example tag: - # <basic_http_authentication user="administrator" password="galaxy" url="http://127.0.0.1" realm="" /> - user, password, url, realm = trans.app.sequencer_actions_registry.basic_http_authentication - # Create a password manager - password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm() - # Add the username, password and realm. - if not realm: - realm = None - password_mgr.add_password( realm, url, user, password ) - handler = urllib2.HTTPBasicAuthHandler( password_mgr ) - # Create "opener" (OpenerDirector instance) - opener = urllib2.build_opener( handler ) - # Install the opener, now all calls to urllib2.urlopen use our opener. - urllib2.install_opener( opener ) - trans.app.sequencer_actions_registry.authenticated = True - if trans.app.sequencer_actions_registry.http_headers_authorization: - # Example tag: - # <http_headers_authorization credentials="administrator:galaxy" url="http://127.0.0.1" /> - url, credentials = trans.app.sequencer_actions_registry.http_headers_authorization - req = urllib2.Request( url ) - req.add_header( 'Authorization', 'Basic %s' % base64.b64encode( credentials ) ) - trans.app.sequencer_actions_registry.authenticated = True - if trans.app.sequencer_actions_registry.http_cookie_processor_authentication: - # Example tag: - # <http_cookie_processor_authentication url="http://127.0.0.1/login"> - # <param name="user" value="administrator"/> - # <param name="password" value="galaxy"/> - # </http_cookie_processor_authentication> - url = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'url' ] - params = trans.app.sequencer_actions_registry.http_cookie_processor_authentication[ 'params' ] - # Build opener with HTTPCookieProcessor - opener = urllib2.build_opener( urllib2.HTTPCookieProcessor() ) - urllib2.install_opener( opener ) - # Perform login with params - page = opener.open( url, urllib.urlencode( params ) ) - response = page.read() - page.close() - # Any additional requests should automatically pass back any - # cookies received during login, thanks to the HTTPCookieProcessor - trans.app.sequencer_actions_registry.authenticated = True - # Handle requests, if there are any - for request_tup in requests: - url, http_method, request_params, response_type = self.parse_request_tup( request_tup, **kwd ) - response = self.handle_request( trans, url, http_method, **request_params ) - # Handle response, currently only handles json - if response_type == 'json': - response = loads( response ) - # Handle response that is an error, for example: - # { "Success":false, "Message":"some error string" } - if 'Success' in response and response[ 'Success' ] == 'false': - message = response[ 'Message' ] - return self.handle_failure( trans, url, message ) - if 'JobId' in response: - JobId = str( response[ 'JobId' ] ) - kwd[ 'JobId' ] = JobId - titles = ','.join( titles ) - return trans.fill_template( "webapps/demo_sequencer/index.mako", - redirect_action=redirect_action, - redirect_delay=redirect_delay, - titles=titles, - sample_id=sample_id, - JobId=JobId, - message=message, - status=status ) - def parse_request_tup( self, request_tup, **kwd ): - redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) ) - titles = util.restore_text( kwd.get( 'titles', '' ) ) - JobId = util.restore_text( kwd.get( 'JobId', '' ) ) - sample_id = util.restore_text( kwd.get( 'sample_id', '' ) ) - message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) - status = kwd.get( 'status', 'done' ) - url, http_method, request_params, response_type = request_tup - url = unquote_plus( url ) - # Handle URLs in which we replace param values, which will look something like: - # http://127.0.0.1/getinfo/{id}. - replace_with_param = url.find( '{' ) > 0 - if replace_with_param: - # Handle the special-case {JobId} param. - if url.find( '{JobId}' ) > 0: - if JobId: - url = url.replace( '{JobId}', str( JobId ) ) - for key, value in kwd.items(): - # Don't attempt to replace if there is nothing with which to do it - # or if the value itself should be replaced with something. - if value and not value.startswith( '{' ): - replace_str = '{%s}' % key - if url.find( replace_str ) > 0: - url = url.replace( replace_str, value ) - # Handle request parameters in which we replace param values. - for key, val in request_params.items(): - if val and val.startswith( '{' ): - replace_key = val.lstrip( '{' ).rstrip( '}' ) - if replace_key in kwd: - request_params[ key ] = kwd[ replace_key ] - return url, http_method, request_params, response_type - def handle_request( self, trans, url, http_method=None, **kwd ): - if 'Name' in kwd and not kwd[ 'Name' ]: - # Hack: specially handle parameters named "Name" if no param_value is given - # by providing a date / time string - guarantees uniqueness, if required. - kwd[ 'Name' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) - if 'Comments' in kwd and not kwd[ 'Comments' ]: - # Hack: specially handle parameters named "Comments" if no param_value is given - # by providing a date / time string. - kwd[ 'Comments' ] = time.strftime( "%a, %d %b %Y %H:%M:%S", time.gmtime() ) - socket.setdefaulttimeout( 600 ) - # The following calls to urllib2.urlopen() will use the above default timeout. - try: - if not http_method or http_method == 'get': - page = urllib2.urlopen( url ) - response = page.read() - page.close() - return response - elif http_method == 'post': - page = urllib2.urlopen( url, urllib.urlencode( kwd ) ) - response = page.read() - page.close() - return response - elif http_method == 'put': - url += '/' + str( kwd.pop( 'id' ) ) + '?key=' + kwd.pop( 'key' ) - output = self.put( url, **kwd ) - except Exception, e: - raise - message = 'Problem sending request to the web application: %s. URL: %s. kwd: %s. Http method: %s' % \ - ( str( e ), str( url ), str( kwd ), str( http_method ) ) - return self.handle_failure( trans, url, message ) - def handle_failure( self, trans, url, message ): - message = '%s, URL: %s' % ( message, url ) - params = dict( message = message, - status = 'error', - redirect_action = 'exit', - titles = 'Error' ) - return trans.response.send_redirect( web.url_for( controller='common', - action='index', - **params ) ) - def put( self, url, **kwd ): - opener = urllib2.build_opener( urllib2.HTTPHandler ) - request = urllib2.Request( url, data=dumps( kwd ) ) - request.add_header( 'Content-Type', 'application/json' ) - request.get_method = lambda: 'PUT' - url = opener.open( request ) - output = url.read() - return loads( output ) - @web.expose - def login( self, trans, **kwd ): - trans.app.sequencer_actions_registry.authenticated = True - return trans.fill_template( "webapps/demo_sequencer/login.mako" ) - @web.expose - def empty_page( self, trans, **kwd ): - # Hack to not display responses in the browser - src for a hidden iframe. - return trans.fill_template( "webapps/demo_sequencer/empty.mako" ) diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/framework/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py +++ /dev/null @@ -1,215 +0,0 @@ -""" -Demo sequencer web application framework -""" - -import json -import os -import pkg_resources -import random -import socket -import string -import sys -import time - -pkg_resources.require( "Cheetah" ) -from Cheetah.Template import Template - -from galaxy.web.framework import helpers - -from galaxy import util -from galaxy.util.json import dumps -from galaxy.util.json import loads -from galaxy.web.framework import url_for -from galaxy.web.framework.decorators import expose -from galaxy.web.framework.decorators import json -from galaxy.web.framework.decorators import json_pretty -from galaxy.web.framework.decorators import require_login -from galaxy.web.framework.decorators import expose_api -from galaxy.web.framework.decorators import error -from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.formbuilder import FormBuilder -from galaxy.web.framework.formbuilder import FormInput -from galaxy.web.framework.formbuilder import FormData -import galaxy.web.framework.base - -from galaxy.util.bunch import Bunch -from galaxy.exceptions import MessageException -from galaxy.util import asbool - -pkg_resources.require( "Mako" ) -import mako.template -import mako.lookup -import mako.runtime - -pkg_resources.require( "pexpect" ) -pkg_resources.require( "amqp" ) - -import logging -log = logging.getLogger( __name__ ) - -class WebApplication( galaxy.web.framework.base.WebApplication ): - def __init__( self, demo_app, session_cookie='demosequencersession' ): - galaxy.web.framework.base.WebApplication.__init__( self ) - self.set_transaction_factory( lambda e: self.transaction_chooser( e, demo_app, session_cookie ) ) - # Mako support - self.mako_template_lookup = mako.lookup.TemplateLookup( - directories = [ demo_app.config.template_path ] , - module_directory = demo_app.config.template_cache, - collection_size = 500, - output_encoding = 'utf-8' ) - # Security helper - self.security = demo_app.security - def handle_controller_exception( self, e, trans, **kwargs ): - if isinstance( e, MessageException ): - return trans.show_message( e.err_msg, e.type ) - def make_body_iterable( self, trans, body ): - if isinstance( body, FormBuilder ): - body = trans.show_form( body ) - return galaxy.web.framework.base.WebApplication.make_body_iterable( self, trans, body ) - def transaction_chooser( self, environ, demo_app, session_cookie ): - if 'is_api_request' in environ: - return DemoWebAPITransaction( environ, demo_app, self ) - else: - return DemoWebUITransaction( environ, demo_app, self, session_cookie ) - -class DemoWebTransaction( galaxy.web.framework.base.DefaultWebTransaction ): - """ - Encapsulates web transaction specific state for the Demo application - (specifically the user's "cookie") - """ - def __init__( self, environ, app, webapp ): - self.app = app - self.webapp = webapp - self.security = webapp.security - galaxy.web.framework.base.DefaultWebTransaction.__init__( self, environ ) - self.debug = asbool( self.app.config.get( 'debug', False ) ) - def get_cookie( self, name='demosequencersession' ): - """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='demosequencersession', path='/', age=90, version='1' ): - """Convenience method for setting a session cookie""" - # The demosequencersession 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 - 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 get_galaxy_session( self ): - """ - Return the current galaxy session - """ - return self.galaxy_session - @galaxy.web.framework.base.lazy_property - def template_context( self ): - return dict() - - 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. - """ - 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, **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 ) - 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 ) - ## return template.render( **data ) - 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 DemoWebAPITransaction( DemoWebTransaction ): - def __init__( self, environ, app, webapp ): - DemoWebTransaction.__init__( self, environ, app, webapp ) - -class DemoWebUITransaction( DemoWebTransaction ): - def __init__( self, environ, app, webapp, session_cookie ): - DemoWebTransaction.__init__( self, environ, app, webapp ) diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/registry.py --- a/lib/galaxy/webapps/demo_sequencer/registry.py +++ /dev/null @@ -1,109 +0,0 @@ -import logging -import galaxy.util -from galaxy.util.odict import odict - -class Registry( object ): - def __init__( self, root_dir=None, config=None ): - self.log = logging.getLogger( __name__ ) - self.log.addHandler( logging.NullHandler() ) - self.redirect_delay = 2.0 # Default to 2 seconds - self.final_redirect = [] - self.sequencer_redirects = odict() - self.sequencer_requests = [] - self.authenticated = False - self.browser_login = None - self.http_headers_authorization = None - self.basic_http_authentication = None - self.http_cookie_processor_authentication = None - if root_dir and config: - tree = galaxy.util.parse_xml( config ) - root = tree.getroot() - self.log.debug( 'Loading sequencer actions from %s' % config ) - try: - # Load the redirect delay value, if any ( default is 2 seconds ). - for redirect_delay in root.findall( 'redirect_delay' ): - delay = redirect_delay.get( 'value', self.redirect_delay ) - self.redirect_delay = float( delay ) - # Load http_headers_authorization information, if any. - for authentication_elem in root.findall( 'http_headers_authorization' ): - # Example tag: - # <http_headers_authorization credentials="administrator:galaxy" url="http://127.0.0.1" /> - url = authentication_elem.get( 'url', '' ) - credentials = authentication_elem.get( 'credentials', '' ) - self.http_headers_authorization = ( url, credentials ) - # Load basic_http_authentication information, if any. - for authentication_elem in root.findall( 'basic_http_authentication' ): - # Example tag: - # <basic_http_authentication user="administrator" password="galaxy" url="http://127.0.0.1" realm="" /> - urls = [] - user = authentication_elem.get( 'user', '' ) - password = authentication_elem.get( 'password', '' ) - url = authentication_elem.get( 'url', '' ) - realm = authentication_elem.get( 'realm', '' ) - self.basic_http_authentication.append( ( user, password, url, realm ) ) - # Load http_cookie_processor_authentication information, if any. - for authentication_elem in root.findall( 'http_cookie_processor_authentication' ): - # Example tag: - # <http_cookie_processor_authentication url="http://127.0.0.1/login"> - # <param name="user" value="administrator"/> - # <param name="password" value="galaxy"/> - # </http_cookie_processor_authentication> - url = authentication_elem.get( 'url', None ) - if url: - # Include parameters, if any - params = {} - for param_elem in authentication_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - self.http_cookie_processor_authentication = dict( url=url, params=params ) - # Load browser_login information, if any. - for authentication_elem in root.findall( 'browser_login' ): - url = authentication_elem.get( 'url', None ) - if url: - # Include parameters, if any - params = {} - for param_elem in authentication_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - self.browser_login = dict( url=url, params=params ) - # Load redirects - for redirect_elem in root.findall( 'redirect' ): - requests = [] - action_dict = {} - action_dict[ 'title' ] = redirect_elem.get( 'title', None ) - action = redirect_elem.get( 'action', None ) - # Load the external webapp requests, if any exist for this redirect action - for request_elem in redirect_elem.findall( 'external_webapp' ): - requests.append( self.parse_request_elem( request_elem ) ) - if requests: - action_dict[ 'requests' ] = requests - self.sequencer_redirects[ action ] = action_dict - # Load the external webapp requests, if any exist for the sequencer action - for request_elem in root.findall( 'external_webapp' ): - self.sequencer_requests.append( self.parse_request_elem( request_elem ) ) - # Load the special final redirect, used to redirect the browser to defined URL. - for request_elem in root.findall( 'final_redirect' ): - self.final_redirect.append( self.parse_request_elem( request_elem ) ) - except Exception, e: - self.log.debug( 'Error loading sequencer action: %s' % str( e ) ) - # Default values - if not self.sequencer_redirects: - self.sequencer_redirects[ 'start_run' ] = dict( title = 'Start run' ) - self.sequencer_redirects[ 'run_finished' ] = dict( title = 'Run finished' ) - def parse_request_elem( self, request_elem ): - request = request_elem.get( 'request', None ) - # Get the http method, default is get - http_method = request_elem.get( 'http_method', 'get' ) - # Include request parameters, if any - params = {} - for param_elem in request_elem.findall( 'param' ): - param_name = param_elem.get( 'name' ) - param_value = param_elem.get( 'value' ) - params[ param_name ] = param_value - # Handle response, if any ( there should only be 0 or 1 ). - response_type = None - for response_elem in request_elem.findall( 'response' ): - response_type = response_elem.get( 'type', None ) - return ( request, http_method, params, response_type ) diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml.sample --- a/lib/galaxy/webapps/demo_sequencer/sequencer_actions.xml.sample +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<sequencer_actions> - <redirect title="Start run" action="start_run"/> - <redirect title="Run finished" action="run_finished"/> -</sequencer_actions> diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 run_demo_sequencer.sh --- a/run_demo_sequencer.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python ./scripts/paster.py serve demo_sequencer_wsgi.ini --pid-file=demo_sequencer_webapp.pid --log-file=demo_sequencer_webapp.log $@ \ No newline at end of file diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 templates/webapps/demo_sequencer/empty.mako --- a/templates/webapps/demo_sequencer/empty.mako +++ /dev/null @@ -1,4 +0,0 @@ -<html> - <body> - </body> -</html> diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 templates/webapps/demo_sequencer/index.mako --- a/templates/webapps/demo_sequencer/index.mako +++ /dev/null @@ -1,54 +0,0 @@ -<%inherit file="/base.mako"/> - -<% - import galaxy.util - titles_list = util.listify( titles ) -%> - -<%def name="javascripts()"> - ${parent.javascripts()} - %if redirect_action != 'exit': - <script type="text/javascript"> - function redirect(){ - top.location.href = "${h.url_for( controller='common', action='index', redirect_action=redirect_action, titles=titles, JobId=JobId, sample_id=sample_id )}"; - } - function set_redirect(){ - %if redirect_delay: - setTimeout("redirect()", ${int(redirect_delay)*1000}); - %else: - setTimeout("redirect()", 2000); - %endif - } - </script> - %endif -</%def> - -## Render a message - can't import because we don't support language encoding here -<%def name="render_message( message, status='done' )"> - <div class="${status}message">${message}</div> - <br/> -</%def> - -%if message: - ${render_message( message, status )} -%endif - -<body onload="set_redirect()"> - <table border="0" align="center" valign="center" cellpadding="5" cellspacing="5"> - <tr><td><img src='static/images/sequencer.png' alt="Sequencer" /></td></tr> - <tr> - <td align="center"> - %if titles_list: - %for title in titles_list: - <h2>${title}</h2> - %endfor - %else: - <h2> </h2> - %endif - </td> - </tr> - </table> - %if not trans.app.sequencer_actions_registry.authenticated and trans.app.sequencer_actions_registry.browser_login: - <iframe name="login" id="login" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="login" )}"></iframe> - %endif -</body> diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 templates/webapps/demo_sequencer/login.mako --- a/templates/webapps/demo_sequencer/login.mako +++ /dev/null @@ -1,10 +0,0 @@ -<html> - <body> - <iframe name="trash" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="empty_page" )}"></iframe> - <form id="logOnForm" name="logOnForm" method="post" action="${trans.app.sequencer_actions_registry.browser_login}" target="trash"> - </form> - <script type="text/javascript"> - document.logOnForm.submit(); - </script> - </body> -</html> diff -r 4b4eee11c31b90eae05db88047a5a675ec645f1b -r d99406f5b690ed130023d8b51cbb5b50a0f4ed12 templates/webapps/demo_sequencer/redirect.mako --- a/templates/webapps/demo_sequencer/redirect.mako +++ /dev/null @@ -1,10 +0,0 @@ -<html> - <head> - <meta http-equiv="refresh" content="1;url=${redirect_url}"> - </head> - <body> - %if trans.app.sequencer_actions_registry.browser_login: - <iframe name="login" id="login" frameborder="0" style="position: absolute; width: 0%; height: 0%;" src="${h.url_for( controller="common", action="login" )}"></iframe> - %endif - </body> -</html> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] 1293cb: update mutable config
by GitHub 20 Feb '15

20 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1293cbbc6d117988b24c6241c396e2057f0de4d0 https://github.com/galaxyproject/usegalaxy-playbook/commit/1293cbbc6d117988… Author: Martin Cech <emulatorer(a)gmail.com> Date: 2015-02-20 (Fri, 20 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- update mutable config

1 0

[galaxyproject/usegalaxy-playbook] b43644: set user_library_import_dir to the ftp dir
by GitHub 20 Feb '15

20 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b436445b888037330f15a39b1b4a529958286008 https://github.com/galaxyproject/usegalaxy-playbook/commit/b436445b88803733… Author: Martin Cech <emulatorer(a)gmail.com> Date: 2015-02-20 (Fri, 20 Feb 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- set user_library_import_dir to the ftp dir

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[galaxyproject/usegalaxy-playbook] b5e4cb: Dropped slide for February 2015 Meetup.
by GitHub 19 Feb '15

19 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b5e4cbda98106790880cbac2ad25816f38af6917 https://github.com/galaxyproject/usegalaxy-playbook/commit/b5e4cbda98106790… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-02-19 (Thu, 19 Feb 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped slide for February 2015 Meetup.

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[galaxyproject/usegalaxy-playbook] 859c4c: Update test.
by GitHub 19 Feb '15

19 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 859c4c0e1078e00f5b089467142196aae51b6d01 https://github.com/galaxyproject/usegalaxy-playbook/commit/859c4c0e1078e00f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-02-19 (Thu, 19 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test.

1 0

commit/galaxy-central: 16 new changesets
by commits-noreply＠bitbucket.org 19 Feb '15

19 Feb '15

16 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3e04f22b499/ Changeset: f3e04f22b499 User: natefoo Date: 2015-02-19 15:34:53+00:00 Summary: Commit convert-mangled .hgtags so the .hgtags removal from git will patch cleanly. Affected #: 1 file diff -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 -r f3e04f22b499b1d602419f86a7757e8bdb304d4f .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,25 +1,25 @@ -a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 -1c717491139269651bb59687563da9410b84c65d release_2013.02.08 -75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 -2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 -524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 -1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 -26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 -5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 -9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 -b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 -9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 -b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 -dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 -db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 -52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 -746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 -ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 -2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 -2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13 +341377bb04676680712f364300e96d70d721df7e release_2013.01.13 +ce310deaf25ee229d05e76f26b5ab263cbd1a226 release_2013.02.08 +3f759aada36a285e85aed002b4912562bce6fb3f release_2013.04.01 +390890ae16e01130b6ad88b0ea33460f7bbda54f security_2013.04.08 +cabc7d8d856fd9d121fc27c7b7db7c8d21274bfe release_2013.06.03 +842e723fdfdb32bfd89dd49606d5d354fc12f544 release_2013.08.12 +6ef33f49b880c8ea5cc2eab9ef3fd76ee0e028d3 release_2013.11.04 +ec716dc9acf551946c24ed41e9f3b98602952c62 release_2014.02.10 +c0271c9b6143c06608fc0d0c50fa38a7e02a9675 release_2014.04.14 +8e38b9ed63b4fd57212f1cfa7003e249fbd07c17 release_2014.06.02 +98c193028cb5f892bcf7dcdd28e4fe5a695c4da4 latest_2014.06.02 +875f1563818f2cf66f867b65836d86d17b76a67f latest_2014.04.14 +a762ca2d670d3412c62a9e56f968a3dca02e37e5 latest_2013.01.13 +1d2795215e72840c76e0888abd80504f960b7129 latest_2013.02.08 +7215b52e6a1ecedf3a960f9b75be8b6ba3771b00 latest_2013.04.01 +59abd0392a52e12e70011863a627b2fe6d64ef20 latest_2013.06.03 +f650fb0cf5b130244b0c35f25ab153dbdd6f1505 latest_2013.08.12 +75e030bbf1b493734dbe98f3df17a31d51f32231 latest_2013.11.04 +9535c43388e4d8e0c9ec3c471a5040d7c22d1c2d latest_2014.02.10 +aac76e72f525efbee1c5ad661e0a036fab97d624 release_2014.08.11 +f26ffe6c2b7a4d157474ff3cdd715900977e91a0 latest_2014.08.11 +3c804ef126e7ab979b76c2ac02bbc0a1fd0ee321 release_2014.10.06 +51005a4e48b624eb79703dd20a32729e474f7a7a latest_2014.10.06 +41027440fcfcb7fc7bc183d9eddbbce6362668d0 release_2015.01.13 +fcdd22776cc21b6f0f64d9dd944174e8503627a6 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/67432ab8f64d/ Changeset: 67432ab8f64d User: erasche2 Date: 2015-02-18 18:15:40+00:00 Summary: Pandoc conversion to rST due to pypi, see #1 Affected #: 2 files diff -r f3e04f22b499b1d602419f86a7757e8bdb304d4f -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 README.md --- a/README.md +++ /dev/null @@ -1,45 +0,0 @@ -# Galaxy - -![Galaxy Logo](https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&… - -[galaxyproject.org](http://galaxyproject.org/) - -The latest information about Galaxy is always available via the Galaxy -website above. - -## Starting Galaxy - -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -```console -$ python -V -Python 2.7.3 -``` - -Start Galaxy: - -```console -$ sh run.sh -``` - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be done -in the `config/galaxy.ini` file. Tools can be either installed from the Tool Shed -or added manually. For details please see the Galaxy wiki: - -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial - -Not all dependencies are included for the tools provided in the sample -`tool_conf.xml`. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies - -## Issues - -Issues can be submitted to trello via the [galaxyproject -website](http://galaxyproject.org/trello/) and viewed on the [Galaxy Trello -Board](https://trello.com/b/75c1kASa/galaxy-development) diff -r f3e04f22b499b1d602419f86a7757e8bdb304d4f -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 README.rst --- /dev/null +++ b/README.rst @@ -0,0 +1,51 @@ +Galaxy +====== + +.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo + + Galaxy Logo +`galaxyproject.org <http://galaxyproject.org/>`__ + +The latest information about Galaxy is always available via the Galaxy +website above. + +Starting Galaxy +--------------- + +Galaxy requires Python 2.6 or 2.7. To check your python version, run: + +.. code:: console + + $ python -V + Python 2.7.3 + +Start Galaxy: + +.. code:: console + + $ sh run.sh + +Once Galaxy completes startup, you should be able to view Galaxy in your +browser at: + +http://localhost:8080 + +You may wish to make changes from the default configuration. This can be +done in the ``config/galaxy.ini`` file. Tools can be either installed +from the Tool Shed or added manually. For details please see the Galaxy +wiki: + +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial + +Not all dependencies are included for the tools provided in the sample +``tool_conf.xml``. A full list of external dependencies is available at: + +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies + +Issues +------ + +Issues can be submitted to trello via the `galaxyproject +website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy +Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__ https://bitbucket.org/galaxy/galaxy-central/commits/c0e79f384381/ Changeset: c0e79f384381 User: erasche2 Date: 2015-02-18 18:17:07+00:00 Summary: Nicer header Affected #: 1 file diff -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 -r c0e79f38438112d7130f63b2cc4aa6ed180fb3e5 README.rst --- a/README.rst +++ b/README.rst @@ -1,14 +1,8 @@ -Galaxy -====== - -.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… - :alt: Galaxy Logo - - Galaxy Logo -`galaxyproject.org <http://galaxyproject.org/>`__ +`.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo <http://galaxyproject.org/>`__ The latest information about Galaxy is always available via the Galaxy -website above. +website: `galaxyproject.org http://galaxyproject.org/>`__ Starting Galaxy --------------- https://bitbucket.org/galaxy/galaxy-central/commits/3704fb0e27bc/ Changeset: 3704fb0e27bc User: erasche2 Date: 2015-02-18 18:20:17+00:00 Summary: Add dev/run instructions to readme Affected #: 1 file diff -r c0e79f38438112d7130f63b2cc4aa6ed180fb3e5 -r 3704fb0e27bcf43c6daa5a5fbaeae27b2330e0fd README.rst --- a/README.rst +++ b/README.rst @@ -4,8 +4,8 @@ The latest information about Galaxy is always available via the Galaxy website: `galaxyproject.org http://galaxyproject.org/>`__ -Starting Galaxy ---------------- +Galaxy Quickstart +================= Galaxy requires Python 2.6 or 2.7. To check your python version, run: @@ -43,3 +43,22 @@ Issues can be submitted to trello via the `galaxyproject website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__ + + +Galaxy Development +================== + +Syncing a Fork +-------------- + +If you fork Galaxy to work on it, you may be interested in keeping your copy +up to date with respect to the main repository. Github has `good documentation +<https://help.github.com/articles/syncing-a-fork/>__` on this. + +.. code:: console + + $ git remote add upstream https://github.com/galaxyproject/galaxy + $ git fetch upstream + $ git checkout dev + $ git merge upstream/dev + https://bitbucket.org/galaxy/galaxy-central/commits/1b98e289d2a7/ Changeset: 1b98e289d2a7 User: erasche2 Date: 2015-02-18 18:22:36+00:00 Summary: Can't write rST to save my life Affected #: 1 file diff -r 3704fb0e27bcf43c6daa5a5fbaeae27b2330e0fd -r 1b98e289d2a73e65fa9af62a0d899b92e4e0f47f README.rst --- a/README.rst +++ b/README.rst @@ -1,8 +1,8 @@ -`.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… - :alt: Galaxy Logo <http://galaxyproject.org/>`__ +.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo The latest information about Galaxy is always available via the Galaxy -website: `galaxyproject.org http://galaxyproject.org/>`__ +website: `http://galaxyproject.org/ <http://galaxyproject.org/>`__ Galaxy Quickstart ================= @@ -53,7 +53,7 @@ If you fork Galaxy to work on it, you may be interested in keeping your copy up to date with respect to the main repository. Github has `good documentation -<https://help.github.com/articles/syncing-a-fork/>__` on this. +<https://help.github.com/articles/syncing-a-fork/>`__ on this. .. code:: console https://bitbucket.org/galaxy/galaxy-central/commits/e386371ff84b/ Changeset: e386371ff84b User: erasche2 Date: 2015-02-18 18:24:11+00:00 Summary: Link to wiki Affected #: 1 file diff -r 1b98e289d2a73e65fa9af62a0d899b92e4e0f47f -r e386371ff84ba4e3d81437b699176b26b58da670 README.rst --- a/README.rst +++ b/README.rst @@ -48,6 +48,9 @@ Galaxy Development ================== +Galaxy welcomes new development! There is extensive documentation on developing +with `Galaxy <https://wiki.galaxyproject.org/Develop>`__ on the wiki. + Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/5222e50ca45d/ Changeset: 5222e50ca45d User: erasche2 Date: 2015-02-18 18:25:04+00:00 Summary: Fix link location Affected #: 1 file diff -r e386371ff84ba4e3d81437b699176b26b58da670 -r 5222e50ca45d5c450173a10b504ead1fd5cb96a7 README.rst --- a/README.rst +++ b/README.rst @@ -49,7 +49,7 @@ ================== Galaxy welcomes new development! There is extensive documentation on developing -with `Galaxy <https://wiki.galaxyproject.org/Develop>`__ on the wiki. +with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__. Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/1600bf5d7532/ Changeset: 1600bf5d7532 User: dannon Date: 2015-02-18 21:37:55+00:00 Summary: Remove old .svn entry and regex def Affected #: 1 file diff -r 5222e50ca45d5c450173a10b504ead1fd5cb96a7 -r 1600bf5d75323ef7d45a4aa79f87cd916f88e1c0 .gitignore --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,3 @@ -syntax: regexp - -\.svn$ - -syntax: glob - .hg* # Downloaded and locally built eggs eggs https://bitbucket.org/galaxy/galaxy-central/commits/0ee5becd6bcf/ Changeset: 0ee5becd6bcf User: dannon Date: 2015-02-18 23:03:31+00:00 Summary: Set datatype extension to default datatype extension when preview=False and to_ext is unsupplied in GET args. Affected #: 1 file diff -r 1600bf5d75323ef7d45a4aa79f87cd916f88e1c0 -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -279,6 +279,7 @@ if chunk: return self.get_chunk(trans, dataset, chunk) elif to_ext or not preview: + to_ext = to_ext or dataset.extension return self._serve_raw(trans, dataset, to_ext) elif dataset.metadata.columns > 50: #Fancy tabular display is only suitable for datasets without an incredibly large number of columns. https://bitbucket.org/galaxy/galaxy-central/commits/19aadae7af81/ Changeset: 19aadae7af81 User: dannon Date: 2015-02-18 23:35:23+00:00 Summary: Style adjustments to tabular dataset headers; use consistent padding. Affected #: 2 files diff -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a -r 19aadae7af81a39edeeda4d10f110008e63a5553 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2286,6 +2286,7 @@ #tool-search{padding-top:5px;padding-bottom:10px;position:relative} #loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif)} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px} +#content_table th{white-space:nowrap;padding:2px 10px} #content_table td.stringalign{text-align:left} #content_table .dark_row{background-color:#DDD} #content_table th{background-color:#AAA} diff -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a -r 19aadae7af81a39edeeda4d10f110008e63a5553 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1548,6 +1548,11 @@ padding:2px 10px; } +#content_table th{ + white-space:nowrap; + padding:2px 10px; +} + #content_table td.stringalign{ text-align:left; } https://bitbucket.org/galaxy/galaxy-central/commits/2480519470a9/ Changeset: 2480519470a9 User: dannon Date: 2015-02-19 12:52:27+00:00 Summary: Custom types cleanup/pep8. Affected #: 1 file diff -r 19aadae7af81a39edeeda4d10f110008e63a5553 -r 2480519470a93059626251a5ec7c8e6cba3eed5d lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,25 +1,23 @@ -from sqlalchemy.types import * +import binascii +import copy +import json +import logging +import uuid -import json -import pickle -import copy -import uuid -import binascii -from galaxy.util.bunch import Bunch +from galaxy import eggs +eggs.require("SQLAlchemy") +import sqlalchemy + from galaxy.util.aliaspickler import AliasPickleModule +from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator -# For monkeypatching BIGINT -import sqlalchemy.dialects.sqlite -import sqlalchemy.dialects.postgresql -import sqlalchemy.dialects.mysql - -import logging log = logging.getLogger( __name__ ) # Default JSON encoder and decoder json_encoder = json.JSONEncoder( sort_keys=True ) json_decoder = json.JSONDecoder( ) + def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue @@ -31,9 +29,10 @@ return binascii.unhexlify( value[2:] ) else: return value - except Exception, ex: + except Exception: return value + class JSONType( TypeDecorator ): """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and @@ -73,9 +72,10 @@ metadata_pickler = AliasPickleModule( { - ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) + ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) + class MetadataType( JSONType ): """ Backward compatible metadata type. Can read pickles or JSON, but always @@ -96,6 +96,7 @@ ret = None return ret + class UUIDType(TypeDecorator): """ Platform-independent UUID type. @@ -129,31 +130,9 @@ class TrimmedString( TypeDecorator ): impl = String + def process_bind_param( self, value, dialect ): """Automatically truncate string values""" if self.impl.length and value is not None: value = value[0:self.impl.length] return value - - -#class BigInteger( Integer ): - #""" - #A type for bigger ``int`` integers. - - #Typically generates a ``BIGINT`` in DDL, and otherwise acts like - #a normal :class:`Integer` on the Python side. - - #""" - -#class BIGINT( BigInteger ): - #"""The SQL BIGINT type.""" - -#class SLBigInteger( BigInteger ): - #def get_col_spec( self ): - #return "BIGINT" - -#sqlalchemy.dialects.sqlite.SLBigInteger = SLBigInteger -#sqlalchemy.dialects.sqlite.colspecs[BigInteger] = SLBigInteger -#sqlalchemy.dialects.sqlite.ischema_names['BIGINT'] = SLBigInteger -#sqlalchemy.dialects.postgres.colspecs[BigInteger] = sqlalchemy.dialects.postgres.PGBigInteger -#sqlalchemy.dialects.mysql.colspecs[BigInteger] = sqlalchemy.dialects.mysql.MSBigInteger https://bitbucket.org/galaxy/galaxy-central/commits/bf564c0703c5/ Changeset: bf564c0703c5 User: nsoranzo Date: 2015-02-19 18:46:29+00:00 Summary: Remove .hgtags file. The hashes got mangled in the transition to Git. Affected #: 1 file diff -r 2480519470a93059626251a5ec7c8e6cba3eed5d -r bf564c0703c57dae79535a4a7ff0c7acd7e87e32 .hgtags --- a/.hgtags +++ /dev/null @@ -1,25 +0,0 @@ -341377bb04676680712f364300e96d70d721df7e release_2013.01.13 -ce310deaf25ee229d05e76f26b5ab263cbd1a226 release_2013.02.08 -3f759aada36a285e85aed002b4912562bce6fb3f release_2013.04.01 -390890ae16e01130b6ad88b0ea33460f7bbda54f security_2013.04.08 -cabc7d8d856fd9d121fc27c7b7db7c8d21274bfe release_2013.06.03 -842e723fdfdb32bfd89dd49606d5d354fc12f544 release_2013.08.12 -6ef33f49b880c8ea5cc2eab9ef3fd76ee0e028d3 release_2013.11.04 -ec716dc9acf551946c24ed41e9f3b98602952c62 release_2014.02.10 -c0271c9b6143c06608fc0d0c50fa38a7e02a9675 release_2014.04.14 -8e38b9ed63b4fd57212f1cfa7003e249fbd07c17 release_2014.06.02 -98c193028cb5f892bcf7dcdd28e4fe5a695c4da4 latest_2014.06.02 -875f1563818f2cf66f867b65836d86d17b76a67f latest_2014.04.14 -a762ca2d670d3412c62a9e56f968a3dca02e37e5 latest_2013.01.13 -1d2795215e72840c76e0888abd80504f960b7129 latest_2013.02.08 -7215b52e6a1ecedf3a960f9b75be8b6ba3771b00 latest_2013.04.01 -59abd0392a52e12e70011863a627b2fe6d64ef20 latest_2013.06.03 -f650fb0cf5b130244b0c35f25ab153dbdd6f1505 latest_2013.08.12 -75e030bbf1b493734dbe98f3df17a31d51f32231 latest_2013.11.04 -9535c43388e4d8e0c9ec3c471a5040d7c22d1c2d latest_2014.02.10 -aac76e72f525efbee1c5ad661e0a036fab97d624 release_2014.08.11 -f26ffe6c2b7a4d157474ff3cdd715900977e91a0 latest_2014.08.11 -3c804ef126e7ab979b76c2ac02bbc0a1fd0ee321 release_2014.10.06 -51005a4e48b624eb79703dd20a32729e474f7a7a latest_2014.10.06 -41027440fcfcb7fc7bc183d9eddbbce6362668d0 release_2015.01.13 -fcdd22776cc21b6f0f64d9dd944174e8503627a6 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/86b814c0bdd2/ Changeset: 86b814c0bdd2 User: dannon Date: 2015-02-19 14:02:31+00:00 Summary: Custom types mutable+pickle fix. Previously failing unit and framework.multi_output functional tests pass now. Affected #: 1 file diff -r bf564c0703c57dae79535a4a7ff0c7acd7e87e32 -r 86b814c0bdd212e0162e358c56feb6ca6350a16d lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -10,6 +10,7 @@ from galaxy.util.aliaspickler import AliasPickleModule from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator +from sqlalchemy.ext.mutable import Mutable log = logging.getLogger( __name__ ) @@ -33,6 +34,40 @@ return value +class MutableDict(Mutable, dict): + # MutableDict following http://docs.sqlalchemy.org/en/latest/orm/extensions/mutable.html + @classmethod + def coerce(cls, key, value): + "Convert plain dictionaries to MutableDict." + + if not isinstance(value, MutableDict): + if isinstance(value, dict): + return MutableDict(value) + + # this call will raise ValueError + return Mutable.coerce(key, value) + else: + return value + + def __setitem__(self, key, value): + "Detect dictionary set events and emit change events." + + dict.__setitem__(self, key, value) + self.changed() + + def __delitem__(self, key): + "Detect dictionary del events and emit change events." + + dict.__delitem__(self, key) + self.changed() + + def __getstate__(self): + return dict(self) + + def __setstate__(self, state): + self.update(state) + + class JSONType( TypeDecorator ): """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and @@ -61,9 +96,6 @@ # return json_encoder.encode( x ) == json_encoder.encode( y ) return ( x == y ) - def is_mutable( self ): - return True - def load_dialect_impl(self, dialect): if dialect.name == "mysql": return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB) @@ -71,6 +103,9 @@ return self.impl +MutableDict.associate_with(JSONType) + + metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) https://bitbucket.org/galaxy/galaxy-central/commits/f862e3546f76/ Changeset: f862e3546f76 User: dannon Date: 2015-02-19 15:14:27+00:00 Summary: Remove .hgignore since it has no relevance to the .git repository; will be maintained downstream in hg as necessary. Affected #: 1 file diff -r 86b814c0bdd212e0162e358c56feb6ca6350a16d -r f862e3546f76d4f7990608cac34f2d0db5491a02 .hgignore --- a/.hgignore +++ /dev/null @@ -1,124 +0,0 @@ -syntax: regexp - -\.svn$ - -syntax: glob - -.hg* -# Downloaded and locally built eggs -eggs -scripts/scramble/build -scripts/scramble/lib -scripts/scramble/archives - -# Python virtualenv -.venv - -# Database stuff -database/beaker_sessions -database/citations -database/community_files -database/compiled_templates -database/files -database/job_working_directory -database/pbs -database/tmp -database/*.sqlite -database/openid_consumer_cache - -# Python bytecode -*.pyc - -# Galaxy Runtime Files -*.lock -*.log -*.pid - -# Tool Shed Runtime Files -tool_shed_webapp.lock -tool_shed_webapp.log -tool_shed_webapp.pid -hgweb.config* -lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml - -# Reports Runtime Files -reports_webapp.lock -reports_webapp.log -reports_webapp.pid - -# Config files -universe_wsgi.ini -reports_wsgi.ini -tool_shed_wsgi.ini - -# Config files. -datatypes_conf.xml -tool_conf.xml -external_service_types_conf.xml -migrated_tools_conf.xml -shed_tool_conf.xml -tool_data_table_conf.xml -tool_sheds_conf.xml -integrated_tool_panel.xml -openid_conf.xml -shed_tool_data_table_conf.xml -job_conf.xml -data_manager_conf.xml -shed_data_manager_conf.xml -object_store_conf.xml -job_metrics_conf.xml -workflow_schedulers_conf.xml -config/* -static/welcome.html.* -static/welcome.html - -# Tool data. -tool-data/annotation_profiler_options.xml -tool-data/annotation_profiler_valid_builds.txt -tool-data/gatk_annotations.txt -tool-data/gd.restriction_enzymes.txt -tool-data/gd.species.txt -tool-data/shared/igv/igv_build_sites.txt -tool-data/shared/rviewer/rviewer_build_sites.txt -tool-data/shared/ncbi/builds.txt -tool-data/shared/ucsc/builds.txt -tool-data/shared/ensembl/builds.txt -tool-data/shared/ucsc/publicbuilds.txt -tool-data/shared/ucsc/ucsc_build_sites.txt -tool-data/*.loc -tool-data/genome/* - -# Test output -test-data-cache -run_functional_tests.html -test/tool_shed/tmp/* -.coverage -htmlcov -run_unit_tests.html -test/unit/**.log - -# Project files -*.kpf - -# Chrom len files -*.len - -# Jars -tool-data/shared/jars/ - -# CSS build artifacts. -sprite-*.less - -# Local node_modules and bower_components directories -node_modules -bower_components - -# Documentation build files. -doc/build - -# Misc -*.orig -.DS_Store -*.rej -*~ - https://bitbucket.org/galaxy/galaxy-central/commits/d11852b77046/ Changeset: d11852b77046 User: natefoo Date: 2015-02-19 15:36:44+00:00 Summary: Recommit correct .hgtags Affected #: 1 file diff -r f862e3546f76d4f7990608cac34f2d0db5491a02 -r d11852b77046481a3cc3ada94ebcc0f2929b524c .hgtags --- /dev/null +++ b/.hgtags @@ -0,0 +1,25 @@ +a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 +1c717491139269651bb59687563da9410b84c65d release_2013.02.08 +75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 +2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 +1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 +26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 +5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 +9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 +7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 +9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 +b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 +dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 +ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 +2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 +d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/503b95e63d0a/ Changeset: 503b95e63d0a User: natefoo Date: 2015-02-19 15:38:16+00:00 Summary: Recommit .hgignore removed from git. Affected #: 1 file diff -r d11852b77046481a3cc3ada94ebcc0f2929b524c -r 503b95e63d0a5268c16a0a87016449bfe969e382 .hgignore --- /dev/null +++ b/.hgignore @@ -0,0 +1,124 @@ +syntax: regexp + +\.svn$ + +syntax: glob + +.hg* +# Downloaded and locally built eggs +eggs +scripts/scramble/build +scripts/scramble/lib +scripts/scramble/archives + +# Python virtualenv +.venv + +# Database stuff +database/beaker_sessions +database/citations +database/community_files +database/compiled_templates +database/files +database/job_working_directory +database/pbs +database/tmp +database/*.sqlite +database/openid_consumer_cache + +# Python bytecode +*.pyc + +# Galaxy Runtime Files +*.lock +*.log +*.pid + +# Tool Shed Runtime Files +tool_shed_webapp.lock +tool_shed_webapp.log +tool_shed_webapp.pid +hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml + +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + +# Config files +universe_wsgi.ini +reports_wsgi.ini +tool_shed_wsgi.ini + +# Config files. +datatypes_conf.xml +tool_conf.xml +external_service_types_conf.xml +migrated_tools_conf.xml +shed_tool_conf.xml +tool_data_table_conf.xml +tool_sheds_conf.xml +integrated_tool_panel.xml +openid_conf.xml +shed_tool_data_table_conf.xml +job_conf.xml +data_manager_conf.xml +shed_data_manager_conf.xml +object_store_conf.xml +job_metrics_conf.xml +workflow_schedulers_conf.xml +config/* +static/welcome.html.* +static/welcome.html + +# Tool data. +tool-data/annotation_profiler_options.xml +tool-data/annotation_profiler_valid_builds.txt +tool-data/gatk_annotations.txt +tool-data/gd.restriction_enzymes.txt +tool-data/gd.species.txt +tool-data/shared/igv/igv_build_sites.txt +tool-data/shared/rviewer/rviewer_build_sites.txt +tool-data/shared/ncbi/builds.txt +tool-data/shared/ucsc/builds.txt +tool-data/shared/ensembl/builds.txt +tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt +tool-data/*.loc +tool-data/genome/* + +# Test output +test-data-cache +run_functional_tests.html +test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html +test/unit/**.log + +# Project files +*.kpf + +# Chrom len files +*.len + +# Jars +tool-data/shared/jars/ + +# CSS build artifacts. +sprite-*.less + +# Local node_modules and bower_components directories +node_modules +bower_components + +# Documentation build files. +doc/build + +# Misc +*.orig +.DS_Store +*.rej +*~ + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 18 Feb '15

18 Feb '15

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ad6939e186d/ Changeset: 7ad6939e186d User: dannon Date: 2015-02-18 16:16:26+00:00 Summary: Add .gitignore Affected #: 1 file diff -r b3a0812f9129f8e1e8bdad3a273c3410edba4e7a -r 7ad6939e186d05233166b6a5fc55f16e14de1309 .gitignore --- /dev/null +++ b/.gitignore @@ -0,0 +1,124 @@ +syntax: regexp + +\.svn$ + +syntax: glob + +.hg* +# Downloaded and locally built eggs +eggs +scripts/scramble/build +scripts/scramble/lib +scripts/scramble/archives + +# Python virtualenv +.venv + +# Database stuff +database/beaker_sessions +database/citations +database/community_files +database/compiled_templates +database/files +database/job_working_directory +database/pbs +database/tmp +database/*.sqlite +database/openid_consumer_cache + +# Python bytecode +*.pyc + +# Galaxy Runtime Files +*.lock +*.log +*.pid + +# Tool Shed Runtime Files +tool_shed_webapp.lock +tool_shed_webapp.log +tool_shed_webapp.pid +hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml + +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + +# Config files +universe_wsgi.ini +reports_wsgi.ini +tool_shed_wsgi.ini + +# Config files. +datatypes_conf.xml +tool_conf.xml +external_service_types_conf.xml +migrated_tools_conf.xml +shed_tool_conf.xml +tool_data_table_conf.xml +tool_sheds_conf.xml +integrated_tool_panel.xml +openid_conf.xml +shed_tool_data_table_conf.xml +job_conf.xml +data_manager_conf.xml +shed_data_manager_conf.xml +object_store_conf.xml +job_metrics_conf.xml +workflow_schedulers_conf.xml +config/* +static/welcome.html.* +static/welcome.html + +# Tool data. +tool-data/annotation_profiler_options.xml +tool-data/annotation_profiler_valid_builds.txt +tool-data/gatk_annotations.txt +tool-data/gd.restriction_enzymes.txt +tool-data/gd.species.txt +tool-data/shared/igv/igv_build_sites.txt +tool-data/shared/rviewer/rviewer_build_sites.txt +tool-data/shared/ncbi/builds.txt +tool-data/shared/ucsc/builds.txt +tool-data/shared/ensembl/builds.txt +tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt +tool-data/*.loc +tool-data/genome/* + +# Test output +test-data-cache +run_functional_tests.html +test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html +test/unit/**.log + +# Project files +*.kpf + +# Chrom len files +*.len + +# Jars +tool-data/shared/jars/ + +# CSS build artifacts. +sprite-*.less + +# Local node_modules and bower_components directories +node_modules +bower_components + +# Documentation build files. +doc/build + +# Misc +*.orig +.DS_Store +*.rej +*~ + https://bitbucket.org/galaxy/galaxy-central/commits/a76dbb051400/ Changeset: a76dbb051400 User: erasche2 Date: 2015-02-18 15:21:38+00:00 Summary: Touch up readme for github Affected #: 2 files diff -r 7ad6939e186d05233166b6a5fc55f16e14de1309 -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 README.md --- /dev/null +++ b/README.md @@ -0,0 +1,37 @@ +# Galaxy + +[galaxyproject.org](http://galaxyproject.org/) + +The latest information about Galaxy is always available via the Galaxy +website above. + +# Starting Galaxy + +Galaxy requires Python 2.6 or 2.7. To check your python version, run: + +```console +$ python -V +Python 2.7.3 +``` + +Start Galaxy: + +```console +$ sh run.sh +``` + +Once Galaxy completes startup, you should be able to view Galaxy in your +browser at: + +http://localhost:8080 + +You may wish to make changes from the default configuration. This can be done +in the `config/galaxy.ini` file. Tools can be either installed from the Tool Shed +or added manually. For details please see the Galaxy wiki: + +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial + +Not all dependencies are included for the tools provided in the sample +`tool_conf.xml`. A full list of external dependencies is available at: + +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 7ad6939e186d05233166b6a5fc55f16e14de1309 -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 README.txt --- a/README.txt +++ /dev/null @@ -1,34 +0,0 @@ -GALAXY -====== -http://galaxyproject.org/ - -The latest information about Galaxy is always available via the Galaxy -website above. - -HOW TO START -============ -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -% python -V -Python 2.7.3 - -Start Galaxy: - -% sh run.sh - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be done -in the config/galaxy.ini file. Tools can be either installed from the Tool Shed -or added manually. For details please see the Galaxy wiki: - -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial - - -Not all dependencies are included for the tools provided in the sample -tool_conf.xml. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies https://bitbucket.org/galaxy/galaxy-central/commits/74a3d684e584/ Changeset: 74a3d684e584 User: erasche2 Date: 2015-02-18 15:22:01+00:00 Summary: Fix section heading Affected #: 1 file diff -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 -r 74a3d684e58419b6d78c75db9b16ac094caf597b README.md --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ The latest information about Galaxy is always available via the Galaxy website above. -# Starting Galaxy +## Starting Galaxy Galaxy requires Python 2.6 or 2.7. To check your python version, run: https://bitbucket.org/galaxy/galaxy-central/commits/0aa8ee4a94d8/ Changeset: 0aa8ee4a94d8 User: erasche2 Date: 2015-02-18 15:29:13+00:00 Summary: Add link to issues Affected #: 1 file diff -r 74a3d684e58419b6d78c75db9b16ac094caf597b -r 0aa8ee4a94d8adda2d71d3f765cebc4eabb865a5 README.md --- a/README.md +++ b/README.md @@ -35,3 +35,9 @@ `tool_conf.xml`. A full list of external dependencies is available at: https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies + +## Issues + +Issues can be submitted to trello via the [galaxyproject +website](http://galaxyproject.org/trello/) and viewed on the [Galaxy Trello +Board](https://trello.com/b/75c1kASa/galaxy-development) https://bitbucket.org/galaxy/galaxy-central/commits/02986af924ce/ Changeset: 02986af924ce User: dannon Date: 2015-02-18 16:37:01+00:00 Summary: Update CONTRIBUTING Affected #: 1 file diff -r 0aa8ee4a94d8adda2d71d3f765cebc4eabb865a5 -r 02986af924ce0f6afbbed78a2829fdc38a8c890c CONTRIBUTING.md --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -25,27 +25,24 @@ ## How to Contribute -* If you are new to Mercurial - please check out this [official - tutorial](http://mercurial.selenic.com/wiki/Tutorial) +* If you are new to Git - please check out the very useful tutorials on the [GitHub training hub](https://training.github.com/kit/) -* Make sure you have a free [Bitbucket - account](https://bitbucket.org/account/signup/) +* Make sure you have a free [GitHub account](https://github.com/) -* Fork the galaxy-central repository on - [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to - make your changes. (Many Galaxy instances target - [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active - development happens on galaxy-central and this is where pull - requests should be made). +* Fork the galaxy repository on + [GitHub](https://github.com/galaxyproject/galaxy) to make your changes. + (While many Galaxy instances track + [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist), active development + happens in the galaxy GitHub repository and this is where pull requests + should be made). -* Choose the correct Mercurial branch to develop your changes against. +* Choose the correct branch to develop your changes against. - * Additions to the code base should be pushed to the `default` - branch (`hg checkout default`). + * Additions to the code base should be pushed to the `dev` branch (`git + checkout dev`). - * Most bug fixes to previously release components (things in - galaxy-dist) should be pushed to the `stable` branch (`hg checkout - stable`). + * Most bug fixes to previously release components (things in galaxy-dist) + should be made against the `master` branch (`git checkout master`). * Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or @@ -76,9 +73,9 @@ with these changes. You pull request message should include: * A description of why the change should be made. - + * A description of implementation of the change. - + * A description of how to test the change. ## Ideas https://bitbucket.org/galaxy/galaxy-central/commits/93b67ff10b23/ Changeset: 93b67ff10b23 User: erasche2 Date: 2015-02-18 16:15:46+00:00 Summary: Add logo Affected #: 1 file diff -r 02986af924ce0f6afbbed78a2829fdc38a8c890c -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 README.md --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # Galaxy +![Galaxy Logo](https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&… + [galaxyproject.org](http://galaxyproject.org/) The latest information about Galaxy is always available via the Galaxy https://bitbucket.org/galaxy/galaxy-central/commits/43b850d3b54a/ Changeset: 43b850d3b54a User: jmchilton Date: 2015-02-18 05:38:06+00:00 Summary: Add --dockerize and --db [postgres|mysql|sqlite] options to run_tests.sh. Runs tests in a Dockerfile with pre-migrated databases and all testing dependencies (postgres, mysql, npm, casper, phantomjs, etc...). Hopefully this makes it easier to run more interesting tests - down the road I would like to add more options for things like condor, slurm, run as real user, etc.... Affected #: 7 files diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 run_tests.sh --- a/run_tests.sh +++ b/run_tests.sh @@ -29,6 +29,9 @@ --no_cleanup Do not delete temp files for Python functional tests (-toolshed, -framework, etc...) --report_file Path of HTML report to produce (for Python Galaxy functional tests). --xunit_report_file Path of XUnit report to produce (for Python Galaxy functional tests). + --dockerize Run tests in a pre-configured Docker container (must be first argument if present). + --db <type> For use with --dockerize, run tests using partially migrated 'postgres', 'mysql', + or 'sqlite' databases. EOF } @@ -60,6 +63,22 @@ driver="python" +if [ "$1" = "--dockerize" ]; +then + shift + if [ "$1" = "--db" ]; then + db_type=$2 + shift 2 + else + db_type="sqlite" + fi + DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""} + DOCKER_RUN_EXTRA_ARGS=${DOCKER_ARGS:-""} + DOCKER_IMAGE=${DOCKER_IMAGE:-"galaxyprojectdotorg/testing-base"} + docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@" + exit $? +fi + while : do case "$1" in diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/README.md --- /dev/null +++ b/test/docker/README.md @@ -0,0 +1,9 @@ +Setup Docker environment for use with testing using the following +commands (until this is on Docker hub). + + % cd test/base + % docker build -t galaxyprojectdotorg/testing-base . + +This will create a docker container ready to run most of Galaxy tests +(functional tests for specific bioinformatics tools may still fail for +now until they are migrated out of Galaxy and to the tool shed). diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/Dockerfile --- /dev/null +++ b/test/docker/base/Dockerfile @@ -0,0 +1,63 @@ +FROM toolshed/requirements +MAINTAINER John Chilton <jmchilton(a)gmail.com> + +ENV MYSQL_MAJOR=5.7 \ + MYSQL_VERSION=5.7.5-m15 + +# Pre-install a bunch of packages to speed up ansible steps. +RUN apt-get update -y && apt-get install -y software-properties-common curl && \ + apt-add-repository -y ppa:ansible/ansible && \ + curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ + echo 'deb https://deb.nodesource.com/node trusty main' > /etc/apt/sources.list.d/nodesource.list && \ + apt-key adv --keyserver pool.sks-keyservers.net --recv-keys A4A9406876FCBD3C456770C88C718D3B5072E1F5 && \ + echo "deb http://repo.mysql.com/apt/ubuntu/ trusty mysql-${MYSQL_MAJOR}-dmr" > /etc/apt/sources.list.d/mysql.list && \ + { \ + echo mysql-community-server mysql-community-server/data-dir select ''; \ + echo mysql-community-server mysql-community-server/root-pass password ''; \ + echo mysql-community-server mysql-community-server/re-root-pass password ''; \ + echo mysql-community-server mysql-community-server/remove-test-db select false; \ + } | debconf-set-selections && \ + apt-get update -y && \ + apt-get install -y libpq-dev postgresql postgresql-client postgresql-plpython-9.3 \ + ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_VERSION}"* \ + nodejs && \ + npm install -g grunt-contrib-qunit grunt grunt-cli casperjs phantomjs && \ + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +RUN mkdir -p /tmp/ansible && \ + mkdir -p /opt/galaxy/db && \ + chown -R postgres:postgres /opt/galaxy/db && \ + sed -Ei 's/^(bind-address|log)/#&/' /etc/mysql/my.cnf + +ADD start_mysql.sh /opt/galaxy/start_mysql.sh +ADD ansible_vars.yml /tmp/ansible/ansible_vars.yml +ADD provision.yml /tmp/ansible/provision.yml + +ENV PYTHON_EGG_CACHE=/root/.python-eggs \ + GALAXY_ROOT=/opt/galaxy/galaxy-app + +RUN cd /tmp/ansible && \ + mkdir roles && \ + mkdir roles/galaxyprojectdotorg.galaxy-os && \ + wget -qO- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \ + mkdir roles/galaxyprojectdotorg.cloudman-database && \ + wget -qO- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.t… | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \ + mkdir roles/galaxyprojectdotorg.galaxy && \ + wget -qO- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \ + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +RUN cd $GALAXY_ROOT && \ + echo "Prepopuating postgres database" && \ + su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \ + GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://galaxy@localhost:5930/galaxy" sh create_db.sh && \ + echo "Prepopuating sqlite database" && \ + GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" sh create_db.sh && \ + sh /opt/galaxy/start_mysql.sh && \ + GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh + +ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh + +ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"] diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/ansible_vars.yml --- /dev/null +++ b/test/docker/base/ansible_vars.yml @@ -0,0 +1,21 @@ +--- +add_system_users: no +galaxyFS_base_dir: /opt/galaxy +# TODO: use GALAXY_ROOT via cmd line instead +galaxy_server_dir: "{{ galaxyFS_base_dir }}/galaxy-app" +galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv" +galxy_egg_cache: "/home/{{ galaxy_user_name }}/.python-eggs" +galaxy_repo: https://bitbucket.org/galaxy/galaxy-central +galaxy_changeset_id: stable +galaxy_manage_clone: no +galaxy_manage_download: yes +galaxy_root: "{{ galaxy_server_dir}}" +galaxy_db_dir: "{{ galaxyFS_base_dir }}/db" +galaxy_db_port: 5930 +galaxy_db_log: /tmp/pSQL.log +psql_galaxyftp_password: ignoredthis +galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini" +configure_docker: no +postgresql_bin_dir: /usr/lib/postgresql/9.3/bin +galaxy_manage_database: no + diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/provision.yml --- /dev/null +++ b/test/docker/base/provision.yml @@ -0,0 +1,15 @@ +- hosts: localhost + connection: local + roles: + - role: galaxyprojectdotorg.galaxy-os + tags: image + sudo: yes + - role: galaxyprojectdotorg.cloudman-database + sudo: yes + sudo_user: postgres + tags: database + - role: galaxyprojectdotorg.galaxy + sudo: yes + tags: galaxy + + diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/run_test_wrapper.sh --- /dev/null +++ b/test/docker/base/run_test_wrapper.sh @@ -0,0 +1,23 @@ +#!/bin/bash +set -e + +# TODO: switch on environment to boot mysql here... +if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ]; +then + su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres + sleep 3 + export GALAXY_TEST_DBURI="postgres://galaxy@localhost:5930/galaxy" +elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ]; +then + sh /opt/galaxy/start_mysql.sh + export GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" +elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ]; +then + export GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite" +else + echo "Unknown database type" + exit 1 +fi +cd /galaxy +GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI" sh manage_db.sh upgrade +sh run_tests.sh $@ diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/start_mysql.sh --- /dev/null +++ b/test/docker/base/start_mysql.sh @@ -0,0 +1,39 @@ +#!/bin/bash +set -e + +MYSQL_USER=galaxy +MYSQL_PASSWORD=galaxy +MYSQL_DATABASE=galaxy + +mkdir -p /var/lib/mysql +chown -R mysql:mysql /var/lib/mysql + +# Derived from +# https://github.com/docker-library/mysql/blob/master/5.7/docker-entrypoint.sh + +DATADIR="$(mysqld --verbose --help 2>/dev/null | awk '$1 == "datadir" { print $2; exit }')" + +tempSqlFile='/tmp/mysql-first-time.sql' +cat > "$tempSqlFile" <<-EOSQL + DELETE FROM mysql.user ; + CREATE USER 'root'@'%' IDENTIFIED BY '${MYSQL_ROOT_PASSWORD}' ; + GRANT ALL ON *.* TO 'root'@'%' WITH GRANT OPTION ; + DROP DATABASE IF EXISTS test ; +EOSQL + +if [ "$MYSQL_DATABASE" ]; then + echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile" +fi + +if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then + echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile" + + if [ "$MYSQL_DATABASE" ]; then + echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile" + fi +fi + +echo 'FLUSH PRIVILEGES ;' >> "$tempSqlFile" + +mysqld_safe --init-file="$tempSqlFile" & +sleep 5 \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge back from next-stable.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3a0812f9129/ Changeset: b3a0812f9129 User: dannon Date: 2015-02-17 20:20:40+00:00 Summary: Merge back from next-stable. 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: 4 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b63caa7dfa98/ Changeset: b63caa7dfa98 Branch: next-stable User: dannon Date: 2015-02-17 20:18:08+00:00 Summary: Fix xml.etree relative import error happening in test/asserts/xml.py Affected #: 1 file diff -r b6d15f14d0b392c4e9d9db56129bc67d6d4ba26b -r b63caa7dfa9865430d87d6023efd45ccf02228ca test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re https://bitbucket.org/galaxy/galaxy-central/commits/9f2731b49115/ Changeset: 9f2731b49115 User: dannon Date: 2015-02-17 20:18:45+00:00 Summary: Merge bugfix from next-stable. Affected #: 1 file diff -r 798e912004b2b26b219d5ed2214f1e65e8c099fa -r 9f2731b49115c44da4dc9bc4d91e9514b4c0b8ba test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re https://bitbucket.org/galaxy/galaxy-central/commits/6310fc863764/ Changeset: 6310fc863764 Branch: next-stable User: dannon Date: 2015-02-17 20:19:00+00:00 Summary: Merge. Affected #: 1 file diff -r b63caa7dfa9865430d87d6023efd45ccf02228ca -r 6310fc863764ef515861a64638bacebad8079514 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) https://bitbucket.org/galaxy/galaxy-central/commits/cc01fa14d826/ Changeset: cc01fa14d826 User: dannon Date: 2015-02-17 20:19:40+00:00 Summary: Merge. Affected #: 1 file diff -r a49498479b2e71f8d2abf955ce4c7c041de730b9 -r cc01fa14d8269a5dc40b09fa3658ff3b58c2bc67 test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re 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: dan: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83fb18cb8c3d/ Changeset: 83fb18cb8c3d Branch: next-stable User: dan Date: 2015-02-17 20:17:17+00:00 Summary: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. Affected #: 1 file diff -r b6d15f14d0b392c4e9d9db56129bc67d6d4ba26b -r 83fb18cb8c3d21351f6267e574ed75c72eeb770a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) 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: dan: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a49498479b2e/ Changeset: a49498479b2e User: dan Date: 2015-02-17 20:17:17+00:00 Summary: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. Affected #: 1 file diff -r 798e912004b2b26b219d5ed2214f1e65e8c099fa -r a49498479b2e71f8d2abf955ce4c7c041de730b9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) 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 17 Feb '15

17 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6d15f14d0b3/ Changeset: b6d15f14d0b3 Branch: next-stable User: dannon Date: 2015-02-17 20:08:45+00:00 Summary: Fix another identity vs value test error in xml handling. Affected #: 1 file diff -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 -r b6d15f14d0b392c4e9d9db56129bc67d6d4ba26b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2947,7 +2947,7 @@ element_attrib = dict( element.attrib ) element_identifier = element_attrib[ "name" ] nested_collection_elem = element.find( "collection" ) - if nested_collection_elem: + if nested_collection_elem is not None: self.elements.append( ( element_identifier, TestCollectionDef( nested_collection_elem, parse_param_elem ) ) ) else: self.elements.append( ( element_identifier, parse_param_elem( element ) ) ) https://bitbucket.org/galaxy/galaxy-central/commits/798e912004b2/ Changeset: 798e912004b2 User: dannon Date: 2015-02-17 20:09:13+00:00 Summary: Apply fix from next-stable. Affected #: 1 file diff -r 41f41e587c3470019855358afb7eaff7377c1ca0 -r 798e912004b2b26b219d5ed2214f1e65e8c099fa lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2947,7 +2947,7 @@ element_attrib = dict( element.attrib ) element_identifier = element_attrib[ "name" ] nested_collection_elem = element.find( "collection" ) - if nested_collection_elem: + if nested_collection_elem is not None: self.elements.append( ( element_identifier, TestCollectionDef( nested_collection_elem, parse_param_elem ) ) ) else: self.elements.append( ( element_identifier, parse_param_elem( 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: jmchilton: Fix tool shed tests for GALAXY_TEST_DB_TEMPLATE unset.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41f41e587c34/ Changeset: 41f41e587c34 User: jmchilton Date: 2015-02-17 19:02:04+00:00 Summary: Fix tool shed tests for GALAXY_TEST_DB_TEMPLATE unset. I guess everyone who has ran tool shed tests in the last couple years has set either that or GALAXY_TEST_DBURI? Odd. Affected #: 1 file diff -r df4ab158d14e2b371ecced7392bcf02bc4e7dd65 -r 41f41e587c3470019855358afb7eaff7377c1ca0 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -224,6 +224,8 @@ # cases (namely tool shed tests expecting clean database). __copy_database_template(os.environ['GALAXY_TEST_DB_TEMPLATE'], db_path) galaxy_database_auto_migrate = True + if not os.path.exists(galaxy_db_path): + os.makedirs(galaxy_db_path) galaxy_database_connection = 'sqlite:///%s' % db_path if 'GALAXY_TEST_INSTALL_DBURI' in os.environ: install_galaxy_database_connection = os.environ[ 'GALAXY_TEST_INSTALL_DBURI' ] 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: 4 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e47493de36f/ Changeset: 7e47493de36f Branch: next-stable User: carlfeberhard Date: 2015-02-17 14:54:36+00:00 Summary: UI: Move action menu rendering into list panel, refactor history contents copying Affected #: 19 files diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 client/galaxy/scripts/mvc/history/history-contents.js --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -25,7 +25,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -185,16 +184,36 @@ return deferred; }, + isCopyable : function( contentsJSON ){ + var copyableModelClasses = [ + 'HistoryDatasetAssociation', + 'HistoryDatasetCollectionAssociation' + ]; + return ( ( _.isObject( contentsJSON ) && contentsJSON.id ) + && ( _.contains( copyableModelClasses, contentsJSON.model_class ) ) ); + }, + /** copy an existing, accessible hda into this collection */ - copy : function( id, contentType ){ - contentType = contentType || 'hda'; - var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), - collection = this; - - var xhr = jQuery.post( this.url(), { - type : type, + copy : function( json ){ + var id, type, contentType; + if( _.isString( json ) ){ + id = json; + contentType = 'hda'; + type = 'dataset'; + } else { + id = json.id; + contentType = ({ + 'HistoryDatasetAssociation' : 'hda', + 'LibraryDatasetDatasetAssociation' : 'ldda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + })[ json.model_class ] || 'hda'; + type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ); + } + var collection = this, + xhr = jQuery.post( this.url(), { + content : id, source : contentType, - content : id + type : type }) .done( function( json ){ collection.add([ json ]); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -69,8 +69,6 @@ /** is the panel currently showing the dataset selection controls? */ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - - this.multiselectActions = attributes.multiselectActions || this._getActions(); }, /** Override to handle history as drag-drop target */ @@ -210,11 +208,6 @@ _super.prototype._setUpBehaviors.call( this, $where ); if( !this.model ){ return; } - // set up the pupup for actions available when multi selecting - if( this.multiselectActions.length ){ - this.actionsPopup = new PopupMenu( $where.find( '.list-action-popup-btn' ), this.multiselectActions ); - } - // anon users shouldn't have access to any of the following if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) || ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){ @@ -245,7 +238,7 @@ /** return a new popup menu for choosing a multi selection action * ajax calls made for multiple datasets are queued */ - _getActions : function(){ + multiselectActions : function(){ var panel = this, actions = [ { html: _l( 'Hide datasets' ), func: function(){ diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 client/galaxy/scripts/mvc/history/history-panel.js --- a/client/galaxy/scripts/mvc/history/history-panel.js +++ b/client/galaxy/scripts/mvc/history/history-panel.js @@ -7,6 +7,7 @@ "mvc/collection/collection-panel", "mvc/user/user-model", "ui/fa-icon-button", + "mvc/ui/popup-menu", "mvc/base-mvc", "utils/localization", "ui/search-input" @@ -19,6 +20,7 @@ COLLECTION_PANEL, USER, faIconButton, + PopupMenu, BASE_MVC, _l ){ @@ -302,7 +304,8 @@ /** In this override, add a btn to toggle the selectors */ _buildNewRender : function(){ var $newRender = _super.prototype._buildNewRender.call( this ); - if( this.multiselectActions.length ){ + //if( this.views.length && this.multiselectActions().length ){ + if( this.multiselectActions().length ){ $newRender.find( '.controls .actions' ).prepend( this._renderSelectButton() ); } return $newRender; @@ -617,10 +620,18 @@ '<div class="actions"></div>', '<div class="messages">', - '<% if( history.deleted ){ %>', + '<% if( history.deleted && history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged and deleted' ), + '</div>', + '<% } else if( history.deleted ){ %>', '<div class="deleted-msg warningmessagesmall">', _l( 'This history has been deleted' ), '</div>', + '<% } else if( history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged' ), + '</div>', '<% } %>', '<% if( history.message ){ %>', @@ -646,8 +657,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - '<button class="list-action-popup-btn btn btn-default">', - _l( 'For all selected' ), '...</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ], 'history' ); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -353,8 +353,8 @@ '</a></li>', '<% } %>', '</ul>', - '<% } %>', - '</div>', + '</div>', + '<% } %>', '</div>' ].join( '' ), { variable: 'data' }), @@ -669,11 +669,7 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this, - modelClassToSource = { - 'HistoryDatasetAssociation' : 'hda', - 'HistoryDatasetCollectionAssociation' : 'hdca' - }; + var multipanel = this; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -691,20 +687,18 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ - //note: this will bad copy sources fail silently + //note: bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( ( _.isObject( json ) && json.id ) - && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); + return panel.model.contents.isCopyable( json ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); toCopy.forEach( function( content ){ - var contentType = modelClassToSource[ content.model_class ]; queue.add({ name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( content.id, contentType ); + return panel.model.contents.copy( content ); } }); }); @@ -714,7 +708,6 @@ }); } }); - }, /** conv. fn to count the columns in columnMap */ diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -46,9 +46,6 @@ /** string used for search placeholder */ searchPlaceholder : _l( 'search' ), - /** actions available for multiselected items */ - multiselectActions : [], - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the list @@ -103,11 +100,6 @@ this.title = attributes.title || ''; this.subtitle = attributes.subtitle || ''; - // allow override of multiselectActions through attributes - this.multiselectActions = attributes.multiselectActions || this.multiselectActions; - /** the popup displayed when 'for all selected...' is clicked */ - this.actionsPopup = null; - this._setUpListeners(); }, @@ -288,9 +280,45 @@ _setUpBehaviors : function( $where ){ $where = $where || this.$el; $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); + // set up the pupup for actions available when multi selecting + this._renderMultiselectActionMenu( $where ); return this; }, + /** render a menu containing the actions available to sets of selected items */ + _renderMultiselectActionMenu : function( $where ){ + $where = $where || this.$el; + var $menu = $where.find( '.list-action-menu' ), + actions = this.multiselectActions(); + if( !actions.length ){ + return $menu.empty(); + } + + var $newMenu = $([ + '<div class="list-action-menu btn-group">', + '<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'For all selected' ), '...', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', '</ul>', + '</div>' + ].join('')); + var $actions = actions.map( function( action ){ + var html = [ '<li><a href="javascript:void(0);">', action.html, '</a></li>' ].join( '' ); + return $( html ).click( action.func ); + }); + $newMenu.find( 'ul' ).append( $actions ); + $menu.replaceWith( $newMenu ); + return $newMenu; + }, + + /** return a list of plain objects used to render multiselect actions menu. Each object should have: + * html: an html string used as the anchor contents + * func: a function called when the anchor is clicked (passed the click event) + */ + multiselectActions : function(){ + return []; + }, + // ------------------------------------------------------------------------ sub-$element shortcuts /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ $scrollContainer : function(){ @@ -790,9 +818,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); @@ -929,9 +956,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -25,7 +25,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -185,16 +184,36 @@ return deferred; }, + isCopyable : function( contentsJSON ){ + var copyableModelClasses = [ + 'HistoryDatasetAssociation', + 'HistoryDatasetCollectionAssociation' + ]; + return ( ( _.isObject( contentsJSON ) && contentsJSON.id ) + && ( _.contains( copyableModelClasses, contentsJSON.model_class ) ) ); + }, + /** copy an existing, accessible hda into this collection */ - copy : function( id, contentType ){ - contentType = contentType || 'hda'; - var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), - collection = this; - - var xhr = jQuery.post( this.url(), { - type : type, + copy : function( json ){ + var id, type, contentType; + if( _.isString( json ) ){ + id = json; + contentType = 'hda'; + type = 'dataset'; + } else { + id = json.id; + contentType = ({ + 'HistoryDatasetAssociation' : 'hda', + 'LibraryDatasetDatasetAssociation' : 'ldda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + })[ json.model_class ] || 'hda'; + type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ); + } + var collection = this, + xhr = jQuery.post( this.url(), { + content : id, source : contentType, - content : id + type : type }) .done( function( json ){ collection.add([ json ]); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -69,8 +69,6 @@ /** is the panel currently showing the dataset selection controls? */ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - - this.multiselectActions = attributes.multiselectActions || this._getActions(); }, /** Override to handle history as drag-drop target */ @@ -210,11 +208,6 @@ _super.prototype._setUpBehaviors.call( this, $where ); if( !this.model ){ return; } - // set up the pupup for actions available when multi selecting - if( this.multiselectActions.length ){ - this.actionsPopup = new PopupMenu( $where.find( '.list-action-popup-btn' ), this.multiselectActions ); - } - // anon users shouldn't have access to any of the following if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) || ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){ @@ -245,7 +238,7 @@ /** return a new popup menu for choosing a multi selection action * ajax calls made for multiple datasets are queued */ - _getActions : function(){ + multiselectActions : function(){ var panel = this, actions = [ { html: _l( 'Hide datasets' ), func: function(){ diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -7,6 +7,7 @@ "mvc/collection/collection-panel", "mvc/user/user-model", "ui/fa-icon-button", + "mvc/ui/popup-menu", "mvc/base-mvc", "utils/localization", "ui/search-input" @@ -19,6 +20,7 @@ COLLECTION_PANEL, USER, faIconButton, + PopupMenu, BASE_MVC, _l ){ @@ -302,7 +304,8 @@ /** In this override, add a btn to toggle the selectors */ _buildNewRender : function(){ var $newRender = _super.prototype._buildNewRender.call( this ); - if( this.multiselectActions.length ){ + //if( this.views.length && this.multiselectActions().length ){ + if( this.multiselectActions().length ){ $newRender.find( '.controls .actions' ).prepend( this._renderSelectButton() ); } return $newRender; @@ -617,10 +620,18 @@ '<div class="actions"></div>', '<div class="messages">', - '<% if( history.deleted ){ %>', + '<% if( history.deleted && history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged and deleted' ), + '</div>', + '<% } else if( history.deleted ){ %>', '<div class="deleted-msg warningmessagesmall">', _l( 'This history has been deleted' ), '</div>', + '<% } else if( history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged' ), + '</div>', '<% } %>', '<% if( history.message ){ %>', @@ -646,8 +657,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - '<button class="list-action-popup-btn btn btn-default">', - _l( 'For all selected' ), '...</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ], 'history' ); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -353,8 +353,8 @@ '</a></li>', '<% } %>', '</ul>', - '<% } %>', - '</div>', + '</div>', + '<% } %>', '</div>' ].join( '' ), { variable: 'data' }), @@ -669,11 +669,7 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this, - modelClassToSource = { - 'HistoryDatasetAssociation' : 'hda', - 'HistoryDatasetCollectionAssociation' : 'hdca' - }; + var multipanel = this; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -691,20 +687,18 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ - //note: this will bad copy sources fail silently + //note: bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( ( _.isObject( json ) && json.id ) - && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); + return panel.model.contents.isCopyable( json ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); toCopy.forEach( function( content ){ - var contentType = modelClassToSource[ content.model_class ]; queue.add({ name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( content.id, contentType ); + return panel.model.contents.copy( content ); } }); }); @@ -714,7 +708,6 @@ }); } }); - }, /** conv. fn to count the columns in columnMap */ diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -46,9 +46,6 @@ /** string used for search placeholder */ searchPlaceholder : _l( 'search' ), - /** actions available for multiselected items */ - multiselectActions : [], - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the list @@ -103,11 +100,6 @@ this.title = attributes.title || ''; this.subtitle = attributes.subtitle || ''; - // allow override of multiselectActions through attributes - this.multiselectActions = attributes.multiselectActions || this.multiselectActions; - /** the popup displayed when 'for all selected...' is clicked */ - this.actionsPopup = null; - this._setUpListeners(); }, @@ -288,9 +280,45 @@ _setUpBehaviors : function( $where ){ $where = $where || this.$el; $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); + // set up the pupup for actions available when multi selecting + this._renderMultiselectActionMenu( $where ); return this; }, + /** render a menu containing the actions available to sets of selected items */ + _renderMultiselectActionMenu : function( $where ){ + $where = $where || this.$el; + var $menu = $where.find( '.list-action-menu' ), + actions = this.multiselectActions(); + if( !actions.length ){ + return $menu.empty(); + } + + var $newMenu = $([ + '<div class="list-action-menu btn-group">', + '<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'For all selected' ), '...', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', '</ul>', + '</div>' + ].join('')); + var $actions = actions.map( function( action ){ + var html = [ '<li><a href="javascript:void(0);">', action.html, '</a></li>' ].join( '' ); + return $( html ).click( action.func ); + }); + $newMenu.find( 'ul' ).append( $actions ); + $menu.replaceWith( $newMenu ); + return $newMenu; + }, + + /** return a list of plain objects used to render multiselect actions menu. Each object should have: + * html: an html string used as the anchor contents + * func: a function called when the anchor is clicked (passed the click event) + */ + multiselectActions : function(){ + return []; + }, + // ------------------------------------------------------------------------ sub-$element shortcuts /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ $scrollContainer : function(){ @@ -790,9 +818,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); @@ -929,9 +956,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/packed/mvc/history/history-contents.js --- a/static/scripts/packed/mvc/history/history-contents.js +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},copy:function(l,k){k=k||"hda";var h=(k==="hdca"?"dataset_collection":"dataset"),j=this;var i=jQuery.post(this.url(),{type:h,source:k,content:l}).done(function(m){j.add([m])}).fail(function(n,m,o){j.trigger("error",j,i,{},"Error copying contents",{type:h,id:l,source:k})});return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file +define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},isCopyable:function(i){var h=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return((_.isObject(i)&&i.id)&&(_.contains(h,i.model_class)))},copy:function(h){var m,i,l;if(_.isString(h)){m=h;l="hda";i="dataset"}else{m=h.id;l=({HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"})[h.model_class]||"hda";i=(l==="hdca"?"dataset_collection":"dataset")}var k=this,j=jQuery.post(this.url(),{content:m,source:l,type:i}).done(function(n){k.add([n])}).fail(function(o,n,p){k.trigger("error",k,j,{},"Error copying contents",{type:i,id:m,source:l})});return j},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(h,j,m,f,e,i,l,c,b,a,d){var k=h.HistoryPanel;var g=k.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:i.HDCAListItemEdit,initialize:function(n){n=n||{};k.prototype.initialize.call(this,n);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=n.purgeAllowed||false;this.annotationEditorShown=n.annotationEditorShown||false;this.tagsEditorShown=n.tagsEditorShown||false;this.multiselectActions=n.multiselectActions||this._getActions()},_setUpListeners:function(){var n=this;k.prototype._setUpListeners.call(n);n.on("drop",function(o,p){n.dataDropped(p);n.dropTargetOff()});n.on("view:attached view:removed",function(){n._renderCounts()},n)},_setUpCollectionListeners:function(){k.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(n){this.model.fetch()},this);return this},_setUpModelListeners:function(){k.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var n=k.prototype._buildNewRender.call(this);if(!this.model){return n}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(n);this._renderAnnotation(n)}return n},renderItems:function(o){var n=k.prototype.renderItems.call(this,o);this._renderCounts(o);return n},_renderCounts:function(p){function o(s,t){return['<a class="',s,'" href="javascript:void(0);">',t,"</a>"].join("")}p=p||this.$el;var n=this.collection.where({deleted:true}),r=this.collection.where({visible:false}),q=[];if(this.views.length){q.push([this.views.length,d("shown")].join(" "))}if(n.length){q.push((!this.showDeleted)?([n.length,o("toggle-deleted-link",d("deleted"))].join(" ")):(o("toggle-deleted-link",d("hide deleted"))))}if(r.length){q.push((!this.showHidden)?([r.length,o("toggle-hidden-link",d("hidden"))].join(" ")):(o("toggle-hidden-link",d("hide hidden"))))}return p.find("> .controls .subtitle").html(q.join(", "))},_renderTags:function(n){var o=this;this.tagsEditor=new l.TagsEditor({model:this.model,el:n.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDATagEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDATagEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(n.find(".controls .actions"))})},_renderAnnotation:function(n){var o=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:n.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDAAnnotationEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDAAnnotationEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(n.find(".controls .actions"))})},_setUpBehaviors:function(n){n=n||this.$el;k.prototype._setUpBehaviors.call(this,n);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new a(n.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var o=this,p=".controls .name";n.find(p).attr("title",d("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(q){var r=o.model.get("name");if(q&&q!==r){o.$el.find(p).text(q);o.model.save({name:q}).fail(function(){o.$el.find(p).text(o.model.previous("name"))})}else{o.$el.find(p).text(r)}}})},_getActions:function(){var n=this,o=[{html:d("Hide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.hide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Unhide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.unhide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Delete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype["delete"];n.getSelectedModels().ajaxQueue(p)}},{html:d("Undelete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.undelete;n.getSelectedModels().ajaxQueue(p)}}];if(n.purgeAllowed){o.push({html:d("Permanently delete datasets"),func:function(){if(confirm(d("This will permanently remove the data in your datasets. Are you sure?"))){var p=f.HistoryDatasetAssociation.prototype.purge;n.getSelectedModels().ajaxQueue(p)}}})}o.push({html:d("Build Dataset List"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"list")}});o.push({html:d("Build Dataset Pair"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"paired")}});o.push({html:d("Build List of Dataset Pairs"),func:_.bind(n._showPairedCollectionModal,n)});return o},_showPairedCollectionModal:function(){var n=this,o=n.getSelectedModels().toJSON().filter(function(p){return p.history_content_type==="dataset"&&p.state===m.OK});if(o.length){require(["mvc/collection/paired-collection-creator"],function(p){window.creator=p.pairedCollectionCreatorModal(o,{historyId:n.model.id})})}else{Galaxy.modal.show({title:d("No valid datasets were selected"),body:d(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:true})}},_attachItems:function(n){this.$list(n).append(this.views.reverse().map(function(o){return o.$el}));return this},_attachView:function(o){var n=this;n.views.unshift(o);n.$list().prepend(o.render(0).$el.hide());n.trigger("view:attached",o);o.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")})},_getItemViewOptions:function(o){var n=k.prototype._getItemViewOptions.call(this,o);_.extend(n,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return n},_handleHdaDeletionChange:function(n){if(n.get("deleted")&&!this.showDeleted){this.removeItemView(n)}this._renderCounts()},_handleHdaVisibleChange:function(n){if(n.hidden()&&!this.storage.showHidden){this.removeItemView(n)}this._renderCounts()},toggleHDATagEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.tagsEditor){p.tagsEditor.toggle.apply(p.tagsEditor,o)}})},toggleHDAAnnotationEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.annotationEditor){p.annotationEditor.toggle.apply(p.annotationEditor,o)}})},events:_.extend(_.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(n){this.toggleShowDeleted()},"click .toggle-hidden-link":function(n){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var o={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var p=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),p]);for(var n in o){if(o.hasOwnProperty(n)){p.on(n,o[n])}}return this},_renderDropTarget:function(){this.$(".history-drop-target").remove();return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){this.$(".history-drop-target-help").remove();return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(d("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;var o=this.$(".history-drop-target").get(0);for(var n in this._dropHandlers){if(this._dropHandlers.hasOwnProperty(n)){console.debug(n,this._dropHandlers[n]);o.off(n,this._dropHandlers[n])}}this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(n){n.preventDefault();n.stopPropagation()},dragleave:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(p){p.preventDefault();p.dataTransfer.dropEffect="move";var n=this,q=p.dataTransfer.getData("text");try{q=JSON.parse(q)}catch(o){this.warn("error parsing JSON from drop:",q)}this.trigger("droptarget:drop",p,q,n);return false},dataDropped:function(o){var n=this;if(_.isObject(o)&&o.model_class==="HistoryDatasetAssociation"&&o.id){return n.model.contents.copy(o.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:g}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(h,j,m,f,e,i,l,c,b,a,d){var k=h.HistoryPanel;var g=k.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:i.HDCAListItemEdit,initialize:function(n){n=n||{};k.prototype.initialize.call(this,n);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=n.purgeAllowed||false;this.annotationEditorShown=n.annotationEditorShown||false;this.tagsEditorShown=n.tagsEditorShown||false},_setUpListeners:function(){var n=this;k.prototype._setUpListeners.call(n);n.on("drop",function(o,p){n.dataDropped(p);n.dropTargetOff()});n.on("view:attached view:removed",function(){n._renderCounts()},n)},_setUpCollectionListeners:function(){k.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(n){this.model.fetch()},this);return this},_setUpModelListeners:function(){k.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var n=k.prototype._buildNewRender.call(this);if(!this.model){return n}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(n);this._renderAnnotation(n)}return n},renderItems:function(o){var n=k.prototype.renderItems.call(this,o);this._renderCounts(o);return n},_renderCounts:function(p){function o(s,t){return['<a class="',s,'" href="javascript:void(0);">',t,"</a>"].join("")}p=p||this.$el;var n=this.collection.where({deleted:true}),r=this.collection.where({visible:false}),q=[];if(this.views.length){q.push([this.views.length,d("shown")].join(" "))}if(n.length){q.push((!this.showDeleted)?([n.length,o("toggle-deleted-link",d("deleted"))].join(" ")):(o("toggle-deleted-link",d("hide deleted"))))}if(r.length){q.push((!this.showHidden)?([r.length,o("toggle-hidden-link",d("hidden"))].join(" ")):(o("toggle-hidden-link",d("hide hidden"))))}return p.find("> .controls .subtitle").html(q.join(", "))},_renderTags:function(n){var o=this;this.tagsEditor=new l.TagsEditor({model:this.model,el:n.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDATagEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDATagEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(n.find(".controls .actions"))})},_renderAnnotation:function(n){var o=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:n.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDAAnnotationEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDAAnnotationEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(n.find(".controls .actions"))})},_setUpBehaviors:function(n){n=n||this.$el;k.prototype._setUpBehaviors.call(this,n);if(!this.model){return}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var o=this,p=".controls .name";n.find(p).attr("title",d("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(q){var r=o.model.get("name");if(q&&q!==r){o.$el.find(p).text(q);o.model.save({name:q}).fail(function(){o.$el.find(p).text(o.model.previous("name"))})}else{o.$el.find(p).text(r)}}})},multiselectActions:function(){var n=this,o=[{html:d("Hide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.hide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Unhide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.unhide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Delete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype["delete"];n.getSelectedModels().ajaxQueue(p)}},{html:d("Undelete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.undelete;n.getSelectedModels().ajaxQueue(p)}}];if(n.purgeAllowed){o.push({html:d("Permanently delete datasets"),func:function(){if(confirm(d("This will permanently remove the data in your datasets. Are you sure?"))){var p=f.HistoryDatasetAssociation.prototype.purge;n.getSelectedModels().ajaxQueue(p)}}})}o.push({html:d("Build Dataset List"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"list")}});o.push({html:d("Build Dataset Pair"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"paired")}});o.push({html:d("Build List of Dataset Pairs"),func:_.bind(n._showPairedCollectionModal,n)});return o},_showPairedCollectionModal:function(){var n=this,o=n.getSelectedModels().toJSON().filter(function(p){return p.history_content_type==="dataset"&&p.state===m.OK});if(o.length){require(["mvc/collection/paired-collection-creator"],function(p){window.creator=p.pairedCollectionCreatorModal(o,{historyId:n.model.id})})}else{Galaxy.modal.show({title:d("No valid datasets were selected"),body:d(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:true})}},_attachItems:function(n){this.$list(n).append(this.views.reverse().map(function(o){return o.$el}));return this},_attachView:function(o){var n=this;n.views.unshift(o);n.$list().prepend(o.render(0).$el.hide());n.trigger("view:attached",o);o.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")})},_getItemViewOptions:function(o){var n=k.prototype._getItemViewOptions.call(this,o);_.extend(n,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return n},_handleHdaDeletionChange:function(n){if(n.get("deleted")&&!this.showDeleted){this.removeItemView(n)}this._renderCounts()},_handleHdaVisibleChange:function(n){if(n.hidden()&&!this.storage.showHidden){this.removeItemView(n)}this._renderCounts()},toggleHDATagEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.tagsEditor){p.tagsEditor.toggle.apply(p.tagsEditor,o)}})},toggleHDAAnnotationEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.annotationEditor){p.annotationEditor.toggle.apply(p.annotationEditor,o)}})},events:_.extend(_.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(n){this.toggleShowDeleted()},"click .toggle-hidden-link":function(n){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var o={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var p=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),p]);for(var n in o){if(o.hasOwnProperty(n)){p.on(n,o[n])}}return this},_renderDropTarget:function(){this.$(".history-drop-target").remove();return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){this.$(".history-drop-target-help").remove();return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(d("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;var o=this.$(".history-drop-target").get(0);for(var n in this._dropHandlers){if(this._dropHandlers.hasOwnProperty(n)){console.debug(n,this._dropHandlers[n]);o.off(n,this._dropHandlers[n])}}this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(n){n.preventDefault();n.stopPropagation()},dragleave:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(p){p.preventDefault();p.dataTransfer.dropEffect="move";var n=this,q=p.dataTransfer.getData("text");try{q=JSON.parse(q)}catch(o){this.warn("error parsing JSON from drop:",q)}this.trigger("droptarget:drop",p,q,n);return false},dataDropped:function(o){var n=this;if(_.isObject(o)&&o.model_class==="HistoryDatasetAssociation"&&o.id){return n.model.contents.copy(o.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:g}}); \ No newline at end of file diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/base-mvc","utils/localization","ui/search-input"],function(e,g,m,c,a,n,h,b,p,f){var k=p.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(q){var r="expandedIds";this.save(r,_.extend(this.get(r),_.object([q.id],[q.get("id")])))},removeExpanded:function(q){var r="expandedIds";this.save(r,_.omit(this.get(r),q.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});k.storageKeyPrefix="history:";k.historyStorageKey=function i(q){if(!q){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+q)}return(k.storageKeyPrefix+q)};k.get=function d(q){return new k({id:k.historyStorageKey(q)})};k.clearAll=function j(r){for(var q in sessionStorage){if(q.indexOf(k.storageKeyPrefix)===0){sessionStorage.removeItem(q)}}};var o=e.ModelListPanel;var l=o.extend({HDAViewClass:c.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:m.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:o.prototype.className+" history-panel",emptyMsg:f("This history is empty"),noneFoundMsg:f("No matching datasets found"),searchPlaceholder:f("search datasets"),initialize:function(q){o.prototype.initialize.call(this,q);this.linkTarget=q.linkTarget||"_blank"},freeModel:function(){o.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){o.prototype._setUpListeners.call(this);this.on("error",function(r,u,q,t,s){this.errorHandler(r,u,q,t,s)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(t,s,r,u){this.info("loadHistoryWithDetails:",t,s,r,u);var q=function(v){return _.values(k.get(v.id).get("expandedIds"))};return this.loadHistory(t,s,r,u,q)},loadHistory:function(u,t,s,v,q){this.info("loadHistory:",u,t,s,v,q);var r=this;t=t||{};r.trigger("loading",r);var w=g.History.getHistoryData(u,{historyFn:s,contentsFn:v,detailIdsFn:t.initiallyExpanded||q});return r._loadHistoryFromXHR(w,t).fail(function(z,x,y){r.trigger("error",r,z,t,f("An error was encountered while "+x),{historyId:u,history:y||{}})}).always(function(){r.trigger("loading-done",r)})},_loadHistoryFromXHR:function(s,r){var q=this;s.then(function(t,u){q.JSONToModel(t,u,r);q.render()});s.fail(function(u,t){q.render()});return s},refreshContents:function(r,q){if(this.model){return this.model.refresh(r,q)}return $.when()},JSONToModel:function(t,q,r){this.log("JSONToModel:",t,q,r);r=r||{};var s=new g.History(t,q,r);this.setModel(s);return s},setModel:function(r,q){q=q||{};o.prototype.setModel.call(this,r,q);if(this.model){this._setUpWebStorage(q.initiallyExpanded,q.show_deleted,q.show_hidden)}},_setUpWebStorage:function(r,q,s){if(this.storage){this.stopListening(this.storage)}this.storage=new k({id:k.historyStorageKey(this.model.get("id"))});if(_.isObject(r)){this.storage.set("expandedIds",r)}if(_.isBoolean(q)){this.storage.set("show_deleted",q)}if(_.isBoolean(s)){this.storage.set("show_hidden",s)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(t,u){this.showDeleted=u},"change:show_hidden":function(t,u){this.showHidden=u}},this);this.showDeleted=(q!==undefined)?q:this.storage.get("show_deleted");this.showHidden=(s!==undefined)?s:this.storage.get("show_hidden");return this},_buildNewRender:function(){var q=o.prototype._buildNewRender.call(this);if(this.multiselectActions.length){q.find(".controls .actions").prepend(this._renderSelectButton())}return q},_renderSelectButton:function(q){return b({title:f("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(q){var r=q.get("history_content_type");switch(r){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+r)},_filterItem:function(r){var q=this;return(o.prototype._filterItem.call(q,r)&&(!r.hidden()||q.showHidden)&&(!r.isDeletedOrPurged()||q.showDeleted))},_getItemViewOptions:function(r){var q=o.prototype._getItemViewOptions.call(this,r);return _.extend(q,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[r.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(r){var q=this;o.prototype._setUpItemViewListeners.call(q,r);r.on("expanded",function(s){q.storage.addExpanded(s.model)});r.on("collapsed",function(s){q.storage.removeExpanded(s.model)});return this},getSelectedModels:function(){var q=o.prototype.getSelectedModels.call(this);q.historyId=this.collection.historyId;return q},events:_.extend(_.clone(o.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(q,r){q=(q!==undefined)?(q):(!this.showDeleted);r=(r!==undefined)?(r):(true);this.showDeleted=q;if(r){this.storage.set("show_deleted",q)}this.trigger("show-hidden",q);this.renderItems();return this.showDeleted},toggleShowHidden:function(q,r){q=(q!==undefined)?(q):(!this.showHidden);r=(r!==undefined)?(r):(true);this.showHidden=q;if(r){this.storage.set("show_hidden",q)}this.trigger("show-hidden",q);this.renderItems();return this.showHidden},_firstSearch:function(q){var r=this,s=".history-search-input";this.log("onFirstSearch",q);if(r.model.contents.haveDetails()){r.searchItems(q);return}r.$el.find(s).searchInput("toggle-loading");r.model.contents.fetchAllDetails({silent:true}).always(function(){r.$el.find(s).searchInput("toggle-loading")}).done(function(){r.searchItems(q)})},errorHandler:function(s,v,r,u,t){this.error(s,v,r,u,t);if(v&&v.status===0&&v.readyState===0){}else{if(v&&v.status===502){}else{var q=this._parseErrorMessage(s,v,r,u,t);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",q.message,q.details)})}else{this.displayMessage("error",q.message,q.details)}}}},_parseErrorMessage:function(u,x,y,s,q,v){var t=Galaxy.currUser,w={message:this._bePolite(s),details:{message:s,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(x)?(_.omit(y,"xhr")):(y),xhr:x,source:(_.isFunction(u.toJSON))?(u.toJSON()):(u+""),user:(t instanceof h.User)?(t.toJSON()):(t+"")}};_.extend(w.details,q||{});if(x&&_.isFunction(x.getAllResponseHeaders)){var r=x.getAllResponseHeaders();r=_.compact(r.split("\n"));r=_.map(r,function(z){return z.split(": ")});w.details.xhr.responseHeaders=_.object(r)}return w},_bePolite:function(q){q=q||f("An error occurred while getting updates from the server");return q+". "+f("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(v,w,u){var s=this;this.scrollToTop();var t=this.$messages(),q=$("<div/>").addClass(v+"message").html(w);if(!_.isEmpty(u)){var r=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(s._messageToModalOptions(v,w,u));return false});q.append(" ",r)}return t.html(q)},_messageToModalOptions:function(t,w,s){var q=this,r={title:"Details"};if(_.isObject(s)){s=_.omit(s,_.functions(s));var v=JSON.stringify(s,null," "),u=$("<pre/>").text(v);r.body=$("<div/>").append(u)}else{r.body=$("<div/>").html(s)}r.buttons={Ok:function(){Galaxy.modal.hide();q.clearMessages()}};return r},clearMessages:function(q){$(q.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(q){return this.scrollToItem(_.first(this.viewsWhereModel({hid:q})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});l.prototype.templates=(function(){var q=p.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',f("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',f("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',f("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',f("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(o.prototype.templates),{controls:q})}());return{HistoryPanel:l}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/ui/popup-menu","mvc/base-mvc","utils/localization","ui/search-input"],function(f,h,n,d,b,o,i,c,a,q,g){var l=q.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(r){var s="expandedIds";this.save(s,_.extend(this.get(s),_.object([r.id],[r.get("id")])))},removeExpanded:function(r){var s="expandedIds";this.save(s,_.omit(this.get(s),r.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});l.storageKeyPrefix="history:";l.historyStorageKey=function j(r){if(!r){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+r)}return(l.storageKeyPrefix+r)};l.get=function e(r){return new l({id:l.historyStorageKey(r)})};l.clearAll=function k(s){for(var r in sessionStorage){if(r.indexOf(l.storageKeyPrefix)===0){sessionStorage.removeItem(r)}}};var p=f.ModelListPanel;var m=p.extend({HDAViewClass:d.HDAListItemView,HDCAViewClass:b.HDCAListItemView,collectionClass:n.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:p.prototype.className+" history-panel",emptyMsg:g("This history is empty"),noneFoundMsg:g("No matching datasets found"),searchPlaceholder:g("search datasets"),initialize:function(r){p.prototype.initialize.call(this,r);this.linkTarget=r.linkTarget||"_blank"},freeModel:function(){p.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){p.prototype._setUpListeners.call(this);this.on("error",function(s,v,r,u,t){this.errorHandler(s,v,r,u,t)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(u,t,s,v){this.info("loadHistoryWithDetails:",u,t,s,v);var r=function(w){return _.values(l.get(w.id).get("expandedIds"))};return this.loadHistory(u,t,s,v,r)},loadHistory:function(v,u,t,w,r){this.info("loadHistory:",v,u,t,w,r);var s=this;u=u||{};s.trigger("loading",s);var x=h.History.getHistoryData(v,{historyFn:t,contentsFn:w,detailIdsFn:u.initiallyExpanded||r});return s._loadHistoryFromXHR(x,u).fail(function(A,y,z){s.trigger("error",s,A,u,g("An error was encountered while "+y),{historyId:v,history:z||{}})}).always(function(){s.trigger("loading-done",s)})},_loadHistoryFromXHR:function(t,s){var r=this;t.then(function(u,v){r.JSONToModel(u,v,s);r.render()});t.fail(function(v,u){r.render()});return t},refreshContents:function(s,r){if(this.model){return this.model.refresh(s,r)}return $.when()},JSONToModel:function(u,r,s){this.log("JSONToModel:",u,r,s);s=s||{};var t=new h.History(u,r,s);this.setModel(t);return t},setModel:function(s,r){r=r||{};p.prototype.setModel.call(this,s,r);if(this.model){this._setUpWebStorage(r.initiallyExpanded,r.show_deleted,r.show_hidden)}},_setUpWebStorage:function(s,r,t){if(this.storage){this.stopListening(this.storage)}this.storage=new l({id:l.historyStorageKey(this.model.get("id"))});if(_.isObject(s)){this.storage.set("expandedIds",s)}if(_.isBoolean(r)){this.storage.set("show_deleted",r)}if(_.isBoolean(t)){this.storage.set("show_hidden",t)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(u,v){this.showDeleted=v},"change:show_hidden":function(u,v){this.showHidden=v}},this);this.showDeleted=(r!==undefined)?r:this.storage.get("show_deleted");this.showHidden=(t!==undefined)?t:this.storage.get("show_hidden");return this},_buildNewRender:function(){var r=p.prototype._buildNewRender.call(this);if(this.multiselectActions().length){r.find(".controls .actions").prepend(this._renderSelectButton())}return r},_renderSelectButton:function(r){return c({title:g("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(r){var s=r.get("history_content_type");switch(s){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+s)},_filterItem:function(s){var r=this;return(p.prototype._filterItem.call(r,s)&&(!s.hidden()||r.showHidden)&&(!s.isDeletedOrPurged()||r.showDeleted))},_getItemViewOptions:function(s){var r=p.prototype._getItemViewOptions.call(this,s);return _.extend(r,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[s.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(s){var r=this;p.prototype._setUpItemViewListeners.call(r,s);s.on("expanded",function(t){r.storage.addExpanded(t.model)});s.on("collapsed",function(t){r.storage.removeExpanded(t.model)});return this},getSelectedModels:function(){var r=p.prototype.getSelectedModels.call(this);r.historyId=this.collection.historyId;return r},events:_.extend(_.clone(p.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(r,s){r=(r!==undefined)?(r):(!this.showDeleted);s=(s!==undefined)?(s):(true);this.showDeleted=r;if(s){this.storage.set("show_deleted",r)}this.trigger("show-hidden",r);this.renderItems();return this.showDeleted},toggleShowHidden:function(r,s){r=(r!==undefined)?(r):(!this.showHidden);s=(s!==undefined)?(s):(true);this.showHidden=r;if(s){this.storage.set("show_hidden",r)}this.trigger("show-hidden",r);this.renderItems();return this.showHidden},_firstSearch:function(r){var s=this,t=".history-search-input";this.log("onFirstSearch",r);if(s.model.contents.haveDetails()){s.searchItems(r);return}s.$el.find(t).searchInput("toggle-loading");s.model.contents.fetchAllDetails({silent:true}).always(function(){s.$el.find(t).searchInput("toggle-loading")}).done(function(){s.searchItems(r)})},errorHandler:function(t,w,s,v,u){this.error(t,w,s,v,u);if(w&&w.status===0&&w.readyState===0){}else{if(w&&w.status===502){}else{var r=this._parseErrorMessage(t,w,s,v,u);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",r.message,r.details)})}else{this.displayMessage("error",r.message,r.details)}}}},_parseErrorMessage:function(v,y,z,t,r,w){var u=Galaxy.currUser,x={message:this._bePolite(t),details:{message:t,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(y)?(_.omit(z,"xhr")):(z),xhr:y,source:(_.isFunction(v.toJSON))?(v.toJSON()):(v+""),user:(u instanceof i.User)?(u.toJSON()):(u+"")}};_.extend(x.details,r||{});if(y&&_.isFunction(y.getAllResponseHeaders)){var s=y.getAllResponseHeaders();s=_.compact(s.split("\n"));s=_.map(s,function(A){return A.split(": ")});x.details.xhr.responseHeaders=_.object(s)}return x},_bePolite:function(r){r=r||g("An error occurred while getting updates from the server");return r+". "+g("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(w,x,v){var t=this;this.scrollToTop();var u=this.$messages(),r=$("<div/>").addClass(w+"message").html(x);if(!_.isEmpty(v)){var s=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(t._messageToModalOptions(w,x,v));return false});r.append(" ",s)}return u.html(r)},_messageToModalOptions:function(u,x,t){var r=this,s={title:"Details"};if(_.isObject(t)){t=_.omit(t,_.functions(t));var w=JSON.stringify(t,null," "),v=$("<pre/>").text(w);s.body=$("<div/>").append(v)}else{s.body=$("<div/>").html(t)}s.buttons={Ok:function(){Galaxy.modal.hide();r.clearMessages()}};return s},clearMessages:function(r){$(r.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(r){return this.scrollToItem(_.first(this.viewsWhereModel({hid:r})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});m.prototype.templates=(function(){var r=q.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',g("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',g("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"],"history");return _.extend(_.clone(p.prototype.templates),{controls:r})}());return{HistoryPanel:m}}); \ No newline at end of file diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.purgeAllowed=!_.isUndefined(C.purgeAllowed)?C.purgeAllowed:false;this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:C,view:this}),this.controlsRightTemplate({history:C,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted change:purged":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")||D.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(D){var E=this,C={HistoryDatasetAssociation:"hda",HistoryDatasetCollectionAssociation:"hdca"};E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return((_.isObject(K)&&K.id)&&(_.contains(_.keys(C),K.model_class)))});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){var L=C[K.model_class];F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id,L)}})});F.start();F.done(function(K){G.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.purgeAllowed=!_.isUndefined(C.purgeAllowed)?C.purgeAllowed:false;this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:C,view:this}),this.controlsRightTemplate({history:C,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted change:purged":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")||D.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return F.model.contents.isCopyable(J)});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(d,f,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(g,h){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this.fxSpeed=_.has(g,"fxSpeed")?(g.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=g.searchFor||"";this.indicator=new f(this.$el);this.selecting=(g.selecting!==undefined)?g.selecting:true;this.selected=g.selected||[];this.lastSelected=null;this.dragItems=g.dragItems||false;this.viewClass=g.viewClass||this.viewClass;this.views=[];this.collection=g.collection||(new this.collectionClass([]));this.filters=g.filters||[];this.$scrollContainer=g.$scrollContainer||this.$scrollContainer;this.title=g.title||"";this.subtitle=g.subtitle||"";this.multiselectActions=g.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(g){g.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(h,k,g,j,i){console.error(h,k,g,j,i)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(h,k,g,j,i){this.trigger("error",h,k,g,j,i)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(g){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(g,h){if(h&&h.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);if(i){this.selectRange(g,i)}}else{if(h&&h.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(g.model.id);this.lastSelected=g.model.id},this);this.on("view:de-selected",function(g,h){this.selected=_.without(this.selected,g.model.id)},this)},render:function(h){this.log(this+".render",h);var g=this._buildNewRender();this._setUpBehaviors(g);this._queueNewRender(g,h);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var g=$(this.templates.el({},this));this._renderControls(g);this._renderTitle(g);this._renderSubtitle(g);this._renderSearch(g);this.renderItems(g);return g},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var g=$(this.templates.controls({},this));h.find(".controls").replaceWith(g);return g},_renderTitle:function(g){},_renderSubtitle:function(g){},_queueNewRender:function(h,i){i=(i===undefined)?(this.fxSpeed):(i);var g=this;g.log("_queueNewRender:",h,i);$(g).queue("fx",[function(j){this.$el.fadeOut(i,j)},function(j){g._swapNewRender(h);j()},function(j){this.$el.fadeIn(i,j)},function(j){g.trigger("rendered",g);j()}])},_swapNewRender:function(g){this.$el.empty().attr("class",this.className).append(g.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(g){g=g||this.$el;g.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(g){return(g||this.$el).find("> .list-items")},$messages:function(g){return(g||this.$el).find("> .controls .messages")},$emptyMessage:function(g){return(g||this.$el).find("> .empty-message")},renderItems:function(i){i=i||this.$el;var g=this;g.log(this+".renderItems",i);var h=g.$list(i);g.views=g._filterCollection().map(function(j){return g._createItemView(j).render(0)});h.empty();if(g.views.length){g._attachItems(i);g.$emptyMessage(i).hide()}else{g._renderEmptyMessage(i).show()}return g.views},_filterCollection:function(){var g=this;return g.collection.filter(_.bind(g._filterItem,g))},_filterItem:function(h){var g=this;return(_.every(g.filters.map(function(i){return i.call(h)})))&&(!g.searchFor||h.matchesAll(g.searchFor))},_createItemView:function(i){var j=this._getItemViewClass(i),h=_.extend(this._getItemViewOptions(i),{model:i}),g=new j(h);this._setUpItemViewListeners(g);return g},_getItemViewClass:function(g){return this.viewClass},_getItemViewOptions:function(g){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,g.id),draggable:this.dragItems}},_setUpItemViewListeners:function(h){var g=this;h.on("all",function(){var i=Array.prototype.slice.call(arguments,0);i[0]="view:"+i[0];g.trigger.apply(g,i)});h.on("draggable:dragstart",function(l,i){var j={},k=this.getSelectedModels();if(k.length){j=k.toJSON()}else{j=[i.model.toJSON()]}l.dataTransfer.setData("text",JSON.stringify(j))},this);return g},_attachItems:function(g){this.$list(g).append(this.views.map(function(h){return h.$el}));return this},_renderEmptyMessage:function(g){this.debug("_renderEmptyMessage",g,this.searchFor);var h=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(g).text(h)},expandAll:function(){_.each(this.views,function(g){g.expand()})},collapseAll:function(){_.each(this.views,function(g){g.collapse()})},addItemView:function(j,k,i){this.log(this+".addItemView:",j);var h=this;if(!h._filterItem(j)){return undefined}var g=h._createItemView(j);$(g).queue("fx",[function(l){h.$emptyMessage().fadeOut(h.fxSpeed,l)},function(l){h._attachView(g);l()}]);return g},_attachView:function(h){var g=this;g.views.push(h);g.$list().append(h.render(0).$el.hide());g.trigger("view:attached",h);h.$el.slideDown(g.fxSpeed,function(){g.trigger("view:attached:rendered")})},removeItemView:function(j,k,i){this.log(this+".removeItemView:",j);var h=this,g=h.viewFromModel(j);if(!g){return undefined}h.views=_.without(h.views,g);h.trigger("view:removed",g);$({}).queue("fx",[function(l){g.$el.fadeOut(h.fxSpeed,l)},function(l){g.remove();h.trigger("view:removed:rendered");if(!h.views.length){h._renderEmptyMessage().fadeIn(h.fxSpeed,l)}else{l()}}]);return g},viewFromModelId:function(h){for(var g=0;g<this.views.length;g++){if(this.views[g].model.id===h){return this.views[g]}}return undefined},viewFromModel:function(g){if(!g){return undefined}return this.viewFromModelId(g.id)},viewsWhereModel:function(g){return this.views.filter(function(h){var j=h.model.toJSON();for(var i in g){if(g.hasOwnProperty(i)){if(j[i]!==h.model.get(i)){return false}}}return true})},viewRange:function(j,i){if(j===i){return(j)?([j]):([])}var h=this.views.indexOf(j),g=this.views.indexOf(i);if(h===-1||g===-1){if(h===g){return[]}return(h===-1)?([i]):([j])}return(h<g)?this.views.slice(h,g+1):this.views.slice(g,h+1)},_renderSearch:function(g){g.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return g},_firstSearch:function(g){this.log("onFirstSearch",g);return this.searchItems(g)},searchItems:function(g){this.searchFor=g;this.trigger("search:searching",g,this);this.renderItems();this.$("> .controls .search-query").val(g);return this},clearSearch:function(g){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(g);_.each(this.views,function(h){h.showSelector(g)})},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(g);_.each(this.views,function(h){h.hideSelector(g)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(g){_.each(this.views,function(h){h.select(g)})},deselectAll:function(g){this.lastSelected=null;_.each(this.views,function(h){h.deselect(g)})},selectRange:function(i,h){var g=this.viewRange(i,h);_.each(g,function(j){j.select()});return g},getSelectedViews:function(){return _.filter(this.views,function(g){return g.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(g){return g.model}))},_showLoadingIndicator:function(h,g,i){this.debug("_showLoadingIndicator",this.indicator,h,g,i);g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new f(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},_hideLoadingIndicator:function(g,h){this.debug("_hideLoadingIndicator",this.indicator,g,h);g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(h,g){g=g||0;this.$scrollContainer().animate({scrollTop:h},g);return this},scrollToTop:function(g){return this.scrollTo(0,g)},scrollToItem:function(g,i){if(!g){return this}var h=g.$el.position().top;return this.scrollTo(h,i)},scrollToId:function(h,g){return this.scrollToItem(this.viewFromModelId(h),g)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var h=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:h,controls:g}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(g){e.prototype.initialize.call(this,g);this.selecting=(g.selecting!==undefined)?g.selecting:false;this.setModel(this.model,g)},setModel:function(h,g){g=g||{};this.debug(this+".setModel:",h,g);this.freeModel();this.freeViews();if(h){var i=this.model?this.model.get("id"):null;this.model=h;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(g.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(i&&h.get("id")!==i){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){var g=Array.prototype.slice.call(arguments,0);g.unshift("error");this.trigger.apply(this,g)},this);return this},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var i=this.model?this.model.toJSON():{},g=$(this.templates.controls(i,this));h.find(".controls").replaceWith(g);return g},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:g})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(d,f,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),initialize:function(g,h){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this.fxSpeed=_.has(g,"fxSpeed")?(g.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=g.searchFor||"";this.indicator=new f(this.$el);this.selecting=(g.selecting!==undefined)?g.selecting:true;this.selected=g.selected||[];this.lastSelected=null;this.dragItems=g.dragItems||false;this.viewClass=g.viewClass||this.viewClass;this.views=[];this.collection=g.collection||(new this.collectionClass([]));this.filters=g.filters||[];this.$scrollContainer=g.$scrollContainer||this.$scrollContainer;this.title=g.title||"";this.subtitle=g.subtitle||"";this._setUpListeners()},freeViews:function(){_.each(this.views,function(g){g.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(h,k,g,j,i){console.error(h,k,g,j,i)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(h,k,g,j,i){this.trigger("error",h,k,g,j,i)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(g){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(g,h){if(h&&h.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);if(i){this.selectRange(g,i)}}else{if(h&&h.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(g.model.id);this.lastSelected=g.model.id},this);this.on("view:de-selected",function(g,h){this.selected=_.without(this.selected,g.model.id)},this)},render:function(h){this.log(this+".render",h);var g=this._buildNewRender();this._setUpBehaviors(g);this._queueNewRender(g,h);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var g=$(this.templates.el({},this));this._renderControls(g);this._renderTitle(g);this._renderSubtitle(g);this._renderSearch(g);this.renderItems(g);return g},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var g=$(this.templates.controls({},this));h.find(".controls").replaceWith(g);return g},_renderTitle:function(g){},_renderSubtitle:function(g){},_queueNewRender:function(h,i){i=(i===undefined)?(this.fxSpeed):(i);var g=this;g.log("_queueNewRender:",h,i);$(g).queue("fx",[function(j){this.$el.fadeOut(i,j)},function(j){g._swapNewRender(h);j()},function(j){this.$el.fadeIn(i,j)},function(j){g.trigger("rendered",g);j()}])},_swapNewRender:function(g){this.$el.empty().attr("class",this.className).append(g.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(g){g=g||this.$el;g.find(".controls [title]").tooltip({placement:"bottom"});this._renderMultiselectActionMenu(g);return this},_renderMultiselectActionMenu:function(g){g=g||this.$el;var h=g.find(".list-action-menu"),k=this.multiselectActions();if(!k.length){return h.empty()}var j=$(['<div class="list-action-menu btn-group">','<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">',c("For all selected"),"...","</button>",'<ul class="dropdown-menu pull-right" role="menu">',"</ul>","</div>"].join(""));var i=k.map(function(m){var l=['<li><a href="javascript:void(0);">',m.html,"</a></li>"].join("");return $(l).click(m.func)});j.find("ul").append(i);h.replaceWith(j);return j},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(g){return(g||this.$el).find("> .list-items")},$messages:function(g){return(g||this.$el).find("> .controls .messages")},$emptyMessage:function(g){return(g||this.$el).find("> .empty-message")},renderItems:function(i){i=i||this.$el;var g=this;g.log(this+".renderItems",i);var h=g.$list(i);g.views=g._filterCollection().map(function(j){return g._createItemView(j).render(0)});h.empty();if(g.views.length){g._attachItems(i);g.$emptyMessage(i).hide()}else{g._renderEmptyMessage(i).show()}return g.views},_filterCollection:function(){var g=this;return g.collection.filter(_.bind(g._filterItem,g))},_filterItem:function(h){var g=this;return(_.every(g.filters.map(function(i){return i.call(h)})))&&(!g.searchFor||h.matchesAll(g.searchFor))},_createItemView:function(i){var j=this._getItemViewClass(i),h=_.extend(this._getItemViewOptions(i),{model:i}),g=new j(h);this._setUpItemViewListeners(g);return g},_getItemViewClass:function(g){return this.viewClass},_getItemViewOptions:function(g){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,g.id),draggable:this.dragItems}},_setUpItemViewListeners:function(h){var g=this;h.on("all",function(){var i=Array.prototype.slice.call(arguments,0);i[0]="view:"+i[0];g.trigger.apply(g,i)});h.on("draggable:dragstart",function(l,i){var j={},k=this.getSelectedModels();if(k.length){j=k.toJSON()}else{j=[i.model.toJSON()]}l.dataTransfer.setData("text",JSON.stringify(j))},this);return g},_attachItems:function(g){this.$list(g).append(this.views.map(function(h){return h.$el}));return this},_renderEmptyMessage:function(g){this.debug("_renderEmptyMessage",g,this.searchFor);var h=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(g).text(h)},expandAll:function(){_.each(this.views,function(g){g.expand()})},collapseAll:function(){_.each(this.views,function(g){g.collapse()})},addItemView:function(j,k,i){this.log(this+".addItemView:",j);var h=this;if(!h._filterItem(j)){return undefined}var g=h._createItemView(j);$(g).queue("fx",[function(l){h.$emptyMessage().fadeOut(h.fxSpeed,l)},function(l){h._attachView(g);l()}]);return g},_attachView:function(h){var g=this;g.views.push(h);g.$list().append(h.render(0).$el.hide());g.trigger("view:attached",h);h.$el.slideDown(g.fxSpeed,function(){g.trigger("view:attached:rendered")})},removeItemView:function(j,k,i){this.log(this+".removeItemView:",j);var h=this,g=h.viewFromModel(j);if(!g){return undefined}h.views=_.without(h.views,g);h.trigger("view:removed",g);$({}).queue("fx",[function(l){g.$el.fadeOut(h.fxSpeed,l)},function(l){g.remove();h.trigger("view:removed:rendered");if(!h.views.length){h._renderEmptyMessage().fadeIn(h.fxSpeed,l)}else{l()}}]);return g},viewFromModelId:function(h){for(var g=0;g<this.views.length;g++){if(this.views[g].model.id===h){return this.views[g]}}return undefined},viewFromModel:function(g){if(!g){return undefined}return this.viewFromModelId(g.id)},viewsWhereModel:function(g){return this.views.filter(function(h){var j=h.model.toJSON();for(var i in g){if(g.hasOwnProperty(i)){if(j[i]!==h.model.get(i)){return false}}}return true})},viewRange:function(j,i){if(j===i){return(j)?([j]):([])}var h=this.views.indexOf(j),g=this.views.indexOf(i);if(h===-1||g===-1){if(h===g){return[]}return(h===-1)?([i]):([j])}return(h<g)?this.views.slice(h,g+1):this.views.slice(g,h+1)},_renderSearch:function(g){g.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return g},_firstSearch:function(g){this.log("onFirstSearch",g);return this.searchItems(g)},searchItems:function(g){this.searchFor=g;this.trigger("search:searching",g,this);this.renderItems();this.$("> .controls .search-query").val(g);return this},clearSearch:function(g){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(g);_.each(this.views,function(h){h.showSelector(g)})},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(g);_.each(this.views,function(h){h.hideSelector(g)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(g){_.each(this.views,function(h){h.select(g)})},deselectAll:function(g){this.lastSelected=null;_.each(this.views,function(h){h.deselect(g)})},selectRange:function(i,h){var g=this.viewRange(i,h);_.each(g,function(j){j.select()});return g},getSelectedViews:function(){return _.filter(this.views,function(g){return g.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(g){return g.model}))},_showLoadingIndicator:function(h,g,i){this.debug("_showLoadingIndicator",this.indicator,h,g,i);g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new f(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},_hideLoadingIndicator:function(g,h){this.debug("_hideLoadingIndicator",this.indicator,g,h);g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(h,g){g=g||0;this.$scrollContainer().animate({scrollTop:h},g);return this},scrollToTop:function(g){return this.scrollTo(0,g)},scrollToItem:function(g,i){if(!g){return this}var h=g.$el.position().top;return this.scrollTo(h,i)},scrollToId:function(h,g){return this.scrollToItem(this.viewFromModelId(h),g)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var h=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return{el:h,controls:g}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(g){e.prototype.initialize.call(this,g);this.selecting=(g.selecting!==undefined)?g.selecting:false;this.setModel(this.model,g)},setModel:function(h,g){g=g||{};this.debug(this+".setModel:",h,g);this.freeModel();this.freeViews();if(h){var i=this.model?this.model.get("id"):null;this.model=h;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(g.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(i&&h.get("id")!==i){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){var g=Array.prototype.slice.call(arguments,0);g.unshift("error");this.trigger.apply(this,g)},this);return this},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var i=this.model?this.model.toJSON():{},g=$(this.templates.controls(i,this));h.find(".controls").replaceWith(g);return g},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:g})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2007,7 +2007,8 @@ .list-panel .controls .list-actions:after{clear:both} .list-panel .controls .list-actions:before,.list-panel .controls .list-actions:after{content:" ";display:table;} .list-panel .controls .list-actions:after{clear:both} -.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%} +.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%;z-index:inherit} +.list-panel .controls .list-actions .list-action-menu{float:right}.list-panel .controls .list-actions .list-action-menu .dropdown-menu{z-index:inherit} .list-panel .list-items .list-item:not(:last-child){border-bottom-width:0px} .list-panel .empty-message{display:none;margin:0px} .list-item .details .list-panel{margin-top:8px;border-radius:3px;background:white;padding:4px}.list-item .details .list-panel .list-items{border:1px solid #bfbfbf;border-radius:3px}.list-item .details .list-panel .list-items .list-item:first-child{border-top-width:0px;border-radius:3px 3px 0px 0px} @@ -2078,7 +2079,6 @@ .history-panel .controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto} .history-panel .controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} .history-panel .controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%} -.history-panel .controls .list-actions .list-action-popup-btn{float:right} .history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-message{margin:0px 10px 0px 10px} .history-panel .dataset-collection .subtitle{margin-top:2px} diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -449,12 +449,6 @@ width: 100%; } } - - .list-actions { - .list-action-popup-btn { - float: right; - } - } } // display only a top border on all diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -167,6 +167,13 @@ padding-top: 2px; padding-bottom: 2px; font-size: 90%; + z-index: inherit; + } + .list-action-menu { + float: right; + .dropdown-menu { + z-index: inherit; + } } } } diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 templates/webapps/galaxy/history/view_multiple.mako --- a/templates/webapps/galaxy/history/view_multiple.mako +++ b/templates/webapps/galaxy/history/view_multiple.mako @@ -43,7 +43,6 @@ multipanel = new MULTI_PANEL.MultiPanelColumns({ el : $( '#center' ).get(0), histories : histories, - //historiesJSON : historiesJSON, order : bootstrapped.order, currentHistoryId : '${current_history_id}' }).render( 0 ); https://bitbucket.org/galaxy/galaxy-central/commits/316080b22578/ Changeset: 316080b22578 User: carlfeberhard Date: 2015-02-17 14:54:52+00:00 Summary: merge Affected #: 19 files diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 client/galaxy/scripts/mvc/history/history-contents.js --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -25,7 +25,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -185,16 +184,36 @@ return deferred; }, + isCopyable : function( contentsJSON ){ + var copyableModelClasses = [ + 'HistoryDatasetAssociation', + 'HistoryDatasetCollectionAssociation' + ]; + return ( ( _.isObject( contentsJSON ) && contentsJSON.id ) + && ( _.contains( copyableModelClasses, contentsJSON.model_class ) ) ); + }, + /** copy an existing, accessible hda into this collection */ - copy : function( id, contentType ){ - contentType = contentType || 'hda'; - var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), - collection = this; - - var xhr = jQuery.post( this.url(), { - type : type, + copy : function( json ){ + var id, type, contentType; + if( _.isString( json ) ){ + id = json; + contentType = 'hda'; + type = 'dataset'; + } else { + id = json.id; + contentType = ({ + 'HistoryDatasetAssociation' : 'hda', + 'LibraryDatasetDatasetAssociation' : 'ldda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + })[ json.model_class ] || 'hda'; + type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ); + } + var collection = this, + xhr = jQuery.post( this.url(), { + content : id, source : contentType, - content : id + type : type }) .done( function( json ){ collection.add([ json ]); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -69,8 +69,6 @@ /** is the panel currently showing the dataset selection controls? */ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - - this.multiselectActions = attributes.multiselectActions || this._getActions(); }, /** Override to handle history as drag-drop target */ @@ -210,11 +208,6 @@ _super.prototype._setUpBehaviors.call( this, $where ); if( !this.model ){ return; } - // set up the pupup for actions available when multi selecting - if( this.multiselectActions.length ){ - this.actionsPopup = new PopupMenu( $where.find( '.list-action-popup-btn' ), this.multiselectActions ); - } - // anon users shouldn't have access to any of the following if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) || ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){ @@ -245,7 +238,7 @@ /** return a new popup menu for choosing a multi selection action * ajax calls made for multiple datasets are queued */ - _getActions : function(){ + multiselectActions : function(){ var panel = this, actions = [ { html: _l( 'Hide datasets' ), func: function(){ diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 client/galaxy/scripts/mvc/history/history-panel.js --- a/client/galaxy/scripts/mvc/history/history-panel.js +++ b/client/galaxy/scripts/mvc/history/history-panel.js @@ -7,6 +7,7 @@ "mvc/collection/collection-panel", "mvc/user/user-model", "ui/fa-icon-button", + "mvc/ui/popup-menu", "mvc/base-mvc", "utils/localization", "ui/search-input" @@ -19,6 +20,7 @@ COLLECTION_PANEL, USER, faIconButton, + PopupMenu, BASE_MVC, _l ){ @@ -302,7 +304,8 @@ /** In this override, add a btn to toggle the selectors */ _buildNewRender : function(){ var $newRender = _super.prototype._buildNewRender.call( this ); - if( this.multiselectActions.length ){ + //if( this.views.length && this.multiselectActions().length ){ + if( this.multiselectActions().length ){ $newRender.find( '.controls .actions' ).prepend( this._renderSelectButton() ); } return $newRender; @@ -617,10 +620,18 @@ '<div class="actions"></div>', '<div class="messages">', - '<% if( history.deleted ){ %>', + '<% if( history.deleted && history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged and deleted' ), + '</div>', + '<% } else if( history.deleted ){ %>', '<div class="deleted-msg warningmessagesmall">', _l( 'This history has been deleted' ), '</div>', + '<% } else if( history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged' ), + '</div>', '<% } %>', '<% if( history.message ){ %>', @@ -646,8 +657,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - '<button class="list-action-popup-btn btn btn-default">', - _l( 'For all selected' ), '...</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ], 'history' ); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -353,8 +353,8 @@ '</a></li>', '<% } %>', '</ul>', - '<% } %>', - '</div>', + '</div>', + '<% } %>', '</div>' ].join( '' ), { variable: 'data' }), @@ -669,11 +669,7 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this, - modelClassToSource = { - 'HistoryDatasetAssociation' : 'hda', - 'HistoryDatasetCollectionAssociation' : 'hdca' - }; + var multipanel = this; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -691,20 +687,18 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ - //note: this will bad copy sources fail silently + //note: bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( ( _.isObject( json ) && json.id ) - && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); + return panel.model.contents.isCopyable( json ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); toCopy.forEach( function( content ){ - var contentType = modelClassToSource[ content.model_class ]; queue.add({ name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( content.id, contentType ); + return panel.model.contents.copy( content ); } }); }); @@ -714,7 +708,6 @@ }); } }); - }, /** conv. fn to count the columns in columnMap */ diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -46,9 +46,6 @@ /** string used for search placeholder */ searchPlaceholder : _l( 'search' ), - /** actions available for multiselected items */ - multiselectActions : [], - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the list @@ -103,11 +100,6 @@ this.title = attributes.title || ''; this.subtitle = attributes.subtitle || ''; - // allow override of multiselectActions through attributes - this.multiselectActions = attributes.multiselectActions || this.multiselectActions; - /** the popup displayed when 'for all selected...' is clicked */ - this.actionsPopup = null; - this._setUpListeners(); }, @@ -288,9 +280,45 @@ _setUpBehaviors : function( $where ){ $where = $where || this.$el; $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); + // set up the pupup for actions available when multi selecting + this._renderMultiselectActionMenu( $where ); return this; }, + /** render a menu containing the actions available to sets of selected items */ + _renderMultiselectActionMenu : function( $where ){ + $where = $where || this.$el; + var $menu = $where.find( '.list-action-menu' ), + actions = this.multiselectActions(); + if( !actions.length ){ + return $menu.empty(); + } + + var $newMenu = $([ + '<div class="list-action-menu btn-group">', + '<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'For all selected' ), '...', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', '</ul>', + '</div>' + ].join('')); + var $actions = actions.map( function( action ){ + var html = [ '<li><a href="javascript:void(0);">', action.html, '</a></li>' ].join( '' ); + return $( html ).click( action.func ); + }); + $newMenu.find( 'ul' ).append( $actions ); + $menu.replaceWith( $newMenu ); + return $newMenu; + }, + + /** return a list of plain objects used to render multiselect actions menu. Each object should have: + * html: an html string used as the anchor contents + * func: a function called when the anchor is clicked (passed the click event) + */ + multiselectActions : function(){ + return []; + }, + // ------------------------------------------------------------------------ sub-$element shortcuts /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ $scrollContainer : function(){ @@ -790,9 +818,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); @@ -929,9 +956,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -25,7 +25,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -185,16 +184,36 @@ return deferred; }, + isCopyable : function( contentsJSON ){ + var copyableModelClasses = [ + 'HistoryDatasetAssociation', + 'HistoryDatasetCollectionAssociation' + ]; + return ( ( _.isObject( contentsJSON ) && contentsJSON.id ) + && ( _.contains( copyableModelClasses, contentsJSON.model_class ) ) ); + }, + /** copy an existing, accessible hda into this collection */ - copy : function( id, contentType ){ - contentType = contentType || 'hda'; - var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), - collection = this; - - var xhr = jQuery.post( this.url(), { - type : type, + copy : function( json ){ + var id, type, contentType; + if( _.isString( json ) ){ + id = json; + contentType = 'hda'; + type = 'dataset'; + } else { + id = json.id; + contentType = ({ + 'HistoryDatasetAssociation' : 'hda', + 'LibraryDatasetDatasetAssociation' : 'ldda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + })[ json.model_class ] || 'hda'; + type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ); + } + var collection = this, + xhr = jQuery.post( this.url(), { + content : id, source : contentType, - content : id + type : type }) .done( function( json ){ collection.add([ json ]); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -69,8 +69,6 @@ /** is the panel currently showing the dataset selection controls? */ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - - this.multiselectActions = attributes.multiselectActions || this._getActions(); }, /** Override to handle history as drag-drop target */ @@ -210,11 +208,6 @@ _super.prototype._setUpBehaviors.call( this, $where ); if( !this.model ){ return; } - // set up the pupup for actions available when multi selecting - if( this.multiselectActions.length ){ - this.actionsPopup = new PopupMenu( $where.find( '.list-action-popup-btn' ), this.multiselectActions ); - } - // anon users shouldn't have access to any of the following if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) || ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){ @@ -245,7 +238,7 @@ /** return a new popup menu for choosing a multi selection action * ajax calls made for multiple datasets are queued */ - _getActions : function(){ + multiselectActions : function(){ var panel = this, actions = [ { html: _l( 'Hide datasets' ), func: function(){ diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -7,6 +7,7 @@ "mvc/collection/collection-panel", "mvc/user/user-model", "ui/fa-icon-button", + "mvc/ui/popup-menu", "mvc/base-mvc", "utils/localization", "ui/search-input" @@ -19,6 +20,7 @@ COLLECTION_PANEL, USER, faIconButton, + PopupMenu, BASE_MVC, _l ){ @@ -302,7 +304,8 @@ /** In this override, add a btn to toggle the selectors */ _buildNewRender : function(){ var $newRender = _super.prototype._buildNewRender.call( this ); - if( this.multiselectActions.length ){ + //if( this.views.length && this.multiselectActions().length ){ + if( this.multiselectActions().length ){ $newRender.find( '.controls .actions' ).prepend( this._renderSelectButton() ); } return $newRender; @@ -617,10 +620,18 @@ '<div class="actions"></div>', '<div class="messages">', - '<% if( history.deleted ){ %>', + '<% if( history.deleted && history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged and deleted' ), + '</div>', + '<% } else if( history.deleted ){ %>', '<div class="deleted-msg warningmessagesmall">', _l( 'This history has been deleted' ), '</div>', + '<% } else if( history.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This history has been purged' ), + '</div>', '<% } %>', '<% if( history.message ){ %>', @@ -646,8 +657,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - '<button class="list-action-popup-btn btn btn-default">', - _l( 'For all selected' ), '...</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ], 'history' ); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -353,8 +353,8 @@ '</a></li>', '<% } %>', '</ul>', - '<% } %>', - '</div>', + '</div>', + '<% } %>', '</div>' ].join( '' ), { variable: 'data' }), @@ -669,11 +669,7 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this, - modelClassToSource = { - 'HistoryDatasetAssociation' : 'hda', - 'HistoryDatasetCollectionAssociation' : 'hdca' - }; + var multipanel = this; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -691,20 +687,18 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ - //note: this will bad copy sources fail silently + //note: bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( ( _.isObject( json ) && json.id ) - && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); + return panel.model.contents.isCopyable( json ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); toCopy.forEach( function( content ){ - var contentType = modelClassToSource[ content.model_class ]; queue.add({ name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( content.id, contentType ); + return panel.model.contents.copy( content ); } }); }); @@ -714,7 +708,6 @@ }); } }); - }, /** conv. fn to count the columns in columnMap */ diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -46,9 +46,6 @@ /** string used for search placeholder */ searchPlaceholder : _l( 'search' ), - /** actions available for multiselected items */ - multiselectActions : [], - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the list @@ -103,11 +100,6 @@ this.title = attributes.title || ''; this.subtitle = attributes.subtitle || ''; - // allow override of multiselectActions through attributes - this.multiselectActions = attributes.multiselectActions || this.multiselectActions; - /** the popup displayed when 'for all selected...' is clicked */ - this.actionsPopup = null; - this._setUpListeners(); }, @@ -288,9 +280,45 @@ _setUpBehaviors : function( $where ){ $where = $where || this.$el; $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); + // set up the pupup for actions available when multi selecting + this._renderMultiselectActionMenu( $where ); return this; }, + /** render a menu containing the actions available to sets of selected items */ + _renderMultiselectActionMenu : function( $where ){ + $where = $where || this.$el; + var $menu = $where.find( '.list-action-menu' ), + actions = this.multiselectActions(); + if( !actions.length ){ + return $menu.empty(); + } + + var $newMenu = $([ + '<div class="list-action-menu btn-group">', + '<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'For all selected' ), '...', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', '</ul>', + '</div>' + ].join('')); + var $actions = actions.map( function( action ){ + var html = [ '<li><a href="javascript:void(0);">', action.html, '</a></li>' ].join( '' ); + return $( html ).click( action.func ); + }); + $newMenu.find( 'ul' ).append( $actions ); + $menu.replaceWith( $newMenu ); + return $newMenu; + }, + + /** return a list of plain objects used to render multiselect actions menu. Each object should have: + * html: an html string used as the anchor contents + * func: a function called when the anchor is clicked (passed the click event) + */ + multiselectActions : function(){ + return []; + }, + // ------------------------------------------------------------------------ sub-$element shortcuts /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ $scrollContainer : function(){ @@ -790,9 +818,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); @@ -929,9 +956,8 @@ '<button class="deselect-all btn btn-default"', 'data-mode="select">', _l( 'None' ), '</button>', '</div>', - //'<button class="list-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', + '<div class="list-action-menu btn-group">', + '</div>', '</div>', '</div>' ]); diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/packed/mvc/history/history-contents.js --- a/static/scripts/packed/mvc/history/history-contents.js +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},copy:function(l,k){k=k||"hda";var h=(k==="hdca"?"dataset_collection":"dataset"),j=this;var i=jQuery.post(this.url(),{type:h,source:k,content:l}).done(function(m){j.add([m])}).fail(function(n,m,o){j.trigger("error",j,i,{},"Error copying contents",{type:h,id:l,source:k})});return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file +define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},isCopyable:function(i){var h=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return((_.isObject(i)&&i.id)&&(_.contains(h,i.model_class)))},copy:function(h){var m,i,l;if(_.isString(h)){m=h;l="hda";i="dataset"}else{m=h.id;l=({HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"})[h.model_class]||"hda";i=(l==="hdca"?"dataset_collection":"dataset")}var k=this,j=jQuery.post(this.url(),{content:m,source:l,type:i}).done(function(n){k.add([n])}).fail(function(o,n,p){k.trigger("error",k,j,{},"Error copying contents",{type:i,id:m,source:l})});return j},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(h,j,m,f,e,i,l,c,b,a,d){var k=h.HistoryPanel;var g=k.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:i.HDCAListItemEdit,initialize:function(n){n=n||{};k.prototype.initialize.call(this,n);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=n.purgeAllowed||false;this.annotationEditorShown=n.annotationEditorShown||false;this.tagsEditorShown=n.tagsEditorShown||false;this.multiselectActions=n.multiselectActions||this._getActions()},_setUpListeners:function(){var n=this;k.prototype._setUpListeners.call(n);n.on("drop",function(o,p){n.dataDropped(p);n.dropTargetOff()});n.on("view:attached view:removed",function(){n._renderCounts()},n)},_setUpCollectionListeners:function(){k.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(n){this.model.fetch()},this);return this},_setUpModelListeners:function(){k.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var n=k.prototype._buildNewRender.call(this);if(!this.model){return n}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(n);this._renderAnnotation(n)}return n},renderItems:function(o){var n=k.prototype.renderItems.call(this,o);this._renderCounts(o);return n},_renderCounts:function(p){function o(s,t){return['<a class="',s,'" href="javascript:void(0);">',t,"</a>"].join("")}p=p||this.$el;var n=this.collection.where({deleted:true}),r=this.collection.where({visible:false}),q=[];if(this.views.length){q.push([this.views.length,d("shown")].join(" "))}if(n.length){q.push((!this.showDeleted)?([n.length,o("toggle-deleted-link",d("deleted"))].join(" ")):(o("toggle-deleted-link",d("hide deleted"))))}if(r.length){q.push((!this.showHidden)?([r.length,o("toggle-hidden-link",d("hidden"))].join(" ")):(o("toggle-hidden-link",d("hide hidden"))))}return p.find("> .controls .subtitle").html(q.join(", "))},_renderTags:function(n){var o=this;this.tagsEditor=new l.TagsEditor({model:this.model,el:n.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDATagEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDATagEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(n.find(".controls .actions"))})},_renderAnnotation:function(n){var o=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:n.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDAAnnotationEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDAAnnotationEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(n.find(".controls .actions"))})},_setUpBehaviors:function(n){n=n||this.$el;k.prototype._setUpBehaviors.call(this,n);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new a(n.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var o=this,p=".controls .name";n.find(p).attr("title",d("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(q){var r=o.model.get("name");if(q&&q!==r){o.$el.find(p).text(q);o.model.save({name:q}).fail(function(){o.$el.find(p).text(o.model.previous("name"))})}else{o.$el.find(p).text(r)}}})},_getActions:function(){var n=this,o=[{html:d("Hide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.hide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Unhide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.unhide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Delete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype["delete"];n.getSelectedModels().ajaxQueue(p)}},{html:d("Undelete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.undelete;n.getSelectedModels().ajaxQueue(p)}}];if(n.purgeAllowed){o.push({html:d("Permanently delete datasets"),func:function(){if(confirm(d("This will permanently remove the data in your datasets. Are you sure?"))){var p=f.HistoryDatasetAssociation.prototype.purge;n.getSelectedModels().ajaxQueue(p)}}})}o.push({html:d("Build Dataset List"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"list")}});o.push({html:d("Build Dataset Pair"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"paired")}});o.push({html:d("Build List of Dataset Pairs"),func:_.bind(n._showPairedCollectionModal,n)});return o},_showPairedCollectionModal:function(){var n=this,o=n.getSelectedModels().toJSON().filter(function(p){return p.history_content_type==="dataset"&&p.state===m.OK});if(o.length){require(["mvc/collection/paired-collection-creator"],function(p){window.creator=p.pairedCollectionCreatorModal(o,{historyId:n.model.id})})}else{Galaxy.modal.show({title:d("No valid datasets were selected"),body:d(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:true})}},_attachItems:function(n){this.$list(n).append(this.views.reverse().map(function(o){return o.$el}));return this},_attachView:function(o){var n=this;n.views.unshift(o);n.$list().prepend(o.render(0).$el.hide());n.trigger("view:attached",o);o.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")})},_getItemViewOptions:function(o){var n=k.prototype._getItemViewOptions.call(this,o);_.extend(n,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return n},_handleHdaDeletionChange:function(n){if(n.get("deleted")&&!this.showDeleted){this.removeItemView(n)}this._renderCounts()},_handleHdaVisibleChange:function(n){if(n.hidden()&&!this.storage.showHidden){this.removeItemView(n)}this._renderCounts()},toggleHDATagEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.tagsEditor){p.tagsEditor.toggle.apply(p.tagsEditor,o)}})},toggleHDAAnnotationEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.annotationEditor){p.annotationEditor.toggle.apply(p.annotationEditor,o)}})},events:_.extend(_.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(n){this.toggleShowDeleted()},"click .toggle-hidden-link":function(n){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var o={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var p=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),p]);for(var n in o){if(o.hasOwnProperty(n)){p.on(n,o[n])}}return this},_renderDropTarget:function(){this.$(".history-drop-target").remove();return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){this.$(".history-drop-target-help").remove();return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(d("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;var o=this.$(".history-drop-target").get(0);for(var n in this._dropHandlers){if(this._dropHandlers.hasOwnProperty(n)){console.debug(n,this._dropHandlers[n]);o.off(n,this._dropHandlers[n])}}this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(n){n.preventDefault();n.stopPropagation()},dragleave:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(p){p.preventDefault();p.dataTransfer.dropEffect="move";var n=this,q=p.dataTransfer.getData("text");try{q=JSON.parse(q)}catch(o){this.warn("error parsing JSON from drop:",q)}this.trigger("droptarget:drop",p,q,n);return false},dataDropped:function(o){var n=this;if(_.isObject(o)&&o.model_class==="HistoryDatasetAssociation"&&o.id){return n.model.contents.copy(o.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:g}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(h,j,m,f,e,i,l,c,b,a,d){var k=h.HistoryPanel;var g=k.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:i.HDCAListItemEdit,initialize:function(n){n=n||{};k.prototype.initialize.call(this,n);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=n.purgeAllowed||false;this.annotationEditorShown=n.annotationEditorShown||false;this.tagsEditorShown=n.tagsEditorShown||false},_setUpListeners:function(){var n=this;k.prototype._setUpListeners.call(n);n.on("drop",function(o,p){n.dataDropped(p);n.dropTargetOff()});n.on("view:attached view:removed",function(){n._renderCounts()},n)},_setUpCollectionListeners:function(){k.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(n){this.model.fetch()},this);return this},_setUpModelListeners:function(){k.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var n=k.prototype._buildNewRender.call(this);if(!this.model){return n}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(n);this._renderAnnotation(n)}return n},renderItems:function(o){var n=k.prototype.renderItems.call(this,o);this._renderCounts(o);return n},_renderCounts:function(p){function o(s,t){return['<a class="',s,'" href="javascript:void(0);">',t,"</a>"].join("")}p=p||this.$el;var n=this.collection.where({deleted:true}),r=this.collection.where({visible:false}),q=[];if(this.views.length){q.push([this.views.length,d("shown")].join(" "))}if(n.length){q.push((!this.showDeleted)?([n.length,o("toggle-deleted-link",d("deleted"))].join(" ")):(o("toggle-deleted-link",d("hide deleted"))))}if(r.length){q.push((!this.showHidden)?([r.length,o("toggle-hidden-link",d("hidden"))].join(" ")):(o("toggle-hidden-link",d("hide hidden"))))}return p.find("> .controls .subtitle").html(q.join(", "))},_renderTags:function(n){var o=this;this.tagsEditor=new l.TagsEditor({model:this.model,el:n.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDATagEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDATagEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(n.find(".controls .actions"))})},_renderAnnotation:function(n){var o=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:n.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){o.toggleHDAAnnotationEditors(true,o.fxSpeed)},onhide:function(){o.toggleHDAAnnotationEditors(false,o.fxSpeed)},$activator:b({title:d("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(n.find(".controls .actions"))})},_setUpBehaviors:function(n){n=n||this.$el;k.prototype._setUpBehaviors.call(this,n);if(!this.model){return}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var o=this,p=".controls .name";n.find(p).attr("title",d("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(q){var r=o.model.get("name");if(q&&q!==r){o.$el.find(p).text(q);o.model.save({name:q}).fail(function(){o.$el.find(p).text(o.model.previous("name"))})}else{o.$el.find(p).text(r)}}})},multiselectActions:function(){var n=this,o=[{html:d("Hide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.hide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Unhide datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.unhide;n.getSelectedModels().ajaxQueue(p)}},{html:d("Delete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype["delete"];n.getSelectedModels().ajaxQueue(p)}},{html:d("Undelete datasets"),func:function(){var p=f.HistoryDatasetAssociation.prototype.undelete;n.getSelectedModels().ajaxQueue(p)}}];if(n.purgeAllowed){o.push({html:d("Permanently delete datasets"),func:function(){if(confirm(d("This will permanently remove the data in your datasets. Are you sure?"))){var p=f.HistoryDatasetAssociation.prototype.purge;n.getSelectedModels().ajaxQueue(p)}}})}o.push({html:d("Build Dataset List"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"list")}});o.push({html:d("Build Dataset Pair"),func:function(){n.getSelectedModels().promoteToHistoryDatasetCollection(n.model,"paired")}});o.push({html:d("Build List of Dataset Pairs"),func:_.bind(n._showPairedCollectionModal,n)});return o},_showPairedCollectionModal:function(){var n=this,o=n.getSelectedModels().toJSON().filter(function(p){return p.history_content_type==="dataset"&&p.state===m.OK});if(o.length){require(["mvc/collection/paired-collection-creator"],function(p){window.creator=p.pairedCollectionCreatorModal(o,{historyId:n.model.id})})}else{Galaxy.modal.show({title:d("No valid datasets were selected"),body:d(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:true})}},_attachItems:function(n){this.$list(n).append(this.views.reverse().map(function(o){return o.$el}));return this},_attachView:function(o){var n=this;n.views.unshift(o);n.$list().prepend(o.render(0).$el.hide());n.trigger("view:attached",o);o.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")})},_getItemViewOptions:function(o){var n=k.prototype._getItemViewOptions.call(this,o);_.extend(n,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return n},_handleHdaDeletionChange:function(n){if(n.get("deleted")&&!this.showDeleted){this.removeItemView(n)}this._renderCounts()},_handleHdaVisibleChange:function(n){if(n.hidden()&&!this.storage.showHidden){this.removeItemView(n)}this._renderCounts()},toggleHDATagEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.tagsEditor){p.tagsEditor.toggle.apply(p.tagsEditor,o)}})},toggleHDAAnnotationEditors:function(n){var o=Array.prototype.slice.call(arguments,1);_.each(this.views,function(p){if(p.annotationEditor){p.annotationEditor.toggle.apply(p.annotationEditor,o)}})},events:_.extend(_.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(n){this.toggleShowDeleted()},"click .toggle-hidden-link":function(n){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var o={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var p=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),p]);for(var n in o){if(o.hasOwnProperty(n)){p.on(n,o[n])}}return this},_renderDropTarget:function(){this.$(".history-drop-target").remove();return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){this.$(".history-drop-target-help").remove();return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(d("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;var o=this.$(".history-drop-target").get(0);for(var n in this._dropHandlers){if(this._dropHandlers.hasOwnProperty(n)){console.debug(n,this._dropHandlers[n]);o.off(n,this._dropHandlers[n])}}this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(n){n.preventDefault();n.stopPropagation()},dragleave:function(n){n.preventDefault();n.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(p){p.preventDefault();p.dataTransfer.dropEffect="move";var n=this,q=p.dataTransfer.getData("text");try{q=JSON.parse(q)}catch(o){this.warn("error parsing JSON from drop:",q)}this.trigger("droptarget:drop",p,q,n);return false},dataDropped:function(o){var n=this;if(_.isObject(o)&&o.model_class==="HistoryDatasetAssociation"&&o.id){return n.model.contents.copy(o.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:g}}); \ No newline at end of file diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/base-mvc","utils/localization","ui/search-input"],function(e,g,m,c,a,n,h,b,p,f){var k=p.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(q){var r="expandedIds";this.save(r,_.extend(this.get(r),_.object([q.id],[q.get("id")])))},removeExpanded:function(q){var r="expandedIds";this.save(r,_.omit(this.get(r),q.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});k.storageKeyPrefix="history:";k.historyStorageKey=function i(q){if(!q){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+q)}return(k.storageKeyPrefix+q)};k.get=function d(q){return new k({id:k.historyStorageKey(q)})};k.clearAll=function j(r){for(var q in sessionStorage){if(q.indexOf(k.storageKeyPrefix)===0){sessionStorage.removeItem(q)}}};var o=e.ModelListPanel;var l=o.extend({HDAViewClass:c.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:m.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:o.prototype.className+" history-panel",emptyMsg:f("This history is empty"),noneFoundMsg:f("No matching datasets found"),searchPlaceholder:f("search datasets"),initialize:function(q){o.prototype.initialize.call(this,q);this.linkTarget=q.linkTarget||"_blank"},freeModel:function(){o.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){o.prototype._setUpListeners.call(this);this.on("error",function(r,u,q,t,s){this.errorHandler(r,u,q,t,s)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(t,s,r,u){this.info("loadHistoryWithDetails:",t,s,r,u);var q=function(v){return _.values(k.get(v.id).get("expandedIds"))};return this.loadHistory(t,s,r,u,q)},loadHistory:function(u,t,s,v,q){this.info("loadHistory:",u,t,s,v,q);var r=this;t=t||{};r.trigger("loading",r);var w=g.History.getHistoryData(u,{historyFn:s,contentsFn:v,detailIdsFn:t.initiallyExpanded||q});return r._loadHistoryFromXHR(w,t).fail(function(z,x,y){r.trigger("error",r,z,t,f("An error was encountered while "+x),{historyId:u,history:y||{}})}).always(function(){r.trigger("loading-done",r)})},_loadHistoryFromXHR:function(s,r){var q=this;s.then(function(t,u){q.JSONToModel(t,u,r);q.render()});s.fail(function(u,t){q.render()});return s},refreshContents:function(r,q){if(this.model){return this.model.refresh(r,q)}return $.when()},JSONToModel:function(t,q,r){this.log("JSONToModel:",t,q,r);r=r||{};var s=new g.History(t,q,r);this.setModel(s);return s},setModel:function(r,q){q=q||{};o.prototype.setModel.call(this,r,q);if(this.model){this._setUpWebStorage(q.initiallyExpanded,q.show_deleted,q.show_hidden)}},_setUpWebStorage:function(r,q,s){if(this.storage){this.stopListening(this.storage)}this.storage=new k({id:k.historyStorageKey(this.model.get("id"))});if(_.isObject(r)){this.storage.set("expandedIds",r)}if(_.isBoolean(q)){this.storage.set("show_deleted",q)}if(_.isBoolean(s)){this.storage.set("show_hidden",s)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(t,u){this.showDeleted=u},"change:show_hidden":function(t,u){this.showHidden=u}},this);this.showDeleted=(q!==undefined)?q:this.storage.get("show_deleted");this.showHidden=(s!==undefined)?s:this.storage.get("show_hidden");return this},_buildNewRender:function(){var q=o.prototype._buildNewRender.call(this);if(this.multiselectActions.length){q.find(".controls .actions").prepend(this._renderSelectButton())}return q},_renderSelectButton:function(q){return b({title:f("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(q){var r=q.get("history_content_type");switch(r){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+r)},_filterItem:function(r){var q=this;return(o.prototype._filterItem.call(q,r)&&(!r.hidden()||q.showHidden)&&(!r.isDeletedOrPurged()||q.showDeleted))},_getItemViewOptions:function(r){var q=o.prototype._getItemViewOptions.call(this,r);return _.extend(q,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[r.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(r){var q=this;o.prototype._setUpItemViewListeners.call(q,r);r.on("expanded",function(s){q.storage.addExpanded(s.model)});r.on("collapsed",function(s){q.storage.removeExpanded(s.model)});return this},getSelectedModels:function(){var q=o.prototype.getSelectedModels.call(this);q.historyId=this.collection.historyId;return q},events:_.extend(_.clone(o.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(q,r){q=(q!==undefined)?(q):(!this.showDeleted);r=(r!==undefined)?(r):(true);this.showDeleted=q;if(r){this.storage.set("show_deleted",q)}this.trigger("show-hidden",q);this.renderItems();return this.showDeleted},toggleShowHidden:function(q,r){q=(q!==undefined)?(q):(!this.showHidden);r=(r!==undefined)?(r):(true);this.showHidden=q;if(r){this.storage.set("show_hidden",q)}this.trigger("show-hidden",q);this.renderItems();return this.showHidden},_firstSearch:function(q){var r=this,s=".history-search-input";this.log("onFirstSearch",q);if(r.model.contents.haveDetails()){r.searchItems(q);return}r.$el.find(s).searchInput("toggle-loading");r.model.contents.fetchAllDetails({silent:true}).always(function(){r.$el.find(s).searchInput("toggle-loading")}).done(function(){r.searchItems(q)})},errorHandler:function(s,v,r,u,t){this.error(s,v,r,u,t);if(v&&v.status===0&&v.readyState===0){}else{if(v&&v.status===502){}else{var q=this._parseErrorMessage(s,v,r,u,t);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",q.message,q.details)})}else{this.displayMessage("error",q.message,q.details)}}}},_parseErrorMessage:function(u,x,y,s,q,v){var t=Galaxy.currUser,w={message:this._bePolite(s),details:{message:s,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(x)?(_.omit(y,"xhr")):(y),xhr:x,source:(_.isFunction(u.toJSON))?(u.toJSON()):(u+""),user:(t instanceof h.User)?(t.toJSON()):(t+"")}};_.extend(w.details,q||{});if(x&&_.isFunction(x.getAllResponseHeaders)){var r=x.getAllResponseHeaders();r=_.compact(r.split("\n"));r=_.map(r,function(z){return z.split(": ")});w.details.xhr.responseHeaders=_.object(r)}return w},_bePolite:function(q){q=q||f("An error occurred while getting updates from the server");return q+". "+f("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(v,w,u){var s=this;this.scrollToTop();var t=this.$messages(),q=$("<div/>").addClass(v+"message").html(w);if(!_.isEmpty(u)){var r=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(s._messageToModalOptions(v,w,u));return false});q.append(" ",r)}return t.html(q)},_messageToModalOptions:function(t,w,s){var q=this,r={title:"Details"};if(_.isObject(s)){s=_.omit(s,_.functions(s));var v=JSON.stringify(s,null," "),u=$("<pre/>").text(v);r.body=$("<div/>").append(u)}else{r.body=$("<div/>").html(s)}r.buttons={Ok:function(){Galaxy.modal.hide();q.clearMessages()}};return r},clearMessages:function(q){$(q.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(q){return this.scrollToItem(_.first(this.viewsWhereModel({hid:q})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});l.prototype.templates=(function(){var q=p.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',f("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',f("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',f("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',f("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(o.prototype.templates),{controls:q})}());return{HistoryPanel:l}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","ui/fa-icon-button","mvc/ui/popup-menu","mvc/base-mvc","utils/localization","ui/search-input"],function(f,h,n,d,b,o,i,c,a,q,g){var l=q.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(r){var s="expandedIds";this.save(s,_.extend(this.get(s),_.object([r.id],[r.get("id")])))},removeExpanded:function(r){var s="expandedIds";this.save(s,_.omit(this.get(s),r.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});l.storageKeyPrefix="history:";l.historyStorageKey=function j(r){if(!r){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+r)}return(l.storageKeyPrefix+r)};l.get=function e(r){return new l({id:l.historyStorageKey(r)})};l.clearAll=function k(s){for(var r in sessionStorage){if(r.indexOf(l.storageKeyPrefix)===0){sessionStorage.removeItem(r)}}};var p=f.ModelListPanel;var m=p.extend({HDAViewClass:d.HDAListItemView,HDCAViewClass:b.HDCAListItemView,collectionClass:n.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:p.prototype.className+" history-panel",emptyMsg:g("This history is empty"),noneFoundMsg:g("No matching datasets found"),searchPlaceholder:g("search datasets"),initialize:function(r){p.prototype.initialize.call(this,r);this.linkTarget=r.linkTarget||"_blank"},freeModel:function(){p.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){p.prototype._setUpListeners.call(this);this.on("error",function(s,v,r,u,t){this.errorHandler(s,v,r,u,t)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(u,t,s,v){this.info("loadHistoryWithDetails:",u,t,s,v);var r=function(w){return _.values(l.get(w.id).get("expandedIds"))};return this.loadHistory(u,t,s,v,r)},loadHistory:function(v,u,t,w,r){this.info("loadHistory:",v,u,t,w,r);var s=this;u=u||{};s.trigger("loading",s);var x=h.History.getHistoryData(v,{historyFn:t,contentsFn:w,detailIdsFn:u.initiallyExpanded||r});return s._loadHistoryFromXHR(x,u).fail(function(A,y,z){s.trigger("error",s,A,u,g("An error was encountered while "+y),{historyId:v,history:z||{}})}).always(function(){s.trigger("loading-done",s)})},_loadHistoryFromXHR:function(t,s){var r=this;t.then(function(u,v){r.JSONToModel(u,v,s);r.render()});t.fail(function(v,u){r.render()});return t},refreshContents:function(s,r){if(this.model){return this.model.refresh(s,r)}return $.when()},JSONToModel:function(u,r,s){this.log("JSONToModel:",u,r,s);s=s||{};var t=new h.History(u,r,s);this.setModel(t);return t},setModel:function(s,r){r=r||{};p.prototype.setModel.call(this,s,r);if(this.model){this._setUpWebStorage(r.initiallyExpanded,r.show_deleted,r.show_hidden)}},_setUpWebStorage:function(s,r,t){if(this.storage){this.stopListening(this.storage)}this.storage=new l({id:l.historyStorageKey(this.model.get("id"))});if(_.isObject(s)){this.storage.set("expandedIds",s)}if(_.isBoolean(r)){this.storage.set("show_deleted",r)}if(_.isBoolean(t)){this.storage.set("show_hidden",t)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(u,v){this.showDeleted=v},"change:show_hidden":function(u,v){this.showHidden=v}},this);this.showDeleted=(r!==undefined)?r:this.storage.get("show_deleted");this.showHidden=(t!==undefined)?t:this.storage.get("show_hidden");return this},_buildNewRender:function(){var r=p.prototype._buildNewRender.call(this);if(this.multiselectActions().length){r.find(".controls .actions").prepend(this._renderSelectButton())}return r},_renderSelectButton:function(r){return c({title:g("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(r){var s=r.get("history_content_type");switch(s){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+s)},_filterItem:function(s){var r=this;return(p.prototype._filterItem.call(r,s)&&(!s.hidden()||r.showHidden)&&(!s.isDeletedOrPurged()||r.showDeleted))},_getItemViewOptions:function(s){var r=p.prototype._getItemViewOptions.call(this,s);return _.extend(r,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[s.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(s){var r=this;p.prototype._setUpItemViewListeners.call(r,s);s.on("expanded",function(t){r.storage.addExpanded(t.model)});s.on("collapsed",function(t){r.storage.removeExpanded(t.model)});return this},getSelectedModels:function(){var r=p.prototype.getSelectedModels.call(this);r.historyId=this.collection.historyId;return r},events:_.extend(_.clone(p.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(r,s){r=(r!==undefined)?(r):(!this.showDeleted);s=(s!==undefined)?(s):(true);this.showDeleted=r;if(s){this.storage.set("show_deleted",r)}this.trigger("show-hidden",r);this.renderItems();return this.showDeleted},toggleShowHidden:function(r,s){r=(r!==undefined)?(r):(!this.showHidden);s=(s!==undefined)?(s):(true);this.showHidden=r;if(s){this.storage.set("show_hidden",r)}this.trigger("show-hidden",r);this.renderItems();return this.showHidden},_firstSearch:function(r){var s=this,t=".history-search-input";this.log("onFirstSearch",r);if(s.model.contents.haveDetails()){s.searchItems(r);return}s.$el.find(t).searchInput("toggle-loading");s.model.contents.fetchAllDetails({silent:true}).always(function(){s.$el.find(t).searchInput("toggle-loading")}).done(function(){s.searchItems(r)})},errorHandler:function(t,w,s,v,u){this.error(t,w,s,v,u);if(w&&w.status===0&&w.readyState===0){}else{if(w&&w.status===502){}else{var r=this._parseErrorMessage(t,w,s,v,u);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",r.message,r.details)})}else{this.displayMessage("error",r.message,r.details)}}}},_parseErrorMessage:function(v,y,z,t,r,w){var u=Galaxy.currUser,x={message:this._bePolite(t),details:{message:t,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(y)?(_.omit(z,"xhr")):(z),xhr:y,source:(_.isFunction(v.toJSON))?(v.toJSON()):(v+""),user:(u instanceof i.User)?(u.toJSON()):(u+"")}};_.extend(x.details,r||{});if(y&&_.isFunction(y.getAllResponseHeaders)){var s=y.getAllResponseHeaders();s=_.compact(s.split("\n"));s=_.map(s,function(A){return A.split(": ")});x.details.xhr.responseHeaders=_.object(s)}return x},_bePolite:function(r){r=r||g("An error occurred while getting updates from the server");return r+". "+g("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(w,x,v){var t=this;this.scrollToTop();var u=this.$messages(),r=$("<div/>").addClass(w+"message").html(x);if(!_.isEmpty(v)){var s=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(t._messageToModalOptions(w,x,v));return false});r.append(" ",s)}return u.html(r)},_messageToModalOptions:function(u,x,t){var r=this,s={title:"Details"};if(_.isObject(t)){t=_.omit(t,_.functions(t));var w=JSON.stringify(t,null," "),v=$("<pre/>").text(w);s.body=$("<div/>").append(v)}else{s.body=$("<div/>").html(t)}s.buttons={Ok:function(){Galaxy.modal.hide();r.clearMessages()}};return s},clearMessages:function(r){$(r.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(r){return this.scrollToItem(_.first(this.viewsWhereModel({hid:r})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});m.prototype.templates=(function(){var r=q.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',g("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',g("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',g("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"],"history");return _.extend(_.clone(p.prototype.templates),{controls:r})}());return{HistoryPanel:m}}); \ No newline at end of file diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.purgeAllowed=!_.isUndefined(C.purgeAllowed)?C.purgeAllowed:false;this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:C,view:this}),this.controlsRightTemplate({history:C,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted change:purged":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")||D.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(D){var E=this,C={HistoryDatasetAssociation:"hda",HistoryDatasetCollectionAssociation:"hdca"};E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return((_.isObject(K)&&K.id)&&(_.contains(_.keys(C),K.model_class)))});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){var L=C[K.model_class];F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id,L)}})});F.start();F.done(function(K){G.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.purgeAllowed=!_.isUndefined(C.purgeAllowed)?C.purgeAllowed:false;this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:C,view:this}),this.controlsRightTemplate({history:C,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted change:purged":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")||D.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return F.model.contents.isCopyable(J)});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(d,f,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(g,h){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this.fxSpeed=_.has(g,"fxSpeed")?(g.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=g.searchFor||"";this.indicator=new f(this.$el);this.selecting=(g.selecting!==undefined)?g.selecting:true;this.selected=g.selected||[];this.lastSelected=null;this.dragItems=g.dragItems||false;this.viewClass=g.viewClass||this.viewClass;this.views=[];this.collection=g.collection||(new this.collectionClass([]));this.filters=g.filters||[];this.$scrollContainer=g.$scrollContainer||this.$scrollContainer;this.title=g.title||"";this.subtitle=g.subtitle||"";this.multiselectActions=g.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(g){g.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(h,k,g,j,i){console.error(h,k,g,j,i)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(h,k,g,j,i){this.trigger("error",h,k,g,j,i)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(g){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(g,h){if(h&&h.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);if(i){this.selectRange(g,i)}}else{if(h&&h.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(g.model.id);this.lastSelected=g.model.id},this);this.on("view:de-selected",function(g,h){this.selected=_.without(this.selected,g.model.id)},this)},render:function(h){this.log(this+".render",h);var g=this._buildNewRender();this._setUpBehaviors(g);this._queueNewRender(g,h);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var g=$(this.templates.el({},this));this._renderControls(g);this._renderTitle(g);this._renderSubtitle(g);this._renderSearch(g);this.renderItems(g);return g},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var g=$(this.templates.controls({},this));h.find(".controls").replaceWith(g);return g},_renderTitle:function(g){},_renderSubtitle:function(g){},_queueNewRender:function(h,i){i=(i===undefined)?(this.fxSpeed):(i);var g=this;g.log("_queueNewRender:",h,i);$(g).queue("fx",[function(j){this.$el.fadeOut(i,j)},function(j){g._swapNewRender(h);j()},function(j){this.$el.fadeIn(i,j)},function(j){g.trigger("rendered",g);j()}])},_swapNewRender:function(g){this.$el.empty().attr("class",this.className).append(g.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(g){g=g||this.$el;g.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(g){return(g||this.$el).find("> .list-items")},$messages:function(g){return(g||this.$el).find("> .controls .messages")},$emptyMessage:function(g){return(g||this.$el).find("> .empty-message")},renderItems:function(i){i=i||this.$el;var g=this;g.log(this+".renderItems",i);var h=g.$list(i);g.views=g._filterCollection().map(function(j){return g._createItemView(j).render(0)});h.empty();if(g.views.length){g._attachItems(i);g.$emptyMessage(i).hide()}else{g._renderEmptyMessage(i).show()}return g.views},_filterCollection:function(){var g=this;return g.collection.filter(_.bind(g._filterItem,g))},_filterItem:function(h){var g=this;return(_.every(g.filters.map(function(i){return i.call(h)})))&&(!g.searchFor||h.matchesAll(g.searchFor))},_createItemView:function(i){var j=this._getItemViewClass(i),h=_.extend(this._getItemViewOptions(i),{model:i}),g=new j(h);this._setUpItemViewListeners(g);return g},_getItemViewClass:function(g){return this.viewClass},_getItemViewOptions:function(g){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,g.id),draggable:this.dragItems}},_setUpItemViewListeners:function(h){var g=this;h.on("all",function(){var i=Array.prototype.slice.call(arguments,0);i[0]="view:"+i[0];g.trigger.apply(g,i)});h.on("draggable:dragstart",function(l,i){var j={},k=this.getSelectedModels();if(k.length){j=k.toJSON()}else{j=[i.model.toJSON()]}l.dataTransfer.setData("text",JSON.stringify(j))},this);return g},_attachItems:function(g){this.$list(g).append(this.views.map(function(h){return h.$el}));return this},_renderEmptyMessage:function(g){this.debug("_renderEmptyMessage",g,this.searchFor);var h=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(g).text(h)},expandAll:function(){_.each(this.views,function(g){g.expand()})},collapseAll:function(){_.each(this.views,function(g){g.collapse()})},addItemView:function(j,k,i){this.log(this+".addItemView:",j);var h=this;if(!h._filterItem(j)){return undefined}var g=h._createItemView(j);$(g).queue("fx",[function(l){h.$emptyMessage().fadeOut(h.fxSpeed,l)},function(l){h._attachView(g);l()}]);return g},_attachView:function(h){var g=this;g.views.push(h);g.$list().append(h.render(0).$el.hide());g.trigger("view:attached",h);h.$el.slideDown(g.fxSpeed,function(){g.trigger("view:attached:rendered")})},removeItemView:function(j,k,i){this.log(this+".removeItemView:",j);var h=this,g=h.viewFromModel(j);if(!g){return undefined}h.views=_.without(h.views,g);h.trigger("view:removed",g);$({}).queue("fx",[function(l){g.$el.fadeOut(h.fxSpeed,l)},function(l){g.remove();h.trigger("view:removed:rendered");if(!h.views.length){h._renderEmptyMessage().fadeIn(h.fxSpeed,l)}else{l()}}]);return g},viewFromModelId:function(h){for(var g=0;g<this.views.length;g++){if(this.views[g].model.id===h){return this.views[g]}}return undefined},viewFromModel:function(g){if(!g){return undefined}return this.viewFromModelId(g.id)},viewsWhereModel:function(g){return this.views.filter(function(h){var j=h.model.toJSON();for(var i in g){if(g.hasOwnProperty(i)){if(j[i]!==h.model.get(i)){return false}}}return true})},viewRange:function(j,i){if(j===i){return(j)?([j]):([])}var h=this.views.indexOf(j),g=this.views.indexOf(i);if(h===-1||g===-1){if(h===g){return[]}return(h===-1)?([i]):([j])}return(h<g)?this.views.slice(h,g+1):this.views.slice(g,h+1)},_renderSearch:function(g){g.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return g},_firstSearch:function(g){this.log("onFirstSearch",g);return this.searchItems(g)},searchItems:function(g){this.searchFor=g;this.trigger("search:searching",g,this);this.renderItems();this.$("> .controls .search-query").val(g);return this},clearSearch:function(g){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(g);_.each(this.views,function(h){h.showSelector(g)})},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(g);_.each(this.views,function(h){h.hideSelector(g)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(g){_.each(this.views,function(h){h.select(g)})},deselectAll:function(g){this.lastSelected=null;_.each(this.views,function(h){h.deselect(g)})},selectRange:function(i,h){var g=this.viewRange(i,h);_.each(g,function(j){j.select()});return g},getSelectedViews:function(){return _.filter(this.views,function(g){return g.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(g){return g.model}))},_showLoadingIndicator:function(h,g,i){this.debug("_showLoadingIndicator",this.indicator,h,g,i);g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new f(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},_hideLoadingIndicator:function(g,h){this.debug("_hideLoadingIndicator",this.indicator,g,h);g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(h,g){g=g||0;this.$scrollContainer().animate({scrollTop:h},g);return this},scrollToTop:function(g){return this.scrollTo(0,g)},scrollToItem:function(g,i){if(!g){return this}var h=g.$el.position().top;return this.scrollTo(h,i)},scrollToId:function(h,g){return this.scrollToItem(this.viewFromModelId(h),g)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var h=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:h,controls:g}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(g){e.prototype.initialize.call(this,g);this.selecting=(g.selecting!==undefined)?g.selecting:false;this.setModel(this.model,g)},setModel:function(h,g){g=g||{};this.debug(this+".setModel:",h,g);this.freeModel();this.freeViews();if(h){var i=this.model?this.model.get("id"):null;this.model=h;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(g.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(i&&h.get("id")!==i){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){var g=Array.prototype.slice.call(arguments,0);g.unshift("error");this.trigger.apply(this,g)},this);return this},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var i=this.model?this.model.toJSON():{},g=$(this.templates.controls(i,this));h.find(".controls").replaceWith(g);return g},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:g})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(d,f,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),initialize:function(g,h){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this.fxSpeed=_.has(g,"fxSpeed")?(g.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=g.searchFor||"";this.indicator=new f(this.$el);this.selecting=(g.selecting!==undefined)?g.selecting:true;this.selected=g.selected||[];this.lastSelected=null;this.dragItems=g.dragItems||false;this.viewClass=g.viewClass||this.viewClass;this.views=[];this.collection=g.collection||(new this.collectionClass([]));this.filters=g.filters||[];this.$scrollContainer=g.$scrollContainer||this.$scrollContainer;this.title=g.title||"";this.subtitle=g.subtitle||"";this._setUpListeners()},freeViews:function(){_.each(this.views,function(g){g.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(h,k,g,j,i){console.error(h,k,g,j,i)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(h,k,g,j,i){this.trigger("error",h,k,g,j,i)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(g){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(g,h){if(h&&h.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);if(i){this.selectRange(g,i)}}else{if(h&&h.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(g.model.id);this.lastSelected=g.model.id},this);this.on("view:de-selected",function(g,h){this.selected=_.without(this.selected,g.model.id)},this)},render:function(h){this.log(this+".render",h);var g=this._buildNewRender();this._setUpBehaviors(g);this._queueNewRender(g,h);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var g=$(this.templates.el({},this));this._renderControls(g);this._renderTitle(g);this._renderSubtitle(g);this._renderSearch(g);this.renderItems(g);return g},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var g=$(this.templates.controls({},this));h.find(".controls").replaceWith(g);return g},_renderTitle:function(g){},_renderSubtitle:function(g){},_queueNewRender:function(h,i){i=(i===undefined)?(this.fxSpeed):(i);var g=this;g.log("_queueNewRender:",h,i);$(g).queue("fx",[function(j){this.$el.fadeOut(i,j)},function(j){g._swapNewRender(h);j()},function(j){this.$el.fadeIn(i,j)},function(j){g.trigger("rendered",g);j()}])},_swapNewRender:function(g){this.$el.empty().attr("class",this.className).append(g.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(g){g=g||this.$el;g.find(".controls [title]").tooltip({placement:"bottom"});this._renderMultiselectActionMenu(g);return this},_renderMultiselectActionMenu:function(g){g=g||this.$el;var h=g.find(".list-action-menu"),k=this.multiselectActions();if(!k.length){return h.empty()}var j=$(['<div class="list-action-menu btn-group">','<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">',c("For all selected"),"...","</button>",'<ul class="dropdown-menu pull-right" role="menu">',"</ul>","</div>"].join(""));var i=k.map(function(m){var l=['<li><a href="javascript:void(0);">',m.html,"</a></li>"].join("");return $(l).click(m.func)});j.find("ul").append(i);h.replaceWith(j);return j},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(g){return(g||this.$el).find("> .list-items")},$messages:function(g){return(g||this.$el).find("> .controls .messages")},$emptyMessage:function(g){return(g||this.$el).find("> .empty-message")},renderItems:function(i){i=i||this.$el;var g=this;g.log(this+".renderItems",i);var h=g.$list(i);g.views=g._filterCollection().map(function(j){return g._createItemView(j).render(0)});h.empty();if(g.views.length){g._attachItems(i);g.$emptyMessage(i).hide()}else{g._renderEmptyMessage(i).show()}return g.views},_filterCollection:function(){var g=this;return g.collection.filter(_.bind(g._filterItem,g))},_filterItem:function(h){var g=this;return(_.every(g.filters.map(function(i){return i.call(h)})))&&(!g.searchFor||h.matchesAll(g.searchFor))},_createItemView:function(i){var j=this._getItemViewClass(i),h=_.extend(this._getItemViewOptions(i),{model:i}),g=new j(h);this._setUpItemViewListeners(g);return g},_getItemViewClass:function(g){return this.viewClass},_getItemViewOptions:function(g){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,g.id),draggable:this.dragItems}},_setUpItemViewListeners:function(h){var g=this;h.on("all",function(){var i=Array.prototype.slice.call(arguments,0);i[0]="view:"+i[0];g.trigger.apply(g,i)});h.on("draggable:dragstart",function(l,i){var j={},k=this.getSelectedModels();if(k.length){j=k.toJSON()}else{j=[i.model.toJSON()]}l.dataTransfer.setData("text",JSON.stringify(j))},this);return g},_attachItems:function(g){this.$list(g).append(this.views.map(function(h){return h.$el}));return this},_renderEmptyMessage:function(g){this.debug("_renderEmptyMessage",g,this.searchFor);var h=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(g).text(h)},expandAll:function(){_.each(this.views,function(g){g.expand()})},collapseAll:function(){_.each(this.views,function(g){g.collapse()})},addItemView:function(j,k,i){this.log(this+".addItemView:",j);var h=this;if(!h._filterItem(j)){return undefined}var g=h._createItemView(j);$(g).queue("fx",[function(l){h.$emptyMessage().fadeOut(h.fxSpeed,l)},function(l){h._attachView(g);l()}]);return g},_attachView:function(h){var g=this;g.views.push(h);g.$list().append(h.render(0).$el.hide());g.trigger("view:attached",h);h.$el.slideDown(g.fxSpeed,function(){g.trigger("view:attached:rendered")})},removeItemView:function(j,k,i){this.log(this+".removeItemView:",j);var h=this,g=h.viewFromModel(j);if(!g){return undefined}h.views=_.without(h.views,g);h.trigger("view:removed",g);$({}).queue("fx",[function(l){g.$el.fadeOut(h.fxSpeed,l)},function(l){g.remove();h.trigger("view:removed:rendered");if(!h.views.length){h._renderEmptyMessage().fadeIn(h.fxSpeed,l)}else{l()}}]);return g},viewFromModelId:function(h){for(var g=0;g<this.views.length;g++){if(this.views[g].model.id===h){return this.views[g]}}return undefined},viewFromModel:function(g){if(!g){return undefined}return this.viewFromModelId(g.id)},viewsWhereModel:function(g){return this.views.filter(function(h){var j=h.model.toJSON();for(var i in g){if(g.hasOwnProperty(i)){if(j[i]!==h.model.get(i)){return false}}}return true})},viewRange:function(j,i){if(j===i){return(j)?([j]):([])}var h=this.views.indexOf(j),g=this.views.indexOf(i);if(h===-1||g===-1){if(h===g){return[]}return(h===-1)?([i]):([j])}return(h<g)?this.views.slice(h,g+1):this.views.slice(g,h+1)},_renderSearch:function(g){g.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return g},_firstSearch:function(g){this.log("onFirstSearch",g);return this.searchItems(g)},searchItems:function(g){this.searchFor=g;this.trigger("search:searching",g,this);this.renderItems();this.$("> .controls .search-query").val(g);return this},clearSearch:function(g){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(g);_.each(this.views,function(h){h.showSelector(g)})},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(g);_.each(this.views,function(h){h.hideSelector(g)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(g){_.each(this.views,function(h){h.select(g)})},deselectAll:function(g){this.lastSelected=null;_.each(this.views,function(h){h.deselect(g)})},selectRange:function(i,h){var g=this.viewRange(i,h);_.each(g,function(j){j.select()});return g},getSelectedViews:function(){return _.filter(this.views,function(g){return g.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(g){return g.model}))},_showLoadingIndicator:function(h,g,i){this.debug("_showLoadingIndicator",this.indicator,h,g,i);g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new f(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},_hideLoadingIndicator:function(g,h){this.debug("_hideLoadingIndicator",this.indicator,g,h);g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(h,g){g=g||0;this.$scrollContainer().animate({scrollTop:h},g);return this},scrollToTop:function(g){return this.scrollTo(0,g)},scrollToItem:function(g,i){if(!g){return this}var h=g.$el.position().top;return this.scrollTo(h,i)},scrollToId:function(h,g){return this.scrollToItem(this.viewFromModelId(h),g)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var h=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return{el:h,controls:g}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(g){e.prototype.initialize.call(this,g);this.selecting=(g.selecting!==undefined)?g.selecting:false;this.setModel(this.model,g)},setModel:function(h,g){g=g||{};this.debug(this+".setModel:",h,g);this.freeModel();this.freeViews();if(h){var i=this.model?this.model.get("id"):null;this.model=h;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(g.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(i&&h.get("id")!==i){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){var g=Array.prototype.slice.call(arguments,0);g.unshift("error");this.trigger.apply(this,g)},this);return this},_renderControls:function(h){this.debug(this+"(ListPanel)._renderControls");var i=this.model?this.model.toJSON():{},g=$(this.templates.controls(i,this));h.find(".controls").replaceWith(g);return g},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:g})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2007,7 +2007,8 @@ .list-panel .controls .list-actions:after{clear:both} .list-panel .controls .list-actions:before,.list-panel .controls .list-actions:after{content:" ";display:table;} .list-panel .controls .list-actions:after{clear:both} -.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%} +.list-panel .controls .list-actions .btn{padding-top:2px;padding-bottom:2px;font-size:90%;z-index:inherit} +.list-panel .controls .list-actions .list-action-menu{float:right}.list-panel .controls .list-actions .list-action-menu .dropdown-menu{z-index:inherit} .list-panel .list-items .list-item:not(:last-child){border-bottom-width:0px} .list-panel .empty-message{display:none;margin:0px} .list-item .details .list-panel{margin-top:8px;border-radius:3px;background:white;padding:4px}.list-item .details .list-panel .list-items{border:1px solid #bfbfbf;border-radius:3px}.list-item .details .list-panel .list-items .list-item:first-child{border-top-width:0px;border-radius:3px 3px 0px 0px} @@ -2078,7 +2079,6 @@ .history-panel .controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto} .history-panel .controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} .history-panel .controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%} -.history-panel .controls .list-actions .list-action-popup-btn{float:right} .history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-message{margin:0px 10px 0px 10px} .history-panel .dataset-collection .subtitle{margin-top:2px} diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -449,12 +449,6 @@ width: 100%; } } - - .list-actions { - .list-action-popup-btn { - float: right; - } - } } // display only a top border on all diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -167,6 +167,13 @@ padding-top: 2px; padding-bottom: 2px; font-size: 90%; + z-index: inherit; + } + .list-action-menu { + float: right; + .dropdown-menu { + z-index: inherit; + } } } } diff -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 -r 316080b22578989fc473e101641c2118a73f6693 templates/webapps/galaxy/history/view_multiple.mako --- a/templates/webapps/galaxy/history/view_multiple.mako +++ b/templates/webapps/galaxy/history/view_multiple.mako @@ -43,7 +43,6 @@ multipanel = new MULTI_PANEL.MultiPanelColumns({ el : $( '#center' ).get(0), histories : histories, - //historiesJSON : historiesJSON, order : bootstrapped.order, currentHistoryId : '${current_history_id}' }).render( 0 ); https://bitbucket.org/galaxy/galaxy-central/commits/df939bc2b7fe/ Changeset: df939bc2b7fe Branch: next-stable User: carlfeberhard Date: 2015-02-17 14:57:18+00:00 Summary: merge Affected #: 5 files diff -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -786,6 +786,14 @@ # public. #new_user_dataset_access_role_default_private = False +# Expose user list. Setting this to true will expose the user list to authenticated users. This +# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and +# have the correct user show up. This makes less sense on large public galaxy instances where +# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the +# username and not email, or vice versa. +#expose_user_name = False +#expose_user_email = False + # -- Beta features # Use new tool form diff -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -106,6 +106,9 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.expose_user_name = kwargs.get( "expose_user_name", False ) + self.expose_user_email = kwargs.get( "expose_user_email", False ) + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) diff -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -131,7 +131,7 @@ histories, credentials, and roles. """ # attributes that will be accessed and returned when calling to_dict( view='collection' ) - dict_collection_visible_keys = ( 'id', 'email' ) + dict_collection_visible_keys = ( 'id', 'email', 'username' ) # attributes that will be accessed and returned when calling to_dict( view='element' ) dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) diff -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -43,11 +43,19 @@ else: query = query.filter( trans.app.model.User.table.c.deleted == False ) # noqa # special case: user can see only their own user - if not trans.user_is_admin(): + # special case2: if the galaxy admin has specified that other user email/names are + # exposed, we don't want special case #1 + if not trans.user_is_admin() and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) return [item] for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) + # If NOT configured to expose_email, do not expose email UNLESS the user is self, or + # the user is an admin + if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin(): + del item['username'] + if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin(): + del item['email'] # TODO: move into api_values rval.append( item ) return rval diff -r 7e47493de36fa37e0fe2e2a29d777cc4356bd6e5 -r df939bc2b7fe0ac410e227acd6e32535a0ad7817 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,10 +36,10 @@ </div><div style="clear: both"></div><div class="form-row"> + <% existing_emails = ','.join([ d.user.email for d in history.users_shared_with ]) %><label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> + <input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"> + </input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users </div> @@ -55,6 +55,94 @@ <input type="submit" name="share_button" value="Submit"></div></form> + <script type="text/javascript"> + // stolen from templates/admin/impersonate.mako + /* This should be ripped out and made generic at some point for the + * various API bindings available, and once the API can filter list + * queries (term, below) */ + + var user_id = "${trans.security.encode_id(trans.user.id)}"; + var history_id = "${trans.security.encode_id( history.id )}"; + + function item_to_label(item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + return text; + //return "id:" + item.id + "|e:" + item.email + "|u:" + item.username; + } + + $("#email_select").select2({ + placeholder: "Select a user", + multiple: true, + initSelection: function(element, callback) { + var data = [ + // Must be here to loop across the users that this has been shared with. + %for i, association in enumerate( history.users_shared_with ): + <% shared_with = association.user %> + { + email: "${ shared_with.email }", + id: "${trans.security.encode_id(shared_with.id)}", + text: item_to_label({"email": "${ shared_with.email }", "username": "${ shared_with.username }" }) + }, + %endfor + ]; + callback(data); + }, + tokenSeparators: [',', ' '], + // Required for initSelection + id: function(object) { + return object.id; + }, + ajax: { + url: "${h.url_for(controller="/api/users", action="index")}", + data: function (term) { + return { + f_email: term + }; + }, + dataType: 'json', + quietMillis: 250, + results: function (data) { + var results = []; + // For every user returned by the API call, + $.each(data, function(index, item){ + // If they aren't the requesting user, add to the + // list that will populate the select + if(item.id != "${trans.security.encode_id(trans.user.id)}"){ + results.push({ + id: item.id, + name: item.username, + text: item_to_label(item), + }); + } + }); + return { + results: results + }; + } + }, + createSearchChoice: function(term, data) { + // Check for a user with a matching email. + var matches = _.filter(data, function(user){ + return user.text.indexOf(term) > -1; + }); + // If there aren't any users with matching object labels, then + // display a "default" entry with whatever text they're entering. + // id is set to term as that will be used in + if(matches.length == 0){ + return {id: term, text:term}; + }else{ + // No extra needed + } + } + }); + </script> %else: ## We are sharing restricted histories %if no_change_needed or can_change: https://bitbucket.org/galaxy/galaxy-central/commits/df4ab158d14e/ Changeset: df4ab158d14e User: carlfeberhard Date: 2015-02-17 14:57:34+00:00 Summary: merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge PR over from default.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80f553f98f2f/ Changeset: 80f553f98f2f Branch: next-stable User: dannon Date: 2015-02-17 14:50:58+00:00 Summary: Merge PR over from default. Affected #: 5 files diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 80f553f98f2fabe60173f9d1f361c11e7c7105b8 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -786,6 +786,14 @@ # public. #new_user_dataset_access_role_default_private = False +# Expose user list. Setting this to true will expose the user list to authenticated users. This +# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and +# have the correct user show up. This makes less sense on large public galaxy instances where +# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the +# username and not email, or vice versa. +#expose_user_name = False +#expose_user_email = False + # -- Beta features # Use new tool form diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 80f553f98f2fabe60173f9d1f361c11e7c7105b8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -106,6 +106,9 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.expose_user_name = kwargs.get( "expose_user_name", False ) + self.expose_user_email = kwargs.get( "expose_user_email", False ) + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 80f553f98f2fabe60173f9d1f361c11e7c7105b8 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -131,7 +131,7 @@ histories, credentials, and roles. """ # attributes that will be accessed and returned when calling to_dict( view='collection' ) - dict_collection_visible_keys = ( 'id', 'email' ) + dict_collection_visible_keys = ( 'id', 'email', 'username' ) # attributes that will be accessed and returned when calling to_dict( view='element' ) dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 80f553f98f2fabe60173f9d1f361c11e7c7105b8 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -43,11 +43,19 @@ else: query = query.filter( trans.app.model.User.table.c.deleted == False ) # noqa # special case: user can see only their own user - if not trans.user_is_admin(): + # special case2: if the galaxy admin has specified that other user email/names are + # exposed, we don't want special case #1 + if not trans.user_is_admin() and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) return [item] for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) + # If NOT configured to expose_email, do not expose email UNLESS the user is self, or + # the user is an admin + if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin(): + del item['username'] + if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin(): + del item['email'] # TODO: move into api_values rval.append( item ) return rval diff -r 9bb938ddd02e88abce8570049049982acc934690 -r 80f553f98f2fabe60173f9d1f361c11e7c7105b8 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,10 +36,10 @@ </div><div style="clear: both"></div><div class="form-row"> + <% existing_emails = ','.join([ d.user.email for d in history.users_shared_with ]) %><label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> + <input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"> + </input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users </div> @@ -55,6 +55,94 @@ <input type="submit" name="share_button" value="Submit"></div></form> + <script type="text/javascript"> + // stolen from templates/admin/impersonate.mako + /* This should be ripped out and made generic at some point for the + * various API bindings available, and once the API can filter list + * queries (term, below) */ + + var user_id = "${trans.security.encode_id(trans.user.id)}"; + var history_id = "${trans.security.encode_id( history.id )}"; + + function item_to_label(item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + return text; + //return "id:" + item.id + "|e:" + item.email + "|u:" + item.username; + } + + $("#email_select").select2({ + placeholder: "Select a user", + multiple: true, + initSelection: function(element, callback) { + var data = [ + // Must be here to loop across the users that this has been shared with. + %for i, association in enumerate( history.users_shared_with ): + <% shared_with = association.user %> + { + email: "${ shared_with.email }", + id: "${trans.security.encode_id(shared_with.id)}", + text: item_to_label({"email": "${ shared_with.email }", "username": "${ shared_with.username }" }) + }, + %endfor + ]; + callback(data); + }, + tokenSeparators: [',', ' '], + // Required for initSelection + id: function(object) { + return object.id; + }, + ajax: { + url: "${h.url_for(controller="/api/users", action="index")}", + data: function (term) { + return { + f_email: term + }; + }, + dataType: 'json', + quietMillis: 250, + results: function (data) { + var results = []; + // For every user returned by the API call, + $.each(data, function(index, item){ + // If they aren't the requesting user, add to the + // list that will populate the select + if(item.id != "${trans.security.encode_id(trans.user.id)}"){ + results.push({ + id: item.id, + name: item.username, + text: item_to_label(item), + }); + } + }); + return { + results: results + }; + } + }, + createSearchChoice: function(term, data) { + // Check for a user with a matching email. + var matches = _.filter(data, function(user){ + return user.text.indexOf(term) > -1; + }); + // If there aren't any users with matching object labels, then + // display a "default" entry with whatever text they're entering. + // id is set to term as that will be used in + if(matches.length == 0){ + return {id: term, text:term}; + }else{ + // No extra needed + } + } + }); + </script> %else: ## We are sharing restricted histories %if no_change_needed or can_change: 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 erasche2/galaxy-central (pull request #570)
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8519e2f351f8/ Changeset: 8519e2f351f8 User: dannon Date: 2015-02-17 14:46:09+00:00 Summary: Merged in erasche2/galaxy-central (pull request #570) Enable user/email list for sharing of datasets Affected #: 5 files diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -786,6 +786,14 @@ # public. #new_user_dataset_access_role_default_private = False +# Expose user list. Setting this to true will expose the user list to authenticated users. This +# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and +# have the correct user show up. This makes less sense on large public galaxy instances where +# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the +# username and not email, or vice versa. +#expose_user_name = False +#expose_user_email = False + # -- Beta features # Use new tool form diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -106,6 +106,9 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.expose_user_name = kwargs.get( "expose_user_name", False ) + self.expose_user_email = kwargs.get( "expose_user_email", False ) + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -131,7 +131,7 @@ histories, credentials, and roles. """ # attributes that will be accessed and returned when calling to_dict( view='collection' ) - dict_collection_visible_keys = ( 'id', 'email' ) + dict_collection_visible_keys = ( 'id', 'email', 'username' ) # attributes that will be accessed and returned when calling to_dict( view='element' ) dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -43,11 +43,19 @@ else: query = query.filter( trans.app.model.User.table.c.deleted == False ) # noqa # special case: user can see only their own user - if not trans.user_is_admin(): + # special case2: if the galaxy admin has specified that other user email/names are + # exposed, we don't want special case #1 + if not trans.user_is_admin() and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) return [item] for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) + # If NOT configured to expose_email, do not expose email UNLESS the user is self, or + # the user is an admin + if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin(): + del item['username'] + if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin(): + del item['email'] # TODO: move into api_values rval.append( item ) return rval diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,10 +36,10 @@ </div><div style="clear: both"></div><div class="form-row"> + <% existing_emails = ','.join([ d.user.email for d in history.users_shared_with ]) %><label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> + <input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"> + </input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users </div> @@ -55,6 +55,94 @@ <input type="submit" name="share_button" value="Submit"></div></form> + <script type="text/javascript"> + // stolen from templates/admin/impersonate.mako + /* This should be ripped out and made generic at some point for the + * various API bindings available, and once the API can filter list + * queries (term, below) */ + + var user_id = "${trans.security.encode_id(trans.user.id)}"; + var history_id = "${trans.security.encode_id( history.id )}"; + + function item_to_label(item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + return text; + //return "id:" + item.id + "|e:" + item.email + "|u:" + item.username; + } + + $("#email_select").select2({ + placeholder: "Select a user", + multiple: true, + initSelection: function(element, callback) { + var data = [ + // Must be here to loop across the users that this has been shared with. + %for i, association in enumerate( history.users_shared_with ): + <% shared_with = association.user %> + { + email: "${ shared_with.email }", + id: "${trans.security.encode_id(shared_with.id)}", + text: item_to_label({"email": "${ shared_with.email }", "username": "${ shared_with.username }" }) + }, + %endfor + ]; + callback(data); + }, + tokenSeparators: [',', ' '], + // Required for initSelection + id: function(object) { + return object.id; + }, + ajax: { + url: "${h.url_for(controller="/api/users", action="index")}", + data: function (term) { + return { + f_email: term + }; + }, + dataType: 'json', + quietMillis: 250, + results: function (data) { + var results = []; + // For every user returned by the API call, + $.each(data, function(index, item){ + // If they aren't the requesting user, add to the + // list that will populate the select + if(item.id != "${trans.security.encode_id(trans.user.id)}"){ + results.push({ + id: item.id, + name: item.username, + text: item_to_label(item), + }); + } + }); + return { + results: results + }; + } + }, + createSearchChoice: function(term, data) { + // Check for a user with a matching email. + var matches = _.filter(data, function(user){ + return user.text.indexOf(term) > -1; + }); + // If there aren't any users with matching object labels, then + // display a "default" entry with whatever text they're entering. + // id is set to term as that will be used in + if(matches.length == 0){ + return {id: term, text:term}; + }else{ + // No extra needed + } + } + }); + </script> %else: ## We are sharing restricted histories %if no_change_needed or can_change: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 9 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d2168785082/ Changeset: 4d2168785082 User: erasche2 Date: 2014-11-22 19:18:08+00:00 Summary: Enable user/email list for sharing of datasets Affected #: 4 files diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r 4d216878508215489b7434703336f6ad0b3e3e1e config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -740,6 +740,14 @@ # public. #new_user_dataset_access_role_default_private = False +# Expose user list. Setting this to true will expose the user list to authenticated users. This +# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and +# have the correct user show up. This makes less sense on large public galaxy instances where +# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the +# username and not email, or vice versa. +#expose_user_name = False +#expose_user_email = False + # -- Beta features # Use new tool form diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r 4d216878508215489b7434703336f6ad0b3e3e1e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -92,6 +92,9 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.expose_user_name = kwargs.get( "expose_user_name", False ) + self.expose_user_email = kwargs.get( "expose_user_email", False ) + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r 4d216878508215489b7434703336f6ad0b3e3e1e lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -37,11 +37,19 @@ else: query = query.filter( trans.app.model.User.table.c.deleted == False ) # noqa # special case: user can see only their own user - if not trans.user_is_admin(): + # special case2: if the galaxy admin has specified that other user email/names are + # exposed, we don't want special case #1 + if not trans.user_is_admin() and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) return [item] for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) + # If NOT configured to expose_email, do not expose email UNLESS the user is self, or + # the user is an admin + if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin(): + del item['username'] + if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin(): + del item['email'] # TODO: move into api_values rval.append( item ) return rval diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r 4d216878508215489b7434703336f6ad0b3e3e1e templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -37,9 +37,8 @@ <div style="clear: both"></div><div class="form-row"><label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> + <input type="hidden" id="email_select" name="email" style="float: left; width: 250px; margin-right: 10px;"> + </input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users </div> @@ -55,6 +54,47 @@ <input type="submit" name="share_button" value="Submit"></div></form> + <script type="text/javascript"> + // stolen from templates/admin/impersonate.mako + /* This should be ripped out and made generic at some point for the + * various API bindings available, and once the API can filter list + * queries (term, below) */ + $("#email_select").select2({ + placeholder: "Select a user", + ajax: { + url: "${h.url_for(controller="/api/users", action="index")}", + dataType: 'json', + quietMillis: 250, + matcher: function(term, text) { return text.toUpperCase().indexOf(term.toUpperCase())>=0; }, + data: function (term) { + return { + f_email: term + }; + }, + results: function (data) { + var results = []; + $.each(data, function(index, item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + results.push({ + id: item.email, + name: item.username, + text: text + }); + }); + return { + results: results + }; + } + } + }); + </script> %else: ## We are sharing restricted histories %if no_change_needed or can_change: https://bitbucket.org/galaxy/galaxy-central/commits/ec3301ee4783/ Changeset: ec3301ee4783 User: erasche2 Date: 2014-11-25 19:19:28+00:00 Summary: Must expose username in controller as well Affected #: 1 file diff -r 4d216878508215489b7434703336f6ad0b3e3e1e -r ec3301ee47836c121425f21b9f54ab828774c756 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -130,7 +130,7 @@ histories, credentials, and roles. """ # attributes that will be accessed and returned when calling to_dict( view='collection' ) - dict_collection_visible_keys = ( 'id', 'email' ) + dict_collection_visible_keys = ( 'id', 'email', 'username' ) # attributes that will be accessed and returned when calling to_dict( view='element' ) dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) https://bitbucket.org/galaxy/galaxy-central/commits/bf8dcef796da/ Changeset: bf8dcef796da User: erasche2 Date: 2014-12-17 20:15:23+00:00 Summary: Merged galaxy/galaxy-central into default Affected #: 452 files diff -r ec3301ee47836c121425f21b9f54ab828774c756 -r bf8dcef796dafaec6462f89624ee1adb92e5a45d .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 diff -r ec3301ee47836c121425f21b9f54ab828774c756 -r bf8dcef796dafaec6462f89624ee1adb92e5a45d client/galaxy/scripts/galaxy.library.js --- a/client/galaxy/scripts/galaxy.library.js +++ b/client/galaxy/scripts/galaxy.library.js @@ -36,7 +36,7 @@ initialize: function() { this.routesHit = 0; //keep count of number of routes handled by the application - Backbone.history.on('route', function() { this.routesHit++; }, this); + Backbone.history.on( 'route', function() { this.routesHit++; }, this ); }, routes: { @@ -45,6 +45,7 @@ "library/:library_id/permissions" : "library_permissions", "folders/:folder_id/permissions" : "folder_permissions", "folders/:id" : "folder_content", + "folders/:id/page/:show_page" : "folder_page", "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", @@ -53,13 +54,13 @@ }, back: function() { - if(this.routesHit > 1) { + if( this.routesHit > 1 ) { //more than one route hit -> user did not land to current page directly window.history.back(); } else { //otherwise go to the home page. Use replaceState if available so //the navigation doesn't create an extra history entry - this.navigate('#', {trigger:true, replace:true}); + this.navigate( '#', { trigger:true, replace:true } ); } } }); @@ -71,7 +72,8 @@ with_deleted : false, sort_order : 'asc', sort_by : 'name', - library_page_size : 20 + library_page_size : 20, + folder_page_size : 15 } }); @@ -94,10 +96,10 @@ this.library_router = new LibraryRouter(); - this.library_router.on('route:libraries', function() { - Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); - Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); - }); + this.library_router.on( 'route:libraries', function() { + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); this.library_router.on('route:libraries_page', function( show_page ) { if ( Galaxy.libraries.libraryToolbarView === null ){ @@ -108,66 +110,77 @@ } }); - this.library_router.on('route:folder_content', function(id) { + this.library_router.on( 'route:folder_content', function( id ) { if (Galaxy.libraries.folderToolbarView){ - Galaxy.libraries.folderToolbarView.$el.unbind('click'); - } - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); - }); + Galaxy.libraries.folderToolbarView.$el.unbind( 'click' ); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: id } ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id } ); + }); - this.library_router.on('route:download', function(folder_id, format) { - if ($('#folder_list_body').find(':checked').length === 0) { - mod_toastr.info( 'You must select at least one dataset to download' ); - Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); - } else { - Galaxy.libraries.folderToolbarView.download(folder_id, format); - Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); - } - }); + this.library_router.on( 'route:folder_page', function( id, show_page ) { + if ( Galaxy.libraries.folderToolbarView === null ){ + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( {id: id} ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id, show_page: show_page } ); + } else { + Galaxy.libraries.folderListView.render( { id: id, show_page: parseInt( show_page ) } ) + } + }); - this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); - }); - this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); - }); + this.library_router.on( 'route:download', function( folder_id, format ) { + if ( $( '#folder_list_body' ).find( ':checked' ).length === 0 ) { + mod_toastr.info( 'You must select at least one dataset to download' ); + Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: true, replace: true } ); + } else { + Galaxy.libraries.folderToolbarView.download( folder_id, format ); + Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: false, replace: true } ); + } + }); - this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); - }); + this.library_router.on( 'route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); - this.library_router.on('route:library_permissions', function(library_id){ - if (Galaxy.libraries.libraryView){ - Galaxy.libraries.libraryView.$el.unbind('click'); - } - Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); - }); + this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); - this.library_router.on('route:folder_permissions', function(folder_id){ - if (Galaxy.libraries.folderView){ - Galaxy.libraries.folderView.$el.unbind('click'); - } - Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); - }); - this.library_router.on('route:import_datasets', function(folder_id, source){ - if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){ - Galaxy.libraries.folderToolbarView.showImportModal({source:source}); - } else { - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id}); - Galaxy.libraries.folderToolbarView.showImportModal({source: source}); - } - }); + this.library_router.on( 'route:dataset_permissions', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); + + this.library_router.on( 'route:library_permissions', function(library_id){ + if (Galaxy.libraries.libraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + + this.library_router.on( 'route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + + this.library_router.on( 'route:import_datasets', function( folder_id, source ){ + if ( Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView ){ + Galaxy.libraries.folderToolbarView.showImportModal( { source:source } ); + } else { + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: folder_id } ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: folder_id } ); + Galaxy.libraries.folderToolbarView.showImportModal( { source: source } ); + } + }); Backbone.history.start({pushState: false}); } diff -r ec3301ee47836c121425f21b9f54ab828774c756 -r bf8dcef796dafaec6462f89624ee1adb92e5a45d client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r ec3301ee47836c121425f21b9f54ab828774c756 -r bf8dcef796dafaec6462f89624ee1adb92e5a45d client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -24,7 +24,7 @@ var tab_analysis = new mod_masthead.GalaxyMastheadTab({ id : "analysis", title : "Analyze Data", - content : "root/index", + content : "", title_attribute : 'Analysis home view' }); this.masthead.append(tab_analysis); @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r ec3301ee47836c121425f21b9f54ab828774c756 -r bf8dcef796dafaec6462f89624ee1adb92e5a45d client/galaxy/scripts/galaxy.workflow_editor.canvas.js --- a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js +++ b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js @@ -784,6 +784,8 @@ this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; + this.label = data.label; + this.uuid = data.uuid; this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : []; var node = this; @@ -991,6 +993,8 @@ position : $(node.element).position(), annotation: node.annotation, post_job_actions: node.post_job_actions, + uuid: node.uuid, + label: node.label, workflow_outputs: node.workflow_outputs }; nodes[ node.id ] = node_data; This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/bee9255a428c/ Changeset: bee9255a428c User: erasche2 Date: 2014-12-17 20:54:12+00:00 Summary: Merged galaxy/galaxy-central into default Affected #: 10 files diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff client/galaxy/scripts/mvc/data.js --- a/client/galaxy/scripts/mvc/data.js +++ b/client/galaxy/scripts/mvc/data.js @@ -169,7 +169,8 @@ }); this.$el.append(data_table); var column_names = this.model.get_metadata('column_names'), - header_row = $('<tr/>').appendTo(data_table); + header_container = $('<thead/>').appendTo(data_table), + header_row = $('<tr/>').appendTo(header_container); if (column_names) { header_row.append('<th>' + column_names.join('</th><th>') + '</th>'); } else { diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff lib/galaxy/tools/parser/xml.py --- a/lib/galaxy/tools/parser/xml.py +++ b/lib/galaxy/tools/parser/xml.py @@ -186,6 +186,11 @@ rval = dict( outputs=__parse_output_elems(test_elem), inputs=__parse_input_elems(test_elem, i), + command=__parse_assert_list_from_elem( test_elem.find("assert_command") ), + stdout=__parse_assert_list_from_elem( test_elem.find("assert_stdout") ), + stderr=__parse_assert_list_from_elem( test_elem.find("assert_stderr") ), + expect_exit_code=test_elem.get("expect_exit_code"), + expect_failure=string_as_bool(test_elem.get("expect_failure", False)), ) _copy_to_dict_if_present(test_elem, rval, ["interactor", "num_outputs"]) return rval @@ -222,6 +227,11 @@ return name, file, attributes +def __parse_command_elem( test_elem ): + assert_elem = test_elem.find("command") + return __parse_assert_list_from_elem( assert_elem ) + + def __parse_test_attributes( output_elem, attrib ): assert_list = __parse_assert_list( output_elem ) file = attrib.pop( 'file', None ) @@ -252,6 +262,10 @@ def __parse_assert_list( output_elem ): assert_elem = output_elem.find("assert_contents") + return __parse_assert_list_from_elem( assert_elem ) + + +def __parse_assert_list_from_elem( assert_elem ): assert_list = None def convert_elem(elem): diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff lib/galaxy/tools/parser/yaml.py --- a/lib/galaxy/tools/parser/yaml.py +++ b/lib/galaxy/tools/parser/yaml.py @@ -152,27 +152,47 @@ attributes["metadata"] = {} # TODO assert_list = [] - for key, assertion in attributes.get("asserts", {}).iteritems(): - # TODO: not handling nested assertions correctly, - # not sure these are used though. - children = [] - if "children" in assertion: - children = assertion["children"] - del assertion["children"] - assert_dict = dict( - tag=key, - attributes=assertion, - children=children, - ) - assert_list.append(assert_dict) + assert_list = __to_test_assert_list( attributes.get("asserts", [] ) ) attributes["assert_list"] = assert_list - _ensure_has(attributes, defaults) test_dict["outputs"] = new_outputs + test_dict["command"] = __to_test_assert_list( test_dict.get( "command", [] ) ) + test_dict["stdout"] = __to_test_assert_list( test_dict.get( "stdout", [] ) ) + test_dict["stderr"] = __to_test_assert_list( test_dict.get( "stderr", [] ) ) + test_dict["expect_exit_code"] = test_dict.get( "expect_exit_code", None ) + test_dict["expect_failure"] = test_dict.get( "expect_exit_code", False ) return test_dict +def __to_test_assert_list(assertions): + def expand_dict_form(item): + key, value = item + new_value = value.copy() + new_value["that"] = key + return new_value + + if isinstance( assertions, dict ): + assertions = map(expand_dict_form, assertions.items() ) + + assert_list = [] + for assertion in assertions: + # TODO: not handling nested assertions correctly, + # not sure these are used though. + children = [] + if "children" in assertion: + children = assertion["children"] + del assertion["children"] + assert_dict = dict( + tag=assertion["that"], + attributes=assertion, + children=children, + ) + assert_list.append(assert_dict) + + return assert_list or None # XML variant is None if no assertions made + + class YamlPageSource(PageSource): def __init__(self, inputs_list): diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -127,6 +127,11 @@ if num_outputs: num_outputs = int( num_outputs ) self.num_outputs = num_outputs + self.command_line = test_dict.get("command", None) + self.stdout = test_dict.get("stdout", None) + self.stderr = test_dict.get("stderr", None) + self.expect_exit_code = test_dict.get("expect_exit_code", None) + self.expect_failure = test_dict.get("expect_failure", False) except Exception, e: self.error = True self.exception = e diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -59,7 +59,7 @@ # Rewrite* method for passing REMOTE_USER and a user is # un-authenticated. Any other possible values need to go here as well. path_info = environ.get('PATH_INFO', '') - if environ.get(self.remote_user_header, '(null)') != '(null)': + if not environ.get(self.remote_user_header, '(null)').startswith('(null)'): if not environ[ self.remote_user_header ].count( '@' ): if self.maildomain is not None: environ[ self.remote_user_header ] += '@' + self.maildomain diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -169,7 +169,8 @@ }); this.$el.append(data_table); var column_names = this.model.get_metadata('column_names'), - header_row = $('<tr/>').appendTo(data_table); + header_container = $('<thead/>').appendTo(data_table), + header_row = $('<tr/>').appendTo(header_container); if (column_names) { header_row.append('<th>' + column_names.join('</th><th>') + '</th>'); } else { diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames","mvc/ui/icon-button"],function(k,j,f){var h=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){if(!this.get("metadata")){this._set_metadata()}this.on("change",this._set_metadata,this)},_set_metadata:function(){var n=new h();_.each(_.keys(this.attributes),function(o){if(o.indexOf("metadata_")===0){var p=o.split("metadata_")[1];n.set(p,this.attributes[o]);delete this.attributes[o]}},this);this.set("metadata",n,{silent:true})},get_metadata:function(n){return this.attributes.metadata.get(n)},urlRoot:galaxy_config.root+"api/datasets"});var i=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(n){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var n=this,o=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:n.attributes.chunk_index++}).success(function(p){var q;if(p.ck_data!==""){q=p}else{n.attributes.at_eof=true;q=null}o.resolve(q)});return o}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(n){this.row_count=0;this.loading_chunk=false;new d({model:n.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(o){var n=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(n.model.get_next_chunk()).then(function(p){if(p){n._renderChunk(p);n.loading_chunk=false}n.loading_indicator.hide();n.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var r=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(r);var n=this.model.get_metadata("column_names"),s=$("<tr/>").appendTo(r);if(n){s.append("<th>"+n.join("</th><th>")+"</th>")}else{for(var q=1;q<=this.model.get_metadata("columns");q++){s.append("<th>"+q+"</th>")}}var p=this,o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}else{$.when(p.model.get_next_chunk()).then(function(t){p._renderChunk(t)})}this.scroll_elt.scroll(function(){p.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(q,n,r){var o=$("<td>").text(q);var p=this.model.get_metadata("column_types");if(r!==undefined){o.attr("colspan",r).addClass("stringalign")}else{if(p){if(n<p.length){if(p[n]==="str"||p[n]==="list"){o.addClass("stringalign")}}}}return o},_renderRow:function(n){var o=n.split("\t"),q=$("<tr>"),p=this.model.get_metadata("columns");if(this.row_count%2!==0){q.addClass("dark_row")}if(o.length===p){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this)}else{if(o.length>p){_.each(o.slice(0,p-1),function(s,r){q.append(this._renderCell(s,r))},this);q.append(this._renderCell(o.slice(p-1).join("\t"),p-1))}else{if(p>5&&o.length===p-1){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this);q.append($("<td>"))}else{q.append(this._renderCell(n,0,p))}}}this.row_count++;return q},_renderChunk:function(n){var o=this.$el.find("table");_.each(n.ck_data.split("\n"),function(p,q){if(p!==""){o.append(this._renderRow(p))}},this)}});var g=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);scroll_elt=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var m=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(p){var s=parent.Galaxy;if(s&&s.modal){this.modal=s.modal}if(s&&s.frame){this.frame=s.frame}if(!this.modal||!this.frame){return}var o=p.model;var r=o.get("metadata");if(!o.get("file_ext")){return}this.file_ext=o.get("file_ext");if(this.file_ext=="bed"){if(r.get("chromCol")&&r.get("startCol")&&r.get("endCol")){this.col.chrom=r.get("chromCol")-1;this.col.start=r.get("startCol")-1;this.col.end=r.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function q(u,v){for(var t=0;t<v.length;t++){if(v[t].match(u)){return t}}return -1}this.col.chrom=q("Chrom",r.get("column_names"));this.col.start=q("Pos",r.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(o.id){this.dataset_id=o.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(o.get("url_viz")){this.url_viz=o.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(o.get("genome_build")){this.genome_build=o.get("genome_build")}var n=new f.IconButtonView({model:new f.IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(p.$el);this.$el.append(n.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(s){function r(x){return !isNaN(parseFloat(x))&&isFinite(x)}if(this.col.chrom===null){return}var w=$(s.target).parent();var t=w.children().eq(this.col.chrom).html();var n=w.children().eq(this.col.start).html();var p=this.col.end?w.children().eq(this.col.end).html():n;if(!t.match("^#")&&t!==""&&r(n)){var v={dataset_id:this.dataset_id,gene_region:t+":"+n+"-"+p};var q=w.offset();var o=q.left-10;var u=q.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:u+"px",left:o+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,v,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(n,q,p){var o=this;return function(){var r={};if(p){r["f-dbkey"]=p}$.ajax({url:n+"/list_tracks?"+$.param(r),dataType:"html",error:function(){o.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){o.modal.hide()}}})},success:function(s){o.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){o.modal.hide()},"View in saved visualization":function(){o.modal.show({title:"Add Data to Saved Visualization",body:s,buttons:{Cancel:function(){o.modal.hide()},"Add to visualization":function(){o.modal.hide();o.modal.$el.find("input[name=id]:checked").each(function(){var t=$(this).val();q.id=t;o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})})}}})},"View in new visualization":function(){o.modal.hide();o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})}}})}});return false}}});var l=function(q,o,r,n){var p=new o({model:new q(r)});p.render();if(n){n.append(p.$el)}return p};var c=function(p){if(!p.model){p.model=new i(p.dataset_config)}var o=p.parent_elt;var q=p.embedded;delete p.embedded;delete p.parent_elt;delete p.dataset_config;var n=(q?new m(p):new g(p));n.render();if(o){o.append(n.$el);n.expand_to_container()}return n};return{Dataset:b,TabularDataset:i,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames","mvc/ui/icon-button"],function(k,j,f){var h=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){if(!this.get("metadata")){this._set_metadata()}this.on("change",this._set_metadata,this)},_set_metadata:function(){var n=new h();_.each(_.keys(this.attributes),function(o){if(o.indexOf("metadata_")===0){var p=o.split("metadata_")[1];n.set(p,this.attributes[o]);delete this.attributes[o]}},this);this.set("metadata",n,{silent:true})},get_metadata:function(n){return this.attributes.metadata.get(n)},urlRoot:galaxy_config.root+"api/datasets"});var i=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(n){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var n=this,o=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:n.attributes.chunk_index++}).success(function(p){var q;if(p.ck_data!==""){q=p}else{n.attributes.at_eof=true;q=null}o.resolve(q)});return o}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(n){this.row_count=0;this.loading_chunk=false;new d({model:n.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(o){var n=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(n.model.get_next_chunk()).then(function(p){if(p){n._renderChunk(p);n.loading_chunk=false}n.loading_indicator.hide();n.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var r=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(r);var n=this.model.get_metadata("column_names"),s=$("<thead/>").appendTo(r),t=$("<tr/>").appendTo(s);if(n){t.append("<th>"+n.join("</th><th>")+"</th>")}else{for(var q=1;q<=this.model.get_metadata("columns");q++){t.append("<th>"+q+"</th>")}}var p=this,o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}else{$.when(p.model.get_next_chunk()).then(function(u){p._renderChunk(u)})}this.scroll_elt.scroll(function(){p.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(q,n,r){var o=$("<td>").text(q);var p=this.model.get_metadata("column_types");if(r!==undefined){o.attr("colspan",r).addClass("stringalign")}else{if(p){if(n<p.length){if(p[n]==="str"||p[n]==="list"){o.addClass("stringalign")}}}}return o},_renderRow:function(n){var o=n.split("\t"),q=$("<tr>"),p=this.model.get_metadata("columns");if(this.row_count%2!==0){q.addClass("dark_row")}if(o.length===p){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this)}else{if(o.length>p){_.each(o.slice(0,p-1),function(s,r){q.append(this._renderCell(s,r))},this);q.append(this._renderCell(o.slice(p-1).join("\t"),p-1))}else{if(p>5&&o.length===p-1){_.each(o,function(s,r){q.append(this._renderCell(s,r))},this);q.append($("<td>"))}else{q.append(this._renderCell(n,0,p))}}}this.row_count++;return q},_renderChunk:function(n){var o=this.$el.find("table");_.each(n.ck_data.split("\n"),function(p,q){if(p!==""){o.append(this._renderRow(p))}},this)}});var g=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);scroll_elt=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var m=a.extend({initialize:function(n){a.prototype.initialize.call(this,n);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(p){var s=parent.Galaxy;if(s&&s.modal){this.modal=s.modal}if(s&&s.frame){this.frame=s.frame}if(!this.modal||!this.frame){return}var o=p.model;var r=o.get("metadata");if(!o.get("file_ext")){return}this.file_ext=o.get("file_ext");if(this.file_ext=="bed"){if(r.get("chromCol")&&r.get("startCol")&&r.get("endCol")){this.col.chrom=r.get("chromCol")-1;this.col.start=r.get("startCol")-1;this.col.end=r.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function q(u,v){for(var t=0;t<v.length;t++){if(v[t].match(u)){return t}}return -1}this.col.chrom=q("Chrom",r.get("column_names"));this.col.start=q("Pos",r.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(o.id){this.dataset_id=o.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(o.get("url_viz")){this.url_viz=o.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(o.get("genome_build")){this.genome_build=o.get("genome_build")}var n=new f.IconButtonView({model:new f.IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(p.$el);this.$el.append(n.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(s){function r(x){return !isNaN(parseFloat(x))&&isFinite(x)}if(this.col.chrom===null){return}var w=$(s.target).parent();var t=w.children().eq(this.col.chrom).html();var n=w.children().eq(this.col.start).html();var p=this.col.end?w.children().eq(this.col.end).html():n;if(!t.match("^#")&&t!==""&&r(n)){var v={dataset_id:this.dataset_id,gene_region:t+":"+n+"-"+p};var q=w.offset();var o=q.left-10;var u=q.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:u+"px",left:o+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,v,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(n,q,p){var o=this;return function(){var r={};if(p){r["f-dbkey"]=p}$.ajax({url:n+"/list_tracks?"+$.param(r),dataType:"html",error:function(){o.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){o.modal.hide()}}})},success:function(s){o.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){o.modal.hide()},"View in saved visualization":function(){o.modal.show({title:"Add Data to Saved Visualization",body:s,buttons:{Cancel:function(){o.modal.hide()},"Add to visualization":function(){o.modal.hide();o.modal.$el.find("input[name=id]:checked").each(function(){var t=$(this).val();q.id=t;o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})})}}})},"View in new visualization":function(){o.modal.hide();o.frame.add({title:"Trackster",type:"url",content:n+"/trackster?"+$.param(q)})}}})}});return false}}});var l=function(q,o,r,n){var p=new o({model:new q(r)});p.render();if(n){n.append(p.$el)}return p};var c=function(p){if(!p.model){p.model=new i(p.dataset_config)}var o=p.parent_elt;var q=p.embedded;delete p.embedded;delete p.parent_elt;delete p.dataset_config;var n=(q?new m(p):new g(p));n.render();if(o){o.append(n.$el);n.expand_to_container()}return n};return{Dataset:b,TabularDataset:i,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -1,6 +1,7 @@ import new import sys from base.twilltestcase import TwillTestCase +from base.asserts import verify_assertions from base.interactor import build_interactor, stage_data_in_history, RunToolException from base.instrument import register_job_data from galaxy.tools import DataManagerTool @@ -92,6 +93,9 @@ raise Exception( "Test parse failure" ) def _verify_outputs( self, testdef, history, jobs, shed_tool_id, data_list, galaxy_interactor ): + assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job." + job = jobs[ 0 ] + maxseconds = testdef.maxseconds if testdef.num_outputs is not None: expected = testdef.num_outputs @@ -102,7 +106,33 @@ raise Exception( message ) found_exceptions = [] - job_stdio = None + if testdef.expect_failure: + if testdef.outputs: + raise Exception("Cannot specify outputs in a test expecting failure.") + + # Wait for the job to complete and register expections if the final + # status was not what test was expecting. + job_failed = False + try: + galaxy_interactor.wait_for_job( job[ 'id' ], history, maxseconds ) + except Exception as e: + job_failed = True + if not testdef.expect_failure: + found_exceptions.append(e) + + if not job_failed and testdef.expect_failure: + error = AssertionError("Expected job to fail but Galaxy indicated the job successfully completed.") + found_exceptions.append(error) + + job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] ) + + expect_exit_code = testdef.expect_exit_code + if expect_exit_code is not None: + exit_code = job_stdio["exit_code"] + if str(expect_exit_code) != str(exit_code): + error = AssertionError("Expected job to complete with exit code %s, found %s" % (expect_exit_code, exit_code)) + found_exceptions.append(error) + for output_index, output_tuple in enumerate(testdef.outputs): # Get the correct hid name, outfile, attributes = output_tuple @@ -123,14 +153,25 @@ except Exception as e: if not found_exceptions: # Only print this stuff out once. - for job in jobs: - job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] ) - for stream in ['stdout', 'stderr']: - if stream in job_stdio: - print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) + for stream in ['stdout', 'stderr']: + if stream in job_stdio: + print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) found_exceptions.append(e) - if job_stdio is None: - job_stdio = galaxy_interactor.get_job_stdio( jobs[0][ 'id' ] ) + + other_checks = { + "command_line": "Command produced by the job", + "stdout": "Standard output of the job", + "stderr": "Standard error of the job", + } + for what, description in other_checks.items(): + if getattr( testdef, what, None ) is not None: + try: + data = job_stdio[what] + verify_assertions( data, getattr( testdef, what ) ) + except AssertionError, err: + errmsg = '%s different than expected\n' % description + errmsg += str( err ) + found_exceptions.append( AssertionError( errmsg ) ) if found_exceptions: raise JobOutputsError(found_exceptions, job_stdio) diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff test/functional/tools/job_properties.xml --- /dev/null +++ b/test/functional/tools/job_properties.xml @@ -0,0 +1,62 @@ +<tool id="job_properties" name="Test Job Properties"> + <command> + #if $thebool + echo "The bool is true"; + echo "The bool is really true" 1>&2; + echo "This is a line of text." > $out_file1 + #else + echo "The bool is not true"; + echo "The bool is very not true" 1>&2; + echo "This is a different line of text." > $out_file1; + sh -c "exit 2" + #end if + #if $failbool + ; sh -c "exit 127" + #end if + + </command> + <inputs> + <param name="thebool" type="boolean" label="The boolean property" /> + <param name="failbool" type="boolean" label="The failure property" checked="false" /> + </inputs> + <outputs> + <data name="out_file1" /> + </outputs> + <stdio> + <exit_code range="127" level="fatal" description="Failing exit code." /> + </stdio> + <tests> + <test expect_exit_code="0"> + <param name="thebool" value="true" /> + <output name="out_file1" file="simple_line.txt" /> + <assert_command> + <has_text text="really" /> + </assert_command> + <assert_stdout> + <has_line line="The bool is true" /> + </assert_stdout> + <assert_stderr> + <has_line line="The bool is really true" /> + </assert_stderr> + </test> + <test expect_exit_code="2"> + <param name="thebool" value="false" /> + <output name="out_file1" file="simple_line_alternative.txt" /> + <assert_command> + <has_text text="very not" /> + </assert_command> + <assert_stdout> + <has_line line="The bool is not true" /> + </assert_stdout> + <assert_stderr> + <has_line line="The bool is very not true" /> + </assert_stderr> + </test> + <test expect_exit_coded="127" expect_failure="true"> + <param name="thebool" value="true" /> + <param name="failbool" value="true" /> + </test> + </tests> + <help> + </help> +</tool> diff -r bf8dcef796dafaec6462f89624ee1adb92e5a45d -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -13,6 +13,7 @@ <tool file="multi_output_assign_primary.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /> + <tool file="job_properties.xml" /><tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/cf2636a3d9c3/ Changeset: cf2636a3d9c3 User: erasche2 Date: 2015-02-05 20:43:26+00:00 Summary: Merged galaxy/galaxy-central into default Affected #: 449 files diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d .hgignore --- a/.hgignore +++ b/.hgignore @@ -30,9 +30,9 @@ *.pyc # Galaxy Runtime Files -paster.lock -paster.log -paster.pid +*.lock +*.log +*.pid # Tool Shed Runtime Files tool_shed_webapp.lock @@ -108,12 +108,9 @@ # CSS build artifacts. sprite-*.less -# Local node_modules directories +# Local node_modules and bower_components directories node_modules - -# Testing -selenium-server.jar -selenium_results.html +bower_components # Documentation build files. doc/build diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,16 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02 -9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 -6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 -3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 -425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 -9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 -9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 -81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 -2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 +9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 +8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 +b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 +dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 +19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 +cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 +7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 +0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 +f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 +9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 +4039bfd5584aac053f686197a76ac176253e6f3d latest_2015.01.13 diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -47,15 +47,77 @@ options: { spawn: false } + }, + + // call bower to install libraries and other external resources + "bower-install-simple" : { + options: { + color: true + }, + "prod": { + options: { + production: true + } + }, + "dev": { + options: { + production: false + } + } + }, + // where to move fetched bower components into the build structure (libName: [ bower-location, libs-location ]) + libraryLocations : { + "jquery": [ "dist/jquery.js", "jquery/jquery.js" ], + "jquery-migrate": [ "jquery-migrate.js", "jquery/jquery.migrate.js" ], + "traceKit": [ "tracekit.js", "tracekit.js" ], + "ravenjs": [ "dist/raven.js", "raven.js" ], + "underscore": [ "underscore.js", "underscore.js" ], + "handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ], + "lunr.js": [ "lunr.js", "lunr.js" ] + //"backbone": [ "backbone.js", "backbone/backbone.js" ], + + // these need to be updated and tested + //"require": [ "build/require.js", "require.js" ], + //"d3": [ "d3.js", "d3.js" ], + //"farbtastic": [ "src/farbtastic.js", "farbtastic.js" ], + //"jQTouch": [ "src/reference/jqtouch.js", "jquery/jqtouch.js" ], + //"bib2json": [ "Parser.js", "bibtex.js" ], + //"jquery-form": [ "jquery.form.js", "jquery/jquery.form.js" ], + //"jquery-autocomplete": [ "src/jquery.autocomplete.js", "jquery/jquery.autocomplete.js" ], + //"select2": [ "select2.js", "jquery/select2.js" ], + //"jStorage": [ "jstorage.js", "jquery/jstorage.js" ], + //"jquery.cookie": [ "", "jquery/jquery.cookie.js" ], + //"dynatree": [ "dist/jquery.dynatree.js", "jquery/jquery.dynatree.js" ], + //"jquery-mousewheel": [ "jquery.mousewheel.js", "jquery/jquery.mousewheel.js" ], + //"jquery.event.drag-drop": [ + // [ "event.drag/jquery.event.drag.js", "jquery/jquery.event.drag.js" ], + // [ "event.drag/jquery.event.drop.js", "jquery/jquery.event.drop.js" ] + //], + + // these are complicated by additional css/less + //"toastr": [ "toastr.js", "toastr.js" ], + //"wymeditor": [ "dist/wymeditor/jquery.wymeditor.js", "jquery/jquery.wymeditor.js" ], + //"jstree": [ "jstree.js", "jquery/jstree.js" ], + + // these have been customized by Galaxy + //"bootstrap": [ "dist/js/bootstrap.js", "bootstrap.js" ], + //"jquery-ui": [ + // // multiple components now + // [ "", "jquery/jquery-ui.js" ] + //], + } + }); grunt.loadNpmTasks( 'grunt-contrib-watch' ); grunt.loadNpmTasks( 'grunt-contrib-copy'); - grunt.loadNpmTasks('grunt-exec'); + grunt.loadNpmTasks( 'grunt-bower-install-simple'); + grunt.loadNpmTasks( 'grunt-exec' ); grunt.registerTask( 'pack', [ 'exec' ] ); - grunt.registerTask( 'default', [ 'copy', 'pack' ] ); + grunt.registerTask( 'default', [ 'copy:main', 'pack' ] ); + // -------------------------------------------------------------------------- copy,pack only those changed // adapted from grunt-contrib-watch jslint example @@ -85,4 +147,25 @@ onChange(); }); + // -------------------------------------------------------------------------- fetch/update external libraries + /** copy external libraries from bower components to scripts/libs */ + function copyLibs(){ + var libraryLocations = grunt.config( 'libraryLocations' ); + for( var libName in libraryLocations ){ + if( libraryLocations.hasOwnProperty( libName ) ){ + + var BOWER_DIR = 'bower_components', + location = libraryLocations[ libName ], + source = [ BOWER_DIR, libName, location[0] ].join( '/' ), + destination = 'galaxy/scripts/libs/' + location[1]; + grunt.log.writeln( source + ' -> ' + destination ); + grunt.file.copy( source, destination ); + } + } + } + + grunt.registerTask( 'copy-libs', 'copy external libraries to src', copyLibs ); + grunt.registerTask( 'install-libs', 'fetch external libraries and copy to src', + [ 'bower-install-simple:prod', 'copy-libs' ] ); + }; diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/bower.json --- /dev/null +++ b/client/bower.json @@ -0,0 +1,41 @@ +{ + "name": "galaxy-client-libs", + "version": "0.0.0", + "description": "External client-side libraries used by Galaxy", + "keywords": [ + "galaxy", + "galaxyproject" + ], + "homepage": "usegalaxy.org", + "dependencies": { + "jquery": "~1.11.1", + "traceKit": "*", + "ravenjs": "~1.1.16", + "require": "*", + "underscore": "~1.7.0", + "backbone": "~1.1.2", + "bootstrap": "~3.3.2", + "d3": "~3.5.3", + "farbtastic": "~2.0.0-alpha.1", + "toastr": "~2.1.0", + "jQTouch": "git://github.com/senchalabs/jQTouch#~1.0.0", + "bib2json": "git://github.com/mayanklahiri/bib2json", + "jquery-form": "~3.46.0", + "jquery-autocomplete": "git://github.com/dyve/jquery-autocomplete", + "select2": "~3.5.2", + "jStorage": "~0.4.12", + "jquery.cookie": "~1.4.1", + "dynatree": "~1.2.5", + "jquery-mousewheel": "~3.1.12", + "wymeditor": "~1.0.0-rc.1", + "jstree": "~3.0.9", + "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2", + "jquery.event.drag-drop": "~2.2.1", + "handlebars": "~2.0.0", + "jquery-migrate": "~1.2.1", + "lunr.js": "git://github.com/olivernn/lunr.js.git#~0.5.7" + }, + "resolutions": { + "jquery": "~1.11.1" + } +} diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -364,7 +364,7 @@ var $popover_element = $(this.el).find('.head'); $popover_element.popover({ html: true, - content: 'Please <a href="' + galaxy_config.root + '/user/login">log in</a> or <a href="' + galaxy_config.root + '/user/create">register</a> to use this feature.', + content: 'Please <a href="' + galaxy_config.root + 'user/login?use_panels=True">log in</a> or <a href="' + galaxy_config.root + 'user/create?use_panels=True">register</a> to use this feature.', placement: 'bottom' }).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay setTimeout(function() { diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/galaxy/scripts/galaxy.workflow_editor.canvas.js --- a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js +++ b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js @@ -805,7 +805,7 @@ nodeView.addDataOutput( output ); } ); nodeView.render(); - workflow.node_changed( this ); + workflow.node_changed( this, true); }, update_field_data : function( data ) { var node = this; @@ -1089,17 +1089,25 @@ if ( this.active_node != node ) { this.check_changes_in_active_form(); this.clear_active_node(); - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } node.make_active(); this.active_node = node; } }, - node_changed : function ( node ) { + node_changed : function ( node, force ) { this.has_changes = true; - if ( this.active_node == node ) { + if ( this.active_node == node && (!parent.__NEWTOOLFORM__ || force)) { // Reactive with new form_html this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped) - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } } }, layout : function () { @@ -1305,7 +1313,6 @@ return node; } - var ext_to_type = null; var type_to_type = null; @@ -1863,6 +1870,9 @@ left: x, top: y }); + self.cv.css( { "background-position-x": x, + "background-position-y": y + }); self.update_viewport_overlay(); }; // Dragging within canvas background diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/galaxy/scripts/libs/handlebars.runtime.js --- a/client/galaxy/scripts/libs/handlebars.runtime.js +++ b/client/galaxy/scripts/libs/handlebars.runtime.js @@ -1,6 +1,8 @@ -/* +/*! -Copyright (C) 2011 by Yehuda Katz + handlebars v2.0.0 + +Copyright (C) 2011-2014 by Yehuda Katz Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -20,343 +22,639 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +@license */ - -// lib/handlebars/browser-prefix.js -var Handlebars = {}; - -(function(Handlebars, undefined) { -; -// lib/handlebars/base.js - -Handlebars.VERSION = "1.0.0"; -Handlebars.COMPILER_REVISION = 4; - -Handlebars.REVISION_CHANGES = { - 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it - 2: '== 1.0.0-rc.3', - 3: '== 1.0.0-rc.4', - 4: '>= 1.0.0' -}; - -Handlebars.helpers = {}; -Handlebars.partials = {}; - -var toString = Object.prototype.toString, - functionType = '[object Function]', - objectType = '[object Object]'; - -Handlebars.registerHelper = function(name, fn, inverse) { - if (toString.call(name) === objectType) { - if (inverse || fn) { throw new Handlebars.Exception('Arg not supported with multiple helpers'); } - Handlebars.Utils.extend(this.helpers, name); +/* exported Handlebars */ +(function (root, factory) { + if (typeof define === 'function' && define.amd) { + define([], factory); + } else if (typeof exports === 'object') { + module.exports = factory(); } else { - if (inverse) { fn.not = inverse; } - this.helpers[name] = fn; + root.Handlebars = root.Handlebars || factory(); } -}; - -Handlebars.registerPartial = function(name, str) { - if (toString.call(name) === objectType) { - Handlebars.Utils.extend(this.partials, name); - } else { - this.partials[name] = str; - } -}; - -Handlebars.registerHelper('helperMissing', function(arg) { - if(arguments.length === 2) { - return undefined; - } else { - throw new Error("Missing helper: '" + arg + "'"); - } -}); - -Handlebars.registerHelper('blockHelperMissing', function(context, options) { - var inverse = options.inverse || function() {}, fn = options.fn; - - var type = toString.call(context); - - if(type === functionType) { context = context.call(this); } - - if(context === true) { - return fn(this); - } else if(context === false || context == null) { - return inverse(this); - } else if(type === "[object Array]") { - if(context.length > 0) { - return Handlebars.helpers.each(context, options); - } else { - return inverse(this); - } - } else { - return fn(context); - } -}); - -Handlebars.K = function() {}; - -Handlebars.createFrame = Object.create || function(object) { - Handlebars.K.prototype = object; - var obj = new Handlebars.K(); - Handlebars.K.prototype = null; - return obj; -}; - -Handlebars.logger = { - DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, - - methodMap: {0: 'debug', 1: 'info', 2: 'warn', 3: 'error'}, - - // can be overridden in the host environment - log: function(level, obj) { - if (Handlebars.logger.level <= level) { - var method = Handlebars.logger.methodMap[level]; - if (typeof console !== 'undefined' && console[method]) { - console[method].call(console, obj); - } - } - } -}; - -Handlebars.log = function(level, obj) { Handlebars.logger.log(level, obj); }; - -Handlebars.registerHelper('each', function(context, options) { - var fn = options.fn, inverse = options.inverse; - var i = 0, ret = "", data; - - var type = toString.call(context); - if(type === functionType) { context = context.call(this); } - - if (options.data) { - data = Handlebars.createFrame(options.data); +}(this, function () { +// handlebars/safe-string.js +var __module3__ = (function() { + "use strict"; + var __exports__; + // Build out our basic SafeString type + function SafeString(string) { + this.string = string; } - if(context && typeof context === 'object') { - if(context instanceof Array){ - for(var j = context.length; i<j; i++) { - if (data) { data.index = i; } - ret = ret + fn(context[i], { data: data }); - } - } else { - for(var key in context) { - if(context.hasOwnProperty(key)) { - if(data) { data.key = key; } - ret = ret + fn(context[key], {data: data}); - i++; + SafeString.prototype.toString = function() { + return "" + this.string; + }; + + __exports__ = SafeString; + return __exports__; +})(); + +// handlebars/utils.js +var __module2__ = (function(__dependency1__) { + "use strict"; + var __exports__ = {}; + /*jshint -W004 */ + var SafeString = __dependency1__; + + var escape = { + "&": "&", + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /[&<>"'`]/g; + var possible = /[&<>"'`]/; + + function escapeChar(chr) { + return escape[chr]; + } + + function extend(obj /* , ...source */) { + for (var i = 1; i < arguments.length; i++) { + for (var key in arguments[i]) { + if (Object.prototype.hasOwnProperty.call(arguments[i], key)) { + obj[key] = arguments[i][key]; } } } + + return obj; } - if(i === 0){ - ret = inverse(this); + __exports__.extend = extend;var toString = Object.prototype.toString; + __exports__.toString = toString; + // Sourced from lodash + // https://github.com/bestiejs/lodash/blob/master/LICENSE.txt + var isFunction = function(value) { + return typeof value === 'function'; + }; + // fallback for older versions of Chrome and Safari + /* istanbul ignore next */ + if (isFunction(/x/)) { + isFunction = function(value) { + return typeof value === 'function' && toString.call(value) === '[object Function]'; + }; } + var isFunction; + __exports__.isFunction = isFunction; + /* istanbul ignore next */ + var isArray = Array.isArray || function(value) { + return (value && typeof value === 'object') ? toString.call(value) === '[object Array]' : false; + }; + __exports__.isArray = isArray; - return ret; -}); - -Handlebars.registerHelper('if', function(conditional, options) { - var type = toString.call(conditional); - if(type === functionType) { conditional = conditional.call(this); } - - if(!conditional || Handlebars.Utils.isEmpty(conditional)) { - return options.inverse(this); - } else { - return options.fn(this); - } -}); - -Handlebars.registerHelper('unless', function(conditional, options) { - return Handlebars.helpers['if'].call(this, conditional, {fn: options.inverse, inverse: options.fn}); -}); - -Handlebars.registerHelper('with', function(context, options) { - var type = toString.call(context); - if(type === functionType) { context = context.call(this); } - - if (!Handlebars.Utils.isEmpty(context)) return options.fn(context); -}); - -Handlebars.registerHelper('log', function(context, options) { - var level = options.data && options.data.level != null ? parseInt(options.data.level, 10) : 1; - Handlebars.log(level, context); -}); -; -// lib/handlebars/utils.js - -var errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack']; - -Handlebars.Exception = function(message) { - var tmp = Error.prototype.constructor.apply(this, arguments); - - // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work. - for (var idx = 0; idx < errorProps.length; idx++) { - this[errorProps[idx]] = tmp[errorProps[idx]]; - } -}; -Handlebars.Exception.prototype = new Error(); - -// Build out our basic SafeString type -Handlebars.SafeString = function(string) { - this.string = string; -}; -Handlebars.SafeString.prototype.toString = function() { - return this.string.toString(); -}; - -var escape = { - "&": "&", - "<": "<", - ">": ">", - '"': """, - "'": "'", - "`": "`" -}; - -var badChars = /[&<>"'`]/g; -var possible = /[&<>"'`]/; - -var escapeChar = function(chr) { - return escape[chr] || "&"; -}; - -Handlebars.Utils = { - extend: function(obj, value) { - for(var key in value) { - if(value.hasOwnProperty(key)) { - obj[key] = value[key]; - } - } - }, - - escapeExpression: function(string) { + function escapeExpression(string) { // don't escape SafeStrings, since they're already safe - if (string instanceof Handlebars.SafeString) { + if (string instanceof SafeString) { return string.toString(); - } else if (string == null || string === false) { + } else if (string == null) { return ""; + } else if (!string) { + return string + ''; } // Force a string conversion as this will be done by the append regardless and // the regex test will do this transparently behind the scenes, causing issues if // an object's to string has escaped characters in it. - string = string.toString(); + string = "" + string; if(!possible.test(string)) { return string; } return string.replace(badChars, escapeChar); - }, + } - isEmpty: function(value) { + __exports__.escapeExpression = escapeExpression;function isEmpty(value) { if (!value && value !== 0) { return true; - } else if(toString.call(value) === "[object Array]" && value.length === 0) { + } else if (isArray(value) && value.length === 0) { return true; } else { return false; } } -}; -; -// lib/handlebars/runtime.js -Handlebars.VM = { - template: function(templateSpec) { + __exports__.isEmpty = isEmpty;function appendContextPath(contextPath, id) { + return (contextPath ? contextPath + '.' : '') + id; + } + + __exports__.appendContextPath = appendContextPath; + return __exports__; +})(__module3__); + +// handlebars/exception.js +var __module4__ = (function() { + "use strict"; + var __exports__; + + var errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack']; + + function Exception(message, node) { + var line; + if (node && node.firstLine) { + line = node.firstLine; + + message += ' - ' + line + ':' + node.firstColumn; + } + + var tmp = Error.prototype.constructor.call(this, message); + + // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work. + for (var idx = 0; idx < errorProps.length; idx++) { + this[errorProps[idx]] = tmp[errorProps[idx]]; + } + + if (line) { + this.lineNumber = line; + this.column = node.firstColumn; + } + } + + Exception.prototype = new Error(); + + __exports__ = Exception; + return __exports__; +})(); + +// handlebars/base.js +var __module1__ = (function(__dependency1__, __dependency2__) { + "use strict"; + var __exports__ = {}; + var Utils = __dependency1__; + var Exception = __dependency2__; + + var VERSION = "2.0.0"; + __exports__.VERSION = VERSION;var COMPILER_REVISION = 6; + __exports__.COMPILER_REVISION = COMPILER_REVISION; + var REVISION_CHANGES = { + 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it + 2: '== 1.0.0-rc.3', + 3: '== 1.0.0-rc.4', + 4: '== 1.x.x', + 5: '== 2.0.0-alpha.x', + 6: '>= 2.0.0-beta.1' + }; + __exports__.REVISION_CHANGES = REVISION_CHANGES; + var isArray = Utils.isArray, + isFunction = Utils.isFunction, + toString = Utils.toString, + objectType = '[object Object]'; + + function HandlebarsEnvironment(helpers, partials) { + this.helpers = helpers || {}; + this.partials = partials || {}; + + registerDefaultHelpers(this); + } + + __exports__.HandlebarsEnvironment = HandlebarsEnvironment;HandlebarsEnvironment.prototype = { + constructor: HandlebarsEnvironment, + + logger: logger, + log: log, + + registerHelper: function(name, fn) { + if (toString.call(name) === objectType) { + if (fn) { throw new Exception('Arg not supported with multiple helpers'); } + Utils.extend(this.helpers, name); + } else { + this.helpers[name] = fn; + } + }, + unregisterHelper: function(name) { + delete this.helpers[name]; + }, + + registerPartial: function(name, partial) { + if (toString.call(name) === objectType) { + Utils.extend(this.partials, name); + } else { + this.partials[name] = partial; + } + }, + unregisterPartial: function(name) { + delete this.partials[name]; + } + }; + + function registerDefaultHelpers(instance) { + instance.registerHelper('helperMissing', function(/* [args, ]options */) { + if(arguments.length === 1) { + // A missing field in a {{foo}} constuct. + return undefined; + } else { + // Someone is actually trying to call something, blow up. + throw new Exception("Missing helper: '" + arguments[arguments.length-1].name + "'"); + } + }); + + instance.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse, + fn = options.fn; + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if (isArray(context)) { + if(context.length > 0) { + if (options.ids) { + options.ids = [options.name]; + } + + return instance.helpers.each(context, options); + } else { + return inverse(this); + } + } else { + if (options.data && options.ids) { + var data = createFrame(options.data); + data.contextPath = Utils.appendContextPath(options.data.contextPath, options.name); + options = {data: data}; + } + + return fn(context, options); + } + }); + + instance.registerHelper('each', function(context, options) { + if (!options) { + throw new Exception('Must pass iterator to #each'); + } + + var fn = options.fn, inverse = options.inverse; + var i = 0, ret = "", data; + + var contextPath; + if (options.data && options.ids) { + contextPath = Utils.appendContextPath(options.data.contextPath, options.ids[0]) + '.'; + } + + if (isFunction(context)) { context = context.call(this); } + + if (options.data) { + data = createFrame(options.data); + } + + if(context && typeof context === 'object') { + if (isArray(context)) { + for(var j = context.length; i<j; i++) { + if (data) { + data.index = i; + data.first = (i === 0); + data.last = (i === (context.length-1)); + + if (contextPath) { + data.contextPath = contextPath + i; + } + } + ret = ret + fn(context[i], { data: data }); + } + } else { + for(var key in context) { + if(context.hasOwnProperty(key)) { + if(data) { + data.key = key; + data.index = i; + data.first = (i === 0); + + if (contextPath) { + data.contextPath = contextPath + key; + } + } + ret = ret + fn(context[key], {data: data}); + i++; + } + } + } + } + + if(i === 0){ + ret = inverse(this); + } + + return ret; + }); + + instance.registerHelper('if', function(conditional, options) { + if (isFunction(conditional)) { conditional = conditional.call(this); } + + // Default behavior is to render the positive path if the value is truthy and not empty. + // The `includeZero` option may be set to treat the condtional as purely not empty based on the + // behavior of isEmpty. Effectively this determines if 0 is handled by the positive path or negative. + if ((!options.hash.includeZero && !conditional) || Utils.isEmpty(conditional)) { + return options.inverse(this); + } else { + return options.fn(this); + } + }); + + instance.registerHelper('unless', function(conditional, options) { + return instance.helpers['if'].call(this, conditional, {fn: options.inverse, inverse: options.fn, hash: options.hash}); + }); + + instance.registerHelper('with', function(context, options) { + if (isFunction(context)) { context = context.call(this); } + + var fn = options.fn; + + if (!Utils.isEmpty(context)) { + if (options.data && options.ids) { + var data = createFrame(options.data); + data.contextPath = Utils.appendContextPath(options.data.contextPath, options.ids[0]); + options = {data:data}; + } + + return fn(context, options); + } else { + return options.inverse(this); + } + }); + + instance.registerHelper('log', function(message, options) { + var level = options.data && options.data.level != null ? parseInt(options.data.level, 10) : 1; + instance.log(level, message); + }); + + instance.registerHelper('lookup', function(obj, field) { + return obj && obj[field]; + }); + } + + var logger = { + methodMap: { 0: 'debug', 1: 'info', 2: 'warn', 3: 'error' }, + + // State enum + DEBUG: 0, + INFO: 1, + WARN: 2, + ERROR: 3, + level: 3, + + // can be overridden in the host environment + log: function(level, message) { + if (logger.level <= level) { + var method = logger.methodMap[level]; + if (typeof console !== 'undefined' && console[method]) { + console[method].call(console, message); + } + } + } + }; + __exports__.logger = logger; + var log = logger.log; + __exports__.log = log; + var createFrame = function(object) { + var frame = Utils.extend({}, object); + frame._parent = object; + return frame; + }; + __exports__.createFrame = createFrame; + return __exports__; +})(__module2__, __module4__); + +// handlebars/runtime.js +var __module5__ = (function(__dependency1__, __dependency2__, __dependency3__) { + "use strict"; + var __exports__ = {}; + var Utils = __dependency1__; + var Exception = __dependency2__; + var COMPILER_REVISION = __dependency3__.COMPILER_REVISION; + var REVISION_CHANGES = __dependency3__.REVISION_CHANGES; + var createFrame = __dependency3__.createFrame; + + function checkRevision(compilerInfo) { + var compilerRevision = compilerInfo && compilerInfo[0] || 1, + currentRevision = COMPILER_REVISION; + + if (compilerRevision !== currentRevision) { + if (compilerRevision < currentRevision) { + var runtimeVersions = REVISION_CHANGES[currentRevision], + compilerVersions = REVISION_CHANGES[compilerRevision]; + throw new Exception("Template was precompiled with an older version of Handlebars than the current runtime. "+ + "Please update your precompiler to a newer version ("+runtimeVersions+") or downgrade your runtime to an older version ("+compilerVersions+")."); + } else { + // Use the embedded version info since the runtime doesn't know about this revision yet + throw new Exception("Template was precompiled with a newer version of Handlebars than the current runtime. "+ + "Please update your runtime to a newer version ("+compilerInfo[1]+")."); + } + } + } + + __exports__.checkRevision = checkRevision;// TODO: Remove this line and break up compilePartial + + function template(templateSpec, env) { + /* istanbul ignore next */ + if (!env) { + throw new Exception("No environment passed to template"); + } + if (!templateSpec || !templateSpec.main) { + throw new Exception('Unknown template object: ' + typeof templateSpec); + } + + // Note: Using env.VM references rather than local var references throughout this section to allow + // for external users to override these as psuedo-supported APIs. + env.VM.checkRevision(templateSpec.compiler); + + var invokePartialWrapper = function(partial, indent, name, context, hash, helpers, partials, data, depths) { + if (hash) { + context = Utils.extend({}, context, hash); + } + + var result = env.VM.invokePartial.call(this, partial, name, context, helpers, partials, data, depths); + + if (result == null && env.compile) { + var options = { helpers: helpers, partials: partials, data: data, depths: depths }; + partials[name] = env.compile(partial, { data: data !== undefined, compat: templateSpec.compat }, env); + result = partials[name](context, options); + } + if (result != null) { + if (indent) { + var lines = result.split('\n'); + for (var i = 0, l = lines.length; i < l; i++) { + if (!lines[i] && i + 1 === l) { + break; + } + + lines[i] = indent + lines[i]; + } + result = lines.join('\n'); + } + return result; + } else { + throw new Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } + }; + // Just add water var container = { - escapeExpression: Handlebars.Utils.escapeExpression, - invokePartial: Handlebars.VM.invokePartial, + lookup: function(depths, name) { + var len = depths.length; + for (var i = 0; i < len; i++) { + if (depths[i] && depths[i][name] != null) { + return depths[i][name]; + } + } + }, + lambda: function(current, context) { + return typeof current === 'function' ? current.call(context) : current; + }, + + escapeExpression: Utils.escapeExpression, + invokePartial: invokePartialWrapper, + + fn: function(i) { + return templateSpec[i]; + }, + programs: [], - program: function(i, fn, data) { - var programWrapper = this.programs[i]; - if(data) { - programWrapper = Handlebars.VM.program(i, fn, data); + program: function(i, data, depths) { + var programWrapper = this.programs[i], + fn = this.fn(i); + if (data || depths) { + programWrapper = program(this, i, fn, data, depths); } else if (!programWrapper) { - programWrapper = this.programs[i] = Handlebars.VM.program(i, fn); + programWrapper = this.programs[i] = program(this, i, fn); } return programWrapper; }, + + data: function(data, depth) { + while (data && depth--) { + data = data._parent; + } + return data; + }, merge: function(param, common) { var ret = param || common; - if (param && common) { - ret = {}; - Handlebars.Utils.extend(ret, common); - Handlebars.Utils.extend(ret, param); + if (param && common && (param !== common)) { + ret = Utils.extend({}, common, param); } + return ret; }, - programWithDepth: Handlebars.VM.programWithDepth, - noop: Handlebars.VM.noop, - compilerInfo: null + + noop: env.VM.noop, + compilerInfo: templateSpec.compiler }; - return function(context, options) { + var ret = function(context, options) { options = options || {}; - var result = templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + var data = options.data; - var compilerInfo = container.compilerInfo || [], - compilerRevision = compilerInfo[0] || 1, - currentRevision = Handlebars.COMPILER_REVISION; - - if (compilerRevision !== currentRevision) { - if (compilerRevision < currentRevision) { - var runtimeVersions = Handlebars.REVISION_CHANGES[currentRevision], - compilerVersions = Handlebars.REVISION_CHANGES[compilerRevision]; - throw "Template was precompiled with an older version of Handlebars than the current runtime. "+ - "Please update your precompiler to a newer version ("+runtimeVersions+") or downgrade your runtime to an older version ("+compilerVersions+")."; - } else { - // Use the embedded version info since the runtime doesn't know about this revision yet - throw "Template was precompiled with a newer version of Handlebars than the current runtime. "+ - "Please update your runtime to a newer version ("+compilerInfo[1]+")."; - } + ret._setup(options); + if (!options.partial && templateSpec.useData) { + data = initData(context, data); + } + var depths; + if (templateSpec.useDepths) { + depths = options.depths ? [context].concat(options.depths) : [context]; } - return result; + return templateSpec.main.call(container, context, container.helpers, container.partials, data, depths); }; - }, + ret.isTop = true; - programWithDepth: function(i, fn, data /*, $depth */) { - var args = Array.prototype.slice.call(arguments, 3); + ret._setup = function(options) { + if (!options.partial) { + container.helpers = container.merge(options.helpers, env.helpers); - var program = function(context, options) { + if (templateSpec.usePartial) { + container.partials = container.merge(options.partials, env.partials); + } + } else { + container.helpers = options.helpers; + container.partials = options.partials; + } + }; + + ret._child = function(i, data, depths) { + if (templateSpec.useDepths && !depths) { + throw new Exception('must pass parent depths'); + } + + return program(container, i, templateSpec[i], data, depths); + }; + return ret; + } + + __exports__.template = template;function program(container, i, fn, data, depths) { + var prog = function(context, options) { options = options || {}; - return fn.apply(this, [context, options.data || data].concat(args)); + return fn.call(container, context, container.helpers, container.partials, options.data || data, depths && [context].concat(depths)); }; - program.program = i; - program.depth = args.length; - return program; - }, - program: function(i, fn, data) { - var program = function(context, options) { - options = options || {}; + prog.program = i; + prog.depth = depths ? depths.length : 0; + return prog; + } - return fn(context, options.data || data); - }; - program.program = i; - program.depth = 0; - return program; - }, - noop: function() { return ""; }, - invokePartial: function(partial, name, context, helpers, partials, data) { - var options = { helpers: helpers, partials: partials, data: data }; + __exports__.program = program;function invokePartial(partial, name, context, helpers, partials, data, depths) { + var options = { partial: true, helpers: helpers, partials: partials, data: data, depths: depths }; if(partial === undefined) { - throw new Handlebars.Exception("The partial " + name + " could not be found"); + throw new Exception("The partial " + name + " could not be found"); } else if(partial instanceof Function) { return partial(context, options); - } else if (!Handlebars.compile) { - throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); - } else { - partials[name] = Handlebars.compile(partial, {data: data !== undefined}); - return partials[name](context, options); } } -}; -Handlebars.template = Handlebars.VM.template; -; -// lib/handlebars/browser-suffix.js -})(Handlebars); -; + __exports__.invokePartial = invokePartial;function noop() { return ""; } + + __exports__.noop = noop;function initData(context, data) { + if (!data || !('root' in data)) { + data = data ? createFrame(data) : {}; + data.root = context; + } + return data; + } + return __exports__; +})(__module2__, __module4__, __module1__); + +// handlebars.runtime.js +var __module0__ = (function(__dependency1__, __dependency2__, __dependency3__, __dependency4__, __dependency5__) { + "use strict"; + var __exports__; + /*globals Handlebars: true */ + var base = __dependency1__; + + // Each of these augment the Handlebars object. No need to setup here. + // (This is done to easily share code between commonjs and browse envs) + var SafeString = __dependency2__; + var Exception = __dependency3__; + var Utils = __dependency4__; + var runtime = __dependency5__; + + // For compatibility and usage outside of module systems, make the Handlebars object a namespace + var create = function() { + var hb = new base.HandlebarsEnvironment(); + + Utils.extend(hb, base); + hb.SafeString = SafeString; + hb.Exception = Exception; + hb.Utils = Utils; + hb.escapeExpression = Utils.escapeExpression; + + hb.VM = runtime; + hb.template = function(spec) { + return runtime.template(spec, hb); + }; + + return hb; + }; + + var Handlebars = create(); + Handlebars.create = create; + + Handlebars['default'] = Handlebars; + + __exports__ = Handlebars; + return __exports__; +})(__module1__, __module3__, __module4__, __module2__, __module5__); + + return __module0__; +})); diff -r bee9255a428c5fcda5b3d3b03a7a3f38cdf5d7ff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d client/galaxy/scripts/libs/jquery/jquery.js --- a/client/galaxy/scripts/libs/jquery/jquery.js +++ b/client/galaxy/scripts/libs/jquery/jquery.js @@ -1,5 +1,5 @@ /*! - * jQuery JavaScript Library v1.11.1 + * jQuery JavaScript Library v1.11.2 * http://jquery.com/ * * Includes Sizzle.js @@ -9,7 +9,7 @@ * Released under the MIT license * http://jquery.org/license * - * Date: 2014-05-01T17:42Z + * Date: 2014-12-17T15:27Z */ (function( global, factory ) { @@ -64,7 +64,7 @@ var - version = "1.11.1", + version = "1.11.2", // Define a local copy of jQuery jQuery = function( selector, context ) { @@ -269,7 +269,8 @@ // parseFloat NaNs numeric-cast false positives (null|true|false|"") // ...but misinterprets leading-number strings, particularly hex literals ("0x...") // subtraction forces infinities to NaN - return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0; + // adding 1 corrects loss of precision from parseFloat (#15100) + return !jQuery.isArray( obj ) && (obj - parseFloat( obj ) + 1) >= 0; }, isEmptyObject: function( obj ) { @@ -584,14 +585,14 @@ } var Sizzle = /*! - * Sizzle CSS Selector Engine v1.10.19 + * Sizzle CSS Selector Engine v2.2.0-pre * http://sizzlejs.com/ * - * Copyright 2013 jQuery Foundation, Inc. and other contributors + * Copyright 2008, 2014 jQuery Foundation, Inc. and other contributors * Released under the MIT license * http://jquery.org/license * - * Date: 2014-04-18 + * Date: 2014-12-16 */ (function( window ) { @@ -618,7 +619,7 @@ contains, // Instance-specific data - expando = "sizzle" + -(new Date()), + expando = "sizzle" + 1 * new Date(), preferredDoc = window.document, dirruns = 0, done = 0, @@ -633,7 +634,6 @@ }, // General-purpose constants - strundefined = typeof undefined, MAX_NEGATIVE = 1 << 31, // Instance methods @@ -643,12 +643,13 @@ push_native = arr.push, push = arr.push, slice = arr.slice, - // Use a stripped-down indexOf if we can't use a native one - indexOf = arr.indexOf || function( elem ) { + // Use a stripped-down indexOf as it's faster than native + // http://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { var i = 0, - len = this.length; + len = list.length; for ( ; i < len; i++ ) { - if ( this[i] === elem ) { + if ( list[i] === elem ) { return i; } } @@ -688,6 +689,7 @@ ")\\)|)", // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), @@ -739,6 +741,14 @@ String.fromCharCode( high + 0x10000 ) : // Supplemental Plane codepoint (surrogate pair) String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); }; // Optimize for push.apply( _, NodeList ) @@ -781,19 +791,18 @@ context = context || document; results = results || []; - - if ( !selector || typeof selector !== "string" ) { + nodeType = context.nodeType; + + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + return results; } - if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) { - return []; - } - - if ( documentIsHTML && !seed ) { - - // Shortcuts - if ( (match = rquickExpr.exec( selector )) ) { + if ( !seed && documentIsHTML ) { + + // Try to shortcut find operations when possible (e.g., not under DocumentFragment) + if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { // Speed-up: Sizzle("#ID") if ( (m = match[1]) ) { if ( nodeType === 9 ) { @@ -825,7 +834,7 @@ return results; // Speed-up: Sizzle(".CLASS") - } else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) { + } else if ( (m = match[3]) && support.getElementsByClassName ) { push.apply( results, context.getElementsByClassName( m ) ); return results; } @@ -835,7 +844,7 @@ if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { nid = old = expando; newContext = context; - newSelector = nodeType === 9 && selector; + newSelector = nodeType !== 1 && selector; // qSA works strangely on Element-rooted queries // We can work around this by specifying an extra ID on the root @@ -1022,7 +1031,7 @@ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value */ function testContext( context ) { - return context && typeof context.getElementsByTagName !== strundefined && context; + return context && typeof context.getElementsByTagName !== "undefined" && context; } // Expose support vars for convenience @@ -1046,9 +1055,8 @@ * @returns {Object} Returns the current document */ setDocument = Sizzle.setDocument = function( node ) { - var hasCompare, - doc = node ? node.ownerDocument || node : preferredDoc, - parent = doc.defaultView; + var hasCompare, parent, + doc = node ? node.ownerDocument || node : preferredDoc; // If no document and documentElement is available, return if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { @@ -1058,9 +1066,7 @@ // Set our document document = doc; docElem = doc.documentElement; - - // Support tests - documentIsHTML = !isXML( doc ); + parent = doc.defaultView; // Support: IE>8 // If iframe document is assigned to "document" variable and if iframe has been reloaded, @@ -1069,21 +1075,22 @@ if ( parent && parent !== parent.top ) { // IE11 does not have attachEvent, so all must suffer if ( parent.addEventListener ) { - parent.addEventListener( "unload", function() { - setDocument(); - }, false ); + parent.addEventListener( "unload", unloadHandler, false ); } else if ( parent.attachEvent ) { - parent.attachEvent( "onunload", function() { - setDocument(); - }); - } - } + parent.attachEvent( "onunload", unloadHandler ); + } + } + + /* Support tests + ---------------------------------------------------------------------- */ + documentIsHTML = !isXML( doc ); /* Attributes ---------------------------------------------------------------------- */ // Support: IE<8 - // Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans) + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) support.attributes = assert(function( div ) { div.className = "i"; return !div.getAttribute("className"); @@ -1098,17 +1105,8 @@ return !div.getElementsByTagName("*").length; }); - // Check if getElementsByClassName can be trusted - support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) { - div.innerHTML = "<div class='a'></div><div class='a i'></div>"; - - // Support: Safari<4 - // Catch class over-caching - div.firstChild.className = "i"; - // Support: Opera<10 - // Catch gEBCN failure to find non-leading classes - return div.getElementsByClassName("i").length === 2; - }); + // Support: IE<9 + support.getElementsByClassName = rnative.test( doc.getElementsByClassName ); // Support: IE<10 // Check if getElementById returns elements by name @@ -1122,7 +1120,7 @@ // ID find and filter if ( support.getById ) { Expr.find["ID"] = function( id, context ) { - if ( typeof context.getElementById !== strundefined && documentIsHTML ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { var m = context.getElementById( id ); // Check parentNode to catch when Blackberry 4.6 returns // nodes that are no longer in the document #6963 @@ -1143,7 +1141,7 @@ Expr.filter["ID"] = function( id ) { var attrId = id.replace( runescape, funescape ); return function( elem ) { - var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id"); + var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); return node && node.value === attrId; }; }; @@ -1152,14 +1150,20 @@ // Tag Expr.find["TAG"] = support.getElementsByTagName ? function( tag, context ) { - if ( typeof context.getElementsByTagName !== strundefined ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); } } : + function( tag, context ) { var elem, tmp = [], i = 0, + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too results = context.getElementsByTagName( tag ); // Filter out possible comments @@ -1177,7 +1181,7 @@ // Class Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { - if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) { + if ( documentIsHTML ) { return context.getElementsByClassName( className ); } }; @@ -1206,13 +1210,15 @@ // setting a boolean content attribute, // since its presence should be enough // http://bugs.jquery.com/ticket/12359 - div.innerHTML = "<select msallowclip=''><option selected=''></option></select>"; + docElem.appendChild( div ).innerHTML = "<a id='" + expando + "'></a>" + + "<select id='" + expando + "-\f]' msallowcapture=''>" + + "<option selected=''></option></select>"; // Support: IE8, Opera 11-12.16 // Nothing should be selected when empty strings follow ^= or $= or *= // The test attribute must be unknown in Opera but "safe" for WinRT // http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section - if ( div.querySelectorAll("[msallowclip^='']").length ) { + if ( div.querySelectorAll("[msallowcapture^='']").length ) { rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); } @@ -1222,12 +1228,24 @@ rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); } + // Support: Chrome<29, Android<4.2+, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.7+ + if ( !div.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push("~="); + } + // Webkit/Opera - :checked should return selected option elements // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked // IE8 throws error here and will not see later tests if ( !div.querySelectorAll(":checked").length ) { rbuggyQSA.push(":checked"); } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibing-combinator selector` fails + if ( !div.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push(".#.+[+~]"); + } }); assert(function( div ) { @@ -1344,7 +1362,7 @@ // Maintain original order return sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : 0; } @@ -1371,7 +1389,7 @@ aup ? -1 : bup ? 1 : sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : 0; // If the nodes are siblings, we can do a quick check @@ -1434,7 +1452,7 @@ elem.document && elem.document.nodeType !== 11 ) { return ret; } - } catch(e) {} + } catch (e) {} } return Sizzle( expr, document, null, [ elem ] ).length > 0; @@ -1653,7 +1671,7 @@ return pattern || (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && classCache( className, function( elem ) { - return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" ); + return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" ); }); }, @@ -1675,7 +1693,7 @@ operator === "^=" ? check && result.indexOf( check ) === 0 : operator === "*=" ? check && result.indexOf( check ) > -1 : operator === "$=" ? check && result.slice( -check.length ) === check : - operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : false; }; @@ -1795,7 +1813,7 @@ matched = fn( seed, argument ), i = matched.length; while ( i-- ) { - idx = indexOf.call( seed, matched[i] ); + idx = indexOf( seed, matched[i] ); seed[ idx ] = !( matches[ idx ] = matched[i] ); } }) : @@ -1834,6 +1852,8 @@ function( elem, context, xml ) { input[0] = elem; matcher( input, null, xml, results ); + // Don't keep the element (issue #299) + input[0] = null; return !results.pop(); }; }), @@ -1845,6 +1865,7 @@ }), "contains": markFunction(function( text ) { + text = text.replace( runescape, funescape ); return function( elem ) { return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; }; @@ -2266,7 +2287,7 @@ i = matcherOut.length; while ( i-- ) { if ( (elem = matcherOut[i]) && - (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) { + (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) { seed[temp] = !(results[temp] = elem); } @@ -2301,13 +2322,16 @@ return elem === checkContext; }, implicitRelative, true ), matchAnyContext = addCombinator( function( elem ) { - return indexOf.call( checkContext, elem ) > -1; + return indexOf( checkContext, elem ) > -1; }, implicitRelative, true ), matchers = [ function( elem, context, xml ) { - return ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( (checkContext = context).nodeType ? matchContext( elem, context, xml ) : matchAnyContext( elem, context, xml ) ); + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; } ]; for ( ; i < len; i++ ) { @@ -2557,7 +2581,7 @@ // Sort stability support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; -// Support: Chrome<14 +// Support: Chrome 14-35+ // Always assume duplicates if they aren't passed to the comparison function support.detectDuplicates = !!hasDuplicate; @@ -6115,7 +6139,14 @@ if ( window.getComputedStyle ) { getStyles = function( elem ) { - return elem.ownerDocument.defaultView.getComputedStyle( elem, null ); + // Support: IE<=11+, Firefox<=30+ (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + if ( elem.ownerDocument.defaultView.opener ) { + return elem.ownerDocument.defaultView.getComputedStyle( elem, null ); + } + + return window.getComputedStyle( elem, null ); }; curCSS = function( elem, name, computed ) { @@ -6363,6 +6394,8 @@ reliableMarginRightVal = !parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight ); + + div.removeChild( contents ); } // Support: IE8 @@ -9070,7 +9103,8 @@ } // We can fire global events as of now if asked to - fireGlobals = s.global; + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; // Watch for a new set of requests if ( fireGlobals && jQuery.active++ === 0 ) { @@ -9329,13 +9363,6 @@ }; }); -// Attach a bunch of functions for handling common AJAX events -jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) { - jQuery.fn[ type ] = function( fn ) { - return this.on( type, fn ); - }; -}); - jQuery._evalUrl = function( url ) { return jQuery.ajax({ @@ -9561,8 +9588,9 @@ // Support: IE<10 // Open requests must be manually aborted on unload (#5280) -if ( window.ActiveXObject ) { - jQuery( window ).on( "unload", function() { +// See https://support.microsoft.com/kb/2856746 for more info +if ( window.attachEvent ) { + window.attachEvent( "onunload", function() { for ( var key in xhrCallbacks ) { xhrCallbacks[ key ]( undefined, true ); } @@ -9996,6 +10024,16 @@ +// Attach a bunch of functions for handling common AJAX events +jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) { + jQuery.fn[ type ] = function( fn ) { + return this.on( type, fn ); + }; +}); + + + + jQuery.expr.filters.animated = function( elem ) { return jQuery.grep(jQuery.timers, function( fn ) { return elem === fn.elem; This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/35ddbdd32fb3/ Changeset: 35ddbdd32fb3 User: erasche2 Date: 2015-02-05 23:37:10+00:00 Summary: Fixes for allowing custom entry Affected #: 1 file diff -r cf2636a3d9c3e29a4b045b4112de14f388e2168d -r 35ddbdd32fb3f36aadb7de52721f5ad66b753b8e templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -59,38 +59,85 @@ /* This should be ripped out and made generic at some point for the * various API bindings available, and once the API can filter list * queries (term, below) */ + + var user_id = "${trans.security.encode_id(trans.user.id)}"; + var history_id = "${trans.security.encode_id( history.id )}"; + + function item_to_label(item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + return text; + //return "id:" + item.id + "|e:" + item.email + "|u:" + item.username; + } + $("#email_select").select2({ placeholder: "Select a user", + multiple: true, + initSelection: function(element, callback) { + var data = [ + // Must be here to loop across the users that this has been shared with. + %for i, association in enumerate( history.users_shared_with ): + <% shared_with = association.user %> + { + email: "${ shared_with.email }", + id: "${trans.security.encode_id(shared_with.id)}", + text: item_to_label({"email": "${ shared_with.email }", "username": "${ shared_with.username }" }) + }, + %endfor + ]; + callback(data); + }, + tokenSeparators: [',', ' '], + // Required for initSelection + id: function(object) { + return object.id; + }, ajax: { url: "${h.url_for(controller="/api/users", action="index")}", - dataType: 'json', - quietMillis: 250, - matcher: function(term, text) { return text.toUpperCase().indexOf(term.toUpperCase())>=0; }, data: function (term) { return { f_email: term }; }, + dataType: 'json', + quietMillis: 250, results: function (data) { - var results = []; - $.each(data, function(index, item){ - var text = ""; - if(typeof(item.username) === "string" && typeof(item.email) === "string"){ - text = item.username + " <" + item.email + ">"; - }else if(typeof(item.username) === "string"){ - text = item.username; - }else{ - text = item.email; + var results = []; + // For every user returned by the API call, + $.each(data, function(index, item){ + // If they aren't the requesting user, add to the + // list that will populate the select + if(item.id != "${trans.security.encode_id(trans.user.id)}"){ + results.push({ + id: item.id, + name: item.username, + text: item_to_label(item), + }); } - results.push({ - id: item.email, - name: item.username, - text: text - }); - }); - return { - results: results - }; + }); + return { + results: results + }; + } + }, + createSearchChoice: function(term, data) { + // Check for a user with a matching email. + var matches = _.filter(data, function(user){ + return user.text.indexOf(term) > -1; + }); + // If there aren't any users with matching object labels, then + // display a "default" entry with whatever text they're entering. + // id is set to term as that will be used in + if(matches.length == 0){ + return {id: term, text:term}; + }else{ + // No extra needed } } }); https://bitbucket.org/galaxy/galaxy-central/commits/d45c3a08dc0c/ Changeset: d45c3a08dc0c User: erasche2 Date: 2015-02-09 21:17:40+00:00 Summary: Use suggestion from Carl to fix initial selection Affected #: 1 file diff -r 35ddbdd32fb3f36aadb7de52721f5ad66b753b8e -r d45c3a08dc0c3d4eb0cc3d88160253f4213bd1d4 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,8 +36,9 @@ </div><div style="clear: both"></div><div class="form-row"> + <% existing_emails = [ d.user.email for d in history.users_shared_with ] %><label>Galaxy user emails with which to share histories</label> - <input type="hidden" id="email_select" name="email" style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"></input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users https://bitbucket.org/galaxy/galaxy-central/commits/153887a934e6/ Changeset: 153887a934e6 User: erasche2 Date: 2015-02-12 20:32:10+00:00 Summary: Works correctly now Affected #: 1 file diff -r d45c3a08dc0c3d4eb0cc3d88160253f4213bd1d4 -r 153887a934e6ffa1c79b01ede9850126b2db2a76 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,7 +36,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <% existing_emails = [ d.user.email for d in history.users_shared_with ] %> + <% existing_emails = ','.join([ d.user.email for d in history.users_shared_with ]) %><label>Galaxy user emails with which to share histories</label><input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"></input> https://bitbucket.org/galaxy/galaxy-central/commits/8519e2f351f8/ Changeset: 8519e2f351f8 User: dannon Date: 2015-02-17 14:46:09+00:00 Summary: Merged in erasche2/galaxy-central (pull request #570) Enable user/email list for sharing of datasets Affected #: 5 files diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -786,6 +786,14 @@ # public. #new_user_dataset_access_role_default_private = False +# Expose user list. Setting this to true will expose the user list to authenticated users. This +# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and +# have the correct user show up. This makes less sense on large public galaxy instances where +# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the +# username and not email, or vice versa. +#expose_user_name = False +#expose_user_email = False + # -- Beta features # Use new tool form diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -106,6 +106,9 @@ self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.expose_user_name = kwargs.get( "expose_user_name", False ) + self.expose_user_email = kwargs.get( "expose_user_email", False ) + # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -131,7 +131,7 @@ histories, credentials, and roles. """ # attributes that will be accessed and returned when calling to_dict( view='collection' ) - dict_collection_visible_keys = ( 'id', 'email' ) + dict_collection_visible_keys = ( 'id', 'email', 'username' ) # attributes that will be accessed and returned when calling to_dict( view='element' ) dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -43,11 +43,19 @@ else: query = query.filter( trans.app.model.User.table.c.deleted == False ) # noqa # special case: user can see only their own user - if not trans.user_is_admin(): + # special case2: if the galaxy admin has specified that other user email/names are + # exposed, we don't want special case #1 + if not trans.user_is_admin() and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) return [item] for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) + # If NOT configured to expose_email, do not expose email UNLESS the user is self, or + # the user is an admin + if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin(): + del item['username'] + if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin(): + del item['email'] # TODO: move into api_values rval.append( item ) return rval diff -r 2e3855e25b9bdbe6e574a1795fe3dd4334e85eb7 -r 8519e2f351f82229ccec63f5b33ff719b8837fd5 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -36,10 +36,10 @@ </div><div style="clear: both"></div><div class="form-row"> + <% existing_emails = ','.join([ d.user.email for d in history.users_shared_with ]) %><label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> + <input type="hidden" id="email_select" name="email" value="${ existing_emails }" style="float: left; width: 250px; margin-right: 10px;"> + </input><div class="toolParamHelp" style="clear: both;"> Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users </div> @@ -55,6 +55,94 @@ <input type="submit" name="share_button" value="Submit"></div></form> + <script type="text/javascript"> + // stolen from templates/admin/impersonate.mako + /* This should be ripped out and made generic at some point for the + * various API bindings available, and once the API can filter list + * queries (term, below) */ + + var user_id = "${trans.security.encode_id(trans.user.id)}"; + var history_id = "${trans.security.encode_id( history.id )}"; + + function item_to_label(item){ + var text = ""; + if(typeof(item.username) === "string" && typeof(item.email) === "string"){ + text = item.username + " <" + item.email + ">"; + }else if(typeof(item.username) === "string"){ + text = item.username; + }else{ + text = item.email; + } + return text; + //return "id:" + item.id + "|e:" + item.email + "|u:" + item.username; + } + + $("#email_select").select2({ + placeholder: "Select a user", + multiple: true, + initSelection: function(element, callback) { + var data = [ + // Must be here to loop across the users that this has been shared with. + %for i, association in enumerate( history.users_shared_with ): + <% shared_with = association.user %> + { + email: "${ shared_with.email }", + id: "${trans.security.encode_id(shared_with.id)}", + text: item_to_label({"email": "${ shared_with.email }", "username": "${ shared_with.username }" }) + }, + %endfor + ]; + callback(data); + }, + tokenSeparators: [',', ' '], + // Required for initSelection + id: function(object) { + return object.id; + }, + ajax: { + url: "${h.url_for(controller="/api/users", action="index")}", + data: function (term) { + return { + f_email: term + }; + }, + dataType: 'json', + quietMillis: 250, + results: function (data) { + var results = []; + // For every user returned by the API call, + $.each(data, function(index, item){ + // If they aren't the requesting user, add to the + // list that will populate the select + if(item.id != "${trans.security.encode_id(trans.user.id)}"){ + results.push({ + id: item.id, + name: item.username, + text: item_to_label(item), + }); + } + }); + return { + results: results + }; + } + }, + createSearchChoice: function(term, data) { + // Check for a user with a matching email. + var matches = _.filter(data, function(user){ + return user.text.indexOf(term) > -1; + }); + // If there aren't any users with matching object labels, then + // display a "default" entry with whatever text they're entering. + // id is set to term as that will be used in + if(matches.length == 0){ + return {id: term, text:term}; + }else{ + // No extra needed + } + } + }); + </script> %else: ## We are sharing restricted histories %if no_change_needed or can_change: 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: 2 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d6063120517/ Changeset: 1d6063120517 User: dannon Date: 2015-02-17 14:26:53+00:00 Summary: Update requirements.txt for SQLAlchemy 0.9.8 (tip) Affected #: 1 file diff -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e -r 1d60631205172f867df03cb37eb0cb45cb2811fc requirements.txt --- a/requirements.txt +++ b/requirements.txt @@ -14,14 +14,14 @@ # starting a Galaxy server. Use this in conjunction with the # `GALAXY_ENABLE_EGGS=False` environment variable. # -# Note that except in the case of SQLAlchemy and Whoosh, all dependencies will -# be installed at their newest versions. Galaxy has not been tested with these -# and you may (likely?) run into problems! The Galaxy Team does not support -# using Galaxy with dependency versions other than those in eggs.ini, however, -# if you do find an incompatibility between Galaxy and the latest version, we -# would appreciate if you would investigate and provide a code fix for the -# issue. We are trying to move away from our strict version dependency policy -# and this would greatly help in our efforts. +# Note that except in the case of Whoosh, all dependencies will be installed at +# their newest versions. Galaxy has not been tested with these and you may +# (likely?) run into problems! The Galaxy Team does not support using Galaxy +# with dependency versions other than those in eggs.ini, however, if you do +# find an incompatibility between Galaxy and the latest version, we would +# appreciate if you would investigate and provide a code fix for the issue. We +# are trying to move away from our strict version dependency policy and this +# would greatly help in our efforts. Paste PasteDeploy @@ -32,7 +32,7 @@ repoze.lru Routes WebOb -SQLAlchemy<0.8 +SQLAlchemy Cheetah pycrypto MarkupSafe https://bitbucket.org/galaxy/galaxy-central/commits/2e3855e25b9b/ Changeset: 2e3855e25b9b User: dannon Date: 2015-02-17 14:27:27+00:00 Summary: Merge. 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.

1 0

[galaxyproject/usegalaxy-playbook] caf8ef: Update Test
by GitHub 17 Feb '15

17 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: caf8efbfc7325256a8256362c3e61d96f5729d01 https://github.com/galaxyproject/usegalaxy-playbook/commit/caf8efbfc7325256… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-17 (Tue, 17 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/group_vars/all.yml Log Message: ----------- Update Test

1 0

commit/galaxy-central: natefoo: Allow latest SQLAlchemy in requirements.txt
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/963441341870/ Changeset: 963441341870 User: natefoo Date: 2015-02-17 14:23:34+00:00 Summary: Allow latest SQLAlchemy in requirements.txt Affected #: 1 file diff -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e -r 963441341870819e393a8958b8da7633b4eecb28 requirements.txt --- a/requirements.txt +++ b/requirements.txt @@ -14,14 +14,14 @@ # starting a Galaxy server. Use this in conjunction with the # `GALAXY_ENABLE_EGGS=False` environment variable. # -# Note that except in the case of SQLAlchemy and Whoosh, all dependencies will -# be installed at their newest versions. Galaxy has not been tested with these -# and you may (likely?) run into problems! The Galaxy Team does not support -# using Galaxy with dependency versions other than those in eggs.ini, however, -# if you do find an incompatibility between Galaxy and the latest version, we -# would appreciate if you would investigate and provide a code fix for the -# issue. We are trying to move away from our strict version dependency policy -# and this would greatly help in our efforts. +# Note that except in the case of Whoosh, all dependencies will be installed at +# their newest versions. Galaxy has not been tested with these and you may +# (likely?) run into problems! The Galaxy Team does not support using Galaxy +# with dependency versions other than those in eggs.ini, however, if you do +# find an incompatibility between Galaxy and the latest version, we would +# appreciate if you would investigate and provide a code fix for the issue. We +# are trying to move away from our strict version dependency policy and this +# would greatly help in our efforts. Paste PasteDeploy @@ -32,7 +32,7 @@ repoze.lru Routes WebOb -SQLAlchemy<0.8 +SQLAlchemy Cheetah pycrypto MarkupSafe 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: 11 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8863e5c7e686/ Changeset: 8863e5c7e686 User: dannon Date: 2015-02-14 15:16:13+00:00 Summary: Initial update of SQLAlchemy to 0.8.7. Definitely still needs testing. Affected #: 2 files diff -r b5e29b7e30995a1f67384ce50a490383ee16083c -r 8863e5c7e686f18ddbacabbece22ed8a81c8c45c eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,7 @@ pysqlite = 2.5.6 python_lzo = 1.08_2.03_static PyYAML = 3.10 -SQLAlchemy = 0.7.9 +SQLAlchemy = 0.8.7 ; msgpack_python = 0.2.4 [eggs:noplatform] @@ -62,7 +62,8 @@ Routes = 2.1 simplejson = 2.1.1 six = 1.9.0 -sqlalchemy_migrate = 0.7.2 +sqlalchemy_migrate = 0.9.4 +sqlparse = 0.1.14 ssh = 1.7.14 SVGFig = 1.1.6 Tempita = 0.5.1 diff -r b5e29b7e30995a1f67384ce50a490383ee16083c -r 8863e5c7e686f18ddbacabbece22ed8a81c8c45c lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -4,8 +4,10 @@ from galaxy import eggs eggs.require( "SQLAlchemy" ) -eggs.require( "decorator" ) #Required by sqlalchemy-migrate -eggs.require( "Tempita " ) #Required by sqlalchemy-migrate +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate +eggs.require( "decorator" ) # Required by sqlalchemy-migrate +eggs.require( "Tempita " ) # Required by sqlalchemy-migrate eggs.require( "sqlalchemy-migrate" ) from sqlalchemy import * https://bitbucket.org/galaxy/galaxy-central/commits/d98b6a04b8b8/ Changeset: d98b6a04b8b8 User: dannon Date: 2015-02-14 15:16:44+00:00 Summary: Fix references to (long deprecated) sqlalchemy.exceptions Affected #: 2 files diff -r 8863e5c7e686f18ddbacabbece22ed8a81c8c45c -r d98b6a04b8b85dcd2e0f93876a04079576dda168 lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -54,7 +54,7 @@ try: self.app.model.context.flush() #TODO:?? flush needed for permissions below? If not, make optional - except sqlalchemy.exceptions.IntegrityError, db_err: + except sqlalchemy.exc.IntegrityError, db_err: raise exceptions.Conflict( db_err.message ) # can throw an sqlalx.IntegrityError if username not unique diff -r 8863e5c7e686f18ddbacabbece22ed8a81c8c45c -r d98b6a04b8b85dcd2e0f93876a04079576dda168 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1723,7 +1723,7 @@ active_folders=relation( model.LibraryFolder, primaryjoin=( ( model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id ) & ( not_( model.LibraryFolder.table.c.deleted ) ) ), order_by=asc( model.LibraryFolder.table.c.name ), - lazy=True, #"""sqlalchemy.exceptions.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship.""" + lazy=True, #"""sqlalchemy.exc.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship.""" viewonly=True ), datasets=relation( model.LibraryDataset, primaryjoin=( ( model.LibraryDataset.table.c.folder_id == model.LibraryFolder.table.c.id ) ), https://bitbucket.org/galaxy/galaxy-central/commits/489925951973/ Changeset: 489925951973 User: dannon Date: 2015-02-14 15:35:42+00:00 Summary: Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his. Affected #: 6 files diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 lib/galaxy/model/orm/scripts.py --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -9,6 +9,8 @@ eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) +eggs.require( "six" ) # required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # required by sqlalchemy-migrate eggs.require( "sqlalchemy_migrate" ) from galaxy.util.properties import load_app_properties diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 lib/galaxy/model/tool_shed_install/migrate/check.py --- a/lib/galaxy/model/tool_shed_install/migrate/check.py +++ b/lib/galaxy/model/tool_shed_install/migrate/check.py @@ -4,6 +4,8 @@ from galaxy import eggs eggs.require( "SQLAlchemy" ) +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate eggs.require( "decorator" ) # Required by sqlalchemy-migrate eggs.require( "Tempita " ) # Required by sqlalchemy-migrate eggs.require( "sqlalchemy-migrate" ) diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -2,11 +2,12 @@ from galaxy import eggs -import pkg_resources -pkg_resources.require( "SQLAlchemy" ) -pkg_resources.require( "decorator" ) -pkg_resources.require( "sqlalchemy-migrate" ) -pkg_resources.require( "Tempita" ) +eggs.require( "SQLAlchemy" ) +eggs.require( "decorator" ) +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate +eggs.require( "sqlalchemy-migrate" ) +eggs.require( "Tempita" ) from migrate.versioning import repository, schema diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -5,6 +5,8 @@ from galaxy import eggs eggs.require( "decorator" ) eggs.require( "Tempita" ) +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate eggs.require( "SQLAlchemy" ) eggs.require( "sqlalchemy_migrate" ) from migrate.versioning import repository diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -13,6 +13,8 @@ eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate eggs.require( "sqlalchemy_migrate" ) from migrate.versioning.shell import main diff -r d98b6a04b8b85dcd2e0f93876a04079576dda168 -r 48992595197338928f7b92f8574b192f8c54b577 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -8,11 +8,12 @@ from galaxy import eggs -import pkg_resources -pkg_resources.require( "SQLAlchemy" ) -pkg_resources.require( "decorator" ) -pkg_resources.require( "Tempita " ) -pkg_resources.require( "sqlalchemy-migrate" ) +eggs.require( "SQLAlchemy" ) +eggs.require( "decorator" ) +eggs.require( "Tempita " ) +eggs.require( "six" ) # Required by sqlalchemy-migrate +eggs.require( "sqlparse" ) # Required by sqlalchemy-migrate +eggs.require( "sqlalchemy-migrate" ) from migrate.versioning.shell import main from ConfigParser import SafeConfigParser https://bitbucket.org/galaxy/galaxy-central/commits/477ebeedaf0c/ Changeset: 477ebeedaf0c User: dannon Date: 2015-02-14 15:38:09+00:00 Summary: Merge. Affected #: 1 file diff -r 48992595197338928f7b92f8574b192f8c54b577 -r 477ebeedaf0c845811602e28ea0ec3d3362d3c2a requirements.txt --- a/requirements.txt +++ b/requirements.txt @@ -14,14 +14,14 @@ # starting a Galaxy server. Use this in conjunction with the # `GALAXY_ENABLE_EGGS=False` environment variable. # -# Note that except in the case of SQLAlchemy, all dependencies will be -# installed at their newest versions. Galaxy has not been tested with these and -# you may (likely?) run into problems! The Galaxy Team does not support using -# Galaxy with dependency versions other than those in eggs.ini, however, if you -# do find an incompatibility between Galaxy and the latest version, we would -# appreciate if you would investigate and provide a code fix for the issue. We -# are trying to move away from our strict version dependency policy and this -# would greatly help in our efforts. +# Note that except in the case of SQLAlchemy and Whoosh, all dependencies will +# be installed at their newest versions. Galaxy has not been tested with these +# and you may (likely?) run into problems! The Galaxy Team does not support +# using Galaxy with dependency versions other than those in eggs.ini, however, +# if you do find an incompatibility between Galaxy and the latest version, we +# would appreciate if you would investigate and provide a code fix for the +# issue. We are trying to move away from our strict version dependency policy +# and this would greatly help in our efforts. Paste PasteDeploy https://bitbucket.org/galaxy/galaxy-central/commits/7f780e8c98aa/ Changeset: 7f780e8c98aa User: dannon Date: 2015-02-14 15:55:17+00:00 Summary: Merge. Affected #: 1 file diff -r 477ebeedaf0c845811602e28ea0ec3d3362d3c2a -r 7f780e8c98aa951432ccc89eb00a697c8d957048 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -519,7 +519,7 @@ # This can manipulate the input other than just masking password, # so the previous string replace method is preferred when the # password doesn't appear twice in the url - split._replace(netloc=split.netloc.replace("%s:%s" % (split.username, split.password), '%s:********' % split.username)) + split = split._replace(netloc=split.netloc.replace("%s:%s" % (split.username, split.password), '%s:********' % split.username)) url = urlparse.urlunsplit(split) return url https://bitbucket.org/galaxy/galaxy-central/commits/af7603a13e8d/ Changeset: af7603a13e8d User: dannon Date: 2015-02-14 16:05:54+00:00 Summary: Merge. Affected #: 1 file diff -r 7f780e8c98aa951432ccc89eb00a697c8d957048 -r af7603a13e8d5340f064312808b6ebfb56d1a959 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -548,7 +548,7 @@ pass #process change_format tags - if output.change_format: + if output.change_format is not None: new_format_set = False for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): https://bitbucket.org/galaxy/galaxy-central/commits/4909df6a1dbd/ Changeset: 4909df6a1dbd User: dannon Date: 2015-02-16 16:17:51+00:00 Summary: Merge. Affected #: 14 files diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -21,8 +21,8 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; + this.options.text_enable = 'Set in Advance'; + this.options.text_disable = 'Set at Runtime'; // configure workflow style this.options.is_dynamic = false; @@ -33,7 +33,7 @@ // declare fields as optional Utils.deepeach(options.inputs, function(item) { if (item.type) { - item.optional = (['data', 'data_hidden', 'hidden', 'drill_down', 'repeat', 'conditional']).indexOf(item.type) == -1; + item.optional = (['data', 'data_hidden', 'hidden', 'repeat', 'conditional']).indexOf(item.type) == -1; } }); diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -9,52 +9,56 @@ initialize: function(app, options) { // link app this.app = app; - - // set text labels - this.text_enable = app.options.text_enable || 'Enable'; - this.text_disable = app.options.text_disable || 'Disable'; + + // set text labels and icons for optional button + this.text_enable = app.options.text_enable || 'Enable'; + this.text_disable = app.options.text_disable || 'Disable'; + this.cls_enable = app.options.cls_enable || 'fa fa-plus-square'; + this.cls_disable = app.options.cls_disable || 'fa fa-minus-square'; // link field this.field = options.field; this.default_value = options.default_value; - + // set element this.setElement(this._template(options)); - + // link elements this.$field = this.$el.find('.ui-table-form-field'); - this.$title_optional = this.$el.find('.ui-table-form-title-optional'); + this.$optional = this.$el.find('.ui-table-form-optional'); + this.$optional_icon = this.$el.find('.ui-table-form-optional').find('.icon'); this.$error_text = this.$el.find('.ui-table-form-error-text'); this.$error = this.$el.find('.ui-table-form-error'); - + // add field element this.$field.prepend(this.field.$el); - + // decide wether to expand or collapse optional fields this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - (v === null || v == this.default_value || - Number(v) == Number(this.default_value) || - JSON.stringify(v) == JSON.stringify(this.default_value))); + (v === null || v === '' || v === this.default_value || + String(v) === String(this.default_value) || + Number(v) === Number(this.default_value) || + JSON.stringify(v) === JSON.stringify(this.default_value))); // refresh view this._refresh(); - + // add optional hide/show var self = this; - this.$title_optional.on('click', function() { + this.$optional.on('click', function() { // flip flag self.field.skip = !self.field.skip; - + // refresh view self._refresh(); - + // refresh state self.app.trigger('refresh'); }); }, - + /** Set error text */ error: function(text) { @@ -62,27 +66,46 @@ this.$error.show(); this.$el.addClass('ui-error'); }, - + /** Reset this view */ reset: function() { this.$error.hide(); this.$el.removeClass('ui-error'); }, - + /** Refresh element */ _refresh: function() { + // reset optional button + this.$optional_icon.removeClass().addClass('icon'); + + // identify state if (!this.field.skip) { + // enable input field this.$field.fadeIn('fast'); - this.$title_optional.html(this.text_disable); + this._tooltip(this.text_disable, this.cls_disable); + } else { + // disable input field this.$field.hide(); - this.$title_optional.html(this.text_enable); + this._tooltip(this.text_enable, this.cls_enable); + // reset field value this.field.value && this.field.value(this.default_value); } }, - + + /** Set tooltip text + */ + _tooltip: function(title, cls) { + if (this.$optional.length) { + this.$optional_icon.addClass(cls) + .tooltip({ placement: 'bottom' }) + .attr('data-original-title', title) + .tooltip('fixTitle').tooltip('hide'); + } + }, + /** Main Template */ _template: function(options) { @@ -91,30 +114,34 @@ '<div class="ui-table-form-error ui-error">' + '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' + '</div>' + - '<div class="ui-table-form-title-strong">'; - + '<div class="ui-table-form-title">'; + // is optional if (options.optional) { - tmp += options.label + - '<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'; + tmp += '<div class="ui-table-form-optional">' + + '<i class="icon"/>' + options.label + + '</div>'; } else { - tmp += options.label; + tmp += options.label; } - + // finalize title tmp += '</div>' + '<div class="ui-table-form-field">'; + // add help + tmp += '<div class="ui-table-form-info">'; if (options.help) { - tmp += '<div class="ui-table-form-info">' + options.help + '</div>'; + tmp += options.help; } + tmp += '</div>'; // finalize tmp += '</div>' + '</div>'; - + // return input element return tmp; } }); -}); +}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 client/galaxy/scripts/mvc/ui/ui-button-check.js --- a/client/galaxy/scripts/mvc/ui/ui-button-check.js +++ b/client/galaxy/scripts/mvc/ui/ui-button-check.js @@ -35,7 +35,7 @@ if (new_val !== undefined) { this.current = new_val; this.$el.removeClass() - .addClass('ui-checkbutton') + .addClass('ui-button-check') .addClass(this.options.icons[new_val]); this.options.onchange && this.options.onchange(new_val); } diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -447,7 +447,7 @@ _template: function(options) { var tmpl = '<div id="' + options.id + '" >'; if (options.info) { - tmpl += '<label>' + options.info + '</label>'; + tmpl += '<div>' + options.info + '</div>'; } tmpl += '<hidden value="' + options.value + '"/>' + '</div>'; diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -21,8 +21,8 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; + this.options.text_enable = 'Set in Advance'; + this.options.text_disable = 'Set at Runtime'; // configure workflow style this.options.is_dynamic = false; @@ -33,7 +33,7 @@ // declare fields as optional Utils.deepeach(options.inputs, function(item) { if (item.type) { - item.optional = (['data', 'data_hidden', 'hidden', 'drill_down', 'repeat', 'conditional']).indexOf(item.type) == -1; + item.optional = (['data', 'data_hidden', 'hidden', 'repeat', 'conditional']).indexOf(item.type) == -1; } }); diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -9,52 +9,56 @@ initialize: function(app, options) { // link app this.app = app; - - // set text labels - this.text_enable = app.options.text_enable || 'Enable'; - this.text_disable = app.options.text_disable || 'Disable'; + + // set text labels and icons for optional button + this.text_enable = app.options.text_enable || 'Enable'; + this.text_disable = app.options.text_disable || 'Disable'; + this.cls_enable = app.options.cls_enable || 'fa fa-plus-square'; + this.cls_disable = app.options.cls_disable || 'fa fa-minus-square'; // link field this.field = options.field; this.default_value = options.default_value; - + // set element this.setElement(this._template(options)); - + // link elements this.$field = this.$el.find('.ui-table-form-field'); - this.$title_optional = this.$el.find('.ui-table-form-title-optional'); + this.$optional = this.$el.find('.ui-table-form-optional'); + this.$optional_icon = this.$el.find('.ui-table-form-optional').find('.icon'); this.$error_text = this.$el.find('.ui-table-form-error-text'); this.$error = this.$el.find('.ui-table-form-error'); - + // add field element this.$field.prepend(this.field.$el); - + // decide wether to expand or collapse optional fields this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - (v === null || v == this.default_value || - Number(v) == Number(this.default_value) || - JSON.stringify(v) == JSON.stringify(this.default_value))); + (v === null || v === '' || v === this.default_value || + String(v) === String(this.default_value) || + Number(v) === Number(this.default_value) || + JSON.stringify(v) === JSON.stringify(this.default_value))); // refresh view this._refresh(); - + // add optional hide/show var self = this; - this.$title_optional.on('click', function() { + this.$optional.on('click', function() { // flip flag self.field.skip = !self.field.skip; - + // refresh view self._refresh(); - + // refresh state self.app.trigger('refresh'); }); }, - + /** Set error text */ error: function(text) { @@ -62,27 +66,46 @@ this.$error.show(); this.$el.addClass('ui-error'); }, - + /** Reset this view */ reset: function() { this.$error.hide(); this.$el.removeClass('ui-error'); }, - + /** Refresh element */ _refresh: function() { + // reset optional button + this.$optional_icon.removeClass().addClass('icon'); + + // identify state if (!this.field.skip) { + // enable input field this.$field.fadeIn('fast'); - this.$title_optional.html(this.text_disable); + this._tooltip(this.text_disable, this.cls_disable); + } else { + // disable input field this.$field.hide(); - this.$title_optional.html(this.text_enable); + this._tooltip(this.text_enable, this.cls_enable); + // reset field value this.field.value && this.field.value(this.default_value); } }, - + + /** Set tooltip text + */ + _tooltip: function(title, cls) { + if (this.$optional.length) { + this.$optional_icon.addClass(cls) + .tooltip({ placement: 'bottom' }) + .attr('data-original-title', title) + .tooltip('fixTitle').tooltip('hide'); + } + }, + /** Main Template */ _template: function(options) { @@ -91,30 +114,34 @@ '<div class="ui-table-form-error ui-error">' + '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' + '</div>' + - '<div class="ui-table-form-title-strong">'; - + '<div class="ui-table-form-title">'; + // is optional if (options.optional) { - tmp += options.label + - '<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'; + tmp += '<div class="ui-table-form-optional">' + + '<i class="icon"/>' + options.label + + '</div>'; } else { - tmp += options.label; + tmp += options.label; } - + // finalize title tmp += '</div>' + '<div class="ui-table-form-field">'; + // add help + tmp += '<div class="ui-table-form-info">'; if (options.help) { - tmp += '<div class="ui-table-form-info">' + options.help + '</div>'; + tmp += options.help; } + tmp += '</div>'; // finalize tmp += '</div>' + '</div>'; - + // return input element return tmp; } }); -}); +}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/mvc/ui/ui-button-check.js --- a/static/scripts/mvc/ui/ui-button-check.js +++ b/static/scripts/mvc/ui/ui-button-check.js @@ -35,7 +35,7 @@ if (new_val !== undefined) { this.current = new_val; this.$el.removeClass() - .addClass('ui-checkbutton') + .addClass('ui-button-check') .addClass(this.options.icons[new_val]); this.options.onchange && this.options.onchange(new_val); } diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -447,7 +447,7 @@ _template: function(options) { var tmpl = '<div id="' + options.id + '" >'; if (options.info) { - tmpl += '<label>' + options.info + '</label>'; + tmpl += '<div>' + options.info + '</div>'; } tmpl += '<hidden value="' + options.value + '"/>' + '</div>'; diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(e){var d=this;e={tool_id:this.options.id,tool_version:this.options.version,inputs:e};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="Set in Advance";this.options.text_disable="Set at Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(e){var d=this;e={tool_id:this.options.id,tool_version:this.options.version,inputs:e};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(b===null||b==this.default_value||Number(b)==Number(this.default_value)||JSON.stringify(b)==JSON.stringify(this.default_value)));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.cls_enable=d.options.cls_enable||"fa fa-plus-square";this.cls_disable=d.options.cls_disable||"fa fa-minus-square";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$optional=this.$el.find(".ui-table-form-optional");this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(b===null||b===""||b===this.default_value||String(b)===String(this.default_value)||Number(b)===Number(this.default_value)||JSON.stringify(b)===JSON.stringify(this.default_value)));this._refresh();var a=this;this.$optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon");if(!this.field.skip){this.$field.fadeIn("fast");this._tooltip(this.text_disable,this.cls_disable)}else{this.$field.hide();this._tooltip(this.text_enable,this.cls_enable);this.field.value&&this.field.value(this.default_value)}},_tooltip:function(b,a){if(this.$optional.length){this.$optional_icon.addClass(a).tooltip({placement:"bottom"}).attr("data-original-title",b).tooltip("fixTitle").tooltip("hide")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';if(a.optional){b+='<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>"}else{b+=a.label}b+='</div><div class="ui-table-form-field">';b+='<div class="ui-table-form-info">';if(a.help){b+=a.help}b+="</div>";b+="</div></div>";return b}})}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/packed/mvc/ui/ui-button-check.js --- a/static/scripts/packed/mvc/ui/ui-button-check.js +++ b/static/scripts/packed/mvc/ui/ui-button-check.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($("<div/>"));this.value(this.options.value);var b=this;this.$el.on("click",function(){b.current=(!b.current&&2)||0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b){if(b!==undefined){this.current=b;this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($("<div/>"));this.value(this.options.value);var b=this;this.$el.on("click",function(){b.current=(!b.current&&2)||0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b){if(b!==undefined){this.current=b;this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current}})}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,h,i,m,l,r,d,b){var q=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var c=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));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick){s.onclick()}});$(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="'+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:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var s=this;$(this.el).on("click",function(){$(".tooltip").hide();if(t.onclick&&!s.disabled){t.onclick()}});$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(s){this.$("i").removeClass(this.options.icon).addClass(s);this.options.icon=s},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="'+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));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:false},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!t.persistent){var s=this;this.timeout=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:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}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){if(s.area){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}else{return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}}});var k=Backbone.View.extend({initialize:function(s){this.options=s;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(s){if(s!==undefined){this.$("hidden").val(s)}return this.$("hidden").val()},_template:function(t){var s='<div id="'+t.id+'" >';if(t.info){s+="<label>"+t.info+"</label>"}s+='<hidden value="'+t.value+'"/></div>';return s}});return{Anchor:p,Button:g,ButtonIcon:o,ButtonCheck:d,ButtonMenu:r,Icon:c,Image:q,Input:n,Label:j,Message:a,Modal:b,RadioButton:m.RadioButton,Checkbox:m.Checkbox,Radio:m.Radio,Searchbox:f,Select:h,Hidden:k,Slider:i,Drilldown:l}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,h,i,m,l,r,d,b){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 j=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.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(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:"ui-button btn btn-default",icon:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="'+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var o=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var s=this;$(this.el).on("click",function(){$(".tooltip").hide();if(t.onclick&&!s.disabled){t.onclick()}});$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(s){this.$("i").removeClass(this.options.icon).addClass(s);this.options.icon=s},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="'+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(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:null,status:"info",persistent:false},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},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.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!t.persistent){var s=this;this.timeout=window.setTimeout(function(){if(s.$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.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var n=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$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.$el.val()},_template:function(s){if(s.area){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}else{return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}}});var k=Backbone.View.extend({initialize:function(s){this.options=s;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(s){if(s!==undefined){this.$("hidden").val(s)}return this.$("hidden").val()},_template:function(t){var s='<div id="'+t.id+'" >';if(t.info){s+="<div>"+t.info+"</div>"}s+='<hidden value="'+t.value+'"/></div>';return s}});return{Anchor:p,Button:g,ButtonIcon:o,ButtonCheck:d,ButtonMenu:r,Icon:c,Image:q,Input:n,Label:j,Message:a,Modal:b,RadioButton:m.RadioButton,Checkbox:m.Checkbox,Radio:m.Radio,Searchbox:f,Select:h,Hidden:k,Slider:i,Drilldown:l}}); \ No newline at end of file diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 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,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{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{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} @@ -1414,11 +1414,10 @@ .ui-table tbody,.ui-table-plain tbody{cursor:pointer} .ui-table-plain{table-layout:fixed}.ui-table-plain tbody{cursor:auto !important}.ui-table-plain tbody td{padding:0px !important;border:none !important} .ui-table-plain .ui-table-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;margin-bottom:5px;padding-left:10px} -.ui-table-form-element{margin-top:5px;margin-bottom:5px;overflow:hidden}.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} +.ui-table-form-element{margin-top:5px;margin-bottom:5px;overflow:visible}.ui-table-form-element .ui-table-form-title{font-weight:bold}.ui-table-form-element .ui-table-form-title .ui-table-form-optional{cursor:pointer}.ui-table-form-element .ui-table-form-title .ui-table-form-optional .icon{margin-right:5px;font-size:1.2em} .ui-table-form-element .ui-table-form-field{margin-top:5px} -.ui-table-form-title-strong{font-weight:bold} +.ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-table-form-info{clear:both !important} -.ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} .ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-limited .portlet-header .portlet-title .icon,.ui-portlet-narrow .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} @@ -1435,7 +1434,7 @@ .ui-portlet-limited,.ui-portlet-narrow,.ui-portlet-narrow{max-width:900px} .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-input,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{background:transparent} +.ui-input,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{width:100%;display:block;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;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)}.ui-input[disabled],.ui-input[readonly],fieldset[disabled] .ui-input{cursor:not-allowed;background-color:#eee} .ui-textarea{height:100px !important} .ui-options .ui-options-list{height:100% !important}.ui-options .ui-options-list input[type=checkbox],.ui-options .ui-options-list input[type=radio]{display:none} .ui-options .ui-options-list label{margin:0px;cursor:pointer} @@ -1448,15 +1447,15 @@ .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px} .ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em} .ui-radiobutton i{padding-right:5px} -.ui-checkbutton{font-size:1.2em;width:1.2em;cursor:pointer} +.ui-button-check{font-size:1.2em;width:1.2em;cursor:pointer} .ui-select{position:relative}.ui-select .button{position:absolute;top:5px;right:5px} .ui-select .select2-container{width:100%} .ui-select select{position:relative;top:0px;height:27px;width:100%;padding-left:5px;padding-right:20px;cursor:pointer;background:transparent;-webkit-appearance:none;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px} .ui-select-content .ui-options{float:left;padding-top:2px} .ui-color-picker .ui-color-picker-header{cursor:pointer} -.ui-color-picker .ui-color-picker-value{float:left;border-radius:3px;border:solid 1px #000000;width:12px;height:12px;margin-bottom:10px;margin-right:5px} +.ui-color-picker .ui-color-picker-value{float:left;border-radius:3px;border:solid 1px #000000;width:12px;height:12px;margin-right:5px} .ui-color-picker .ui-color-picker-label{float:left;line-height:1.2em} -.ui-color-picker .ui-color-picker-view{display:none;float:left;overflow:auto;height:100%}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{width:210px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} +.ui-color-picker .ui-color-picker-view{height:100%;overflow:auto;display:none;float:left;margin-top:5px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{width:210px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} .ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} diff -r af7603a13e8d5340f064312808b6ebfb56d1a959 -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -57,7 +57,10 @@ height: auto !important; ul { i { - font-size: 1.2em; margin-right: @ui-margin-horizontal; position: relative; top: 1px; + font-size: 1.2em; + margin-right: @ui-margin-horizontal; + position: relative; + top: 1px; } } .button { @@ -142,26 +145,22 @@ // table form elements .ui-table-form-element { - .ui-table-form-title-optional { + .ui-table-form-title { font-weight: bold; - text-decoration: underline; - cursor: pointer; + .ui-table-form-optional { + cursor: pointer; + .icon { + margin-right: 5px; + font-size: 1.2em; + } + } } .ui-table-form-field { margin-top: @ui-margin-vertical; } margin-top: @ui-margin-vertical; margin-bottom: @ui-margin-vertical; - overflow: hidden; -} - -.ui-table-form-title-strong { - font-weight: bold; -} - -.ui-table-form-info { - &:extend(.toolParamHelp); - clear: both !important; + overflow: visible; } .ui-table-form-separator { @@ -169,6 +168,11 @@ font-size: 0.9em; } +.ui-table-form-info { + &:extend(.toolParamHelp); + clear: both !important; +} + .ui-table-form-error { display: none; .ui-table-form-error-text { @@ -312,8 +316,22 @@ // input elements .ui-input { - &:extend(.form-control); - background: transparent; + width: 100%; + display: block; + height: @input-height-base; + padding: @padding-base-vertical @padding-base-horizontal; + font-size: @font-size-base; + line-height: @line-height-base; + color: @input-color; + border: 1px solid @input-border; + border-radius: @input-border-radius; + .box-shadow(inset 0 1px 1px rgba(0,0,0,.075)); + &[disabled], + &[readonly], + fieldset[disabled] & { + cursor: not-allowed; + background-color: @input-bg-disabled; + } } .ui-textarea { @@ -370,7 +388,6 @@ } } - .ui-form-slider { display: inline-block; width: 100%; @@ -400,7 +417,7 @@ } } -.ui-checkbutton { +.ui-button-check { font-size: 1.2em; width: 1.2em; cursor: pointer; @@ -453,7 +470,6 @@ border: solid 1px #000000; width: 12px; height: 12px; - margin-bottom: 10px; margin-right: 5px; } .ui-color-picker-label { @@ -465,6 +481,7 @@ overflow: auto; display: none; float: left; + margin-top: 5px; .ui-color-picker-panel { width: 210px; .ui-color-picker-content { https://bitbucket.org/galaxy/galaxy-central/commits/4589eb71e192/ Changeset: 4589eb71e192 User: dannon Date: 2015-02-16 20:09:42+00:00 Summary: Bump SQLAlchemy all the way to 0.9.8 Affected #: 1 file diff -r 4909df6a1dbde9ece5f8b5dfd0bbe03597826893 -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,7 @@ pysqlite = 2.5.6 python_lzo = 1.08_2.03_static PyYAML = 3.10 -SQLAlchemy = 0.8.7 +SQLAlchemy = 0.9.8 ; msgpack_python = 0.2.4 [eggs:noplatform] https://bitbucket.org/galaxy/galaxy-central/commits/d004eb0d8be7/ Changeset: d004eb0d8be7 User: dannon Date: 2015-02-17 12:26:52+00:00 Summary: Merge. Affected #: 20 files diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 client/galaxy/scripts/mvc/history/history-model.js --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -205,6 +205,11 @@ if( this.get( 'deleted' ) ){ return jQuery.when(); } return this.save( { deleted: true }, options ); }, + /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */ + purge : function( options ){ + if( this.get( 'purged' ) ){ return jQuery.when(); } + return this.save( { purged: true }, options ); + }, /** save this history, _Mark_ing it as undeleted */ undelete : function( options ){ if( !this.get( 'deleted' ) ){ return jQuery.when(); } diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -128,12 +128,9 @@ /** set up passed-in panel (if any) and listeners */ initialize : function initialize( options ){ options = options || {}; + this.purgeAllowed = !_.isUndefined( options.purgeAllowed )? options.purgeAllowed: false; + this.panel = options.panel || this.createPanel( options ); - //this.log( this + '.init', options ); - // if model, set up model - // create panel sub-view -//TODO: use current-history-panel for current - this.panel = options.panel || this.createPanel( options ); this.setUpListeners(); }, @@ -143,6 +140,7 @@ model : this.model, //el : this.$panel(), // non-current panels should set their hdas to draggable + purgeAllowed: this.purgeAllowed, dragItems : true }, panelOptions ); //this.log( 'panelOptions:', panelOptions ); @@ -245,9 +243,9 @@ }); return $([ '<div class="panel-controls clear flex-row">', - this.controlsLeftTemplate( data ), + this.controlsLeftTemplate({ history: data, view: this }), //'<button class="btn btn-default">Herp</button>', - this.controlsRightTemplate( data ), + this.controlsRightTemplate({ history: data, view: this }), '</div>', '<div class="inner flex-row flex-column-container">', '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', @@ -317,24 +315,24 @@ /** controls template displaying controls above the panel based on this.currentHistory */ controlsLeftTemplate : _.template([ '<div class="pull-left">', - '<% if( history.isCurrentHistory ){ %>', + '<% if( data.history.isCurrentHistory ){ %>', '<strong class="current-label">', _l( 'Current History' ), '</strong>', '<% } else { %>', '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', '<% } %>', '</div>' - ].join( '' ), { variable : 'history' }), + ].join( '' ), { variable : 'data' }), /** controls template displaying controls above the panel based on this.currentHistory */ controlsRightTemplate : _.template([ '<div class="pull-right">', - '<% if( !history.purged ){ %>', + '<% if( !data.history.purged ){ %>', '<div class="panel-menu btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', '<span class="caret"></span>', '</button>', '<ul class="dropdown-menu pull-right" role="menu">', - '<% if( !history.deleted ){ %>', + '<% if( !data.history.deleted ){ %>', '<li><a href="javascript:void(0);" class="copy-history">', _l( 'Copy' ), '</a></li>', @@ -349,14 +347,16 @@ _l( 'Undelete' ), '</a></li>', '<% } %>', - //'<li><a href="javascript:void(0);" class="purge-history">', - // _l( 'Purge' ), - //'</a></li>', + '<% if( data.view.purgeAllowed ){ %>', + '<li><a href="javascript:void(0);" class="purge-history">', + _l( 'Purge' ), + '</a></li>', + '<% } %>', '</ul>', '<% } %>', '</div>', '</div>' - ].join( '' ), { variable: 'history' }), + ].join( '' ), { variable: 'data' }), // ------------------------------------------------------------------------ misc /** String rep */ @@ -491,7 +491,7 @@ // handle setting a history as current, triggered by history.setAsCurrent 'set-as-current': multipanel.setCurrentHistory, // handle deleting a history (depends on whether panels is including deleted or not) - 'change:deleted': multipanel.handleDeletedHistory, + 'change:deleted change:purged': multipanel.handleDeletedHistory, 'sort' : function(){ multipanel.renderColumns( 0 ); } }); @@ -519,7 +519,7 @@ * based on collection.includeDeleted */ handleDeletedHistory : function handleDeletedHistory( history ){ - if( history.get( 'deleted' ) ){ + if( history.get( 'deleted' ) || history.get( 'purged' ) ){ this.log( 'handleDeletedHistory', this.collection.includeDeleted, history ); var multipanel = this; column = multipanel.columnMap[ history.id ]; @@ -584,7 +584,10 @@ /** create a column and its panel and set up any listeners to them */ createColumn : function createColumn( history, options ){ // options passed can be re-used, so extend them before adding the model to prevent pollution for the next - options = _.extend( {}, options, { model: history }); + options = _.extend( {}, options, { + model : history, + purgeAllowed: Galaxy.config.allow_user_dataset_purge + }); var column = new HistoryPanelColumn( options ); if( history.id === this.currentHistoryId ){ column.currentHistory = true; } this.setUpColumnListeners( column ); @@ -1047,21 +1050,19 @@ mainTemplate : _.template([ '<div class="header flex-column-container">', '<div class="control-column control-column-left flex-column">', - '<button class="create-new btn btn-default">', _l( 'Create new' ), '</button> ', + '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ', '<div id="search-histories" class="search-control"></div>', '<div id="search-datasets" class="search-control"></div>', - '<button class="open-more-options btn btn-default">', - //TODO: tip not working - '<span class="fa fa-ellipsis-h" title="More options"></span>', - '</button>', + '<a class="open-more-options btn btn-default" tabindex="3">', + '<span class="fa fa-ellipsis-h"></span>', + '</a>', '</div>', // feedback '<div class="control-column control-column-center flex-column">', - '<div class="header-info">', - '</div>', + '<div class="header-info">', '</div>', '</div>', '<div class="control-column control-column-right flex-column">', - '<button class="done btn btn-default">', _l( 'Done' ), '</button>', + '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>', '</div>', '</div>', // middle - where the columns go diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -36,73 +36,75 @@ 'mvc/visualization/visualization-model' )} ${h.javascript_link( root + 'plugins/visualizations/scatterplot/static/scatterplot-edit.js' )} + +<script type="text/javascript"> +function getModel(){ + return new ScatterplotModel({ + id : ${h.dumps( visualization_id )} || undefined, + title : "${title}", + config : ${h.dumps( config, indent=2 )} + }); +} +function getHDAJSON(){ + return ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}; +} +</script> + </head> ## ---------------------------------------------------------------------------- <body> -%if embedded and saved_visualization: -<figcaption> - <span class="title">${title}</span> - <span class="title-info">${info}</span> -</figcaption> -<figure class="scatterplot-display"></div> + %if embedded and saved_visualization: + <figcaption> + <span class="title">${title}</span> + <span class="title-info">${info}</span> + </figcaption> + <figure class="scatterplot-display"></figure> -<script type="text/javascript"> -$(function(){ - var model = new ScatterplotModel({ - id : ${h.dumps( visualization_id )} || undefined, - title : "${title}", - config : ${h.dumps( config, indent=2 )} + <script type="text/javascript"> + $(function(){ + var display = new ScatterplotDisplay({ + el : $( '.scatterplot-display' ).attr( 'id', 'scatterplot-display-' + '${visualization_id}' ), + model : getModel(), + dataset : getHDAJSON(), + embedded: "${embedded}" + }).render(); + display.fetchData(); + //window.model = model; + //window.display = display; }); - hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, - display = new ScatterplotDisplay({ - el : $( '.scatterplot-display' ).attr( 'id', 'scatterplot-display-' + '${visualization_id}' ), - model : model, - dataset : hdaJson, - embedded: "${embedded}" - }).render(); - display.fetchData(); - //window.model = model; - //window.display = display; -}); + </script> -</script> + %else: + <div class="chart-header"> + <h2>${title or default_title}</h2> + <p>${info}</p> + </div> -%else: -<div class="chart-header"> - <h2>${title or default_title}</h2> - <p>${info}</p> -</div> + <div class="scatterplot-editor"></div> + <script type="text/javascript"> + $(function(){ + var model = getModel(), + hdaJSON = getHDAJSON(), + editor = new ScatterplotConfigEditor({ + el : $( '.scatterplot-editor' ).attr( 'id', 'scatterplot-editor-hda-' + hdaJSON.id ), + model : getModel(), + dataset : hdaJSON + }).render(); + window.editor = editor; -<div class="scatterplot-editor"></div> -<script type="text/javascript"> -$(function(){ - var model = new ScatterplotModel({ - id : ${h.dumps( visualization_id )} || undefined, - title : "${title or default_title}", - config : ${h.dumps( config, indent=2 )} - }), - hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, - editor = new ScatterplotConfigEditor({ - el : $( '.scatterplot-editor' ).attr( 'id', 'scatterplot-editor-hda-' + hdaJson.id ), - model : model, - dataset : hdaJson - }).render(); - window.editor = editor; - - $( '.chart-header h2' ).click( function(){ - var returned = prompt( 'Enter a new title:' ); - if( returned ){ - model.set( 'title', returned ); - } - }); - model.on( 'change:title', function(){ - $( '.chart-header h2' ).text( model.get( 'title' ) ); - document.title = model.get( 'title' ) + ' | ' + '${visualization_display_name}'; - }) -}); - -</script> -%endif + $( '.chart-header h2' ).click( function(){ + var returned = prompt( 'Enter a new title:' ); + if( returned ){ + model.set( 'title', returned ); + } + }); + model.on( 'change:title', function(){ + $( '.chart-header h2' ).text( model.get( 'title' ) ); + document.title = model.get( 'title' ) + ' | ' + '${visualization_display_name}'; + }) + }); + </script> + %endif </body> diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -116,8 +116,8 @@ self.column_filters.append( parsed ) def parse_filter( self, filter_param_str ): - split = filter_param_str.split( '-', 3 ) - if not len( split ) == 3: + split = filter_param_str.split( '-', 2 ) + if not len( split ) >= 3: return None column, op, val = split diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/managers/deletable.py --- a/lib/galaxy/managers/deletable.py +++ b/lib/galaxy/managers/deletable.py @@ -105,7 +105,7 @@ return item.purged if new_purged: self.manager.purge( trans, item, flush=False ) - return self.purged + return item.purged class PurgableFiltersMixin( DeletableFiltersMixin ): diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -260,7 +260,7 @@ 'model_class', 'name', 'deleted', - #'purged', + 'purged', #'count' 'url', #TODO: why these? diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -965,7 +965,7 @@ # Old style dynamic options, no dependency information so there isn't # a lot we can do: if we're dealing with workflows, have to assume # late validation no matter what. - if (self.dynamic_options is not None or self.is_dynamic is not None) and ( trans is None or trans.workflow_building_mode ): + if self.dynamic_options is not None and ( trans is None or trans.workflow_building_mode ): return True # If we got this far, we can actually look at the dependencies # to see if their values will not be available until runtime. diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -63,11 +63,11 @@ self.add_view( 'all', self.serializers.keys() ) def default_serializer( self, trans, config, key ): - return config.get( key, None ) + return getattr( config, key, None ) def add_serializers( self ): def _defaults_to( default ): - return lambda t, i, k: i.get( k, default ) + return lambda t, i, k: getattr( i, k, default ) self.serializers = { #TODO: this is available from user data, remove @@ -90,7 +90,6 @@ 'biostar_url_redirect' : lambda *a: self.url_for( controller='biostar', action='biostar_redirect', qualified=True ), - 'allow_user_creation' : _defaults_to( False ), 'use_remote_user' : _defaults_to( None ), 'remote_user_logout_href' : _defaults_to( '' ), 'enable_cloud_launch' : _defaults_to( False ), @@ -111,7 +110,7 @@ def add_serializers( self ): super( AdminConfigSerializer, self ).add_serializers() def _defaults_to( default ): - return lambda t, i, k: i.get( k, default ) + return lambda t, i, k: getattr( i, k, default ) self.serializers.update({ #TODO: this is available from user data, remove diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -259,23 +259,23 @@ :type id: str :param id: the encoded id of the history to delete :type kwd: dict - :param kwd: (optional) dictionary structure containing: + :param kwd: (optional) dictionary structure containing extra parameters - * payload: a dictionary itself containing: - * purge: if True, purge the history and all of its HDAs + You can purge a history, removing all it's datasets from disk (if unshared), + by passing in ``purge=True`` in the url. :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict - :returns: an error object if an error occurred or a dictionary containing: - * id: the encoded id of the history, - * deleted: if the history was marked as deleted, - * purged: if the history was purged + :returns: the deleted or purged history """ history_id = id # a request body is optional here purge = False + if 'purge' in kwd: + purge = string_as_bool( kwd.get( 'purge' ) ) + # for backwards compat, keep the payload sub-dictionary if kwd.get( 'payload', None ): purge = string_as_bool( kwd['payload'].get( 'purge', False ) ) diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -801,7 +801,6 @@ raise HTTPNotFound( 'No visualization registry (possibly disabled in galaxy.ini)' ) if visualization_name not in registry.plugins: raise HTTPNotFound( 'Unknown or invalid visualization: ' + visualization_name ) - # or redirect to list? plugin = registry.plugins[ visualization_name ] returned = None @@ -824,15 +823,21 @@ # look up template and render template_path = plugin.config[ 'template' ] returned = registry.fill_template( trans, plugin, template_path, - visualization_name=visualization_name, visualization_display_name=visualization_display_name, - title=title, saved_visualization=visualization, visualization_id=encoded_visualization_id, - embedded=embedded, query=kwargs, vars={}, config=config, **resources ) - #NOTE: passing *unparsed* kwargs as query - #NOTE: vars is a dictionary for shared data in the template - # this feels hacky to me but it's what mako recommends: - # http://docs.makotemplates.org/en/latest/runtime.html - #TODO: should vars contain all the passed in arguments? is that even necessary? - #TODO: embedded + visualization_name=visualization_name, + visualization_display_name=visualization_display_name, + title=title, + saved_visualization=visualization, + visualization_id=encoded_visualization_id, + embedded=embedded, + #NOTE: passing *unparsed* kwargs as query + query=kwargs, + #NOTE: vars is a dictionary for shared data in the template + # this feels hacky to me but it's what mako recommends: + # http://docs.makotemplates.org/en/latest/runtime.html + vars={}, + config=config, + **resources + ) except Exception, exception: log.exception( 'error rendering visualization (%s): %s', visualization_name, str( exception ) ) diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -652,9 +652,6 @@ trans.workflow_building_mode = True module = module_factory.new( trans, type, **kwargs ) tool_model = None - if type == 'tool': - tool_model = module.tool.to_json(trans, is_dynamic=False) - module.state.inputs = copy.deepcopy(tool_model['state_inputs']) return { 'type': module.type, 'name': module.get_name(), diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -205,6 +205,11 @@ if( this.get( 'deleted' ) ){ return jQuery.when(); } return this.save( { deleted: true }, options ); }, + /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */ + purge : function( options ){ + if( this.get( 'purged' ) ){ return jQuery.when(); } + return this.save( { purged: true }, options ); + }, /** save this history, _Mark_ing it as undeleted */ undelete : function( options ){ if( !this.get( 'deleted' ) ){ return jQuery.when(); } diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -128,12 +128,9 @@ /** set up passed-in panel (if any) and listeners */ initialize : function initialize( options ){ options = options || {}; + this.purgeAllowed = !_.isUndefined( options.purgeAllowed )? options.purgeAllowed: false; + this.panel = options.panel || this.createPanel( options ); - //this.log( this + '.init', options ); - // if model, set up model - // create panel sub-view -//TODO: use current-history-panel for current - this.panel = options.panel || this.createPanel( options ); this.setUpListeners(); }, @@ -143,6 +140,7 @@ model : this.model, //el : this.$panel(), // non-current panels should set their hdas to draggable + purgeAllowed: this.purgeAllowed, dragItems : true }, panelOptions ); //this.log( 'panelOptions:', panelOptions ); @@ -245,9 +243,9 @@ }); return $([ '<div class="panel-controls clear flex-row">', - this.controlsLeftTemplate( data ), + this.controlsLeftTemplate({ history: data, view: this }), //'<button class="btn btn-default">Herp</button>', - this.controlsRightTemplate( data ), + this.controlsRightTemplate({ history: data, view: this }), '</div>', '<div class="inner flex-row flex-column-container">', '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', @@ -317,24 +315,24 @@ /** controls template displaying controls above the panel based on this.currentHistory */ controlsLeftTemplate : _.template([ '<div class="pull-left">', - '<% if( history.isCurrentHistory ){ %>', + '<% if( data.history.isCurrentHistory ){ %>', '<strong class="current-label">', _l( 'Current History' ), '</strong>', '<% } else { %>', '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', '<% } %>', '</div>' - ].join( '' ), { variable : 'history' }), + ].join( '' ), { variable : 'data' }), /** controls template displaying controls above the panel based on this.currentHistory */ controlsRightTemplate : _.template([ '<div class="pull-right">', - '<% if( !history.purged ){ %>', + '<% if( !data.history.purged ){ %>', '<div class="panel-menu btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', '<span class="caret"></span>', '</button>', '<ul class="dropdown-menu pull-right" role="menu">', - '<% if( !history.deleted ){ %>', + '<% if( !data.history.deleted ){ %>', '<li><a href="javascript:void(0);" class="copy-history">', _l( 'Copy' ), '</a></li>', @@ -349,14 +347,16 @@ _l( 'Undelete' ), '</a></li>', '<% } %>', - //'<li><a href="javascript:void(0);" class="purge-history">', - // _l( 'Purge' ), - //'</a></li>', + '<% if( data.view.purgeAllowed ){ %>', + '<li><a href="javascript:void(0);" class="purge-history">', + _l( 'Purge' ), + '</a></li>', + '<% } %>', '</ul>', '<% } %>', '</div>', '</div>' - ].join( '' ), { variable: 'history' }), + ].join( '' ), { variable: 'data' }), // ------------------------------------------------------------------------ misc /** String rep */ @@ -491,7 +491,7 @@ // handle setting a history as current, triggered by history.setAsCurrent 'set-as-current': multipanel.setCurrentHistory, // handle deleting a history (depends on whether panels is including deleted or not) - 'change:deleted': multipanel.handleDeletedHistory, + 'change:deleted change:purged': multipanel.handleDeletedHistory, 'sort' : function(){ multipanel.renderColumns( 0 ); } }); @@ -519,7 +519,7 @@ * based on collection.includeDeleted */ handleDeletedHistory : function handleDeletedHistory( history ){ - if( history.get( 'deleted' ) ){ + if( history.get( 'deleted' ) || history.get( 'purged' ) ){ this.log( 'handleDeletedHistory', this.collection.includeDeleted, history ); var multipanel = this; column = multipanel.columnMap[ history.id ]; @@ -584,7 +584,10 @@ /** create a column and its panel and set up any listeners to them */ createColumn : function createColumn( history, options ){ // options passed can be re-used, so extend them before adding the model to prevent pollution for the next - options = _.extend( {}, options, { model: history }); + options = _.extend( {}, options, { + model : history, + purgeAllowed: Galaxy.config.allow_user_dataset_purge + }); var column = new HistoryPanelColumn( options ); if( history.id === this.currentHistoryId ){ column.currentHistory = true; } this.setUpColumnListeners( column ); @@ -1047,21 +1050,19 @@ mainTemplate : _.template([ '<div class="header flex-column-container">', '<div class="control-column control-column-left flex-column">', - '<button class="create-new btn btn-default">', _l( 'Create new' ), '</button> ', + '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ', '<div id="search-histories" class="search-control"></div>', '<div id="search-datasets" class="search-control"></div>', - '<button class="open-more-options btn btn-default">', - //TODO: tip not working - '<span class="fa fa-ellipsis-h" title="More options"></span>', - '</button>', + '<a class="open-more-options btn btn-default" tabindex="3">', + '<span class="fa fa-ellipsis-h"></span>', + '</a>', '</div>', // feedback '<div class="control-column control-column-center flex-column">', - '<div class="header-info">', - '</div>', + '<div class="header-info">', '</div>', '</div>', '<div class="control-column control-column-right flex-column">', - '<button class="done btn btn-default">', _l( 'Done' ), '</button>', + '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>', '</div>', '</div>', // middle - where the columns go diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(D){var E=this,C={HistoryDatasetAssociation:"hda",HistoryDatasetCollectionAssociation:"hdca"};E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return((_.isObject(K)&&K.id)&&(_.contains(_.keys(C),K.model_class)))});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){var L=C[K.model_class];F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id,L)}})});F.start();F.done(function(K){G.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.purgeAllowed=!_.isUndefined(C.purgeAllowed)?C.purgeAllowed:false;this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:C,view:this}),this.controlsRightTemplate({history:C,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted change:purged":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")||D.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(D){var E=this,C={HistoryDatasetAssociation:"hda",HistoryDatasetCollectionAssociation:"hdca"};E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return((_.isObject(K)&&K.id)&&(_.contains(_.keys(C),K.model_class)))});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){var L=C[K.model_class];F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id,L)}})});F.start();F.done(function(K){G.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -64,7 +64,10 @@ // remove tmp files clean: { - clean : [ fmt('%s/tmp-site-config.less', out) ] + clean : [ + fmt( '%s/tmp-site-config.less', out ), + fmt( '%s/jstree.css', out ) + ] } }); diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2101,14 +2101,14 @@ .multi-panel-history .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row} .multi-panel-history .flex-row,.multi-panel-history .flex-column{-webkit-flex:1 1 auto;-ms-flex:1 1 auto;flex:1 1 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto} .multi-panel-history .header,.multi-panel-history .footer{width:100%;background-color:lightgrey}.multi-panel-history .header .btn,.multi-panel-history .footer .btn{height:21px} -.multi-panel-history .header{min-height:29px;max-height:29px} +.multi-panel-history .header{min-height:29px;max-height:29px}.multi-panel-history .header .more-options .btn{height:26px} +.multi-panel-history .header .more-options input[type=checkbox]{margin-top:1px} .multi-panel-history .footer{min-height:0;max-height:0} .multi-panel-history .smaller-btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} .multi-panel-history .control-column{margin-top:4px}.multi-panel-history .control-column .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} .multi-panel-history .control-column .search-control{display:inline-block;width:40%}.multi-panel-history .control-column .search-control .search-clear,.multi-panel-history .control-column .search-control .search-loading{margin-top:-22px} .multi-panel-history .control-column input.search-query{font-size:90%;height:21px;line-height:normal;padding:2px 2px 1px 2px} .multi-panel-history .control-column .open-more-options{padding:2px 6px 2px 6px;font-size:100%} -.multi-panel-history .control-column .more-options input[type=checkbox]{margin-top:2px} .multi-panel-history .control-column .header-info{display:inline-block;padding:2px 4px 2px 4px;color:grey} .multi-panel-history .control-column.control-column-right,.multi-panel-history .control-column.control-column-left{margin-right:8px;margin-left:8px}.multi-panel-history .control-column.control-column-right>*,.multi-panel-history .control-column.control-column-left>*{margin:0px 4px 4px 0px} .multi-panel-history .control-column.control-column-center{text-align:center;max-height:22px;-webkit-flex:0 1 auto;-ms-flex:0 1 auto;flex:0 1 auto;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;max-height:22px} diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -650,6 +650,15 @@ .header { min-height: @mph-header_height; max-height: @mph-header_height; + // popover containing sorting and filters + .more-options { + .btn { + height: 26px; + } + input[type=checkbox] { + margin-top: 1px; + } + } } .footer { min-height: @mph-footer_height; @@ -691,9 +700,6 @@ padding: 2px 6px 2px 6px; font-size: 100%; } - .more-options input[type=checkbox] { - margin-top: 2px; - } .header-info { display: inline-block; padding: 2px 4px 2px 4px; diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -118,7 +118,7 @@ "Id of last history (from index) DOES appear after undeletion: " + newFirstHistory.id ); //TODO: show, deleted flag - //TODO: delete, purge flag + // ------------------------------------------------------------------------------------------- UPDATE // ........................................................................................... name @@ -294,6 +294,28 @@ //this.test.comment( 'calling show with /deleted should raise a bad request' ); /* */ + + // ------------------------------------------------------------------------------------------- PURGE + var newHistoryId = null; + spaceghost.then( function(){ + this.test.comment( 'calling purge should mark a history, its datasets, and remove the files' ); + // create new history + var newHistory = this.api.histories.create({ name: 'To Purge' }); + newHistoryId = newHistory.id; + }); + spaceghost.openHomePage().api.tools.thenUploadToCurrent({ + filepath: '../../test-data/1.sam' + }); + spaceghost.then( function(){ + var recent = this.api.histories.show( newHistoryId ); + this.debug( 'size:\n' + recent.size ); + + this.api.assertRaises( function(){ + this.api.histories.delete_( recent.id, true ); + }, 403, 'This instance does not allow user dataset purging', 'Config does not allow thrown' ); + }); + //TODO: a way to set the config to allow user purging and then being able to test this would be good. + //this.debug( this.jsonStr( historyShow ) ); }); diff -r 4589eb71e192251691fbf82aac75b9b0d6f47c18 -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -267,10 +267,12 @@ this.api.spaceghost.info( 'histories.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); // py.payload <-> ajax.data - var payload = ( purge )?({ purge: true }):({}); - return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), { - type : 'DELETE', - data : payload + var url = utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ); + if( purge ){ + url += '?purge=True'; + } + return this.api._ajax( url, { + type : 'DELETE' }); }; https://bitbucket.org/galaxy/galaxy-central/commits/17dd62d9a0b0/ Changeset: 17dd62d9a0b0 User: dannon Date: 2015-02-17 13:37:37+00:00 Summary: Supply remote annotation for complex mappings (also squelches a warning which was causing job failures) Affected #: 1 file diff -r d004eb0d8be7f7b64974f368d16d5fd217a08bd8 -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1457,7 +1457,8 @@ backref=backref( "parent", primaryjoin=( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ), remote_side=[model.HistoryDatasetAssociation.table.c.id], uselist=False ) ), visible_children=relation( model.HistoryDatasetAssociation, - primaryjoin=( ( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ) & ( model.HistoryDatasetAssociation.table.c.visible == True ) ) ), + primaryjoin=( ( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ) & ( model.HistoryDatasetAssociation.table.c.visible == True ) ), + remote_side=[model.HistoryDatasetAssociation.table.c.id] ), tags=relation( model.HistoryDatasetAssociationTagAssociation, order_by=model.HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations' ), annotations=relation( model.HistoryDatasetAssociationAnnotationAssociation, order_by=model.HistoryDatasetAssociationAnnotationAssociation.table.c.id, backref="hdas" ), ratings=relation( model.HistoryDatasetAssociationRatingAssociation, order_by=model.HistoryDatasetAssociationRatingAssociation.table.c.id, backref="hdas" ), @@ -1784,7 +1785,8 @@ backref=backref( "parent", primaryjoin=( model.LibraryDatasetDatasetAssociation.table.c.parent_id == model.LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[model.LibraryDatasetDatasetAssociation.table.c.id] ) ), visible_children=relation( model.LibraryDatasetDatasetAssociation, - primaryjoin=( ( model.LibraryDatasetDatasetAssociation.table.c.parent_id == model.LibraryDatasetDatasetAssociation.table.c.id ) & ( model.LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ), + primaryjoin=( ( model.LibraryDatasetDatasetAssociation.table.c.parent_id == model.LibraryDatasetDatasetAssociation.table.c.id ) & ( model.LibraryDatasetDatasetAssociation.table.c.visible == True ) ), + remote_side=[model.LibraryDatasetDatasetAssociation.table.c.id]), extended_metadata=relation( model.ExtendedMetadata, primaryjoin=( ( model.LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id ) ) https://bitbucket.org/galaxy/galaxy-central/commits/1374a75dfeb1/ Changeset: 1374a75dfeb1 User: dannon Date: 2015-02-17 14:16:11+00:00 Summary: Merge. Affected #: 11 files diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -577b270034b48d90e58ffbea296e700d229545c9 latest_2015.01.13 +d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13 diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -443,7 +443,7 @@ @web.require_admin def import_workflow( self, trans, workflow_name, repository_id, **kwd ): """Import a workflow contained in an installed tool shed repository into Galaxy.""" - message = escape( kwd.get( 'message', '' ) ) + message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) @@ -480,7 +480,7 @@ tool shed repository. """ # Get the tool_shed_repository from one of the tool_dependencies. - message = escape( kwd.get( 'message', '' ) ) + message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) err_msg = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/galaxy/controllers/library_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/library_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_admin.py @@ -162,14 +162,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - message = "The new library named '%s' has been created" % library.name + message = "The new library named '%s' has been created" % escape( library.name ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( library.id ), message=message, status='done' ) ) - return trans.fill_template( '/admin/library/new_library.mako', message=escape( message ), status=escape( status ) ) + return trans.fill_template( '/admin/library/new_library.mako', message=message, status=escape( status ) ) @web.expose @web.require_admin def delete_library( self, trans, id, **kwd ): @@ -222,7 +222,7 @@ trans.sa_session.add( library_folder ) trans.sa_session.flush() if not library.deleted: - message = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) + message = "Library '%s' has not been marked deleted, so it cannot be purged" % escape( library.name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', message=message, @@ -232,7 +232,7 @@ library.purged = True trans.sa_session.add( library ) trans.sa_session.flush() - message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name + message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % escape( library.name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', message=message, diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -248,7 +248,7 @@ trans.sa_session.refresh( library ) # Copy the permissions to the root folder trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) - message = "Permissions updated for library '%s'." % library.name + message = "Permissions updated for library '%s'." % escape( library.name ) return trans.response.send_redirect( web.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, @@ -310,7 +310,7 @@ if info_association and ( not( inherited ) or info_association.inheritable ): widgets = new_folder.get_template_widgets( trans ) if info_association: - message = "The new folder named '%s' has been added to the data library. " % new_folder.name + message = "The new folder named '%s' has been added to the data library. " % escape( new_folder.name ) message += "Additional information about this folder may be added using the inherited template." return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, @@ -325,7 +325,7 @@ message=escape( message ), status='done' ) # If not inheritable info_association, redirect to the library. - message = "The new folder named '%s' has been added to the data library." % new_folder.name + message = "The new folder named '%s' has been added to the data library." % escape( new_folder.name ) # SM: This is the second place where the API controller would # reference the library id: return trans.response.send_redirect( web.url_for( controller='library_common', @@ -373,7 +373,7 @@ folder.description = new_description trans.sa_session.add( folder ) trans.sa_session.flush() - message = "Information updated for folder '%s'." % folder.name + message = "Information updated for folder '%s'." % escape( folder.name ) return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_info', cntrller=cntrller, @@ -429,7 +429,7 @@ permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles trans.app.security_agent.set_all_library_permissions( trans, folder, permissions ) trans.sa_session.refresh( folder ) - message = "Permissions updated for folder '%s'." % folder.name + message = "Permissions updated for folder '%s'." % escape( folder.name ) return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, @@ -498,10 +498,10 @@ if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( kwd.get( 'datatype' ) ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, kwd.get( 'datatype' ) ) trans.sa_session.flush() - message = "Data type changed for library dataset '%s'." % ldda.name + message = "Data type changed for library dataset '%s'." % escape( ldda.name ) status = 'done' else: - message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, kwd.get( 'datatype' ) ) + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( escape( ldda.extension ), escape( kwd.get( 'datatype' ) ) ) status = 'error' else: message = "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." @@ -532,7 +532,7 @@ setattr( ldda.metadata, name, spec.unwrap( kwd.get( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_setting_metadata( ldda ) - message = "Attributes updated for library dataset '%s'." % ldda.name + message = "Attributes updated for library dataset '%s'." % escape( ldda.name ) status = 'done' else: message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." @@ -546,7 +546,7 @@ if name not in [ 'name', 'info', 'dbkey' ]: if spec.get( 'default' ): setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - message = "Attributes have been queued to be updated for library dataset '%s'." % ldda.name + message = "Attributes have been queued to be updated for library dataset '%s'." % escape( ldda.name ) status = 'done' trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':ldda } ) else: @@ -570,7 +570,7 @@ self.delete_extended_metadata(trans, ex_obj) ex_obj = self.create_extended_metadata(trans, payload) self.set_item_extended_metadata_obj(trans, ldda, ex_obj) - message = "Updated Extended metadata '%s'." % ldda.name + message = "Updated Extended metadata '%s'." % escape( ldda.name ) status = 'done' else: message = "LDDA not found" @@ -581,7 +581,7 @@ if ex_obj is not None: self.unset_item_extended_metadata_obj(trans, ldda) self.delete_extended_metadata(trans, ex_obj) - message = "Deleted Extended metadata '%s'." % ldda.name + message = "Deleted Extended metadata '%s'." % escape( ldda.name ) status = 'done' @@ -658,7 +658,7 @@ @web.expose def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ): - message = escape( kwd.get( 'message', '' ) ) + message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) @@ -744,7 +744,7 @@ trans.app.security_agent.set_all_library_permissions( trans, ldda, permissions ) trans.sa_session.refresh( ldda ) if len( lddas ) == 1: - message = "Permissions updated for dataset '%s'." % ldda.name + message = "Permissions updated for dataset '%s'." % escape( ldda.name ) else: message = 'Permissions updated for %d datasets.' % len( lddas ) status= 'done' @@ -937,13 +937,13 @@ ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] created_ldda_ids=",".join( ldda_id_list ) if replace_dataset: - message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, escape( replace_dataset_name ), escape( folder.name ) ) else: if not folder.parent: # Libraries have the same name as their root_folder - message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, escape( folder.name ) ) else: - message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, escape( folder.name ) ) if cntrller == 'library_admin': message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." status='done' @@ -1399,13 +1399,13 @@ ldda_id_list = created_ldda_ids.split( ',' ) total_added = len( ldda_id_list ) if replace_dataset: - message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, escape( replace_dataset.name ), escape( folder.name ) ) else: if not folder.parent: # Libraries have the same name as their root_folder - message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, escape( folder.name ) ) else: - message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, escape( folder.name ) ) if cntrller == 'library_admin': message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." else: @@ -1591,7 +1591,7 @@ library_dataset.info = new_info trans.sa_session.add( library_dataset ) trans.sa_session.flush() - message = "Information updated for library dataset '%s'." % library_dataset.name + message = "Information updated for library dataset '%s'." % escape( library_dataset.name ) status = 'done' # See if we have any associated templates widgets = [] @@ -1648,7 +1648,7 @@ # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation trans.app.security_agent.set_all_library_permissions( trans, library_dataset.library_dataset_dataset_association, permissions ) trans.sa_session.refresh( library_dataset.library_dataset_dataset_association ) - message = "Permisisons updated for library dataset '%s'." % library_dataset.name + message = "Permisisons updated for library dataset '%s'." % escape( library_dataset.name ) status = 'done' roles = trans.app.security_agent.get_legitimate_roles( trans, library_dataset, cntrller ) return trans.fill_template( '/library/common/library_dataset_permissions.mako', @@ -1677,23 +1677,23 @@ contents = util.string_as_bool( kwd.get( 'contents', 'False' ) ) trans.app.security_agent.make_library_public( library, contents=contents ) if contents: - message = "The data library (%s) and all its contents have been made publicly accessible." % library.name + message = "The data library (%s) and all its contents have been made publicly accessible." % escape( library.name ) else: - message = "The data library (%s) has been made publicly accessible, but access to its contents has been left unchanged." % library.name + message = "The data library (%s) has been made publicly accessible, but access to its contents has been left unchanged." % escape( library.name ) elif item_type == 'folder': folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( id ) ) self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted ) self._check_manage( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted ) trans.app.security_agent.make_folder_public( folder ) - message = "All of the contents of folder (%s) have been made publicly accessible." % folder.name + message = "All of the contents of folder (%s) have been made publicly accessible." % escape( folder.name ) elif item_type == 'ldda': ldda = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) self._check_access( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted ) self._check_manage( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted ) trans.app.security_agent.make_dataset_public( ldda.dataset ) - message = "The libary dataset (%s) has been made publicly accessible." % ldda.name + message = "The libary dataset (%s) has been made publicly accessible." % escape( ldda.name ) else: - message = "Invalid item_type (%s) received." % str( item_type ) + message = "Invalid item_type (%s) received." % escape( str( item_type ) ) status = 'error' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', @@ -1803,7 +1803,7 @@ if invalid_lddas: message += "You are not authorized to manage permissions on %s: " % inflector.cond_plural( len( invalid_lddas ), "dataset" ) for ldda in invalid_lddas: - message += '(%s)' % ldda.name + message += '(%s)' % escape( ldda.name ) message += '. ' if valid_ldda_ids: encoded_ldda_ids = [ trans.security.encode_id( ldda_id ) for ldda_id in valid_ldda_ids ] @@ -1967,7 +1967,7 @@ return archive.stream else: status = 'error' - message = 'Invalid action (%s) specified.' % str( action ) + message = 'Invalid action (%s) specified.' % escape( str( action ) ) if library_id: # If we have a library_id, browse the associated library return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2053,11 +2053,11 @@ status = 'error' invalid_datasets += 1 elif ldda.dataset.state not in [ trans.model.Dataset.states.OK, trans.model.Dataset.states.ERROR ]: - message += "You cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) + message += "You cannot import dataset '%s' since its state is '%s'. " % ( escape( ldda.name ), ldda.dataset.state ) status = 'error' invalid_datasets += 1 elif not ldda.has_data(): - message += "You cannot import empty dataset '%s'. " % ldda.name + message += "You cannot import empty dataset '%s'. " % escape( ldda.name ) status = 'error' invalid_datasets += 1 else: @@ -2140,7 +2140,7 @@ except ValueError: return None if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): - message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name ) + message = "You are not authorized to modify %s '%s'." % ( escape( item_desc ), escape( item.name ) ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -2151,9 +2151,9 @@ info_association, inherited = item.get_info_association( restrict=True ) if info_association: if info_association.inheritable: - message = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will no longer be inherited to contained folders and datasets." % escape( item_desc ) else: - message = "The template for this %s will now be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will now be inherited to contained folders and datasets." % escape( item_desc ) info_association.inheritable = not( info_association.inheritable ) trans.sa_session.add( info_association ) trans.sa_session.flush() @@ -2260,7 +2260,7 @@ elif invalid_lddas: message += "You are not authorized to move %s: " % inflector.cond_plural( len( invalid_lddas ), "dataset" ) for ldda in invalid_lddas: - message += '(%s)' % ldda.name + message += '(%s)' % escape( ldda.name ) message += '. ' num_source = len( move_ldda_ids ) - invalid_items message = "%i %s moved to folder (%s) within data library (%s)" % ( num_source, @@ -2278,9 +2278,9 @@ move_folder.parent = target_folder trans.sa_session.add( move_folder ) flush_required = True - message = "Moved folder (%s) to folder (%s) within data library (%s) " % ( move_folder.name, - target_folder.name, - target_library.name ) + message = "Moved folder (%s) to folder (%s) within data library (%s) " % ( escape( move_folder.name ), + escape( target_folder.name ), + escape( target_library.name ) ) if flush_required: trans.sa_session.flush() if target_library: @@ -2400,7 +2400,7 @@ is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' ) current_user_roles = trans.get_current_user_roles() if item_type not in item_types: - message = 'Bad item_type specified: %s' % str( item_type ) + message = 'Bad item_type specified: %s' % escape( str( item_type ) ) status = 'error' else: if item_type == 'library_dataset': @@ -2430,12 +2430,12 @@ if flush_needed: trans.sa_session.flush() if valid_items: - message += "%d %s marked deleted. " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) ) + message += "%d %s marked deleted. " % ( valid_items, escape( inflector.cond_plural( valid_items, item_desc ) ) ) if invalid_items: - message += '%d invalid %s specifield. ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) ) + message += '%d invalid %s specifield. ' % ( invalid_items, escape( inflector.cond_plural( invalid_items, item_desc ) ) ) status = 'error' if not_authorized_items: - message += 'You are not authorized to delete %d %s. ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) ) + message += 'You are not authorized to delete %d %s. ' % ( not_authorized_items, escape( inflector.cond_plural( not_authorized_items, item_desc ) ) ) status = 'error' if item_type == 'library': return trans.response.send_redirect( web.url_for( controller=cntrller, @@ -2462,7 +2462,7 @@ is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' ) current_user_roles = trans.get_current_user_roles() if item_type not in item_types: - message = 'Bad item_type specified: %s' % str( item_type ) + message = 'Bad item_type specified: %s' % escape( str( item_type ) ) status = 'error' else: if item_type == 'library_dataset': @@ -2496,15 +2496,15 @@ if flush_needed: trans.sa_session.flush() if valid_items: - message += "%d %s marked undeleted. " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) ) + message += "%d %s marked undeleted. " % ( valid_items, escape( inflector.cond_plural( valid_items, item_desc ) ) ) if invalid_items: - message += '%d invalid %s specifield. ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) ) + message += '%d invalid %s specifield. ' % ( invalid_items, escape( inflector.cond_plural( invalid_items, item_desc ) ) ) status = 'error' if not_authorized_items: - message += 'You are not authorized to undelete %d %s. ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) ) + message += 'You are not authorized to undelete %d %s. ' % ( not_authorized_items, escape( inflector.cond_plural( not_authorized_items, item_desc ) ) ) status = 'error' if purged_items: - message += '%d %s marked purged, so cannot be undeleted. ' % ( purged_items, inflector.cond_plural( purged_items, item_desc ) ) + message += '%d %s marked purged, so cannot be undeleted. ' % ( purged_items, escape( inflector.cond_plural( purged_items, item_desc ) ) ) status = 'error' if item_type == 'library': return trans.response.send_redirect( web.url_for( controller=cntrller, @@ -2525,7 +2525,7 @@ if isinstance( item, trans.model.HistoryDatasetAssociation ): # Make sure the user has the DATASET_ACCESS permission on the history_dataset_association. if not item: - message = "Invalid history dataset (%s) specified." % str( item ) + message = "Invalid history dataset (%s) specified." % escape( str( item ) ) can_access = False elif not trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user: message = "You do not have permission to access the history dataset with id (%s)." % str( item.id ) @@ -2533,7 +2533,7 @@ else: # Make sure the user has the LIBRARY_ACCESS permission on the library item. if not item: - message = "Invalid library item (%s) specified." % str( item ) + message = "Invalid library item (%s) specified." % escape( str( item ) ) can_access = False elif not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ): if isinstance( item, trans.model.Library ): @@ -2542,7 +2542,7 @@ item_type = 'folder' else: item_type = '(unknown item type)' - message = "You do not have permission to access the %s with id (%s)." % ( item_type, str( item.id ) ) + message = "You do not have permission to access the %s with id (%s)." % ( escape( item_type ), str( item.id ) ) can_access = False if not can_access: if cntrller == 'api': @@ -2566,7 +2566,7 @@ def _check_add( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny access if the user is not an admin and does not have the LIBRARY_ADD permission. if not ( is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, item ) ): - message = "You are not authorized to add an item to (%s)." % item.name + message = "You are not authorized to add an item to (%s)." % escape( item.name ) # Redirect to the real parent library since we know we have access to it. if cntrller == 'api': return 403, message @@ -2585,7 +2585,7 @@ if not ( is_admin or \ ( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ): - message = "You are not authorized to manage permissions on library dataset (%s)." % library_dataset.name + message = "You are not authorized to manage permissions on library dataset (%s)." % escape( library_dataset.name ) if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2597,7 +2597,7 @@ status='error' ) ) # Deny access if the user is not an admin and does not have the LIBRARY_MANAGE permission. if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, item ) ): - message = "You are not authorized to manage permissions on (%s)." % item.name + message = "You are not authorized to manage permissions on (%s)." % escape( item.name ) if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2611,7 +2611,7 @@ def _check_modify( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny modification if the user is not an admin and does not have the LIBRARY_MODIFY permission. if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): - message = "You are not authorized to modify (%s)." % item.name + message = "You are not authorized to modify (%s)." % escape( item.name ) if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -574,7 +574,7 @@ username = trans.user.username is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: - message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( email, url_for( '/' ) ) + message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( escape( email ), url_for( '/' ) ) status = 'error' else: message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.<br><a target="_top" href="%s">Return to the home page</a>.' % url_for( '/' ) @@ -678,7 +678,7 @@ trans.log_event( "User created a new account" ) trans.log_event( "User logged in" ) if success and is_admin: - message = 'Created new user account (%s)' % user.email + message = 'Created new user account (%s)' % escape( user.email ) trans.response.send_redirect( web.url_for( controller='admin', action='users', cntrller=cntrller, @@ -775,7 +775,7 @@ if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on: is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: - message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) + message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target="_top" href="%s">Return to the home page.</a>' % ( escape( user.email ), url_for( '/' ) ) success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' @@ -783,7 +783,7 @@ message += ' Contact: %s' % trans.app.config.error_email_to success = False else: # User activation is OFF, proceed without sending the activation email. - message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) + message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( escape( user.email ), url_for( '/' ) ) success = True return ( message, status, user, success ) @@ -793,7 +793,7 @@ """ if username is None: username = trans.user.username - activation_link = self.prepare_activation_link( trans, email ) + activation_link = self.prepare_activation_link( trans, escape( email ) ) body = ("Hello %s,\n\n" "In order to complete the activation process for %s begun on %s at %s, please click on the following link to verify your account:\n\n" @@ -801,7 +801,7 @@ "By clicking on the above link and opening a Galaxy account you are also confirming that you have read and agreed to Galaxy's Terms and Conditions for use of this service (%s). This includes a quota limit of one account per user. Attempts to subvert this limit by creating multiple accounts or through any other method may result in termination of all associated accounts and data.\n\n" "Please contact us if you need help with your account at: %s. You can also browse resources available at: %s. \n\n" "More about the Galaxy Project can be found at galaxyproject.org\n\n" - "Your Galaxy Team" % (username, email, + "Your Galaxy Team" % (escape( username ), escape( email ), datetime.utcnow().strftime( "%D"), trans.request.host, activation_link, trans.app.config.terms_url, @@ -1178,7 +1178,7 @@ if not username: return "A public user name is required in the tool shed." if username in [ 'repos' ]: - return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a public user name." % username + return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a public user name." % escape( username ) message = "\n".join( [ validate_email( trans, email ), validate_password( trans, password, confirm ), validate_publicname( trans, username ) ] ).rstrip() diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -826,7 +826,7 @@ """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) - message = escape( kwd.get( 'message', '' ) ) + message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) # The special Galaxy integration landing page's URL on myExperiment diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -140,7 +140,7 @@ trans.sa_session.flush() # Update the Tool Shed's repository registry. trans.app.repository_registry.add_category_entry( category ) - message = "Category '%s' has been created" % category.name + message = "Category '%s' has been created" % escape( category.name ) status = 'done' trans.response.send_redirect( web.url_for( controller='admin', action='manage_categories', @@ -184,7 +184,7 @@ count += 1 deleted_repositories += " %s " % repository.name if count: - message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), deleted_repositories ) + message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), escape( deleted_repositories ) ) else: message = "All selected repositories were already marked deleted." else: @@ -258,7 +258,7 @@ if original_category_name != new_name: # Update the Tool Shed's repository registry. trans.app.repository_registry.edit_category_entry( original_category_name, new_name ) - message = "The information has been saved for category '%s'" % ( category.name ) + message = "The information has been saved for category '%s'" % escape( category.name ) status = 'done' return trans.response.send_redirect( web.url_for( controller='admin', action='manage_categories', @@ -431,7 +431,7 @@ trans.sa_session.flush() # Update the Tool Shed's repository registry. trans.app.repository_registry.remove_category_entry( category ) - message += " %s " % category.name + message += " %s " % escape( category.name ) else: message = "No category ids received for deleting." status = 'error' @@ -462,7 +462,7 @@ trans.sa_session.delete( rca ) trans.sa_session.flush() purged_categories += " %s " % category.name - message = "Purged %d categories: %s" % ( count, purged_categories ) + message = "Purged %d categories: %s" % ( count, escape( purged_categories ) ) else: message = "No category ids received for purging." status = 'error' @@ -491,7 +491,7 @@ trans.app.repository_registry.add_category_entry( category ) count += 1 undeleted_categories += " %s" % category.name - message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) + message = "Undeleted %d categories: %s" % ( count, escape( undeleted_categories ) ) else: message = "No category ids received for undeleting." status = 'error' diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1126,11 +1126,11 @@ if mark_deprecated: # Update the repository registry. trans.app.repository_registry.remove_entry( repository ) - message = 'The repository <b>%s</b> has been marked as deprecated.' % repository.name + message = 'The repository <b>%s</b> has been marked as deprecated.' % escape( repository.name ) else: # Update the repository registry. trans.app.repository_registry.add_entry( repository ) - message = 'The repository <b>%s</b> has been marked as not deprecated.' % repository.name + message = 'The repository <b>%s</b> has been marked as not deprecated.' % escape( repository.name ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own', @@ -1388,8 +1388,8 @@ else: kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ ( basic_util.stringify( tool_ids ), - basic_util.stringify( tool_names ), - basic_util.stringify( tool_versions ), + escape( basic_util.stringify( tool_names ) ), + escape( basic_util.stringify( tool_versions ) ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching tools" return self.matched_repository_grid( trans, **kwd ) @@ -1479,7 +1479,7 @@ return self.install_matched_repository_grid( trans, **kwd ) else: kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( basic_util.stringify( workflow_names ), str( exact_matches_checked ) ) + ( escape( basic_util.stringify( workflow_names ) ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching workflows" return self.matched_repository_grid( trans, **kwd ) else: @@ -3076,7 +3076,7 @@ changeset_revision=changeset_revision ) ) else: message = "The change log for the repository named <b>%s</b> owned by <b>%s</b> does not include revision <b>%s</b>." % \ - ( str( name ), str( owner ), str( changeset_revision ) ) + ( escape( str( name ) ), escape( str( owner ) ), escape( str( changeset_revision ) ) ) return trans.response.send_redirect( web.url_for( controller='repository', action='index', repository_id=repository_id, diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -51,7 +51,7 @@ review.approved = approved_select_field_value trans.sa_session.add( review ) trans.sa_session.flush() - message = 'Approved value <b>%s</b> saved for this revision.' % approved_select_field_value + message = 'Approved value <b>%s</b> saved for this revision.' % escape( approved_select_field_value ) repository_id = trans.security.encode_id( review.repository_id ) changeset_revision = review.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository_review', @@ -121,7 +121,7 @@ component = trans.app.model.Component( name=name, description=description ) trans.sa_session.add( component ) trans.sa_session.flush() - message = "Component '%s' has been created" % component.name + message = "Component '%s' has been created" % escape( component.name ) status = 'done' trans.response.send_redirect( web.url_for( controller='repository_review', action='manage_components', @@ -151,7 +151,7 @@ repository_id=repository_id, changeset_revision=changeset_revision, user_id=trans.security.encode_id( trans.user.id ) ): - message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name ) + message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, escape( repository.name ) ) status = "error" else: # See if there are any reviews for previous changeset revisions that the user can copy. @@ -188,7 +188,7 @@ status=status ) ) else: message = "A new review cannot be created for revision <b>%s</b> of repository <b>%s</b>. Select a valid revision and try again." \ - % ( changeset_revision, repository.name ) + % ( changeset_revision, escape( repository.name ) ) kwd[ 'message' ] = message kwd[ 'status' ] = 'error' else: @@ -218,7 +218,7 @@ component.description = new_description trans.sa_session.add( component ) trans.sa_session.flush() - message = "The information has been saved for the component named <b>%s</b>" % ( component.name ) + message = "The information has been saved for the component named <b>%s</b>" % escape( component.name ) status = 'done' return trans.response.send_redirect( web.url_for( controller='repository_review', action='manage_components', diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -256,7 +256,7 @@ source_type = "file" source = uploaded_file_filename message = "The %s <b>%s</b> has been successfully%suploaded to the repository. " % \ - ( source_type, source, uncompress_str ) + ( source_type, escape( source ), uncompress_str ) if istar and ( undesirable_dirs_removed or undesirable_files_removed ): items_removed = undesirable_dirs_removed + undesirable_files_removed message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) " % items_removed diff -r 17dd62d9a0b0614f5b7fd1fbf360450855c7ab18 -r 1374a75dfeb17af8913e4fffa8b6f11bdf6f668e lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -167,7 +167,7 @@ sa_session.flush() # Update the repository registry. app.repository_registry.add_entry( repository ) - message = "Repository <b>%s</b> has been created." % str( repository.name ) + message = "Repository <b>%s</b> has been created." % escape( str( repository.name ) ) return repository, message def create_repository_admin_role( app, repository ): @@ -285,7 +285,7 @@ repositories=in_repositories ) sa_session.refresh( role ) message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \ - ( str( role.name ), len( in_users ), len( in_groups ), len( in_repositories ) ) + ( escape( str( role.name ) ), len( in_users ), len( in_groups ), len( in_repositories ) ) in_users = [] out_users = [] in_groups = [] 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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