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commit/galaxy-central: greg: Enhance the Galaxy API to display the list of exported workflows contained in an installed tool shed repository and to import one or more of those exported workflows into Galaxy. This change set is loosely based on John Chilton's pull request # 223 titled "Implement API methods for interfacing with an installed tool shed repository's workflows", but the implementation has been re-worked. All of John's contributed features should be available in this change set.
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6431d6796645/ Changeset: 6431d6796645 User: greg Date: 2013-09-24 18:05:17 Summary: Enhance the Galaxy API to display the list of exported workflows contained in an installed tool shed repository and to import one or more of those exported workflows into Galaxy. This change set is loosely based on John Chilton's pull request # 223 titled "Implement API methods for interfacing with an installed tool shed repository's workflows", but the implementation has been re-worked. All of John's contributed features should be available in this change set. Affected #: 7 files diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2327,9 +2327,12 @@ self.id = None self.user = None + class StoredWorkflow( object, Dictifiable): + dict_collection_visible_keys = ( 'id', 'name', 'published' ) dict_element_visible_keys = ( 'id', 'name', 'published' ) + def __init__( self ): self.id = None self.user = None @@ -2357,7 +2360,11 @@ return rval -class Workflow( object ): +class Workflow( object, Dictifiable ): + + dict_collection_visible_keys = ( 'name', 'has_cycles', 'has_errors' ) + dict_element_visible_keys = ( 'name', 'has_cycles', 'has_errors' ) + def __init__( self ): self.user = None self.name = None @@ -2365,7 +2372,9 @@ self.has_errors = None self.steps = [] + class WorkflowStep( object ): + def __init__( self ): self.id = None self.type = None @@ -2376,36 +2385,48 @@ self.input_connections = [] self.config = None + class WorkflowStepConnection( object ): + def __init__( self ): self.output_step_id = None self.output_name = None self.input_step_id = None self.input_name = None + class WorkflowOutput(object): + def __init__( self, workflow_step, output_name): self.workflow_step = workflow_step self.output_name = output_name + class StoredWorkflowUserShareAssociation( object ): + def __init__( self ): self.stored_workflow = None self.user = None + class StoredWorkflowMenuEntry( object ): + def __init__( self ): self.stored_workflow = None self.user = None self.order_index = None + class WorkflowInvocation( object ): pass + class WorkflowInvocationStep( object ): pass + class MetadataFile( object ): + def __init__( self, dataset = None, name = None ): if isinstance( dataset, HistoryDatasetAssociation ): self.history_dataset = dataset diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -10,6 +10,7 @@ from tool_shed.galaxy_install import repository_util from tool_shed.util import common_util from tool_shed.util import encoding_util +from tool_shed.util import workflow_util import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) @@ -33,6 +34,102 @@ """RESTful controller for interactions with tool shed repositories.""" @web.expose_api + def exported_workflows( self, trans, id, **kwd ): + """ + GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/exported_workflows + + Display a list of dictionaries containing information about this tool shed repository's exported workflows. + + :param id: the encoded id of the ToolShedRepository object + """ + # Example URL: http://localhost:8763/api/tool_shed_repositories/f2db41e1fa331b3e/exported_… + # Since exported workflows are dictionaries with very few attributes that differentiate them from each other, we'll build the + # list based on the following dictionary of those few attributes. + exported_workflows = [] + repository = suc.get_tool_shed_repository_by_id( trans, id ) + metadata = repository.metadata + if metadata: + exported_workflow_tups = metadata.get( 'workflows', [] ) + else: + exported_workflow_tups = [] + for index, exported_workflow_tup in enumerate( exported_workflow_tups ): + # The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of relative_path is the location + # on disk (relative to the root of the installed repository) where the exported_workflow_dict file (.ga file) is located. + exported_workflow_dict = exported_workflow_tup[ 1 ] + annotation = exported_workflow_dict.get( 'annotation', '' ) + format_version = exported_workflow_dict.get( 'format-version', '' ) + workflow_name = exported_workflow_dict.get( 'name', '' ) + # Since we don't have an in-memory object with an id, we'll identify the exported workflow via it's location (i.e., index) in the list. + display_dict = dict( index=index, annotation=annotation, format_version=format_version, workflow_name=workflow_name ) + exported_workflows.append( display_dict ) + return exported_workflows + + @web.expose_api + def import_workflow( self, trans, payload, **kwd ): + """ + POST /api/tool_shed_repositories/import_workflow + + Import the specified exported workflow contained in the specified installed tool shed repository into Galaxy. + + :param key: the API key of the Galaxy user with which the imported workflow will be associated. + :param id: the encoded id of the ToolShedRepository object + + The following parameters are included in the payload. + :param index: the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository + """ + api_key = kwd.get( 'key', None ) + if api_key is None: + raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) + tool_shed_repository_id = kwd.get( 'id', '' ) + if not tool_shed_repository_id: + raise HTTPBadRequest( detail="Missing required parameter 'id'." ) + index = payload.get( 'index', None ) + if index is None: + raise HTTPBadRequest( detail="Missing required parameter 'index'." ) + repository = suc.get_tool_shed_repository_by_id( trans, tool_shed_repository_id ) + exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) ) + # Since we don't have an in-memory object with an id, we'll identify the exported workflow via it's location (i.e., index) in the list. + exported_workflow = exported_workflows[ int( index ) ] + workflow_name = exported_workflow[ 'workflow_name' ] + workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) + if status == 'error': + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + else: + return workflow.to_dict( view='element' ) + + @web.expose_api + def import_workflows( self, trans, **kwd ): + """ + POST /api/tool_shed_repositories/import_workflow + + Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy. + + :param key: the API key of the Galaxy user with which the imported workflows will be associated. + :param id: the encoded id of the ToolShedRepository object + """ + api_key = kwd.get( 'key', None ) + if api_key is None: + raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." ) + tool_shed_repository_id = kwd.get( 'id', '' ) + if not tool_shed_repository_id: + raise HTTPBadRequest( detail="Missing required parameter 'id'." ) + repository = suc.get_tool_shed_repository_by_id( trans, tool_shed_repository_id ) + exported_workflows = json.from_json_string( self.exported_workflows( trans, tool_shed_repository_id ) ) + imported_workflow_dicts = [] + for exported_workflow_dict in exported_workflows: + workflow_name = exported_workflow_dict[ 'workflow_name' ] + workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) + if status == 'error': + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + else: + imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) + return imported_workflow_dicts + + @web.expose_api def index( self, trans, **kwd ): """ GET /api/tool_shed_repositories @@ -58,28 +155,6 @@ return message @web.expose_api - def show( self, trans, id, **kwd ): - """ - GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id} - Display a dictionary containing information about a specified tool_shed_repository. - - :param id: the encoded id of the ToolShedRepository object - """ - # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e - try: - tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) - tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', - action='show', - id=trans.security.encode_id( tool_shed_repository.id ) ) - return tool_shed_repository_dict - except Exception, e: - message = "Error in tool_shed_repositories API in index: " + str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - - @web.expose_api def install_repository_revision( self, trans, payload, **kwd ): """ POST /api/tool_shed_repositories/install_repository_revision @@ -412,3 +487,25 @@ tool_shed_repositories.append( repository_dict ) # Display the list of repaired repositories. return tool_shed_repositories + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id} + Display a dictionary containing information about a specified tool_shed_repository. + + :param id: the encoded id of the ToolShedRepository object + """ + # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e + try: + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) + tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', + action='show', + id=trans.security.encode_id( tool_shed_repository.id ) ) + return tool_shed_repository_dict + except Exception, e: + message = "Error in tool_shed_repositories API in index: " + str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -176,7 +176,10 @@ # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', - member={ 'repair_repository_revision' : 'POST' }, + member={ 'repair_repository_revision' : 'POST', + 'exported_workflows' : 'GET', + 'import_workflow' : 'POST', + 'import_workflows' : 'POST' }, controller='tool_shed_repositories', name_prefix='tool_shed_repository_', path_prefix='/api', diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 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 @@ -358,66 +358,26 @@ @web.expose @web.require_admin def import_workflow( self, trans, workflow_name, repository_id, **kwd ): - """Import a workflow contained in an installed tool shed repository into the Galaxy instance.""" + """Import a workflow contained in an installed tool shed repository into Galaxy.""" message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) - changeset_revision = repository.changeset_revision - metadata = repository.metadata - workflows = metadata.get( 'workflows', [] ) - tools_metadata = metadata.get( 'tools', [] ) - workflow_dict = None - for workflow_data_tuple in workflows: - # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ). - relative_path_to_workflow_file, exported_workflow_dict = workflow_data_tuple - if exported_workflow_dict[ 'name' ] == workflow_name: - # If the exported workflow is available on disk, import it. - if os.path.exists( relative_path_to_workflow_file ): - workflow_file = open( relative_path_to_workflow_file, 'rb' ) - workflow_data = workflow_file.read() - workflow_file.close() - workflow_dict = json.from_json_string( workflow_data ) + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + if repository: + workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) + if workflow: + workflow_name = encoding_util.tool_shed_encode( str( workflow.name ) ) else: - # Use the current exported_workflow_dict. - workflow_dict = exported_workflow_dict - break - if workflow_dict: - # Create workflow if possible. - workflow, missing_tool_tups = workflow_util.get_workflow_from_dict( trans=trans, - workflow_dict=workflow_dict, - tools_metadata=tools_metadata, - repository_id=repository_id, - changeset_revision=changeset_revision ) - # Save the workflow in the Galaxy database. - # Pass workflow_dict along to create annotation at this point - stored_workflow = workflow_util.save_workflow( trans, workflow, workflow_dict ) - # Use the latest version of the saved workflow. - workflow = stored_workflow.latest_workflow - if workflow_name: - workflow.name = workflow_name - # Provide user feedback and show workflow list. - if workflow.has_errors: - message += "Imported, but some steps in this workflow have validation errors. " - status = "error" - if workflow.has_cycles: - message += "Imported, but this workflow contains cycles. " - status = "error" + message += 'Unable to locate a workflow named <b>%s</b> within the installed tool shed repository named <b>%s</b>' % \ + ( str( workflow_name ), str( repository.name ) ) + status = 'error' else: - message += "Workflow <b>%s</b> imported successfully. " % workflow.name - if missing_tool_tups: - # TODO: rework this since it is used in the tool shed, but shoudn't be used in Galaxy. - name_and_id_str = '' - for missing_tool_tup in missing_tool_tups: - tool_id, tool_name, other = missing_tool_tup - name_and_id_str += 'name: %s, id: %s' % ( str( tool_id ), str( tool_name ) ) - log.debug( "The following tools required by this workflow are missing from this Galaxy instance: %s" % name_and_id_str ) + message = 'Invalid repository id <b>%s</b> received.' % str( repository_id ) + status = 'error' else: - message += 'The workflow named %s is not included in the metadata for revision %s of repository %s' % \ - ( str( workflow_name ), str( changeset_revision ), str( repository.name ) ) + message = 'The value of workflow_name is required, but was not received.' status = 'error' - workflow_name = encoding_util.tool_shed_encode( workflow.name ), return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='view_workflow', workflow_name=workflow_name, diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1896,7 +1896,7 @@ changeset_revisions.append( changeset_revision ) add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions ) elif len( repo ) == 1 and not invalid_file_tups: - message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) ) + message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % str( repository.tip( trans.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" if invalid_file_tups: diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -1,4 +1,5 @@ import logging +import os import galaxy.tools import galaxy.tools.parameters import galaxy.webapps.galaxy.controllers.workflow @@ -151,7 +152,7 @@ def new( self, trans, type, tools_metadata=None, tool_id=None ): """Return module for type and (optional) tool_id initialized with new / default state.""" assert type in self.module_types - return self.module_types[type].new( trans, tool_id ) + return self.module_types[ type ].new( trans, tool_id ) def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): """Return module initialized from the data in dictionary `step_dict`.""" @@ -219,13 +220,11 @@ tool_errors = module.type == 'tool' and not module.tool module_data_inputs = get_workflow_data_inputs( step, module ) module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps ) - step_dict = { - 'id' : step.order_index, - 'data_inputs' : module_data_inputs, - 'data_outputs' : module_data_outputs, - 'position' : step.position, - 'tool_errors' : tool_errors - } + step_dict = { 'id' : step.order_index, + 'data_inputs' : module_data_inputs, + 'data_outputs' : module_data_outputs, + 'position' : step.position, + 'tool_errors' : tool_errors } input_conn_dict = {} for conn in step.input_connections: input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) @@ -401,8 +400,9 @@ post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): trans.model.PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) + step, + pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) steps.append( step ) steps_by_external_id[ step_dict[ 'id' ] ] = step # Second pass to deal with connections between steps. @@ -433,6 +433,64 @@ break return module_name +def import_workflow( trans, repository, workflow_name ): + """Import a workflow contained in an installed tool shed repository into Galaxy (this method is called only from Galaxy).""" + status = 'done' + message = '' + changeset_revision = repository.changeset_revision + metadata = repository.metadata + workflows = metadata.get( 'workflows', [] ) + tools_metadata = metadata.get( 'tools', [] ) + workflow_dict = None + for workflow_data_tuple in workflows: + # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ). + relative_path_to_workflow_file, exported_workflow_dict = workflow_data_tuple + if exported_workflow_dict[ 'name' ] == workflow_name: + # If the exported workflow is available on disk, import it. + if os.path.exists( relative_path_to_workflow_file ): + workflow_file = open( relative_path_to_workflow_file, 'rb' ) + workflow_data = workflow_file.read() + workflow_file.close() + workflow_dict = json.from_json_string( workflow_data ) + else: + # Use the current exported_workflow_dict. + workflow_dict = exported_workflow_dict + break + if workflow_dict: + # Create workflow if possible. + workflow, missing_tool_tups = get_workflow_from_dict( trans=trans, + workflow_dict=workflow_dict, + tools_metadata=tools_metadata, + repository_id=repository.id, + changeset_revision=changeset_revision ) + # Save the workflow in the Galaxy database. Pass workflow_dict along to create annotation at this point. + stored_workflow = save_workflow( trans, workflow, workflow_dict ) + # Use the latest version of the saved workflow. + workflow = stored_workflow.latest_workflow + if workflow_name: + workflow.name = workflow_name + # Provide user feedback and show workflow list. + if workflow.has_errors: + message += "Imported, but some steps in this workflow have validation errors. " + status = "error" + if workflow.has_cycles: + message += "Imported, but this workflow contains cycles. " + status = "error" + else: + message += "Workflow <b>%s</b> imported successfully. " % workflow.name + if missing_tool_tups: + name_and_id_str = '' + for missing_tool_tup in missing_tool_tups: + tool_id, tool_name, other = missing_tool_tup + name_and_id_str += 'name: %s, id: %s' % ( str( tool_id ), str( tool_name ) ) + message += "The following tools required by this workflow are missing from this Galaxy instance: %s. " % name_and_id_str + else: + workflow = None + message += 'The workflow named %s is not included in the metadata for revision %s of repository %s' % \ + ( str( workflow_name ), str( changeset_revision ), str( repository.name ) ) + status = 'error' + return workflow, status, message + def save_workflow( trans, workflow, workflow_dict = None): """Use the received in-memory Workflow object for saving to the Galaxy database.""" stored = trans.model.StoredWorkflow() diff -r 7df8d81544c39cde769a5ead49be182294ba58b1 -r 6431d67966450d1c4e6946d54a94584e343049a4 scripts/api/import_workflows_from_installed_tool_shed_repository.py --- /dev/null +++ b/scripts/api/import_workflows_from_installed_tool_shed_repository.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python +""" +Import one or more exported workflows contained within a specified tool shed repository installed into Galaxy. + +Here is a working example of how to use this script to repair a repository installed into Galaxy. +python ./import_workflows_from_installed_tool_shed_repository.py -a 22be3b -l http://localhost:8763/ -n workflow_with_tools -o test -r ef45bb64237e -u http://localhost:9009/ +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import display +from common import submit + +def clean_url( url ): + if url.find( '//' ) > 0: + # We have an url that includes a protocol, something like: http://localhost:9009 + items = url.split( '//' ) + return items[ 1 ].rstrip( '/' ) + return url.rstrip( '/' ) + +def main( options ): + api_key = options.api + base_galaxy_url = options.local_url.rstrip( '/' ) + base_tool_shed_url = options.tool_shed_url.rstrip( '/' ) + cleaned_tool_shed_url = clean_url( base_tool_shed_url ) + installed_tool_shed_repositories_url = '%s/api/tool_shed_repositories' % base_galaxy_url + tool_shed_repository_id = None + installed_tool_shed_repositories = display( api_key, installed_tool_shed_repositories_url, return_formatted=False ) + for installed_tool_shed_repository in installed_tool_shed_repositories: + tool_shed = str( installed_tool_shed_repository[ 'tool_shed' ] ) + name = str( installed_tool_shed_repository[ 'name' ] ) + owner = str( installed_tool_shed_repository[ 'owner' ] ) + changeset_revision = str( installed_tool_shed_repository[ 'changeset_revision' ] ) + if tool_shed == cleaned_tool_shed_url and name == options.name and owner == options.owner and changeset_revision == options.changeset_revision: + tool_shed_repository_id = installed_tool_shed_repository[ 'id' ] + break + if tool_shed_repository_id: + # Get the list of exported workflows contained in the installed repository. + url = '%s%s' % ( base_galaxy_url, '/api/tool_shed_repositories/%s/exported_workflows' % str( tool_shed_repository_id ) ) + exported_workflows = display( api_key, url, return_formatted=False ) + if exported_workflows: + # Import all of the workflows in the list of exported workflows. + data = {} + # NOTE: to import a single workflow, add an index to data (e.g., + # data[ 'index' ] = 0 + # and change the url to be ~/import_workflow (simgular). For example, + # url = '%s%s' % ( base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflow' % str( tool_shed_repository_id ) ) + url = '%s%s' % ( base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflows' % str( tool_shed_repository_id ) ) + submit( options.api, url, data ) + else: + print "Invalid tool_shed / name / owner / changeset_revision." + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Import workflows contained in an installed tool shed repository via the Galaxy API.' ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) + parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) + parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." ) + parser.add_argument( "-n", "--name", required=True, help="Repository name." ) + parser.add_argument( "-o", "--owner", required=True, help="Repository owner." ) + parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." ) + options = parser.parse_args() + main( options ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/079ce0488cdc/ Changeset: 079ce0488cdc User: Dave Bouvier Date: 2013-09-24 15:10:13 Summary: Fix for backwards compatibility with a Galaxy instance running the latest revision installing repositories from a tool shed running the stable branch. Affected #: 5 files diff -r fd7f14161d3537abf1f676f14ec763d150ee611f -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -100,19 +100,14 @@ continue # rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635f…' # rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']] - try: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - container_util.get_components_from_key( rd_key ) - except: - tool_shed, name, owner, changeset_revision = container_util.get_components_from_key( rd_val ) + repository_components_tuple = container_util.get_components_from_key( rd_key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + tool_shed, name, owner, changeset_revision = components_list[ 0:4 ] installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) for rd_val in rd_vals: - try: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_val - except: - tool_shed, name, owner, changeset_revision = rd_val + tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ] installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) @@ -631,13 +626,10 @@ # Change the folder id so it won't confict with others being merged. old_container_repository_dependencies_folder.id = folder_id folder_id += 1 + repository_components_tuple = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + name = components_list[ 1 ] # Generate the label by retrieving the repository name. - try: - toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release. - toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) old_container_repository_dependencies_folder.label = str( name ) repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) # Merge tool_dependencies. diff -r fd7f14161d3537abf1f676f14ec763d150ee611f -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -352,19 +352,20 @@ for key, val in repository_dependencies.items(): if key in [ 'root_key', 'description' ]: continue - try: - toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - container_util.get_components_from_key( key ) - components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ] - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required and only_if_compiling_contained_td - # to False in the caller. - toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) - components_list = [ toolshed, name, owner, changeset_revision ] - only_if_compiling_contained_td = 'False' + repository_components_tuple = container_util.get_components_from_key( key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since # in this case, the repository dependency is really a dependency of the dependent repository's contained tool dependency, and only if # that tool dependency requires compilation. + # For backward compatibility to the 12/20/12 Galaxy release. + prior_installation_required = 'False' + only_if_compiling_contained_td = 'False' + if len( components_list ) == 4: + prior_installation_required = 'False' + only_if_compiling_contained_td = 'False' + elif len( components_list ) == 5: + prior_installation_required = components_list[ 4 ] + only_if_compiling_contained_td = 'False' if not util.asbool( only_if_compiling_contained_td ): if components_list not in required_repository_tups: required_repository_tups.append( components_list ) diff -r fd7f14161d3537abf1f676f14ec763d150ee611f -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -855,7 +855,7 @@ folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder except Exception, e: - log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) + log.exception( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) finally: lock.release() return containers_dict @@ -1325,29 +1325,31 @@ repository_name = items[ 1 ] repository_owner = items[ 2 ] changeset_revision = items[ 3 ] - if len( items ) >= 5: - try: - prior_installation_required = items[ 4 ] - except: - prior_installation_required = 'False' - try: - only_if_compiling_contained_td = items[ 5 ] - except: - only_if_compiling_contained_td = 'False' + if len( items ) == 5: + prior_installation_required = items[ 4 ] + return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required + elif len( items ) == 6: + prior_installation_required = items[ 4 ] + only_if_compiling_contained_td = items[ 5 ] return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td else: # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions. return toolshed_base_url, repository_name, repository_owner, changeset_revision def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): - try: - toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - get_components_from_key( rd_key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required and only_if_compiling_contained_td to 'False'. - toolshed, repository_name, repository_owner, changeset_revision = get_components_from_key( rd_key ) + repository_components_tuple = get_components_from_key( rd_key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ] + # For backward compatibility to the 12/20/12 Galaxy release. + if len( components_list ) == 4: prior_installation_required = 'False' only_if_compiling_contained_td = 'False' + elif len( components_list ) == 5: + prior_installation_required = components_list[ 4 ] + only_if_compiling_contained_td = 'False' + elif len( components_list ) == 6: + prior_installation_required = components_list[ 4 ] + only_if_compiling_contained_td = components_list[ 5 ] folder = get_folder( repository_dependencies_folder, rd_key ) label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, @@ -1416,14 +1418,19 @@ return False def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ): - try: - toolshed_base_url, key_name, key_owner, key_changeset_revision, key_prior_installation_required, key_only_if_compiling_contained_td = \ - get_components_from_key( key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release, default key_prior_installation_required to False. - toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) + repository_components_tuple = get_components_from_key( key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + toolshed, key_name, key_owner, key_changeset_revision = components_list[ 0:4 ] + # For backward compatibility to the 12/20/12 Galaxy release. + if len( components_list ) == 4: key_prior_installation_required = 'False' key_only_if_compiling_contained_td = 'False' + elif len( components_list ) == 5: + key_prior_installation_required = components_list[ 4 ] + key_only_if_compiling_contained_td = 'False' + elif len( components_list ) == 6: + key_prior_installation_required = components_list[ 4 ] + key_only_if_compiling_contained_td = components_list[ 5 ] if repository_name == key_name and \ repository_owner == key_owner and \ changeset_revision == key_changeset_revision and \ diff -r fd7f14161d3537abf1f676f14ec763d150ee611f -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -36,12 +36,9 @@ if key in [ 'root_key', 'description' ]: continue d_repository = None - try: - d_toolshed, d_name, d_owner, d_changeset_revision, d_prior_installation_required, d_only_if_compiling_contained_td = \ - container_util.get_components_from_key( key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release. - d_toolshed, d_name, d_owner, d_changeset_revision = container_util.get_components_from_key( key ) + repository_components_tuple = container_util.get_components_from_key( key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + d_toolshed, d_name, d_owner, d_changeset_revision = components_list[ 0:4 ] for tsr in tool_shed_repositories: # Get the the tool_shed_repository defined by name, owner and changeset_revision. This is the repository that will be # dependent upon each of the tool shed repositories contained in val. We'll need to check tool_shed_repository.tool_shed @@ -437,22 +434,22 @@ # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) else: - try: - toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required, rd_only_if_compiling_contained_td = \ - container_util.get_components_from_key( key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release. - toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + repository_components_tuple = container_util.get_components_from_key( key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ] + # For backward compatibility to the 12/20/12 Galaxy release. + if len( components_list ) == 4: + prior_installation_required = 'False' + rd_only_if_compiling_contained_td = 'False' + elif len( components_list ) == 5: + rd_only_if_compiling_contained_td = 'False' message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) else: - try: - toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - container_util.get_components_from_key( key ) - except ValueError: - # For backward compatibility to the 12/20/12 Galaxy release. - toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + repository_components_tuple = container_util.get_components_from_key( key ) + components_list = suc.extract_components_from_tuple( repository_components_tuple ) + toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ] message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) diff -r fd7f14161d3537abf1f676f14ec763d150ee611f -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -307,6 +307,21 @@ sa_session.flush() return tool_shed_repository +def extract_components_from_tuple( repository_components_tuple ): + '''Extract the repository components from the provided tuple in a backward-compatible manner.''' + toolshed = repository_components_tuple[ 0 ] + name = repository_components_tuple[ 1 ] + owner = repository_components_tuple[ 2 ] + changeset_revision = repository_components_tuple[ 3 ] + components_list = [ toolshed, name, owner, changeset_revision ] + if len( repository_components_tuple ) == 5: + toolshed, name, owner, changeset_revision, prior_installation_required = repository_components_tuple + components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ] + elif len( repository_components_tuple ) == 6: + toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_components_tuple + components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ] + return components_list + def generate_clone_url_for_installed_repository( app, repository ): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed ) https://bitbucket.org/galaxy/galaxy-central/commits/78836810e69e/ Changeset: 78836810e69e User: Dave Bouvier Date: 2013-09-24 15:21:41 Summary: Update functional tests to reflect changes in HTML output. Add the ability to browse a running test instance of Galaxy or the tool shed with styles and javascript enabled. Affected #: 9 files diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -38,7 +38,7 @@ self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, - 'Repository %s has been created' % "'%s'" % repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % repository_name ] self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py --- a/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py +++ b/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -58,7 +58,7 @@ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name, - 'Repository %s has been created' % "'%s'" % datatypes_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ] repository = self.get_or_create_repository( name=datatypes_repository_name, description=datatypes_repository_description, long_description=datatypes_repository_long_description, @@ -98,7 +98,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name, - 'Repository %s has been created' % "'%s'" % tool_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % tool_repository_name ] repository = self.get_or_create_repository( name=tool_repository_name, description=tool_repository_description, long_description=tool_repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0400_repository_component_reviews.py --- a/test/tool_shed/functional/test_0400_repository_component_reviews.py +++ b/test/tool_shed/functional/test_0400_repository_component_reviews.py @@ -93,7 +93,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, - 'Repository %s has been created' % "'%s'" % repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % repository_name ] repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0410_repository_component_review_access_control.py --- a/test/tool_shed/functional/test_0410_repository_component_review_access_control.py +++ b/test/tool_shed/functional/test_0410_repository_component_review_access_control.py @@ -72,7 +72,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, - 'Repository %s has been created' % "'%s'" % repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % repository_name ] repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0420_citable_urls_for_repositories.py --- a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py +++ b/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py @@ -52,7 +52,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, - 'Repository %s has been created' % "'%s'" % repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % repository_name ] repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0430_browse_utilities.py --- a/test/tool_shed/functional/test_0430_browse_utilities.py +++ b/test/tool_shed/functional/test_0430_browse_utilities.py @@ -57,7 +57,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name, - 'Repository %s has been created' % "'%s'" % datatypes_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ] repository = self.get_or_create_repository( name=datatypes_repository_name, description=datatypes_repository_description, long_description=datatypes_repository_long_description, @@ -85,7 +85,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % emboss_repository_name, - 'Repository %s has been created' % "'%s'" % emboss_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % emboss_repository_name ] emboss_repository = self.get_or_create_repository( name=emboss_repository_name, description=emboss_repository_description, long_description=emboss_repository_long_description, @@ -122,7 +122,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % freebayes_repository_name, - 'Repository %s has been created' % "'%s'" % freebayes_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % freebayes_repository_name ] repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_0450_skip_tool_tests.py --- a/test/tool_shed/functional/test_0450_skip_tool_tests.py +++ b/test/tool_shed/functional/test_0450_skip_tool_tests.py @@ -76,7 +76,7 @@ self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = test_db_util.get_category_by_name( category_name ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, - 'Repository %s has been created' % "'%s'" % repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % repository_name ] repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py --- a/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py +++ b/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py @@ -63,7 +63,7 @@ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name, - 'Repository %s has been created' % "'%s'" % datatypes_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ] repository = self.get_or_create_repository( name=datatypes_repository_name, description=datatypes_repository_description, long_description=datatypes_repository_long_description, @@ -105,7 +105,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name, - 'Repository %s has been created' % "'%s'" % tool_repository_name ] + 'Repository %s has been created' % "<b>%s</b>" % tool_repository_name ] repository = self.get_or_create_repository( name=tool_repository_name, description=tool_repository_description, long_description=tool_repository_long_description, diff -r 079ce0488cdcf4ee882ba3cd4e5413dcab3f9412 -r 78836810e69e016a56597f8e273c9baeb13e94dc test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -56,6 +56,40 @@ default_galaxy_test_port_max = 9999 default_galaxy_test_host = 'localhost' +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED = True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_factory. + """ + # (was originally sent 'dict()') - nothing here for now except static settings + global_conf = dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + tool_sheds_conf_xml_template = '''<?xml version="1.0"?><tool_sheds><tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/> @@ -144,6 +178,9 @@ galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir + hgweb_config_dir = hgweb_config_file_path + os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir + print "Directory location for hgweb.config:", hgweb_config_dir if 'TOOL_SHED_TEST_DBURI' in os.environ: toolshed_database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] else: @@ -152,7 +189,29 @@ galaxy_database_connection = os.environ[ 'GALAXY_TEST_DBURI' ] else: galaxy_database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'universe_test.sqlite' ) - kwargs = {} + tool_shed_global_conf = get_webapp_global_conf() + tool_shed_global_conf[ '__file__' ] = 'tool_shed_wsgi.ini.sample' + kwargs = dict( admin_users = 'test(a)bx.psu.edu', + allow_user_creation = True, + allow_user_deletion = True, + database_connection = toolshed_database_connection, + datatype_converters_config_file = 'datatype_converters_conf.xml.sample', + file_path = shed_file_path, + global_conf = tool_shed_global_conf, + hgweb_config_dir = hgweb_config_dir, + job_queue_workers = 5, + id_secret = 'changethisinproductiontoo', + log_destination = "stdout", + new_file_path = new_repos_path, + running_functional_tests = True, + shed_tool_data_table_config = shed_tool_data_table_conf_file, + smtp_server = 'smtp.dummy.string.tld', + email_from = 'functional@localhost', + template_path = 'templates', + tool_path=tool_path, + tool_parse_help = False, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + use_heartbeat = False ) for dir in [ tool_shed_test_tmp_dir ]: try: os.makedirs( dir ) @@ -162,11 +221,6 @@ print "Tool shed database connection:", toolshed_database_connection print "Galaxy database connection:", galaxy_database_connection - hgweb_config_dir = hgweb_config_file_path - os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir - - print "Directory location for hgweb.config:", hgweb_config_dir - # Generate the tool_data_table_conf.xml file. file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) # Generate the shed_tool_data_table_conf.xml file. @@ -174,7 +228,6 @@ os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Build Tool Shed Application -------------------------------------------------- toolshedapp = None - global_conf = { '__file__' : 'tool_shed_wsgi.ini.sample' } # if not toolshed_database_connection.startswith( 'sqlite://' ): # kwargs[ 'database_engine_option_max_overflow' ] = '20' if tool_dependency_dir is not None: @@ -183,41 +236,22 @@ kwargs[ 'object_store' ] = 'distributed' kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' + kwargs[ 'global_conf' ] = tool_shed_global_conf if not toolshed_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' - toolshedapp = ToolshedUniverseApplication( admin_users = 'test(a)bx.psu.edu', - allow_user_creation = True, - allow_user_deletion = True, - database_connection = toolshed_database_connection, - datatype_converters_config_file = 'datatype_converters_conf.xml.sample', - file_path = shed_file_path, - global_conf = global_conf, - hgweb_config_dir = hgweb_config_dir, - job_queue_workers = 5, - id_secret = 'changethisinproductiontoo', - log_destination = "stdout", - new_file_path = new_repos_path, - running_functional_tests = True, - shed_tool_data_table_config = shed_tool_data_table_conf_file, - smtp_server = 'smtp.dummy.string.tld', - email_from = 'functional@localhost', - template_path = 'templates', - tool_path=tool_path, - tool_parse_help = False, - tool_data_table_config_path = galaxy_tool_data_table_conf_file, - use_heartbeat = False, - **kwargs ) + toolshedapp = ToolshedUniverseApplication( **kwargs ) log.info( "Embedded Toolshed application started" ) # ---- Run tool shed webserver ------------------------------------------------------ tool_shed_server = None - toolshedwebapp = toolshedbuildapp.app_factory( dict( database_connection=toolshed_database_connection ), - use_translogger=False, - static_enabled=False, - app=toolshedapp ) + tool_shed_global_conf[ 'database_connection' ] = toolshed_database_connection + toolshedwebapp = toolshedbuildapp.app_factory( tool_shed_global_conf, + use_translogger=False, + static_enabled=True, + app=toolshedapp ) if tool_shed_test_port is not None: tool_shed_server = httpserver.serve( toolshedwebapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False ) else: @@ -268,50 +302,53 @@ migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file + galaxy_global_conf = get_webapp_global_conf() + galaxy_global_conf[ '__file__' ] = 'universe_wsgi.ini.sample' + + kwargs = dict( allow_user_creation = True, + allow_user_deletion = True, + admin_users = 'test(a)bx.psu.edu', + allow_library_path_paste = True, + database_connection = galaxy_database_connection, + datatype_converters_config_file = "datatype_converters_conf.xml.sample", + enable_tool_shed_check = True, + file_path = galaxy_file_path, + global_conf = galaxy_global_conf, + hours_between_check = 0.001, + id_secret = 'changethisinproductiontoo', + job_queue_workers = 5, + log_destination = "stdout", + migrated_tools_config = galaxy_migrated_tool_conf_file, + new_file_path = galaxy_tempfiles, + running_functional_tests=True, + shed_tool_data_table_config = shed_tool_data_table_conf_file, + shed_tool_path = galaxy_shed_tool_path, + template_path = "templates", + tool_data_path = tool_data_path, + tool_dependency_dir = galaxy_tool_dependency_dir, + tool_path = tool_path, + tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], + tool_sheds_config_file = galaxy_tool_sheds_conf_file, + tool_parse_help = False, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + update_integrated_tool_panel = False, + use_heartbeat = False ) # ---- Build Galaxy Application -------------------------------------------------- - galaxy_global_conf = { '__file__' : 'universe_wsgi.ini.sample' } if not galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' kwargs[ 'database_engine_option_max_overflow' ] = '20' - galaxyapp = GalaxyUniverseApplication( allow_user_creation = True, - allow_user_deletion = True, - admin_users = 'test(a)bx.psu.edu', - allow_library_path_paste = True, - database_connection = galaxy_database_connection, - datatype_converters_config_file = "datatype_converters_conf.xml.sample", - enable_tool_shed_check = True, - file_path = galaxy_file_path, - global_conf = global_conf, - hours_between_check = 0.001, - id_secret = 'changethisinproductiontoo', - job_queue_workers = 5, - log_destination = "stdout", - migrated_tools_config = galaxy_migrated_tool_conf_file, - new_file_path = galaxy_tempfiles, - running_functional_tests=True, - shed_tool_data_table_config = shed_tool_data_table_conf_file, - shed_tool_path = galaxy_shed_tool_path, - template_path = "templates", - tool_data_path = tool_data_path, - tool_dependency_dir = galaxy_tool_dependency_dir, - tool_path = tool_path, - tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], - tool_sheds_config_file = galaxy_tool_sheds_conf_file, - tool_parse_help = False, - tool_data_table_config_path = galaxy_tool_data_table_conf_file, - update_integrated_tool_panel = False, - use_heartbeat = False, - **kwargs ) + galaxyapp = GalaxyUniverseApplication( **kwargs ) log.info( "Embedded Galaxy application started" ) # ---- Run galaxy webserver ------------------------------------------------------ galaxy_server = None - galaxywebapp = galaxybuildapp.app_factory( dict( database_file=galaxy_database_connection ), - use_translogger=False, - static_enabled=False, - app=galaxyapp ) + galaxy_global_conf[ 'database_file' ] = galaxy_database_connection + galaxywebapp = galaxybuildapp.app_factory( galaxy_global_conf, + use_translogger=False, + static_enabled=True, + app=galaxyapp ) if galaxy_test_port is not None: galaxy_server = httpserver.serve( galaxywebapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) @@ -412,4 +449,8 @@ return 1 if __name__ == "__main__": - sys.exit( main() ) + try: + sys.exit( main() ) + except Exception, e: + log.exception( str( e ) ) + exit(1) https://bitbucket.org/galaxy/galaxy-central/commits/7df8d81544c3/ Changeset: 7df8d81544c3 User: Dave Bouvier Date: 2013-09-24 15:23:44 Summary: Update for automated repository installation and testing framework to record cases where a repository installation fails before a record is created in the embedded Galaxy instance's database. Affected #: 1 file diff -r 78836810e69e016a56597f8e273c9baeb13e94dc -r 7df8d81544c39cde769a5ead49be182294ba58b1 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -254,6 +254,49 @@ success = result.wasSuccessful() return success +def extract_log_data( test_result, from_tool_test=True ): + '''Extract any useful data from the test_result.failures and test_result.errors attributes.''' + for failure in test_result.failures + test_result.errors: + # Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing. + test_id = str( failure[0] ) + if not from_tool_test: + tool_id = None + tool_version = None + else: + tool_id, tool_version = get_tool_info_from_test_id( test_id ) + test_status = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) + log_output = failure[1].replace( '\\n', '\n' ) + # Remove debug output that the reviewer or owner doesn't need. + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + # Iterate through the functional test output and extract only the important data. Captured logging and stdout are not recorded. + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif '>> end captured' in line or '>> end tool' in line: + continue + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in [ 'stderr', 'traceback' ]: + if output_type in tmp_output: + test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + return test_status + def get_api_url( base, parts=[], params=None, key=None ): if 'api' in parts and parts.index( 'api' ) != 0: parts.pop( parts.index( 'api' ) ) @@ -1054,43 +1097,7 @@ params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.', changeset_revision, name ) else: - # If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API. - for failure in result.failures + result.errors: - # Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing. - test_id = str( failure[0] ) - tool_id, tool_version = get_tool_info_from_test_id( test_id ) - test_status = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) - log_output = failure[1].replace( '\\n', '\n' ) - # Remove debug output that the reviewer or owner doesn't need. - log_output = re.sub( r'control \d+:.+', r'', log_output ) - log_output = re.sub( r'\n+', r'\n', log_output ) - appending_to = 'output' - tmp_output = {} - output = {} - # Iterate through the functional test output and extract only the important data. Captured logging and stdout are not recorded. - for line in log_output.split( '\n' ): - if line.startswith( 'Traceback' ): - appending_to = 'traceback' - elif '>> end captured' in line or '>> end tool' in line: - continue - elif 'request returned None from get_history' in line: - continue - elif '>> begin captured logging <<' in line: - appending_to = 'logging' - continue - elif '>> begin captured stdout <<' in line: - appending_to = 'stdout' - continue - elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line: - appending_to = 'stderr' - continue - if appending_to not in tmp_output: - tmp_output[ appending_to ] = [] - tmp_output[ appending_to ].append( line ) - for output_type in [ 'stderr', 'traceback' ]: - if output_type in tmp_output: - test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) - repository_status[ 'failed_tests' ].append( test_status ) + repository_status[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True ) # Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome # of the tests, and updates tool_test_results with the relevant log data. # This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested @@ -1129,7 +1136,7 @@ name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision, - error_message=repository.error_message ) + error_message=extract_log_data( result, from_tool_test=False ) ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) params[ 'tools_functionally_correct' ] = False params[ 'test_install_error' ] = True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Improve scratchbook style sheet
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd7f14161d35/ Changeset: fd7f14161d35 User: guerler Date: 2013-09-24 07:43:30 Summary: Improve scratchbook style sheet Affected #: 2 files diff -r 2a2457d3bad09740d48cd2ba4de98936aafe2105 -r fd7f14161d3537abf1f676f14ec763d150ee611f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1116,9 +1116,9 @@ .galaxy-frame .frame{z-index:1002;overflow:hidden;position:absolute;background:#fff;border:1px solid #888;-webkit-box-shadow:0 0 5px rgba(0,0,0,0.3);}.galaxy-frame .frame .f-content{position:absolute;overflow:hidden;background:#fff;border:none;top:24px;bottom:3px;left:3px;right:3px} .galaxy-frame .frame .f-cover{position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.0;background:#fff} .galaxy-frame .frame .f-iframe{border:none;width:100%;height:100%} -.galaxy-frame .frame .f-header{height:17px;margin:2px;cursor:pointer;border:1px solid #000;background:#2c3143;color:#fff;font-weight:bold} +.galaxy-frame .frame .f-header{height:17px;margin:2px;cursor:pointer;border:1px solid #000;background:#2c3143;color:#fff} .galaxy-frame .frame .f-title{position:absolute;top:2px;left:16px;right:16px;font-size:12px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;text-align:center} -.galaxy-frame .frame .f-icon{position:absolute;cursor:pointer;font-style:normal} +.galaxy-frame .frame .f-icon{position:absolute;cursor:pointer} .galaxy-frame .frame .f-not-allowed{cursor:not-allowed} .galaxy-frame .frame .f-close{right:5px;top:1px} .galaxy-frame .frame .f-pin{left:6px;top:1px} diff -r 2a2457d3bad09740d48cd2ba4de98936aafe2105 -r fd7f14161d3537abf1f676f14ec763d150ee611f static/style/src/less/frame.less --- a/static/style/src/less/frame.less +++ b/static/style/src/less/frame.less @@ -111,7 +111,6 @@ border : 1px solid @black; background : @base-color-1; color : @white; - font-weight : bold; } .f-title @@ -133,7 +132,6 @@ { position : absolute; cursor : pointer; - font-style : normal; } .f-not-allowed 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: guerler: Show dataset title in scratchbook frame header
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2a2457d3bad0/ Changeset: 2a2457d3bad0 User: guerler Date: 2013-09-24 07:11:41 Summary: Show dataset title in scratchbook frame header Affected #: 2 files diff -r 6acc907464869c92c4bb366f6574c52714f60ae7 -r 2a2457d3bad09740d48cd2ba4de98936aafe2105 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -163,22 +163,7 @@ // success event_success : function(index, file, message) - { - // get element - var it = this.get_upload_item(index); - - // update progress frame - it.addClass('panel-success'); - it.removeClass('panel-default'); - - // update icon - var sy = it.find('.symbol'); - sy.addClass(this.state.done); - - // remove spin - sy.removeClass('fa-icon-spin'); - sy.removeClass('fa-icon-spinner'); - + { // update galaxy history Galaxy.currHistoryPanel.refresh(); @@ -194,32 +179,26 @@ // update on screen info this.update_screen(); + + // get element + var it = this.get_upload_item(index); + + // update progress frame + it.addClass('panel-success'); + it.removeClass('panel-default'); + + // update icon + var sy = it.find('.symbol'); + sy.removeClass('fa-icon-spin'); + sy.removeClass('fa-icon-spinner'); + + // set status + sy.addClass(this.state.done); }, // error event_error : function(index, file, message) { - // get element - var it = this.get_upload_item(index); - - // update progress frame - it.addClass('panel-danger'); - it.removeClass('panel-default'); - - // update icon - var sy = it.find('.symbol'); - sy.addClass(this.state.done); - - // remove spin - sy.removeClass('fa-icon-spin'); - sy.removeClass('fa-icon-spinner'); - - // remove progress bar - it.find('.progress').remove(); - - // write error message - it.find('.error').html('<strong>Failed:</strong> ' + message); - // make sure progress is shown correctly this.event_progress(index, file, 0); @@ -232,6 +211,27 @@ // update on screen info this.update_screen(); + + // get element + var it = this.get_upload_item(index); + + // update progress frame + it.addClass('panel-danger'); + it.removeClass('panel-default'); + + // remove progress bar + it.find('.progress').remove(); + + // write error message + it.find('.error').html('<strong>Failed:</strong> ' + message); + + // update icon + var sy = it.find('.symbol'); + sy.removeClass('fa-icon-spin'); + sy.removeClass('fa-icon-spinner'); + + // set status + sy.addClass(this.state.done); }, // start upload process @@ -241,13 +241,6 @@ if (this.counter.announce == 0 || this.counter.running > 0) return; - // update running - this.counter.running = this.counter.announce; - this.update_screen(); - - // hide configuration - $(this.el).find('.panel-body').hide(); - // switch icons for new uploads var self = this; $(this.el).find('.symbol').each(function() @@ -259,6 +252,13 @@ $(this).addClass('fa-icon-spin'); } }); + + // hide configuration + $(this.el).find('.panel-body').hide(); + + // update running + this.counter.running = this.counter.announce; + this.update_screen(); // configure url var current_history = Galaxy.currHistoryPanel.model.get('id'); diff -r 6acc907464869c92c4bb366f6574c52714f60ae7 -r 2a2457d3bad09740d48cd2ba4de98936aafe2105 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -251,7 +251,7 @@ var self = this; displayBtnData.on_click = function(){ Galaxy.frame_manager.frame_new({ - title : "Data Viewer", + title : "Data Viewer: " + self.model.get('name'), type : "url", location: "center", content : self.urls.display 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: guerler: Drag&drop multiple file upload: add status icon
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6acc90746486/ Changeset: 6acc90746486 User: guerler Date: 2013-09-24 05:38:26 Summary: Drag&drop multiple file upload: add status icon Affected #: 4 files diff -r 8c464ada320ff611112d5b71febe394112a02daf -r 6acc907464869c92c4bb366f6574c52714f60ae7 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -24,6 +24,12 @@ 'ab1' : 'ab1' }, + // states + state : { + init : 'fa-icon-trash', + done : 'fa-icon-caret-down' + }, + // counter counter : { // stats @@ -80,7 +86,7 @@ event_mouseleave : function (e) { }, - + // start event_announce : function(index, file, message) { @@ -107,7 +113,7 @@ // add functionality to remove button var self = this; - it.find('.remove').on('click', function() { self.event_remove (index) }); + it.find('.symbol').on('click', function() { self.event_remove (index) }); // initialize progress this.event_progress(index, file, 0); @@ -155,7 +161,7 @@ it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size)); }, - // end + // success event_success : function(index, file, message) { // get element @@ -165,6 +171,14 @@ it.addClass('panel-success'); it.removeClass('panel-default'); + // update icon + var sy = it.find('.symbol'); + sy.addClass(this.state.done); + + // remove spin + sy.removeClass('fa-icon-spin'); + sy.removeClass('fa-icon-spinner'); + // update galaxy history Galaxy.currHistoryPanel.refresh(); @@ -182,7 +196,7 @@ this.update_screen(); }, - // end + // error event_error : function(index, file, message) { // get element @@ -192,6 +206,14 @@ it.addClass('panel-danger'); it.removeClass('panel-default'); + // update icon + var sy = it.find('.symbol'); + sy.addClass(this.state.done); + + // remove spin + sy.removeClass('fa-icon-spin'); + sy.removeClass('fa-icon-spinner'); + // remove progress bar it.find('.progress').remove(); @@ -226,11 +248,16 @@ // hide configuration $(this.el).find('.panel-body').hide(); - // switch icon - $(this.el).find('.remove').each(function() + // switch icons for new uploads + var self = this; + $(this.el).find('.symbol').each(function() { - $(this).removeClass('fa-icon-trash'); - $(this).addClass('fa-icon-caret-down'); + if($(this).hasClass(self.state.init)) + { + $(this).removeClass(self.state.init); + $(this).addClass('fa-icon-spinner'); + $(this).addClass('fa-icon-spin'); + } }); // configure url @@ -273,12 +300,13 @@ // remove item from upload list event_remove : function(index) { - // only remove from queue if paused - if (this.counter.running == 0) + // get item + var it = this.get_upload_item(index); + var sy = it.find('.symbol'); + + // only remove from queue if not in processing line + if (sy.hasClass(this.state.init) || sy.hasClass(this.state.done)) { - // get item - var it = this.get_upload_item(index); - // reduce counter if (it.hasClass('panel-default')) this.counter.announce--; @@ -428,7 +456,7 @@ '<div class="panel-heading">' + '<h5 class="title"></h5>' + '<h5 class="info"></h5>' + - '<div class="remove fa-icon-trash"></div>' + + '<div class="symbol ' + this.state.init + '"></div>' + '</div>' + '<div class="panel-body">' + '<div class="menu">' + diff -r 8c464ada320ff611112d5b71febe394112a02daf -r 6acc907464869c92c4bb366f6574c52714f60ae7 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -65,6 +65,9 @@ { // add files to queue add(e.target.files); + + // reset + $(this).val(''); }); // drop event @@ -323,7 +326,7 @@ // verify browser compatibility function compatible() { - return window.File && window.FileReader && window.FormData && window.XMLHttpRequest; + return window.File && window.FileReader && window.FormData && window.XMLHttpRequest && window.FileList; } // export functions diff -r 8c464ada320ff611112d5b71febe394112a02daf -r 6acc907464869c92c4bb366f6574c52714f60ae7 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1126,7 +1126,7 @@ .upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} .upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} -.upload-box .panel .panel-heading .remove{position:absolute;cursor:pointer;top:0px;right:3px} +.upload-box .panel .panel-heading .symbol{position:absolute;cursor:pointer;top:0px;right:3px} .upload-box .panel .panel-body{position:relative;padding:5px} .upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px} .upload-box .panel .panel-footer .error{font-weight:normal;margin:2px} diff -r 8c464ada320ff611112d5b71febe394112a02daf -r 6acc907464869c92c4bb366f6574c52714f60ae7 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -49,7 +49,7 @@ margin: 0px; } - .remove + .symbol { position: absolute; cursor: pointer; 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: natefoo: Merge stable branch, pack scripts.
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c464ada320f/ Changeset: 8c464ada320f User: natefoo Date: 2013-09-24 02:10:18 Summary: Merge stable branch, pack scripts. Affected #: 6 files diff -r e1bc855165bc857d6afd19d37a0542798601d85a -r 8c464ada320ff611112d5b71febe394112a02daf static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){this.uploadbox.info().hide();var i="#upload-"+e;$(this.el).append(this.template_file(i));$(this.el).scrollTop($(this.el).prop("scrollHeight"));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);g.find("#extension").select2({placeholder:"Auto-detect",width:"copy",ajax:{url:"http://www.weighttraining.com/sm/search",dataType:"jsonp",quietMillis:100,data:function(j,k){return{types:["exercise"],limit:-1,term:j}},results:function(k,j){return{results:k.results.exercise}}},formatResult:function(j){return"<div class='select2-user-result'>"+j.term+"</div>"},formatSelection:function(j){return j.term},initSelection:function(j,l){var k=$(j).attr("data-init-text");l({term:k})}});var d=this;g.find(".remove").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.modal.enable("Upload");this.modal.enable("Reset")},event_initialize:function(d,e,g){this.button_show.number(g);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("")},event_error:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.button_show.number("")},event_upload:function(){$(this.el).find(".panel-body").hide();$(this.el).find(".remove").each(function(){$(this).removeClass("fa-icon-trash");$(this).addClass("fa-icon-caret-down")});this.modal.disable("Upload");var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_reset:function(){var e=$(this.el).find(".panel");var d=this;e.fadeOut({complete:function(){e.remove();d.uploadbox.info().fadeIn()}});this.modal.disable("Upload");this.modal.disable("Reset");this.uploadbox.reset()},event_remove:function(e){var d=this;var f=this.get_upload_item(e);f.fadeOut({complete:function(){f.remove();d.uploadbox.remove(e);if($(d.el).find(".panel").length>0){d.modal.enable("Reset")}else{d.modal.disable("Reset");d.uploadbox.info().fadeIn()}if(d.uploadbox.length()>0){d.modal.enable("Upload")}else{d.modal.disable("Upload")}}})},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}}});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},});this.modal.disable("Upload");this.modal.disable("Reset")}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(d){return'<div id="'+d+'" class="upload-box"></div>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="remove fa-icon-trash"></div></div><div class="panel-body"><div class="menu"><span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{"":"Auto-detect",bed:"bed",ab1:"ab1"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){var i="#upload-"+e;$(this.el).append(this.template_file(i,this.select_extension));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);var d=this;g.find(".remove").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.counter.announce++;this.update_screen()},event_initialize:function(d,e,g){this.button_show.number(this.counter.announce);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen()},event_error:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen()},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}this.counter.running=this.counter.announce;this.update_screen();$(this.el).find(".panel-body").hide();$(this.el).find(".remove").each(function(){$(this).removeClass("fa-icon-trash");$(this).addClass("fa-icon-caret-down")});var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_complete:function(){this.counter.running=0;this.update_screen()},event_reset:function(){if(this.counter.running==0){var d=$(this.el).find(".panel");d.fadeOut({complete:function(){d.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(d){if(this.counter.running==0){var e=this.get_upload_item(d);if(e.hasClass("panel-default")){this.counter.announce--}else{if(e.hasClass("panel-success")){this.counter.success--}else{if(e.hasClass("panel-danger")){this.counter.error--}}}this.update_screen();this.uploadbox.remove(d);e.remove()}},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}}});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},complete:function(){d.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+' file(s) to the queue. Add more files or click "Upload" to proceed.'}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enable("Reset")}else{this.modal.disable("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enable("Upload")}else{this.modal.disable("Upload")}if(this.counter.running==0){this.modal.enable("Select")}else{this.modal.disable("Select")}},template:function(d){return'<div id="'+d+'" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'},template_file:function(f,e){var d='<div id="'+f.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="remove fa-icon-trash"></div></div><div class="panel-body"><div class="menu">Select file type: <select id="extension">';for(key in e){d+='<option value="'+key+'">'+e[key]+"</option>"}d+='</select>, <span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>';return d}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r e1bc855165bc857d6afd19d37a0542798601d85a -r 8c464ada320ff611112d5b71febe394112a02daf static/scripts/packed/libs/jquery/select2.js --- a/static/scripts/packed/libs/jquery/select2.js +++ b/static/scripts/packed/libs/jquery/select2.js @@ -1,1 +1,1 @@ -(function(a){if(typeof a.fn.each2=="undefined"){a.extend(a.fn,{each2:function(f){var d=a([0]),e=-1,b=this.length;while(++e<b&&(d.context=d[0]=this[e])&&f.call(d[0],e,d)!==false){}return this}})}})(jQuery);(function(D,m){if(window.Select2!==m){return}var 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aa=this.search,U=this.results,O=this.opts,T,Z=this,X,S=aa.val(),Q=D.data(this.container,"select2-last-term"),Y;if(W!==true&&Q&&t(S,Q)){return}D.data(this.container,"select2-last-term",S);if(W!==true&&(this.showSearchInput===false||!this.opened())){return}function V(){aa.removeClass("select2-active");Z.positionDropdown()}function P(ab){U.html(ab);V()}Y=++this.queryCount;var R=this.getMaximumSelectionSize();if(R>=1){T=this.data();if(D.isArray(T)&&T.length>=R&&y(O.formatSelectionTooBig,"formatSelectionTooBig")){P("<li class='select2-selection-limit'>"+O.formatSelectionTooBig(R)+"</li>");return}}if(aa.val().length<O.minimumInputLength){if(y(O.formatInputTooShort,"formatInputTooShort")){P("<li class='select2-no-results'>"+O.formatInputTooShort(aa.val(),O.minimumInputLength)+"</li>")}else{P("")}if(W&&this.showSearch){this.showSearch(true)}return}if(O.maximumInputLength&&aa.val().length>O.maximumInputLength){if(y(O.formatInputTooLong,"formatInputTooLong")){P("<li class='select2-no-results'>"+O.formatInputTooLong(aa.val(),O.maximumInputLength)+"</li>")}else{P("")}return}if(O.formatSearching&&this.findHighlightableChoices().length===0){P("<li class='select2-searching'>"+O.formatSearching()+"</li>")}aa.addClass("select2-active");this.removeHighlight();X=this.tokenize();if(X!=m&&X!=null){aa.val(X)}this.resultsPage=1;O.query({element:O.element,term:aa.val(),page:this.resultsPage,context:null,matcher:O.matcher,callback:this.bind(function(ac){var ab;if(Y!=this.queryCount){return}if(!this.opened()){this.search.removeClass("select2-active");return}this.context=(ac.context===m)?null:ac.context;if(this.opts.createSearchChoice&&aa.val()!==""){ab=this.opts.createSearchChoice.call(Z,aa.val(),ac.results);if(ab!==m&&ab!==null&&Z.id(ab)!==m&&Z.id(ab)!==null){if(D(ac.results).filter(function(){return t(Z.id(this),Z.id(ab))}).length===0){ac.results.unshift(ab)}}}if(ac.results.length===0&&y(O.formatNoMatches,"formatNoMatches")){P("<li class='select2-no-results'>"+O.formatNoMatches(aa.val())+"</li>");return}U.empty();Z.opts.populateResults.call(this,U,ac.results,{term:aa.val(),page:this.resultsPage,context:null});if(ac.more===true&&y(O.formatLoadMore,"formatLoadMore")){U.append("<li class='select2-more-results'>"+Z.opts.escapeMarkup(O.formatLoadMore(this.resultsPage))+"</li>");window.setTimeout(function(){Z.loadMoreIfNeeded()},10)}this.postprocessResults(ac,W);V();this.opts.element.trigger({type:"select2-loaded",items:ac})})})},cancel:function(){this.close()},blur:function(){if(this.opts.selectOnBlur){this.selectHighlighted({noFocus:true})}this.close();this.container.removeClass("select2-container-active");if(this.search[0]===document.activeElement){this.search.blur()}this.clearSearch();this.selection.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")},focusSearch:function(){I(this.search)},selectHighlighted:function(P){var O=this.highlight(),Q=this.results.find(".select2-highlighted"),R=Q.closest(".select2-result").data("select2-data");if(R){this.highlight(O);this.onSelect(R,P)}else{if(P&&P.noFocus){this.close()}}},getPlaceholder:function(){var O;return this.opts.element.attr("placeholder")||this.opts.element.attr("data-placeholder")||this.opts.element.data("placeholder")||this.opts.placeholder||((O=this.getPlaceholderOption())!==m?O.text():m)},getPlaceholderOption:function(){if(this.select){var O=this.select.children().first();if(this.opts.placeholderOption!==m){return(this.opts.placeholderOption==="first"&&O)||(typeof this.opts.placeholderOption==="function"&&this.opts.placeholderOption(this.select))}else{if(O.text()===""&&O.val()===""){return O}}}},initContainerWidth:function(){function P(){var T,R,U,S,Q;if(this.opts.width==="off"){return null}else{if(this.opts.width==="element"){return this.opts.element.outerWidth(false)===0?"auto":this.opts.element.outerWidth(false)+"px"}else{if(this.opts.width==="copy"||this.opts.width==="resolve"){T=this.opts.element.attr("style");if(T!==m){R=T.split(";");for(S=0,Q=R.length;S<Q;S=S+1){U=R[S].replace(/\s/g,"").match(/[^-]width:(([-+]?([0-9]*\.)?[0-9]+)(px|em|ex|%|in|cm|mm|pt|pc))/i);if(U!==null&&U.length>=1){return U[1]}}}if(this.opts.width==="resolve"){T=this.opts.element.css("width");if(T.indexOf("%")>0){return T}return(this.opts.element.outerWidth(false)===0?"auto":this.opts.element.outerWidth(false)+"px")}return null}else{if(D.isFunction(this.opts.width)){return this.opts.width()}else{return this.opts.width}}}}}var O=P.call(this);if(O!==null){this.container.css("width",O)}}});x=L(N,{createContainer:function(){var O=D(document.createElement("div")).attr({"class":"select2-container"}).html(["<a href='javascript:void(0)' onclick='return false;' class='select2-choice' tabindex='-1'>"," <span class='select2-chosen'> </span><abbr class='select2-search-choice-close'></abbr>"," <span class='select2-arrow'><b></b></span>","</a>","<input class='select2-focusser select2-offscreen' type='text'/>","<div class='select2-drop select2-display-none'>"," <div class='select2-search'>"," <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'/>"," </div>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return O},enableInterface:function(){if(this.parent.enableInterface.apply(this,arguments)){this.focusser.prop("disabled",!this.isInterfaceEnabled())}},opening:function(){var Q,P,O;if(this.opts.minimumResultsForSearch>=0){this.showSearch(true)}this.parent.opening.apply(this,arguments);if(this.showSearchInput!==false){this.search.val(this.focusser.val())}this.search.focus();Q=this.search.get(0);if(Q.createTextRange){P=Q.createTextRange();P.collapse(false);P.select()}else{if(Q.setSelectionRange){O=this.search.val().length;Q.setSelectionRange(O,O)}}if(this.search.val()===""){if(this.nextSearchTerm!=m){this.search.val(this.nextSearchTerm);this.search.select()}}this.focusser.prop("disabled",true).val("");this.updateResults(true);this.opts.element.trigger(D.Event("select2-open"))},close:function(O){if(!this.opened()){return}this.parent.close.apply(this,arguments);O=O||{focus:true};this.focusser.removeAttr("disabled");if(O.focus){this.focusser.focus()}},focus:function(){if(this.opened()){this.close()}else{this.focusser.removeAttr("disabled");this.focusser.focus()}},isFocused:function(){return this.container.hasClass("select2-container-active")},cancel:function(){this.parent.cancel.apply(this,arguments);this.focusser.removeAttr("disabled");this.focusser.focus()},destroy:function(){D("label[for='"+this.focusser.attr("id")+"']").attr("for",this.opts.element.attr("id"));this.parent.destroy.apply(this,arguments)},initContainer:function(){var P,O=this.container,Q=this.dropdown;if(this.opts.minimumResultsForSearch<0){this.showSearch(false)}else{this.showSearch(true)}this.selection=P=O.find(".select2-choice");this.focusser=O.find(".select2-focusser");this.focusser.attr("id","s2id_autogen"+a());D("label[for='"+this.opts.element.attr("id")+"']").attr("for",this.focusser.attr("id"));this.focusser.attr("tabindex",this.elementTabIndex);this.search.on("keydown",this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(R.which===K.PAGE_UP||R.which===K.PAGE_DOWN){A(R);return}switch(R.which){case K.UP:case K.DOWN:this.moveHighlight((R.which===K.UP)?-1:1);A(R);return;case K.ENTER:this.selectHighlighted();A(R);return;case K.TAB:if(this.opts.selectOnBlur){this.selectHighlighted({noFocus:true})}return;case K.ESC:this.cancel(R);A(R);return}}));this.search.on("blur",this.bind(function(R){if(document.activeElement===this.body().get(0)){window.setTimeout(this.bind(function(){this.search.focus()}),0)}}));this.focusser.on("keydown",this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(R.which===K.TAB||K.isControl(R)||K.isFunctionKey(R)||R.which===K.ESC){return}if(this.opts.openOnEnter===false&&R.which===K.ENTER){A(R);return}if(R.which==K.DOWN||R.which==K.UP||(R.which==K.ENTER&&this.opts.openOnEnter)){if(R.altKey||R.ctrlKey||R.shiftKey||R.metaKey){return}this.open();A(R);return}if(R.which==K.DELETE||R.which==K.BACKSPACE){if(this.opts.allowClear){this.clear()}A(R);return}}));F(this.focusser);this.focusser.on("keyup-change input",this.bind(function(R){if(this.opts.minimumResultsForSearch>=0){R.stopPropagation();if(this.opened()){return}this.open()}}));P.on("mousedown","abbr",this.bind(function(R){if(!this.isInterfaceEnabled()){return}this.clear();b(R);this.close();this.selection.focus()}));P.on("mousedown",this.bind(function(R){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}if(this.opened()){this.close()}else{if(this.isInterfaceEnabled()){this.open()}}A(R)}));Q.on("mousedown",this.bind(function(){this.search.focus()}));P.on("focus",this.bind(function(R){A(R)}));this.focusser.on("focus",this.bind(function(){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active")})).on("blur",this.bind(function(){if(!this.opened()){this.container.removeClass("select2-container-active");this.opts.element.trigger(D.Event("select2-blur"))}}));this.search.on("focus",this.bind(function(){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active")}));this.initContainerWidth();this.opts.element.addClass("select2-offscreen");this.setPlaceholder()},clear:function(P){var Q=this.selection.data("select2-data");if(Q){var O=this.getPlaceholderOption();this.opts.element.val(O?O.val():"");this.selection.find(".select2-chosen").empty();this.selection.removeData("select2-data");this.setPlaceholder();if(P!==false){this.opts.element.trigger({type:"select2-removed",val:this.id(Q),choice:Q});this.triggerChange({removed:Q})}}},initSelection:function(){var P;if(this.isPlaceholderOptionSelected()){this.updateSelection(null);this.close();this.setPlaceholder()}else{var O=this;this.opts.initSelection.call(null,this.opts.element,function(Q){if(Q!==m&&Q!==null){O.updateSelection(Q);O.close();O.setPlaceholder()}})}},isPlaceholderOptionSelected:function(){var O;if(!this.opts.placeholder){return false}return((O=this.getPlaceholderOption())!==m&&O.is(":selected"))||(this.opts.element.val()==="")||(this.opts.element.val()===m)||(this.opts.element.val()===null)},prepareOpts:function(){var P=this.parent.prepareOpts.apply(this,arguments),O=this;if(P.element.get(0).tagName.toLowerCase()==="select"){P.initSelection=function(Q,S){var R=Q.find(":selected");S(O.optionToData(R))}}else{if("data" in P){P.initSelection=P.initSelection||function(R,T){var S=R.val();var Q=null;P.query({matcher:function(U,X,V){var W=t(S,P.id(V));if(W){Q=V}return W},callback:!D.isFunction(T)?D.noop:function(){T(Q)}})}}}return P},getPlaceholder:function(){if(this.select){if(this.getPlaceholderOption()===m){return m}}return this.parent.getPlaceholder.apply(this,arguments)},setPlaceholder:function(){var O=this.getPlaceholder();if(this.isPlaceholderOptionSelected()&&O!==m){if(this.select&&this.getPlaceholderOption()===m){return}this.selection.find(".select2-chosen").html(this.opts.escapeMarkup(O));this.selection.addClass("select2-default");this.container.removeClass("select2-allowclear")}},postprocessResults:function(T,P,S){var R=0,O=this,U=true;this.findHighlightableChoices().each2(function(V,W){if(t(O.id(W.data("select2-data")),O.opts.element.val())){R=V;return false}});if(S!==false){if(P===true&&R>=0){this.highlight(R)}else{this.highlight(0)}}if(P===true){var Q=this.opts.minimumResultsForSearch;if(Q>=0){this.showSearch(r(T.results)>=Q)}}},showSearch:function(O){if(this.showSearchInput===O){return}this.showSearchInput=O;this.dropdown.find(".select2-search").toggleClass("select2-search-hidden",!O);this.dropdown.find(".select2-search").toggleClass("select2-offscreen",!O);D(this.dropdown,this.container).toggleClass("select2-with-searchbox",O)},onSelect:function(Q,P){if(!this.triggerSelect(Q)){return}var O=this.opts.element.val(),R=this.data();this.opts.element.val(this.id(Q));this.updateSelection(Q);this.opts.element.trigger({type:"select2-selected",val:this.id(Q),choice:Q});this.nextSearchTerm=this.opts.nextSearchTerm(Q,this.search.val());this.close();if(!P||!P.noFocus){this.selection.focus()}if(!t(O,this.id(Q))){this.triggerChange({added:Q,removed:R})}},updateSelection:function(R){var P=this.selection.find(".select2-chosen"),Q,O;this.selection.data("select2-data",R);P.empty();if(R!==null){Q=this.opts.formatSelection(R,P,this.opts.escapeMarkup)}if(Q!==m){P.append(Q)}O=this.opts.formatSelectionCssClass(R,P);if(O!==m){P.addClass(O)}this.selection.removeClass("select2-default");if(this.opts.allowClear&&this.getPlaceholder()!==m){this.container.addClass("select2-allowclear")}},val:function(){var S,P=false,Q=null,O=this,R=this.data();if(arguments.length===0){return this.opts.element.val()}S=arguments[0];if(arguments.length>1){P=arguments[1]}if(this.select){this.select.val(S).find(":selected").each2(function(T,U){Q=O.optionToData(U);return false});this.updateSelection(Q);this.setPlaceholder();if(P){this.triggerChange({added:Q,removed:R})}}else{if(!S&&S!==0){this.clear(P);return}if(this.opts.initSelection===m){throw new Error("cannot call val() if initSelection() is not defined")}this.opts.element.val(S);this.opts.initSelection(this.opts.element,function(T){O.opts.element.val(!T?"":O.id(T));O.updateSelection(T);O.setPlaceholder();if(P){O.triggerChange({added:T,removed:R})}})}},clearSearch:function(){this.search.val("");this.focusser.val("")},data:function(Q){var P,O=false;if(arguments.length===0){P=this.selection.data("select2-data");if(P==m){P=null}return P}else{if(arguments.length>1){O=arguments[1]}if(!Q){this.clear(O)}else{P=this.data();this.opts.element.val(!Q?"":this.id(Q));this.updateSelection(Q);if(O){this.triggerChange({added:Q,removed:P})}}}}});c=L(N,{createContainer:function(){var O=D(document.createElement("div")).attr({"class":"select2-container select2-container-multi"}).html(["<ul class='select2-choices'>"," <li class='select2-search-field'>"," <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'>"," </li>","</ul>","<div class='select2-drop select2-drop-multi select2-display-none'>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return O},prepareOpts:function(){var P=this.parent.prepareOpts.apply(this,arguments),O=this;if(P.element.get(0).tagName.toLowerCase()==="select"){P.initSelection=function(Q,S){var R=[];Q.find(":selected").each2(function(T,U){R.push(O.optionToData(U))});S(R)}}else{if("data" in P){P.initSelection=P.initSelection||function(Q,T){var R=i(Q.val(),P.separator);var S=[];P.query({matcher:function(U,X,V){var W=D.grep(R,function(Y){return t(Y,P.id(V))}).length;if(W){S.push(V)}return W},callback:!D.isFunction(T)?D.noop:function(){var U=[];for(var X=0;X<R.length;X++){var Y=R[X];for(var W=0;W<S.length;W++){var V=S[W];if(t(Y,P.id(V))){U.push(V);S.splice(W,1);break}}}T(U)}})}}}return P},selectChoice:function(O){var P=this.container.find(".select2-search-choice-focus");if(P.length&&O&&O[0]==P[0]){}else{if(P.length){this.opts.element.trigger("choice-deselected",P)}P.removeClass("select2-search-choice-focus");if(O&&O.length){this.close();O.addClass("select2-search-choice-focus");this.opts.element.trigger("choice-selected",O)}}},destroy:function(){D("label[for='"+this.search.attr("id")+"']").attr("for",this.opts.element.attr("id"));this.parent.destroy.apply(this,arguments)},initContainer:function(){var O=".select2-choices",P;this.searchContainer=this.container.find(".select2-search-field");this.selection=P=this.container.find(O);var Q=this;this.selection.on("click",".select2-search-choice",function(R){Q.search[0].focus();Q.selectChoice(D(this))});this.search.attr("id","s2id_autogen"+a());D("label[for='"+this.opts.element.attr("id")+"']").attr("for",this.search.attr("id"));this.search.on("input paste",this.bind(function(){if(!this.isInterfaceEnabled()){return}if(!this.opened()){this.open()}}));this.search.attr("tabindex",this.elementTabIndex);this.keydowns=0;this.search.on("keydown",this.bind(function(V){if(!this.isInterfaceEnabled()){return}++this.keydowns;var T=P.find(".select2-search-choice-focus");var U=T.prev(".select2-search-choice:not(.select2-locked)");var S=T.next(".select2-search-choice:not(.select2-locked)");var W=f(this.search);if(T.length&&(V.which==K.LEFT||V.which==K.RIGHT||V.which==K.BACKSPACE||V.which==K.DELETE||V.which==K.ENTER)){var R=T;if(V.which==K.LEFT&&U.length){R=U}else{if(V.which==K.RIGHT){R=S.length?S:null}else{if(V.which===K.BACKSPACE){this.unselect(T.first());this.search.width(10);R=U.length?U:S}else{if(V.which==K.DELETE){this.unselect(T.first());this.search.width(10);R=S.length?S:null}else{if(V.which==K.ENTER){R=null}}}}}this.selectChoice(R);A(V);if(!R||!R.length){this.open()}return}else{if(((V.which===K.BACKSPACE&&this.keydowns==1)||V.which==K.LEFT)&&(W.offset==0&&!W.length)){this.selectChoice(P.find(".select2-search-choice:not(.select2-locked)").last());A(V);return}else{this.selectChoice(null)}}if(this.opened()){switch(V.which){case K.UP:case K.DOWN:this.moveHighlight((V.which===K.UP)?-1:1);A(V);return;case K.ENTER:this.selectHighlighted();A(V);return;case K.TAB:if(this.opts.selectOnBlur){this.selectHighlighted({noFocus:true})}this.close();return;case K.ESC:this.cancel(V);A(V);return}}if(V.which===K.TAB||K.isControl(V)||K.isFunctionKey(V)||V.which===K.BACKSPACE||V.which===K.ESC){return}if(V.which===K.ENTER){if(this.opts.openOnEnter===false){return}else{if(V.altKey||V.ctrlKey||V.shiftKey||V.metaKey){return}}}this.open();if(V.which===K.PAGE_UP||V.which===K.PAGE_DOWN){A(V)}if(V.which===K.ENTER){A(V)}}));this.search.on("keyup",this.bind(function(R){this.keydowns=0;this.resizeSearch()}));this.search.on("blur",this.bind(function(R){this.container.removeClass("select2-container-active");this.search.removeClass("select2-focused");this.selectChoice(null);if(!this.opened()){this.clearSearch()}R.stopImmediatePropagation();this.opts.element.trigger(D.Event("select2-blur"))}));this.container.on("click",O,this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(D(R.target).closest(".select2-search-choice").length>0){return}this.selectChoice(null);this.clearPlaceholder();if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.open();this.focusSearch();R.preventDefault()}));this.container.on("focus",O,this.bind(function(){if(!this.isInterfaceEnabled()){return}if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active");this.dropdown.addClass("select2-drop-active");this.clearPlaceholder()}));this.initContainerWidth();this.opts.element.addClass("select2-offscreen");this.clearSearch()},enableInterface:function(){if(this.parent.enableInterface.apply(this,arguments)){this.search.prop("disabled",!this.isInterfaceEnabled())}},initSelection:function(){var P;if(this.opts.element.val()===""&&this.opts.element.text()===""){this.updateSelection([]);this.close();this.clearSearch()}if(this.select||this.opts.element.val()!==""){var O=this;this.opts.initSelection.call(null,this.opts.element,function(Q){if(Q!==m&&Q!==null){O.updateSelection(Q);O.close();O.clearSearch()}})}},clearSearch:function(){var P=this.getPlaceholder(),O=this.getMaxSearchWidth();if(P!==m&&this.getVal().length===0&&this.search.hasClass("select2-focused")===false){this.search.val(P).addClass("select2-default");this.search.width(O>0?O:this.container.css("width"))}else{this.search.val("").width(10)}},clearPlaceholder:function(){if(this.search.hasClass("select2-default")){this.search.val("").removeClass("select2-default")}},opening:function(){this.clearPlaceholder();this.resizeSearch();this.parent.opening.apply(this,arguments);this.focusSearch();this.updateResults(true);this.search.focus();this.opts.element.trigger(D.Event("select2-open"))},close:function(){if(!this.opened()){return}this.parent.close.apply(this,arguments)},focus:function(){this.close();this.search.focus()},isFocused:function(){return this.search.hasClass("select2-focused")},updateSelection:function(R){var Q=[],P=[],O=this;D(R).each(function(){if(q(O.id(this),Q)<0){Q.push(O.id(this));P.push(this)}});R=P;this.selection.find(".select2-search-choice").remove();D(R).each(function(){O.addSelectedChoice(this)});O.postprocessResults()},tokenize:function(){var 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O=this.highlight(),Q=this.results.find(".select2-highlighted"),R=Q.closest(".select2-result").data("select2-data");if(R){this.highlight(O);this.onSelect(R,P)}else{if(P&&P.noFocus){this.close()}}},getPlaceholder:function(){var O;return this.opts.element.attr("placeholder")||this.opts.element.attr("data-placeholder")||this.opts.element.data("placeholder")||this.opts.placeholder||((O=this.getPlaceholderOption())!==m?O.text():m)},getPlaceholderOption:function(){if(this.select){var O=this.select.children().first();if(this.opts.placeholderOption!==m){return(this.opts.placeholderOption==="first"&&O)||(typeof this.opts.placeholderOption==="function"&&this.opts.placeholderOption(this.select))}else{if(O.text()===""&&O.val()===""){return O}}}},initContainerWidth:function(){function P(){var T,R,U,S,Q;if(this.opts.width==="off"){return null}else{if(this.opts.width==="element"){return this.opts.element.outerWidth(false)===0?"auto":this.opts.element.outerWidth(false)+"px"}else{if(this.opts.width==="copy"||this.opts.width==="resolve"){T=this.opts.element.attr("style");if(T!==m){R=T.split(";");for(S=0,Q=R.length;S<Q;S=S+1){U=R[S].replace(/\s/g,"").match(/[^-]width:(([-+]?([0-9]*\.)?[0-9]+)(px|em|ex|%|in|cm|mm|pt|pc))/i);if(U!==null&&U.length>=1){return U[1]}}}if(this.opts.width==="resolve"){T=this.opts.element.css("width");if(T.indexOf("%")>0){return T}return(this.opts.element.outerWidth(false)===0?"auto":this.opts.element.outerWidth(false)+"px")}return null}else{if(D.isFunction(this.opts.width)){return this.opts.width()}else{return this.opts.width}}}}}var O=P.call(this);if(O!==null){this.container.css("width",O)}}});x=L(N,{createContainer:function(){var O=D(document.createElement("div")).attr({"class":"select2-container"}).html(["<a href='javascript:void(0)' onclick='return false;' class='select2-choice' tabindex='-1'>"," <span class='select2-chosen'> </span><abbr class='select2-search-choice-close'></abbr>"," <span class='select2-arrow'><b></b></span>","</a>","<input class='select2-focusser select2-offscreen' type='text'/>","<div class='select2-drop select2-display-none'>"," <div class='select2-search'>"," <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'/>"," </div>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return O},enableInterface:function(){if(this.parent.enableInterface.apply(this,arguments)){this.focusser.prop("disabled",!this.isInterfaceEnabled())}},opening:function(){var Q,P,O;if(this.opts.minimumResultsForSearch>=0){this.showSearch(true)}this.parent.opening.apply(this,arguments);if(this.showSearchInput!==false){this.search.val(this.focusser.val())}this.search.focus();Q=this.search.get(0);if(Q.createTextRange){P=Q.createTextRange();P.collapse(false);P.select()}else{if(Q.setSelectionRange){O=this.search.val().length;Q.setSelectionRange(O,O)}}if(this.search.val()===""){if(this.nextSearchTerm!=m){this.search.val(this.nextSearchTerm);this.search.select()}}this.focusser.prop("disabled",true).val("");this.updateResults(true);this.opts.element.trigger(D.Event("select2-open"))},close:function(O){if(!this.opened()){return}this.parent.close.apply(this,arguments);O=O||{focus:true};this.focusser.removeAttr("disabled");if(O.focus){this.focusser.focus()}},focus:function(){if(this.opened()){this.close()}else{this.focusser.removeAttr("disabled");this.focusser.focus()}},isFocused:function(){return this.container.hasClass("select2-container-active")},cancel:function(){this.parent.cancel.apply(this,arguments);this.focusser.removeAttr("disabled");this.focusser.focus()},destroy:function(){D("label[for='"+this.focusser.attr("id")+"']").attr("for",this.opts.element.attr("id"));this.parent.destroy.apply(this,arguments)},initContainer:function(){var P,O=this.container,Q=this.dropdown;if(this.opts.minimumResultsForSearch<0){this.showSearch(false)}else{this.showSearch(true)}this.selection=P=O.find(".select2-choice");this.focusser=O.find(".select2-focusser");this.focusser.attr("id","s2id_autogen"+a());D("label[for='"+this.opts.element.attr("id")+"']").attr("for",this.focusser.attr("id"));this.focusser.attr("tabindex",this.elementTabIndex);this.search.on("keydown",this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(R.which===K.PAGE_UP||R.which===K.PAGE_DOWN){A(R);return}switch(R.which){case K.UP:case K.DOWN:this.moveHighlight((R.which===K.UP)?-1:1);A(R);return;case K.ENTER:this.selectHighlighted();A(R);return;case K.TAB:this.selectHighlighted({noFocus:true});return;case K.ESC:this.cancel(R);A(R);return}}));this.search.on("blur",this.bind(function(R){if(document.activeElement===this.body().get(0)){window.setTimeout(this.bind(function(){this.search.focus()}),0)}}));this.focusser.on("keydown",this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(R.which===K.TAB||K.isControl(R)||K.isFunctionKey(R)||R.which===K.ESC){return}if(this.opts.openOnEnter===false&&R.which===K.ENTER){A(R);return}if(R.which==K.DOWN||R.which==K.UP||(R.which==K.ENTER&&this.opts.openOnEnter)){if(R.altKey||R.ctrlKey||R.shiftKey||R.metaKey){return}this.open();A(R);return}if(R.which==K.DELETE||R.which==K.BACKSPACE){if(this.opts.allowClear){this.clear()}A(R);return}}));F(this.focusser);this.focusser.on("keyup-change input",this.bind(function(R){if(this.opts.minimumResultsForSearch>=0){R.stopPropagation();if(this.opened()){return}this.open()}}));P.on("mousedown","abbr",this.bind(function(R){if(!this.isInterfaceEnabled()){return}this.clear();b(R);this.close();this.selection.focus()}));P.on("mousedown",this.bind(function(R){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}if(this.opened()){this.close()}else{if(this.isInterfaceEnabled()){this.open()}}A(R)}));Q.on("mousedown",this.bind(function(){this.search.focus()}));P.on("focus",this.bind(function(R){A(R)}));this.focusser.on("focus",this.bind(function(){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active")})).on("blur",this.bind(function(){if(!this.opened()){this.container.removeClass("select2-container-active");this.opts.element.trigger(D.Event("select2-blur"))}}));this.search.on("focus",this.bind(function(){if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active")}));this.initContainerWidth();this.opts.element.addClass("select2-offscreen");this.setPlaceholder()},clear:function(Q){var R=this.selection.data("select2-data");if(R){var P=D.Event("select2-clearing");this.opts.element.trigger(P);if(P.isDefaultPrevented()){return}var O=this.getPlaceholderOption();this.opts.element.val(O?O.val():"");this.selection.find(".select2-chosen").empty();this.selection.removeData("select2-data");this.setPlaceholder();if(Q!==false){this.opts.element.trigger({type:"select2-removed",val:this.id(R),choice:R});this.triggerChange({removed:R})}}},initSelection:function(){var P;if(this.isPlaceholderOptionSelected()){this.updateSelection(null);this.close();this.setPlaceholder()}else{var O=this;this.opts.initSelection.call(null,this.opts.element,function(Q){if(Q!==m&&Q!==null){O.updateSelection(Q);O.close();O.setPlaceholder()}})}},isPlaceholderOptionSelected:function(){var O;if(!this.getPlaceholder()){return false}return((O=this.getPlaceholderOption())!==m&&O.is(":selected"))||(this.opts.element.val()==="")||(this.opts.element.val()===m)||(this.opts.element.val()===null)},prepareOpts:function(){var P=this.parent.prepareOpts.apply(this,arguments),O=this;if(P.element.get(0).tagName.toLowerCase()==="select"){P.initSelection=function(Q,S){var R=Q.find(":selected");S(O.optionToData(R))}}else{if("data" in P){P.initSelection=P.initSelection||function(R,T){var S=R.val();var Q=null;P.query({matcher:function(U,X,V){var W=t(S,P.id(V));if(W){Q=V}return W},callback:!D.isFunction(T)?D.noop:function(){T(Q)}})}}}return P},getPlaceholder:function(){if(this.select){if(this.getPlaceholderOption()===m){return m}}return this.parent.getPlaceholder.apply(this,arguments)},setPlaceholder:function(){var O=this.getPlaceholder();if(this.isPlaceholderOptionSelected()&&O!==m){if(this.select&&this.getPlaceholderOption()===m){return}this.selection.find(".select2-chosen").html(this.opts.escapeMarkup(O));this.selection.addClass("select2-default");this.container.removeClass("select2-allowclear")}},postprocessResults:function(T,P,S){var R=0,O=this,U=true;this.findHighlightableChoices().each2(function(V,W){if(t(O.id(W.data("select2-data")),O.opts.element.val())){R=V;return false}});if(S!==false){if(P===true&&R>=0){this.highlight(R)}else{this.highlight(0)}}if(P===true){var Q=this.opts.minimumResultsForSearch;if(Q>=0){this.showSearch(r(T.results)>=Q)}}},showSearch:function(O){if(this.showSearchInput===O){return}this.showSearchInput=O;this.dropdown.find(".select2-search").toggleClass("select2-search-hidden",!O);this.dropdown.find(".select2-search").toggleClass("select2-offscreen",!O);D(this.dropdown,this.container).toggleClass("select2-with-searchbox",O)},onSelect:function(Q,P){if(!this.triggerSelect(Q)){return}var O=this.opts.element.val(),R=this.data();this.opts.element.val(this.id(Q));this.updateSelection(Q);this.opts.element.trigger({type:"select2-selected",val:this.id(Q),choice:Q});this.nextSearchTerm=this.opts.nextSearchTerm(Q,this.search.val());this.close();if(!P||!P.noFocus){this.focusser.focus()}if(!t(O,this.id(Q))){this.triggerChange({added:Q,removed:R})}},updateSelection:function(R){var P=this.selection.find(".select2-chosen"),Q,O;this.selection.data("select2-data",R);P.empty();if(R!==null){Q=this.opts.formatSelection(R,P,this.opts.escapeMarkup)}if(Q!==m){P.append(Q)}O=this.opts.formatSelectionCssClass(R,P);if(O!==m){P.addClass(O)}this.selection.removeClass("select2-default");if(this.opts.allowClear&&this.getPlaceholder()!==m){this.container.addClass("select2-allowclear")}},val:function(){var S,P=false,Q=null,O=this,R=this.data();if(arguments.length===0){return this.opts.element.val()}S=arguments[0];if(arguments.length>1){P=arguments[1]}if(this.select){this.select.val(S).find(":selected").each2(function(T,U){Q=O.optionToData(U);return false});this.updateSelection(Q);this.setPlaceholder();if(P){this.triggerChange({added:Q,removed:R})}}else{if(!S&&S!==0){this.clear(P);return}if(this.opts.initSelection===m){throw new Error("cannot call val() if initSelection() is not defined")}this.opts.element.val(S);this.opts.initSelection(this.opts.element,function(T){O.opts.element.val(!T?"":O.id(T));O.updateSelection(T);O.setPlaceholder();if(P){O.triggerChange({added:T,removed:R})}})}},clearSearch:function(){this.search.val("");this.focusser.val("")},data:function(Q){var P,O=false;if(arguments.length===0){P=this.selection.data("select2-data");if(P==m){P=null}return P}else{if(arguments.length>1){O=arguments[1]}if(!Q){this.clear(O)}else{P=this.data();this.opts.element.val(!Q?"":this.id(Q));this.updateSelection(Q);if(O){this.triggerChange({added:Q,removed:P})}}}}});c=L(N,{createContainer:function(){var O=D(document.createElement("div")).attr({"class":"select2-container select2-container-multi"}).html(["<ul class='select2-choices'>"," <li class='select2-search-field'>"," <input type='text' autocomplete='off' autocorrect='off' autocapitalize='off' spellcheck='false' class='select2-input'>"," </li>","</ul>","<div class='select2-drop select2-drop-multi select2-display-none'>"," <ul class='select2-results'>"," </ul>","</div>"].join(""));return O},prepareOpts:function(){var P=this.parent.prepareOpts.apply(this,arguments),O=this;if(P.element.get(0).tagName.toLowerCase()==="select"){P.initSelection=function(Q,S){var R=[];Q.find(":selected").each2(function(T,U){R.push(O.optionToData(U))});S(R)}}else{if("data" in P){P.initSelection=P.initSelection||function(Q,T){var R=i(Q.val(),P.separator);var S=[];P.query({matcher:function(U,X,V){var W=D.grep(R,function(Y){return t(Y,P.id(V))}).length;if(W){S.push(V)}return W},callback:!D.isFunction(T)?D.noop:function(){var U=[];for(var X=0;X<R.length;X++){var Y=R[X];for(var W=0;W<S.length;W++){var V=S[W];if(t(Y,P.id(V))){U.push(V);S.splice(W,1);break}}}T(U)}})}}}return P},selectChoice:function(O){var P=this.container.find(".select2-search-choice-focus");if(P.length&&O&&O[0]==P[0]){}else{if(P.length){this.opts.element.trigger("choice-deselected",P)}P.removeClass("select2-search-choice-focus");if(O&&O.length){this.close();O.addClass("select2-search-choice-focus");this.opts.element.trigger("choice-selected",O)}}},destroy:function(){D("label[for='"+this.search.attr("id")+"']").attr("for",this.opts.element.attr("id"));this.parent.destroy.apply(this,arguments)},initContainer:function(){var O=".select2-choices",P;this.searchContainer=this.container.find(".select2-search-field");this.selection=P=this.container.find(O);var Q=this;this.selection.on("click",".select2-search-choice:not(.select2-locked)",function(R){Q.search[0].focus();Q.selectChoice(D(this))});this.search.attr("id","s2id_autogen"+a());D("label[for='"+this.opts.element.attr("id")+"']").attr("for",this.search.attr("id"));this.search.on("input paste",this.bind(function(){if(!this.isInterfaceEnabled()){return}if(!this.opened()){this.open()}}));this.search.attr("tabindex",this.elementTabIndex);this.keydowns=0;this.search.on("keydown",this.bind(function(V){if(!this.isInterfaceEnabled()){return}++this.keydowns;var T=P.find(".select2-search-choice-focus");var U=T.prev(".select2-search-choice:not(.select2-locked)");var S=T.next(".select2-search-choice:not(.select2-locked)");var W=f(this.search);if(T.length&&(V.which==K.LEFT||V.which==K.RIGHT||V.which==K.BACKSPACE||V.which==K.DELETE||V.which==K.ENTER)){var R=T;if(V.which==K.LEFT&&U.length){R=U}else{if(V.which==K.RIGHT){R=S.length?S:null}else{if(V.which===K.BACKSPACE){this.unselect(T.first());this.search.width(10);R=U.length?U:S}else{if(V.which==K.DELETE){this.unselect(T.first());this.search.width(10);R=S.length?S:null}else{if(V.which==K.ENTER){R=null}}}}}this.selectChoice(R);A(V);if(!R||!R.length){this.open()}return}else{if(((V.which===K.BACKSPACE&&this.keydowns==1)||V.which==K.LEFT)&&(W.offset==0&&!W.length)){this.selectChoice(P.find(".select2-search-choice:not(.select2-locked)").last());A(V);return}else{this.selectChoice(null)}}if(this.opened()){switch(V.which){case K.UP:case K.DOWN:this.moveHighlight((V.which===K.UP)?-1:1);A(V);return;case K.ENTER:this.selectHighlighted();A(V);return;case K.TAB:this.selectHighlighted({noFocus:true});this.close();return;case K.ESC:this.cancel(V);A(V);return}}if(V.which===K.TAB||K.isControl(V)||K.isFunctionKey(V)||V.which===K.BACKSPACE||V.which===K.ESC){return}if(V.which===K.ENTER){if(this.opts.openOnEnter===false){return}else{if(V.altKey||V.ctrlKey||V.shiftKey||V.metaKey){return}}}this.open();if(V.which===K.PAGE_UP||V.which===K.PAGE_DOWN){A(V)}if(V.which===K.ENTER){A(V)}}));this.search.on("keyup",this.bind(function(R){this.keydowns=0;this.resizeSearch()}));this.search.on("blur",this.bind(function(R){this.container.removeClass("select2-container-active");this.search.removeClass("select2-focused");this.selectChoice(null);if(!this.opened()){this.clearSearch()}R.stopImmediatePropagation();this.opts.element.trigger(D.Event("select2-blur"))}));this.container.on("click",O,this.bind(function(R){if(!this.isInterfaceEnabled()){return}if(D(R.target).closest(".select2-search-choice").length>0){return}this.selectChoice(null);this.clearPlaceholder();if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.open();this.focusSearch();R.preventDefault()}));this.container.on("focus",O,this.bind(function(){if(!this.isInterfaceEnabled()){return}if(!this.container.hasClass("select2-container-active")){this.opts.element.trigger(D.Event("select2-focus"))}this.container.addClass("select2-container-active");this.dropdown.addClass("select2-drop-active");this.clearPlaceholder()}));this.initContainerWidth();this.opts.element.addClass("select2-offscreen");this.clearSearch()},enableInterface:function(){if(this.parent.enableInterface.apply(this,arguments)){this.search.prop("disabled",!this.isInterfaceEnabled())}},initSelection:function(){var P;if(this.opts.element.val()===""&&this.opts.element.text()===""){this.updateSelection([]);this.close();this.clearSearch()}if(this.select||this.opts.element.val()!==""){var O=this;this.opts.initSelection.call(null,this.opts.element,function(Q){if(Q!==m&&Q!==null){O.updateSelection(Q);O.close();O.clearSearch()}})}},clearSearch:function(){var P=this.getPlaceholder(),O=this.getMaxSearchWidth();if(P!==m&&this.getVal().length===0&&this.search.hasClass("select2-focused")===false){this.search.val(P).addClass("select2-default");this.search.width(O>0?O:this.container.css("width"))}else{this.search.val("").width(10)}},clearPlaceholder:function(){if(this.search.hasClass("select2-default")){this.search.val("").removeClass("select2-default")}},opening:function(){this.clearPlaceholder();this.resizeSearch();this.parent.opening.apply(this,arguments);this.focusSearch();this.updateResults(true);this.search.focus();this.opts.element.trigger(D.Event("select2-open"))},close:function(){if(!this.opened()){return}this.parent.close.apply(this,arguments)},focus:function(){this.close();this.search.focus()},isFocused:function(){return this.search.hasClass("select2-focused")},updateSelection:function(R){var Q=[],P=[],O=this;D(R).each(function(){if(q(O.id(this),Q)<0){Q.push(O.id(this));P.push(this)}});R=P;this.selection.find(".select2-search-choice").remove();D(R).each(function(){O.addSelectedChoice(this)});O.postprocessResults()},tokenize:function(){var O=this.search.val();O=this.opts.tokenizer.call(this,O,this.data(),this.bind(this.onSelect),this.opts);if(O!=null&&O!=m){this.search.val(O);if(O.length>0){this.open()}}},onSelect:function(P,O){if(!this.triggerSelect(P)){return}this.addSelectedChoice(P);this.opts.element.trigger({type:"selected",val:this.id(P),choice:P});if(this.select||!this.opts.closeOnSelect){this.postprocessResults(P,false,this.opts.closeOnSelect===true)}if(this.opts.closeOnSelect){this.close();this.search.width(10)}else{if(this.countSelectableResults()>0){this.search.width(10);this.resizeSearch();if(this.getMaximumSelectionSize()>0&&this.val().length>=this.getMaximumSelectionSize()){this.updateResults(true)}this.positionDropdown()}else{this.close();this.search.width(10)}}this.triggerChange({added:P});if(!O||!O.noFocus){this.focusSearch()}},cancel:function(){this.close();this.focusSearch()},addSelectedChoice:function(S){var U=!S.locked,Q=D("<li class='select2-search-choice'><div></div><a href='#' onclick='return 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You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Remove unmaintained RGENETICS tools from Galaxy Main
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4b1c7ad464ea/ Changeset: 4b1c7ad464ea Branch: stable User: natefoo Date: 2013-09-24 01:38:30 Summary: Remove unmaintained RGENETICS tools from Galaxy Main Affected #: 1 file diff -r 1f34ec186fcf79e5d82ea2a7e73ba5f537fb80f9 -r 4b1c7ad464ea5b181d9d5d95e8751518b170fca8 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -336,33 +336,4 @@ <label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> - <label text="RGENETICS" id="rgenetics" /> - <section name="SNP/WGA: Data; Filters" id="rgdat"> - <label text="Data: Import and upload" id="rgimport" /> - <tool file="data_source/upload.xml"/> - <tool file="data_source/access_libraries.xml" /> - <tool file="data_source/hapmapmart.xml" /> - <label text="Data: Filter and Clean" id="rgfilter" /> - <tool file="rgenetics/rgClean.xml"/> - <tool file="rgenetics/rgPedSub.xml"/> - <tool file="rgenetics/rgLDIndep.xml"/> - <label text="Simulate" id="rgsim" /> - <tool file="rgenetics/rgfakePhe.xml"/> - <tool file="rgenetics/rgfakePed.xml"/> - </section> - <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> - <label text="QC; Eigenstrat" id="rgvisual" /> - <tool file="rgenetics/rgQC.xml"/> - <tool file="rgenetics/rgEigPCA.xml"/> - <label text="LD; Manhattan/QQ; GRR" id="rgld" /> - <tool file="rgenetics/rgHaploView.xml"/> - <tool file="rgenetics/rgManQQ.xml"/> - <tool file="rgenetics/rgGRR.xml"/> - </section> - <section name="SNP/WGA: Statistical Models" id="rgmodel"> - <tool file="rgenetics/rgCaCo.xml"/> - <tool file="rgenetics/rgTDT.xml"/> - <tool file="rgenetics/rgGLM.xml"/> - <tool file="rgenetics/rgManQQ.xml"/> - </section></toolbox> 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 24 Sep '13

24 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a35cebc5735/ Changeset: 5a35cebc5735 User: natefoo Date: 2013-09-24 00:44:47 Summary: Drop old platforms from dist-eggs.ini. Affected #: 1 file diff -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe -r 5a35cebc573591fb9dc15e9712d8d8a4ebc12c65 dist-eggs.ini --- a/dist-eggs.ini +++ b/dist-eggs.ini @@ -1,88 +1,54 @@ ; ; Config for building eggs for distribution (via a site such as -; eggs.g2.bx.psu.edu) Probably only useful to Galaxy developers at -; Penn State. This file is used by scripts/dist-scramble.py +; eggs.galaxyproject.org) Probably only useful to members of the Galaxy Team +; building eggs for distribution. This file is used by +; scripts/dist-scramble.py ; -; More information: http://wiki.g2.bx.psu.edu/Admin/Config/Eggs +; More information: http://wiki.galaxyproject.org/Admin/Config/Eggs ; [hosts] -py2.5-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.5 -py2.5-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.5 py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7 py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7 -py2.5-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.5 -py2.5-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7 py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 -py2.5-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 py2.7-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.7 -py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 -py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 -py2.7-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.7 -py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 -py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 -py2.7-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.7 -py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 -py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 -py2.7-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.7 -py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.5 -py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.6 -py2.7-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.7 - +; ; these hosts are used to build eggs with no C extensions -py2.5 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 [groups] -py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 -py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.6-linux-x86_64 = py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-i686 = py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.7-linux-x86_64 = py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 -py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 py2.6-linux = py2.6-linux-i686 py2.6-linux-x86_64 py2.7-linux = py2.7-linux-i686 py2.7-linux-x86_64 -linux-i686 = py2.5-linux-i686 py2.6-linux-i686 py2.7-linux-i686 -linux-x86_64 = py2.5-linux-x86_64 py2.6-linux-x86_64 py2.7-linux-x86_64 +linux-i686 = py2.6-linux-i686 py2.7-linux-i686 +linux-x86_64 = py2.6-linux-x86_64 py2.7-linux-x86_64 linux = linux-i686 linux-x86_64 -py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 py2.7-macosx-10.6-intel-ucs2 -macosx = py2.5-macosx py2.6-macosx py2.7-macosx -py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 -py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 -py2.7-solaris-i86pc = py2.7-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 -py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 -py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 -py2.7-solaris-sun4u = py2.7-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 -py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u -py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u -py2.7-solaris = py2.7-solaris-i86pc py2.7-solaris-sun4u -solaris-i86pc = py2.5-solaris-i86pc py2.6-solaris-i86pc py2.7-solaris-i86pc -solaris-sun4u = py2.5-solaris-sun4u py2.6-solaris-sun4u py2.7-solaris-sun4u -solaris = solaris-i86pc solaris-sun4u -py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris -py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris -py2.7-all = py2.7-linux py2.7-macosx py2.7-solaris +macosx = py2.6-macosx py2.7-macosx +py2.6-all = py2.6-linux py2.6-macosx +py2.7-all = py2.7-linux py2.7-macosx ; the 'all' key is used internally by the build system to specify which hosts ; to build on when no hosts are specified on the dist-eggs.py command line. -all = linux macosx solaris +all = linux macosx ; the 'noplatform' key, likewise, is for which build hosts should be used when ; building pure python (noplatform) eggs. -noplatform = py2.5 py2.6 py2.7 +noplatform = py2.6 py2.7 ; don't build these eggs on these platforms: [ignore] -ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx-10.3-fat-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2 +;ctypes = https://bitbucket.org/galaxy/galaxy-central/commits/e1bc855165bc/ Changeset: e1bc855165bc User: natefoo Date: 2013-09-24 00:45:58 Summary: Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4). Affected #: 1 file diff -r 5a35cebc573591fb9dc15e9712d8d8a4ebc12c65 -r e1bc855165bc857d6afd19d37a0542798601d85a eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -21,7 +21,7 @@ PyRods = 3.2.4 numpy = 1.6.0 pbs_python = 4.3.5 -psycopg2 = 2.0.13 +psycopg2 = 2.5.1 pycrypto = 2.5 pysam = 0.4.2 pysqlite = 2.5.6 @@ -72,7 +72,7 @@ ; extra version information [tags] -psycopg2 = _8.4.2_static +psycopg2 = _9.2.4_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static bx_python = _7b95ff194725 @@ -83,7 +83,7 @@ ; the wiki page above [source] MySQL_python = mysql-5.1.41 -psycopg2 = postgresql-8.4.2 +psycopg2 = postgresql-9.2.4 pysqlite = sqlite-amalgamation-3_6_17 [dependencies] 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: guerler: Drag&drop multiple file upload: add status line, improve queueing, update select2
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72308af0df64/ Changeset: 72308af0df64 User: guerler Date: 2013-09-23 22:16:06 Summary: Drag&drop multiple file upload: add status line, improve queueing, update select2 Affected #: 6 files diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -17,6 +17,28 @@ // upload mod uploadbox: null, + // extension types + select_extension : { + '' : 'Auto-detect', + 'bed' : 'bed', + 'ab1' : 'ab1' + }, + + // counter + counter : { + // stats + announce : 0, + success : 0, + error : 0, + running : 0, + + // reset stats + reset : function() + { + this.announce = this.success = this.error = this.running = 0; + } + }, + // initialize initialize : function() { @@ -62,17 +84,14 @@ // start event_announce : function(index, file, message) { - // hide info - this.uploadbox.info().hide(); - // make id var id = '#upload-' + index; - + // add upload item - $(this.el).append(this.template_file(id)); + $(this.el).append(this.template_file(id, this.select_extension)); // scroll to bottom - $(this.el).scrollTop($(this.el).prop('scrollHeight')); + //$(this.el).scrollTop($(this.el).prop('scrollHeight')); // access upload item var it = this.get_upload_item(index); @@ -84,41 +103,7 @@ it.find('.title').html(file.name); // configure select field - it.find('#extension').select2( - { - placeholder: 'Auto-detect', - width: 'copy', - ajax: { - url: "http://www.weighttraining.com/sm/search", - dataType: 'jsonp', - quietMillis: 100, - data: function(term, page) - { - return { - types: ["exercise"], - limit: -1, - term: term - }; - }, - results: function(data, page) - { - return { results: data.results.exercise } - } - }, - formatResult: function(exercise) - { - return "<div class='select2-user-result'>" + exercise.term + "</div>"; - }, - formatSelection: function(exercise) - { - return exercise.term; - }, - initSelection : function (element, callback) - { - var elementText = $(element).attr('data-init-text'); - callback({"term":elementText}); - } - }); + //it.find('#extension').select2(); // add functionality to remove button var self = this; @@ -127,16 +112,18 @@ // initialize progress this.event_progress(index, file, 0); - // update button status - this.modal.enable('Upload'); - this.modal.enable('Reset'); + // update counter + this.counter.announce++; + + // update screen + this.update_screen(); }, // start event_initialize : function(index, file, message) { // update on screen counter - this.button_show.number(message); + this.button_show.number(this.counter.announce); // get element var it = this.get_upload_item(index); @@ -186,6 +173,13 @@ // update on screen counter this.button_show.number(''); + + // update counter + this.counter.announce--; + this.counter.success++; + + // update on screen info + this.update_screen(); }, // end @@ -209,11 +203,26 @@ // update on screen counter this.button_show.number(''); + + // update counter + this.counter.announce--; + this.counter.error++; + + // update on screen info + this.update_screen(); }, // start upload process event_upload : function() { + // check + if (this.counter.announce == 0 || this.counter.running > 0) + return; + + // update running + this.counter.running = this.counter.announce; + this.update_screen(); + // hide configuration $(this.el).find('.panel-body').hide(); @@ -223,10 +232,7 @@ $(this).removeClass('fa-icon-trash'); $(this).addClass('fa-icon-caret-down'); }); - - // update button status - this.modal.disable('Upload'); - + // configure url var current_history = Galaxy.currHistoryPanel.model.get('id'); this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); @@ -235,62 +241,61 @@ this.uploadbox.upload(); }, + // queue is done + event_complete: function() + { + // update running + this.counter.running = 0; + this.update_screen(); + }, + // remove all event_reset : function() { - // remove from screen - var panels = $(this.el).find('.panel'); - var self = this; - panels.fadeOut({complete: function() + // make sure queue is not running + if (this.counter.running == 0) { - // remove panels - panels.remove(); - + // remove from screen + var panels = $(this.el).find('.panel'); + panels.fadeOut({complete: function() { panels.remove(); }}); + + // reset counter + this.counter.reset(); + // show on screen info - self.uploadbox.info().fadeIn(); - }}); - - // update button status - this.modal.disable('Upload'); - this.modal.disable('Reset'); - - // remove from queue - this.uploadbox.reset(); + this.update_screen(); + + // remove from queue + this.uploadbox.reset(); + } }, // remove item from upload list event_remove : function(index) { - // remove - var self = this; - var it = this.get_upload_item(index); + // only remove from queue if paused + if (this.counter.running == 0) + { + // get item + var it = this.get_upload_item(index); - // fade out and update button status - it.fadeOut({complete: function() - { - // remove from screen + // reduce counter + if (it.hasClass('panel-default')) + this.counter.announce--; + else if (it.hasClass('panel-success')) + this.counter.success--; + else if (it.hasClass('panel-danger')) + this.counter.error--; + + // show on screen info + this.update_screen(); + + // remove from queue + this.uploadbox.remove(index); + + // remove element it.remove(); - - // remove from queue - self.uploadbox.remove(index); - - // update reset button - if ($(self.el).find('.panel').length > 0) - self.modal.enable('Reset'); - else { - // disable reset button - self.modal.disable('Reset'); - - // show on screen info - self.uploadbox.info().fadeIn(); - } - - // update upload button - if (self.uploadbox.length() > 0) - self.modal.enable('Upload'); - else - self.modal.disable('Upload'); - }}); + } }, // show/hide upload frame @@ -330,11 +335,11 @@ success : function(index, file, message) { self.event_success(index, file, message) }, progress : function(index, file, message) { self.event_progress(index, file, message) }, error : function(index, file, message) { self.event_error(index, file, message) }, + complete : function() { self.event_complete() }, }); - // update button status - this.modal.disable('Upload'); - this.modal.disable('Reset'); + // setup info + this.update_screen(); } // show modal @@ -362,34 +367,93 @@ return "<strong>" + (Math.round(size) / 10) + "</strong> " + unit; }, + // set screen + update_screen: function () + { + /* + update on screen info + */ + + // check default message + if(this.counter.announce == 0) + { + if (this.uploadbox.compatible) + message = 'Drag&drop files into this box or click \'Select\' to select files!'; + else + message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.' + } else { + if (this.counter.running == 0) + message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click "Upload" to proceed.'; + else + message = 'Please wait...' + this.counter.announce + ' out of ' + this.counter.running + ' remaining.'; + } + + // set html content + $('#upload-info').html(message); + + /* + update button status + */ + + // update reset button + if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0) + this.modal.enable('Reset'); + else + this.modal.disable('Reset'); + + // update upload button + if (this.counter.running == 0 && this.counter.announce > 0) + this.modal.enable('Upload'); + else + this.modal.disable('Upload'); + + // select upload button + if (this.counter.running == 0) + this.modal.enable('Select'); + else + this.modal.disable('Select'); + }, + // load html template template: function(id) { - return '<div id="' + id + '" class="upload-box"></div>'; + return '<div id="' + id + '" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'; }, // load html template - template_file: function(id) + template_file: function(id, select_extension) { - return '<div id="' + id.substr(1) + '" class="panel panel-default">' + - '<div class="panel-heading">' + - '<h5 class="title"></h5>' + - '<h5 class="info"></h5>' + - '<div class="remove fa-icon-trash"></div>' + - '</div>' + - '<div class="panel-body">' + - '<div class="menu">' + - //'<input id="extension" type="hidden" width="10px"/> ' + - '<span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span>' + + // start template + var tmpl = '<div id="' + id.substr(1) + '" class="panel panel-default">' + + '<div class="panel-heading">' + + '<h5 class="title"></h5>' + + '<h5 class="info"></h5>' + + '<div class="remove fa-icon-trash"></div>' + '</div>' + - '</div>' + - '<div class="panel-footer">' + - '<div class="progress">' + - '<div class="progress-bar progress-bar-success"></div>' + + '<div class="panel-body">' + + '<div class="menu">' + + 'Select file type: ' + + '<select id="extension">'; + + // add file types to selection + for (key in select_extension) + tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>'; + + // continue template + tmpl += '</select>, ' + + '<span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span>' + + '</div>' + '</div>' + - '<h6 class="error"></h6>' + - '</div>' + - '</div>'; + '<div class="panel-footer">' + + '<div class="progress">' + + '<div class="progress-bar progress-bar-success"></div>' + + '</div>' + + '<h6 class="error"></h6>' + + '</div>' + + '</div>'; + + // return html string + return tmpl; } }); diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/scripts/libs/jquery/select2.js --- a/static/scripts/libs/jquery/select2.js +++ b/static/scripts/libs/jquery/select2.js @@ -1,7 +1,7 @@ /* Copyright 2012 Igor Vaynberg -Version: 3.4.2 Timestamp: Mon Aug 12 15:04:12 PDT 2013 +Version: 3.4.3 Timestamp: Tue Sep 17 06:47:14 PDT 2013 This software is licensed under the Apache License, Version 2.0 (the "Apache License") or the GNU General Public License version 2 (the "GPL License"). You may choose either license to govern your @@ -688,14 +688,18 @@ this.opts.element .data("select2", this) .attr("tabindex", "-1") - .before(this.container); + .before(this.container) + .on("click.select2", killEvent); // do not leak click events + this.container.data("select2", this); this.dropdown = this.container.find(".select2-drop"); + + syncCssClasses(this.dropdown, this.opts.element, this.opts.adaptDropdownCssClass); + this.dropdown.addClass(evaluate(opts.dropdownCssClass)); this.dropdown.data("select2", this); - - syncCssClasses(this.dropdown, this.opts.element, this.opts.adaptDropdownCssClass); + this.dropdown.on("click", killEvent); this.results = results = this.container.find(resultsSelector); this.search = search = this.container.find("input.select2-input"); @@ -707,6 +711,8 @@ // initialize the container this.initContainer(); + this.container.on("click", killEvent); + installFilteredMouseMove(this.results); this.dropdown.on("mousemove-filtered touchstart touchmove touchend", resultsSelector, this.bind(this.highlightUnderEvent)); @@ -968,10 +974,11 @@ opts.initSelection = function (element, callback) { var data = []; $(splitVal(element.val(), opts.separator)).each(function () { - var id = this, text = this, tags=opts.tags; + var obj = { id: this, text: this }, + tags = opts.tags; if ($.isFunction(tags)) tags=tags(); - $(tags).each(function() { if (equal(this.id, id)) { text = this.text; return false; } }); - data.push({id: id, text: text}); + $(tags).each(function() { if (equal(this.id, obj.id)) { obj = this; return false; } }); + data.push(obj); }); callback(data); @@ -1320,7 +1327,7 @@ $("#select2-drop-mask").hide(); this.dropdown.removeAttr("id"); // only the active dropdown has the select2-drop id this.dropdown.hide(); - this.container.removeClass("select2-dropdown-open"); + this.container.removeClass("select2-dropdown-open").removeClass("select2-container-active"); this.results.empty(); @@ -1395,7 +1402,7 @@ // abstract findHighlightableChoices: function() { - return this.results.find(".select2-result-selectable:not(.select2-selected):not(.select2-disabled)"); + return this.results.find(".select2-result-selectable:not(.select2-disabled)"); }, // abstract @@ -1926,10 +1933,7 @@ killEvent(e); return; case KEY.TAB: - // if selectOnBlur == true, select the currently highlighted option - if (this.opts.selectOnBlur) { - this.selectHighlighted({noFocus: true}); - } + this.selectHighlighted({noFocus: true}); return; case KEY.ESC: this.cancel(e); @@ -2046,6 +2050,11 @@ clear: function(triggerChange) { var data=this.selection.data("select2-data"); if (data) { // guard against queued quick consecutive clicks + var evt = $.Event("select2-clearing"); + this.opts.element.trigger(evt); + if (evt.isDefaultPrevented()) { + return; + } var placeholderOption = this.getPlaceholderOption(); this.opts.element.val(placeholderOption ? placeholderOption.val() : ""); this.selection.find(".select2-chosen").empty(); @@ -2083,7 +2092,7 @@ isPlaceholderOptionSelected: function() { var placeholderOption; - if (!this.opts.placeholder) return false; // no placeholder specified so no option should be considered + if (!this.getPlaceholder()) return false; // no placeholder specified so no option should be considered return ((placeholderOption = this.getPlaceholderOption()) !== undefined && placeholderOption.is(':selected')) || (this.opts.element.val() === "") || (this.opts.element.val() === undefined) @@ -2216,7 +2225,7 @@ this.close(); if (!options || !options.noFocus) - this.selection.focus(); + this.focusser.focus(); if (!equal(old, this.id(data))) { this.triggerChange({added:data,removed:oldData}); } }, @@ -2442,7 +2451,7 @@ this.selection = selection = this.container.find(selector); var _this = this; - this.selection.on("click", ".select2-search-choice", function (e) { + this.selection.on("click", ".select2-search-choice:not(.select2-locked)", function (e) { //killEvent(e); _this.search[0].focus(); _this.selectChoice($(this)); @@ -2521,10 +2530,7 @@ killEvent(e); return; case KEY.TAB: - // if selectOnBlur == true, select the currently highlighted option - if (this.opts.selectOnBlur) { - this.selectHighlighted({noFocus:true}); - } + this.selectHighlighted({noFocus:true}); this.close(); return; case KEY.ESC: @@ -2842,9 +2848,7 @@ return; } - index = indexOf(this.id(data), val); - - if (index >= 0) { + while((index = indexOf(this.id(data), val)) >= 0) { val.splice(index, 1); this.setVal(val); if (this.select) this.postprocessResults(); @@ -2925,7 +2929,7 @@ searchWidth = minimumWidth; } - this.search.width(searchWidth); + this.search.width(Math.floor(searchWidth)); }, // multi diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -19,11 +19,10 @@ progress : function() {}, success : function() {}, error : function(index, file, message) { alert(message); }, + complete : function() {}, error_browser : "Your browser does not support drag-and-drop file uploads.", error_filesize : "This file is too large (>250MB). Please use an FTP client to upload it.", - error_default : "Please make sure the file is available.", - text_default : "Drag&drop files into this box or click 'Select' to select files!", - text_degrade : "Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+." + error_default : "Please make sure the file is available." } // options @@ -32,7 +31,7 @@ // file queue var queue = {}; - // counter for file being currently processed + // queue index counter var queue_index = 0; // queue length @@ -50,21 +49,11 @@ // parse options opts = $.extend({}, default_opts, options); - // compatibility - var mode = window.File && window.FileReader && window.FormData && window.XMLHttpRequest; - // element el = this; // append upload button el.append('<input id="uploadbox_input" type="file" style="display: none" multiple>'); - el.append('<div id="uploadbox_info"></div>'); - - // set info text - if (mode) - el.find('#uploadbox_info').html(opts.text_default); - else - el.find('#uploadbox_info').html(opts.text_degrade); // attach events el.on('drop', drop); @@ -120,11 +109,15 @@ // respond to an upload request function add(files) { + // only allow adding file if current batch is complete + if (queue_status) + return; + // add new files to queue for (var i = 0; i < files.length; i++) { // new identifier - var index = String(++queue_index); + var index = String(queue_index++); // add to queue queue[index] = files[i]; @@ -153,6 +146,15 @@ // process an upload, recursive function process() { + // validate + if (queue_length == 0) + { + queue_status = false; + opts.complete(); + return; + } else + queue_status = true; + // get an identifier from the queue var index = -1; for (var key in queue) @@ -161,10 +163,6 @@ break; } - // validate - if (queue_length == 0) - return; - // get current file from queue var file = queue[index]; @@ -172,7 +170,7 @@ remove(index) // start - var data = opts.initialize(index, file, length); + var data = opts.initialize(index, file); // add file to queue try @@ -312,12 +310,6 @@ process(); } - // current queue length - function length() - { - return queue_length; - } - // set options function configure(options) { @@ -328,21 +320,20 @@ return opts; } - // visibility of on screen information - function info() + // verify browser compatibility + function compatible() { - return el.find('#uploadbox_info'); + return window.File && window.FileReader && window.FormData && window.XMLHttpRequest; } // export functions return { - 'select' : select, - 'remove' : remove, - 'upload' : upload, - 'reset' : reset, - 'length' : length, - 'configure' : configure, - 'info' : info + 'select' : select, + 'remove' : remove, + 'upload' : upload, + 'reset' : reset, + 'configure' : configure, + 'compatible' : compatible }; } })(jQuery); \ No newline at end of file diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1123,6 +1123,7 @@ .galaxy-frame .frame .f-close{right:5px;top:1px} .galaxy-frame .frame .f-pin{left:6px;top:1px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} +.upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} .upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} .upload-box .panel .panel-heading .remove{position:absolute;cursor:pointer;top:0px;right:3px} @@ -1167,12 +1168,12 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#fce1ba} .panel-done-message{background-image:url(ok_small.png);background-color:#aff1af} .panel-info-message{background-image:url(info_small.png);background-color:#a6e4f7} -#masthead{position:absolute;top:0;left:0;width:100%;min-width:980px;padding:0}#masthead .nav{z-index:15001} +#masthead{position:absolute;top:0;left:0;width:100%;min-width:990px;padding:0}#masthead .nav{z-index:15001} #masthead .nav>li>a{cursor:pointer;text-decoration:none}#masthead .nav>li>a:hover{color:gold} #masthead li.dropdown>a:hover .caret{border-top-color:gold;border-bottom-color:gold} #masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top} #masthead .navbar-brand a{color:white;text-decoration:none} -#masthead .iconbar{position:absolute;top:2px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 8px} +#masthead .iconbar{position:absolute;top:2px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px} #masthead .iconbar .symbol .number{font-weight:bold;font-size:12px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-18px} #masthead .iconbar .toggle{color:#BCC800} .quota-meter-container{position:absolute;top:0;right:0;height:32px} diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -324,7 +324,7 @@ top:0; left:0; width:100%; - min-width:980px; + min-width:990px; padding: 0; .nav { @@ -387,7 +387,7 @@ .symbol { float : left; - margin : 0px 8px; + margin : 0px 10px; } .symbol .number diff -r 4ef6df129520040017cfd4a287cb01558c6af35f -r 72308af0df6416a4cc888ee2cb5af90b3fd8f9fe static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -1,3 +1,9 @@ +.upload-info +{ + font-weight: normal; + text-align: center; +} + .upload-box { width : 100%; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Style: add proper alert macro for warning, add errormessagesmall; pack scripts
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ef6df129520/ Changeset: 4ef6df129520 User: carlfeberhard Date: 2013-09-23 21:23:38 Summary: Style: add proper alert macro for warning, add errormessagesmall; pack scripts Affected #: 10 files diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -82,6 +82,10 @@ this.$el.attr( 'id', 'historyItemContainer-' + id ); + //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide + // handle that here by removing previous view's tooltips + this.$el.find("[title]").tooltip( "destroy" ); + /** web controller urls for functions relating to this hda. * These are rendered from urlTemplates using the model data. */ this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() ); diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -166,6 +166,7 @@ success: function() { // FIXME: setting model attribute causes re-rendering, which is unnecessary. //self.$el.remove(); + self.model.set({ deleted: true }); } }); diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var 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a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var 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p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($("<button></button>").text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($('<button id="'+String(e).toLowerCase()+'"></button>').text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){$("#galaxy-upload-box").addClass("highlight")},event_mouseleave:function(d){$("#galaxy-upload-box").removeClass("highlight")},event_start:function(d,e,f){var g="#galaxy-upload-file-"+d;$("#galaxy-upload-box").append(this.template_file(g));$("#galaxy-upload-file-"+d).find(".title").html(e.name);this.event_progress(d,e,0);this.file_counter++;this.refresh()},event_progress:function(e,f,h){var g=$("#galaxy-upload-file-"+e);var d=parseInt(h);g.find(".progress").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,f){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(d,e,g){var f=$("#galaxy-upload-file-"+d);f.find(".progress-frame").addClass("failed");f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.file_counter--;this.refresh()},event_show:function(g){g.preventDefault();if(!Galaxy.currHistoryPanel){var f=this;window.setTimeout(function(){f.event_show(g)},200);return}if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template(),buttons:{Close:function(){f.modal.hide()}}});var d=Galaxy.currHistoryPanel.model.get("id");var f=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+d+"/contents",dragover:f.event_mouseover,dragleave:f.event_mouseleave,start:function(e,h,i){f.event_start(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box"></form>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="file corner-soft shadow"><div class="title"></div><div class="error"></div><div class="progress-frame corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){this.uploadbox.info().hide();var i="#upload-"+e;$(this.el).append(this.template_file(i));$(this.el).scrollTop($(this.el).prop("scrollHeight"));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);g.find("#extension").select2({placeholder:"Auto-detect",width:"copy",ajax:{url:"http://www.weighttraining.com/sm/search",dataType:"jsonp",quietMillis:100,data:function(j,k){return{types:["exercise"],limit:-1,term:j}},results:function(k,j){return{results:k.results.exercise}}},formatResult:function(j){return"<div class='select2-user-result'>"+j.term+"</div>"},formatSelection:function(j){return j.term},initSelection:function(j,l){var k=$(j).attr("data-init-text");l({term:k})}});var d=this;g.find(".remove").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.modal.enable("Upload");this.modal.enable("Reset")},event_initialize:function(d,e,g){this.button_show.number(g);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("")},event_error:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.button_show.number("")},event_upload:function(){$(this.el).find(".panel-body").hide();$(this.el).find(".remove").each(function(){$(this).removeClass("fa-icon-trash");$(this).addClass("fa-icon-caret-down")});this.modal.disable("Upload");var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_reset:function(){var e=$(this.el).find(".panel");var d=this;e.fadeOut({complete:function(){e.remove();d.uploadbox.info().fadeIn()}});this.modal.disable("Upload");this.modal.disable("Reset");this.uploadbox.reset()},event_remove:function(e){var d=this;var f=this.get_upload_item(e);f.fadeOut({complete:function(){f.remove();d.uploadbox.remove(e);if($(d.el).find(".panel").length>0){d.modal.enable("Reset")}else{d.modal.disable("Reset");d.uploadbox.info().fadeIn()}if(d.uploadbox.length()>0){d.modal.enable("Upload")}else{d.modal.disable("Upload")}}})},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}}});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},});this.modal.disable("Upload");this.modal.disable("Reset")}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(d){return'<div id="'+d+'" class="upload-box"></div>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="remove fa-icon-trash"></div></div><div class="panel-body"><div class="menu"><span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.$el.find("[title]").tooltip("destroy");this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: 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\ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1245,9 +1245,10 @@ .errormessage .alert-link,.warningmessage .alert-link,.donemessage .alert-link,.infomessage .alert-link,.errormessagesmall .alert-link,.warningmessagesmall .alert-link,.donemessagesmall .alert-link,.infomessagesmall .alert-link{font-weight:bold} .errormessage>p,.warningmessage>p,.donemessage>p,.infomessage>p,.errormessagesmall>p,.warningmessagesmall>p,.donemessagesmall>p,.infomessagesmall>p,.errormessage>ul,.warningmessage>ul,.donemessage>ul,.infomessage>ul,.errormessagesmall>ul,.warningmessagesmall>ul,.donemessagesmall>ul,.infomessagesmall>ul{margin-bottom:0} .errormessage>p+p,.warningmessage>p+p,.donemessage>p+p,.infomessage>p+p,.errormessagesmall>p+p,.warningmessagesmall>p+p,.donemessagesmall>p+p,.infomessagesmall>p+p{margin-top:5px} -.errormessage{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr{border-top-color:#c61913} -.errormessage .alert-link{color:#571d1b} -.warningmessage,.warningmessagesmall{background-image:url(warn_small.png)} +.errormessage,.errormessagesmall{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr,.errormessagesmall hr{border-top-color:#c61913} +.errormessage .alert-link,.errormessagesmall .alert-link{color:#571d1b} +.warningmessage,.warningmessagesmall{background-color:#fce1ba;border-color:#e28709;color:#80571e;background-image:url(warn_small.png)}.warningmessage hr,.warningmessagesmall hr{border-top-color:#c97908} +.warningmessage .alert-link,.warningmessagesmall .alert-link{color:#573b14} .donemessage,.donemessagesmall{background-color:#aff1af;border-color:#20b420;color:#295f29;background-image:url(ok_small.png)}.donemessage hr,.donemessagesmall hr{border-top-color:#1c9e1c} .donemessage .alert-link,.donemessagesmall .alert-link{color:#193b19} .infomessage,.infomessagesmall{background-color:#a6e4f7;border-color:#1197c0;color:#1f5566;background-image:url(info_small.png)}.infomessage hr,.infomessagesmall hr{border-top-color:#0f85a8} diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -759,28 +759,23 @@ background-position: 5px 5px; } -.errormessage { +.errormessage, .errormessagesmall { .alert-danger(); } .warningmessage, .warningmessagesmall { + .alert-warning(); background-image: url(warn_small.png); - //border-color: @warn_message_border; - //background-color: @warn_message_bg; } .donemessage, .donemessagesmall { .alert-success(); background-image: url(ok_small.png); - // border-color: @done_message_border; - // background-color: @done_message_bg; } .infomessage, .infomessagesmall { .alert-info(); background-image: url(info_small.png); - //border-color: @info_message_border; - //background-color: @info_message_bg; } .errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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