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commit/galaxy-central: greg: Eliminate the use of trans when exporting repository capsules from the Tool SHed and move the new tag_attribute_haldler.py module where it was meant to be located.
by commits-noreply＠bitbucket.org 22 Jun '14

22 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/344e84a6554a/ Changeset: 344e84a6554a User: greg Date: 2014-06-23 00:25:22 Summary: Eliminate the use of trans when exporting repository capsules from the Tool SHed and move the new tag_attribute_haldler.py module where it was meant to be located. Affected #: 7 files diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -53,7 +53,8 @@ log.debug( error_message ) return None, error_message repository_id = trans.security.encode_id( repository.id ) - return export_util.export_repository( trans, + return export_util.export_repository( trans.app, + trans.user, tool_shed_url, repository_id, str( repository.name ), diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1172,7 +1172,8 @@ file_type = 'gz' export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies ) tool_shed_url = web.url_for( '/', qualified=True ) - repositories_archive, error_message = export_util.export_repository( trans, + repositories_archive, error_message = export_util.export_repository( trans.app, + trans.user, tool_shed_url, repository_id, str( repository.name ), diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/dependency_manager.py --- a/lib/tool_shed/dependencies/dependency_manager.py +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -5,7 +5,7 @@ from galaxy.util.odict import odict from galaxy.web import url_for -from tool_shed.dependencies import tag_attribute_handler +from tool_shed.dependencies.tool import tag_attribute_handler from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME from tool_shed.util import hg_util diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/tag_attribute_handler.py --- a/lib/tool_shed/dependencies/tag_attribute_handler.py +++ /dev/null @@ -1,199 +0,0 @@ -import copy -import logging - -log = logging.getLogger( __name__ ) - - -class TagAttributeHandler( object ): - - def __init__( self, app, rdd, unpopulate ): - self.app = app - self.altered = False - self.rdd = rdd - self.unpopulate = unpopulate - - def process_action_tag_set( self, elem, message ): - # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . - # <action> - # <repository name="package_readline_6_2" owner="devteam"> - # <package name="readline" version="6.2" /> - # </repository> - # </action> - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'repository': - altered, new_sub_elem, error_message = \ - self.process_repository_tag_set( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_actions_tag_set( self, elem, message ): - # <actions> - # <package name="libgtextutils" version="0.6"> - # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> - # </package> - from tool_shed.util import xml_util - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'package': - altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, - message=message ) - elif sub_elem.tag == 'action': - # <action type="set_environment_for_install"> - # <repository name="package_readline_6_2" owner="devteam""> - # <package name="readline" version="6.2" /> - # </repository> - # </action> - altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, - message=message ) - else: - # Inspect the sub elements of elem to locate all <repository> tags and - # populate them with toolshed and changeset_revision attributes if necessary. - altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): - # Inspect all entries in the <actions_group> tag set, skipping <actions> - # tag sets that define os and architecture attributes. We want to inspect - # only the last <actions> tag set contained within the <actions_group> tag - # set to see if a complex repository dependency is defined. - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'actions': - if skip_actions_tags: - # Skip all actions tags that include os or architecture attributes. - system = sub_elem.get( 'os' ) - architecture = sub_elem.get( 'architecture' ) - if system or architecture: - continue - altered, new_sub_elem, error_message = \ - self.process_actions_tag_set( elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_config( self, root ): - error_message = '' - new_root = copy.deepcopy( root ) - if root.tag == 'tool_dependency': - for elem_index, elem in enumerate( root ): - altered = False - if elem.tag == 'package': - # <package name="eigen" version="2.0.17"> - altered, new_elem, error_message = \ - self.process_package_tag_set( elem=elem, - message=error_message ) - if altered: - if not self.altered: - self.altered = True - new_root[ elem_index ] = new_elem - else: - error_message = "Invalid tool_dependencies.xml file." - return self.altered, new_root, error_message - - def process_install_tag_set( self, elem, message ): - # <install version="1.0"> - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'actions_group': - altered, new_sub_elem, error_message = \ - self.process_actions_group_tag_set( elem=sub_elem, - message=message, - skip_actions_tags=True ) - elif sub_elem.tag == 'actions': - altered, new_sub_elem, error_message = \ - self.process_actions_tag_set( elem=sub_elem, - message=message ) - else: - package_name = elem.get( 'name', '' ) - package_version = elem.get( 'version', '' ) - error_message += 'Version %s of the %s package cannot be installed because ' % \ - ( str( package_version ), str( package_name ) ) - error_message += 'the recipe for installing the package is missing either an ' - error_message += '<actions> tag set or an <actions_group> tag set.' - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_package_tag_set( self, elem, message ): - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'install': - altered, new_sub_elem, error_message = \ - self.process_install_tag_set( elem=sub_elem, - message=message ) - elif sub_elem.tag == 'repository': - altered, new_sub_elem, error_message = \ - self.process_repository_tag_set( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): - # We have a complex repository dependency. - altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, - elem_index=elem_index, - elem=elem ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - return altered, new_elem, message diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/tool/tag_attribute_handler.py --- /dev/null +++ b/lib/tool_shed/dependencies/tool/tag_attribute_handler.py @@ -0,0 +1,199 @@ +import copy +import logging + +log = logging.getLogger( __name__ ) + + +class TagAttributeHandler( object ): + + def __init__( self, app, rdd, unpopulate ): + self.app = app + self.altered = False + self.rdd = rdd + self.unpopulate = unpopulate + + def process_action_tag_set( self, elem, message ): + # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . + # <action> + # <repository name="package_readline_6_2" owner="devteam"> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_tag_set( self, elem, message ): + # <actions> + # <package name="libgtextutils" version="0.6"> + # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> + # </package> + from tool_shed.util import xml_util + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'package': + altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'action': + # <action type="set_environment_for_install"> + # <repository name="package_readline_6_2" owner="devteam""> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, + message=message ) + else: + # Inspect the sub elements of elem to locate all <repository> tags and + # populate them with toolshed and changeset_revision attributes if necessary. + altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): + # Inspect all entries in the <actions_group> tag set, skipping <actions> + # tag sets that define os and architecture attributes. We want to inspect + # only the last <actions> tag set contained within the <actions_group> tag + # set to see if a complex repository dependency is defined. + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions': + if skip_actions_tags: + # Skip all actions tags that include os or architecture attributes. + system = sub_elem.get( 'os' ) + architecture = sub_elem.get( 'architecture' ) + if system or architecture: + continue + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_config( self, root ): + error_message = '' + new_root = copy.deepcopy( root ) + if root.tag == 'tool_dependency': + for elem_index, elem in enumerate( root ): + altered = False + if elem.tag == 'package': + # <package name="eigen" version="2.0.17"> + altered, new_elem, error_message = \ + self.process_package_tag_set( elem=elem, + message=error_message ) + if altered: + if not self.altered: + self.altered = True + new_root[ elem_index ] = new_elem + else: + error_message = "Invalid tool_dependencies.xml file." + return self.altered, new_root, error_message + + def process_install_tag_set( self, elem, message ): + # <install version="1.0"> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions_group': + altered, new_sub_elem, error_message = \ + self.process_actions_group_tag_set( elem=sub_elem, + message=message, + skip_actions_tags=True ) + elif sub_elem.tag == 'actions': + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + else: + package_name = elem.get( 'name', '' ) + package_version = elem.get( 'version', '' ) + error_message += 'Version %s of the %s package cannot be installed because ' % \ + ( str( package_version ), str( package_name ) ) + error_message += 'the recipe for installing the package is missing either an ' + error_message += '<actions> tag set or an <actions_group> tag set.' + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_package_tag_set( self, elem, message ): + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'install': + altered, new_sub_elem, error_message = \ + self.process_install_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): + # We have a complex repository dependency. + altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, + elem_index=elem_index, + elem=elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + return altered, new_elem, message diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -7,7 +7,6 @@ from time import gmtime from time import strftime import tool_shed.repository_types.util as rt_util -from galaxy import eggs from galaxy import web from galaxy.util.odict import odict from tool_shed.dependencies import dependency_manager @@ -21,11 +20,6 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager -eggs.require( 'mercurial' ) - -from mercurial import commands -from mercurial import ui - log = logging.getLogger( __name__ ) CAPSULE_FILENAME = 'capsule' @@ -36,24 +30,9 @@ def __init__( self ): self.exported_repository_elems = [] -def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ): - '''Create an un-versioned archive of a repository.''' - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) - options_dict = hg_util.get_mercurial_default_options_dict( 'archive' ) - options_dict[ 'rev' ] = changeset_revision - error_message = '' - return_code = None - try: - return_code = commands.archive( ui, repo, archive_dir, **options_dict ) - except Exception, e: - error_message = "Error attempting to archive revision <b>%s</b> of repository %s: %s\nReturn code: %s\n" % \ - ( str( changeset_revision ), str( repository.name ), str( e ), str( return_code ) ) - log.exception( error_message ) - return return_code, error_message - -def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, +def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) + repository = suc.get_repository_in_tool_shed( app, repository_id ) repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, str( repository.name ), str( repository.user.username ), @@ -62,16 +41,16 @@ export_repository_dependencies=export_repository_dependencies, use_tmp_archive_dir=True ) if export_repository_dependencies: - repo_info_dicts = get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ) - repository_ids = get_repository_ids( trans, repo_info_dicts ) + repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ) + repository_ids = get_repository_ids( app, repo_info_dicts ) ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ - order_components_for_import( trans, repository_id, repository_ids, repo_info_dicts ) + order_components_for_import( app, repository_id, repository_ids, repo_info_dicts ) else: ordered_repository_ids = [] ordered_repositories = [] ordered_changeset_revisions = [] if repository: - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans.app, + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ) if repository_metadata: @@ -89,7 +68,7 @@ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) ordered_repository = ordered_repositories[ index ] ordered_changeset_revision = ordered_changeset_revisions[ index ] - repository_archive, error_message = generate_repository_archive( trans, + repository_archive, error_message = generate_repository_archive( app, work_dir, tool_shed_url, ordered_repository, @@ -128,12 +107,15 @@ return dict( download_url=download_url, error_messages=error_messages ) return repositories_archive, error_messages -def generate_repository_archive( trans, work_dir, tool_shed_url, repository, changeset_revision, file_type ): - rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=True ) - tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=True ) +def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True ) file_type_str = get_file_type_str( changeset_revision, file_type ) file_name = '%s-%s' % ( repository.name, file_type_str ) - return_code, error_message = archive_repository_revision( trans, ui, repository, work_dir, changeset_revision ) + return_code, error_message = hg_util.archive_repository_revision( app, + repository, + work_dir, + changeset_revision ) if return_code: return None, error_message repository_archive_name = os.path.join( work_dir, file_name ) @@ -195,7 +177,7 @@ sub_elements[ 'exported_via_api' ] = str( api ) return sub_elements -def get_components_from_repo_info_dict( trans, repo_info_dict ): +def get_components_from_repo_info_dict( app, repo_info_dict ): """ Return the repository and the associated latest installable changeset_revision (including updates) for the repository defined by the received repo_info_dict. @@ -204,8 +186,8 @@ # There should only be one entry in the received repo_info_dict. description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans.app, + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ) if repository_metadata: @@ -235,30 +217,30 @@ return repo_info_dict return None -def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ): +def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ): """ Return a list of dictionaries defining repositories that are required by the repository associated with the received repository_id. """ - rdm = RepositoryDependencyManager( trans.app ) - repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) + rdm = RepositoryDependencyManager( app ) + repository = suc.get_repository_in_tool_shed( app, repository_id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = {} # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ), + common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ), str( changeset_revision ), str( ctx.rev() ), str( repository.user.username ), @@ -292,18 +274,24 @@ sub_elements[ 'categories' ] = categories return attributes, sub_elements -def get_repository_ids( trans, repo_info_dicts ): +def get_repository_ids( app, repo_info_dicts ): """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" repository_ids = [] for repo_info_dict in repo_info_dicts: for repository_name, repo_info_tup in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) - repository_ids.append( trans.security.encode_id( repository.id ) ) + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + repository_ids.append( app.security.encode_id( repository.id ) ) return repository_ids -def order_components_for_import( trans, primary_repository_id, repository_ids, repo_info_dicts ): +def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ): """ Some repositories may have repository dependencies that must be imported and have metadata set on them before the dependent repository is imported. This method will inspect the list of repositories @@ -322,7 +310,7 @@ # Create a dictionary whose keys are the received repository_ids and whose values are a list of # repository_ids, each of which is contained in the received list of repository_ids and whose associated # repository must be imported prior to the repository associated with the repository_id key. - prior_import_required_dict = suc.get_prior_import_or_install_required_dict( trans.app, repository_ids, repo_info_dicts ) + prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts ) processed_repository_ids = [] # Process the list of repository dependencies defined for the repository associated with the received # primary_repository_id. @@ -340,20 +328,20 @@ if prior_import_required_id not in ordered_repository_ids: # Import the associated repository dependency first. prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts ) - prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( trans, prior_repo_info_dict ) + prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict ) if prior_repository and prior_import_changeset_revision: ordered_repository_ids.append( prior_import_required_id ) ordered_repositories.append( prior_repository ) ordered_changeset_revisions.append( prior_import_changeset_revision ) repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( trans, repo_info_dict ) + repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) if repository and changeset_revision: ordered_repository_ids.append( repository_id ) ordered_repositories.append( repository ) ordered_changeset_revisions.append( changeset_revision ) # Process the repository associated with the received primary_repository_id last. repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( trans, repo_info_dict ) + repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) if repository and changeset_revision: ordered_repository_ids.append( repository_id ) ordered_repositories.append( repository ) diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/util/hg_util.py --- a/lib/tool_shed/util/hg_util.py +++ b/lib/tool_shed/util/hg_util.py @@ -28,6 +28,21 @@ def add_changeset( repo_ui, repo, path_to_filename_in_archive ): commands.add( repo_ui, repo, path_to_filename_in_archive ) +def archive_repository_revision( app, repository, archive_dir, changeset_revision ): + '''Create an un-versioned archive of a repository.''' + repo = get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) + options_dict = get_mercurial_default_options_dict( 'archive' ) + options_dict[ 'rev' ] = changeset_revision + error_message = '' + return_code = None + try: + return_code = commands.archive( get_configured_ui, repo, archive_dir, **options_dict ) + except Exception, e: + error_message = "Error attempting to archive revision <b>%s</b> of repository %s: %s\nReturn code: %s\n" % \ + ( str( changeset_revision ), str( repository.name ), str( e ), str( return_code ) ) + log.exception( error_message ) + return return_code, error_message + def bundle_to_json( fh ): """ Convert the received HG10xx data stream (a mercurial 1.0 bundle created using hg push from the Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Move 2 Tool Shed utility functions into the middleware hg class.
by commits-noreply＠bitbucket.org 22 Jun '14

22 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae53980fad82/ Changeset: ae53980fad82 User: greg Date: 2014-06-22 14:00:57 Summary: Move 2 Tool Shed utility functions into the middleware hg class. Affected #: 3 files diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -11,7 +11,6 @@ from galaxy.util import asbool from galaxy.util.hash_util import new_secure_hash -from tool_shed.util import commit_util from tool_shed.util import hg_util import tool_shed.repository_types.util as rt_util @@ -54,13 +53,15 @@ connection = engine.connect() path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) user_id, repository_name = self.__get_user_id_repository_name_from_path_info( connection, path_info ) - sql_cmd = "SELECT times_downloaded FROM repository WHERE user_id = %d AND name = '%s'" % ( user_id, repository_name.lower() ) + sql_cmd = "SELECT times_downloaded FROM repository WHERE user_id = %d AND name = '%s'" % \ + ( user_id, repository_name.lower() ) result_set = connection.execute( sql_cmd ) for row in result_set: # Should only be 1 row... times_downloaded = row[ 'times_downloaded' ] times_downloaded += 1 - sql_cmd = "UPDATE repository SET times_downloaded = %d WHERE user_id = %d AND name = '%s'" % ( times_downloaded, user_id, repository_name.lower() ) + sql_cmd = "UPDATE repository SET times_downloaded = %d WHERE user_id = %d AND name = '%s'" % \ + ( times_downloaded, user_id, repository_name.lower() ) connection.execute( sql_cmd ) connection.close() elif cmd in [ 'unbundle', 'pushkey' ]: @@ -132,7 +133,7 @@ if filename and isinstance( filename, str ): if filename == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Make sure the any complex repository dependency definitions contain valid <repository> tags. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -151,7 +152,7 @@ if filename and isinstance( filename, str ): if filename == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Make sure the any complex repository dependency definitions contain valid <repository> tags. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -174,7 +175,7 @@ rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # We check both files since tool dependency definitions files can contain complex # repository dependency definitions. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -186,6 +187,54 @@ return result.wsgi_application( environ, start_response ) return self.app( environ, start_response ) + def __authenticate( self, username, password ): + db_password = None + # Instantiate a database connection + engine = sqlalchemy.create_engine( self.db_url ) + connection = engine.connect() + result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) + for row in result_set: + # Should only be 1 row... + db_email = row[ 'email' ] + db_password = row[ 'password' ] + connection.close() + if db_password: + # Check if password matches db_password when hashed. + return new_secure_hash( text_type=password ) == db_password + return False + + def __authenticate_remote_user( self, environ, username, password ): + """ + Look after a remote user and "authenticate" - upstream server should already have achieved + this for us, but we check that the user exists at least. Hg allow_push = must include username + - some versions of mercurial blow up with 500 errors. + """ + db_username = None + ru_email = environ[ 'HTTP_REMOTE_USER' ].lower() + ## Instantiate a database connection... + engine = sqlalchemy.create_engine( self.db_url ) + connection = engine.connect() + result_set = connection.execute( "select email, username, password from galaxy_user where email = '%s'" % ru_email ) + for row in result_set: + # Should only be 1 row... + db_email = row[ 'email' ] + db_password = row[ 'password' ] + db_username = row[ 'username' ] + connection.close() + if db_username: + # We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() + # does some random generation of a password - so that no-one knows the password and only the hash is stored... + return db_username == username + return False + + def __basic_authentication( self, environ, username, password ): + """The environ parameter is needed in basic authentication. We also check it if use_remote_user is true.""" + if asbool( self.config.get( 'use_remote_user', False ) ): + assert "HTTP_REMOTE_USER" in environ, "use_remote_user is set but no HTTP_REMOTE_USER variable" + return self.__authenticate_remote_user( environ, username, password ) + else: + return self.__authenticate( username, password ) + def __display_exception_remotely( self, start_response, msg ): # Display the exception to the remote user's command line. status = "500 %s" % msg @@ -213,49 +262,37 @@ user_id = row[ 'id' ] return user_id, repository_name - def __basic_authentication( self, environ, username, password ): - """The environ parameter is needed in basic authentication. We also check it if use_remote_user is true.""" - if asbool( self.config.get( 'use_remote_user', False ) ): - assert "HTTP_REMOTE_USER" in environ, "use_remote_user is set but no HTTP_REMOTE_USER variable" - return self.__authenticate_remote_user( environ, username, password ) - else: - return self.__authenticate( username, password ) - - def __authenticate( self, username, password ): - db_password = None - # Instantiate a database connection - engine = sqlalchemy.create_engine( self.db_url ) - connection = engine.connect() - result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) - for row in result_set: - # Should only be 1 row... - db_email = row[ 'email' ] - db_password = row[ 'password' ] - connection.close() - if db_password: - # Check if password matches db_password when hashed. - return new_secure_hash( text_type=password ) == db_password - return False - - def __authenticate_remote_user( self, environ, username, password ): + def repository_tag_is_valid( self, filename, line ): """ - Look after a remote user and "authenticate" - upstream server should already have achieved this for us, but we check that the - user exists at least. Hg allow_push = must include username - some versions of mercurial blow up with 500 errors. + Checks changes made to <repository> tags in a dependency definition file being pushed to the + Tool Shed from the command line to ensure that all required attributes exist. """ - db_username = None - ru_email = environ[ 'HTTP_REMOTE_USER' ].lower() - ## Instantiate a database connection... - engine = sqlalchemy.create_engine( self.db_url ) - connection = engine.connect() - result_set = connection.execute( "select email, username, password from galaxy_user where email = '%s'" % ru_email ) - for row in result_set: - # Should only be 1 row... - db_email = row[ 'email' ] - db_password = row[ 'password' ] - db_username = row[ 'username' ] - connection.close() - if db_username: - # We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() does some random generation of - # a password - so that no-one knows the password and only the hash is stored... - return db_username == username - return False + required_attributes = [ 'toolshed', 'name', 'owner', 'changeset_revision' ] + defined_attributes = line.split() + for required_attribute in required_attributes: + defined = False + for defined_attribute in defined_attributes: + if defined_attribute.startswith( required_attribute ): + defined = True + break + if not defined: + error_msg = 'The %s file contains a <repository> tag that is missing the required attribute %s. ' % \ + ( filename, required_attribute ) + error_msg += 'Automatically populating dependency definition attributes occurs only when using ' + error_msg += 'the Tool Shed upload utility. ' + return False, error_msg + return True, '' + + def repository_tags_are_valid( self, filename, change_list ): + """ + Make sure the any complex repository dependency definitions contain valid <repository> tags when pushing + changes to the tool shed on the command line. + """ + tag = '<repository' + for change_dict in change_list: + lines = get_change_lines_in_file_for_tag( tag, change_dict ) + for line in lines: + is_valid, error_msg = repository_tag_is_valid( filename, line ) + if not is_valid: + return False, error_msg + return True, '' diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/tool_shed/dependencies/dependency_manager.py --- a/lib/tool_shed/dependencies/dependency_manager.py +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -177,6 +177,7 @@ new_root[ index ] = new_elem return root_altered, new_root, error_message + class ToolDependencyAttributeHandler( object ): def __init__( self, app, unpopulate ): diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -221,41 +221,6 @@ gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def repository_tag_is_valid( filename, line ): - """ - Checks changes made to <repository> tags in a dependency definition file being pushed to the - Tool Shed from the command line to ensure that all required attributes exist. - """ - required_attributes = [ 'toolshed', 'name', 'owner', 'changeset_revision' ] - defined_attributes = line.split() - for required_attribute in required_attributes: - defined = False - for defined_attribute in defined_attributes: - if defined_attribute.startswith( required_attribute ): - defined = True - break - if not defined: - error_msg = 'The %s file contains a <repository> tag that is missing the required attribute %s. ' % \ - ( filename, required_attribute ) - error_msg += 'Automatically populating dependency definition attributes occurs only when using ' - error_msg += 'the Tool Shed upload utility. ' - return False, error_msg - return True, '' - -def repository_tags_are_valid( filename, change_list ): - """ - Make sure the any complex repository dependency definitions contain valid <repository> tags when pushing - changes to the tool shed on the command line. - """ - tag = '<repository' - for change_dict in change_list: - lines = get_change_lines_in_file_for_tag( tag, change_dict ) - for line in lines: - is_valid, error_msg = repository_tag_is_valid( filename, line ) - if not is_valid: - return False, error_msg - return True, '' - def uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip=False, isbz2=False ): if isgzip: handle_gzip( repository, uploaded_file_name ) 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: greg: Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed.
by commits-noreply＠bitbucket.org 21 Jun '14

21 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63919647ca84/ Changeset: 63919647ca84 User: greg Date: 2014-06-21 20:15:20 Summary: Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed. Affected #: 9 files diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -8,13 +8,14 @@ from galaxy import util from galaxy import web from galaxy.datatypes import checkers +from tool_shed.dependencies import dependency_manager import tool_shed.repository_types.util as rt_util -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_dependency_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util @@ -95,6 +96,8 @@ uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file or uploaded_directory: + rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) ok = True isgzip = False isbz2 = False @@ -124,6 +127,8 @@ if istar: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_tar( trans, + rdah, + tdah, repository, tar, uploaded_file, @@ -134,6 +139,8 @@ elif uploaded_directory: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_directory( trans, + rdah, + tdah, repository, uploaded_directory, upload_point, @@ -164,12 +171,9 @@ full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) # Move some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME ]: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, - # set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: ok = False message = error_message @@ -179,12 +183,10 @@ shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) - elif uploaded_file_filename in [ rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: + elif uploaded_file_filename in [ rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if changeset_revision values are # missing and if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: ok = False message = error_message @@ -333,7 +335,7 @@ message=message, status=status ) - def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, + def upload_directory( self, trans, rdah, tdah, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -364,20 +366,18 @@ if ok: uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and - # if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] if altered: @@ -406,7 +406,8 @@ undesirable_dirs_removed, undesirable_files_removed ) - def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): + def upload_tar( self, trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, + commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -442,18 +443,18 @@ for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] if altered: diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/dependencies/dependency_manager.py --- /dev/null +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -0,0 +1,202 @@ +import copy +import logging + +from galaxy.util import asbool +from galaxy.util.odict import odict +from galaxy.web import url_for + +from tool_shed.dependencies import tag_attribute_handler +from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +log = logging.getLogger( __name__ ) + + +class RepositoryDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def check_tag_attributes( self, elem ): + # <repository name="molecule_datatypes" owner="test" /> + error_message = '' + name = elem.get( 'name' ) + if not name: + error_message += 'The tag is missing the required name attribute. ' + owner = elem.get( 'owner' ) + if not owner: + error_message += 'The tag is missing the required owner attribute. ' + log.debug( error_message ) + return error_message + + def handle_complex_dependency_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag that defines a complex repository dependency. + """ + # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message += ' The %s file contains an invalid <repository> tag.' % TOOL_DEPENDENCY_DEFINITION_FILENAME + return altered, new_elem, error_message + + def handle_elem( self, elem ): + """Populate or unpopulate the changeset_revision and toolshed attributes of repository tags.""" + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> + # <package name="xorg_macros" version="1.17.1" /> + # </repository> + error_message = '' + name = elem.get( 'name' ) + owner = elem.get( 'owner' ) + # The name and owner attributes are always required, so if either are missing, return the error message. + if not name or not owner: + error_message = self.check_tag_attributes( elem ) + return False, elem, error_message + altered = False + toolshed = elem.get( 'toolshed' ) + changeset_revision = elem.get( 'changeset_revision' ) + # Over a short period of time a bug existed which caused the prior_installation_required attribute + # to be set to False and included in the <repository> tag when a repository was exported along with + # its dependencies. The following will eliminate this problematic attribute upon import. + prior_installation_required = elem.get( 'prior_installation_required' ) + if prior_installation_required is not None and not asbool( prior_installation_required ): + del elem.attrib[ 'prior_installation_required' ] + sub_elems = [ child_elem for child_elem in list( elem ) ] + if len( sub_elems ) > 0: + # At this point, a <repository> tag will point only to a package. + # <package name="xorg_macros" version="1.17.1" /> + # Coerce the list to an odict(). + sub_elements = odict() + packages = [] + for sub_elem in sub_elems: + sub_elem_type = sub_elem.tag + sub_elem_name = sub_elem.get( 'name' ) + sub_elem_version = sub_elem.get( 'version' ) + if sub_elem_type and sub_elem_name and sub_elem_version: + packages.append( ( sub_elem_name, sub_elem_version ) ) + sub_elements[ 'packages' ] = packages + else: + # Set to None. + sub_elements = None + if self.unpopulate: + # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes + # from the <repository> tag. + if toolshed or changeset_revision: + attributes = odict() + attributes[ 'name' ] = name + attributes[ 'owner' ] = owner + prior_installation_required = elem.get( 'prior_installation_required' ) + if asbool( prior_installation_required ): + attributes[ 'prior_installation_required' ] = 'True' + new_elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + altered = True + return altered, new_elem, error_message + # From here on we're populating the toolshed and changeset_revision attributes if necessary. + if not toolshed: + # Default the setting to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + elem.attrib[ 'toolshed' ] = toolshed + altered = True + if not changeset_revision: + # Populate the changeset_revision attribute with the latest installable metadata revision for + # the defined repository. We use the latest installable revision instead of the latest metadata + # revision to ensure that the contents of the revision are valid. + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository: + repo = hg_util.get_repo_for_repository( self.app, + repository=repository, + repo_path=None, + create=False ) + lastest_installable_changeset_revision = \ + suc.get_latest_downloadable_changeset_revision( self.app, repository, repo ) + if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: + elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision + altered = True + else: + error_message = 'Invalid latest installable changeset_revision %s ' % \ + str( lastest_installable_changeset_revision ) + error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) + else: + error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) + return altered, elem, error_message + + def handle_sub_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes for each of + the following tag sets. + <action type="set_environment_for_install"> + <action type="setup_r_environment"> + <action type="setup_ruby_environment"> + """ + sub_elem_altered = False + error_message = '' + for sub_index, sub_elem in enumerate( elem ): + # Make sure to skip comments and tags that are not <repository>. + if sub_elem.tag == 'repository': + altered, new_sub_elem, message = self.handle_elem( sub_elem ) + if message: + error_message += 'The %s file contains an invalid <repository> tag. %s' % \ + ( TOOL_DEPENDENCY_DEFINITION_FILENAME, message ) + if altered: + if not sub_elem_altered: + sub_elem_altered = True + elem[ sub_index ] = new_sub_elem + if sub_elem_altered: + parent_elem[ elem_index ] = elem + return sub_elem_altered, parent_elem, error_message + + def handle_tag_attributes( self, config ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag. Populating will occur when a dependency definition file + is being uploaded to the repository, while unpopulating will occur when the + repository is being exported. + """ + # Make sure we're looking at a valid repository_dependencies.xml file. + tree, error_message = xml_util.parse_xml( config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + root_altered = False + new_root = copy.deepcopy( root ) + for index, elem in enumerate( root ): + if elem.tag == 'repository': + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message = 'The %s file contains an invalid <repository> tag. %s' % ( self.file_name, error_message ) + return False, None, error_message + if altered: + if not root_altered: + root_altered = True + new_root[ index ] = new_elem + return root_altered, new_root, error_message + +class ToolDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def handle_tag_attributes( self, tool_dependencies_config ): + """ + Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> + tag defined within a tool_dependencies.xml file. + """ + rdah = RepositoryDependencyAttributeHandler( self.app, self.unpopulate ) + tah = tag_attribute_handler.TagAttributeHandler( self.app, rdah, self.unpopulate ) + altered = False + error_message = '' + # Make sure we're looking at a valid tool_dependencies.xml file. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + altered, new_root, error_message = tah.process_config( root ) + return altered, new_root, error_message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/dependencies/tag_attribute_handler.py --- /dev/null +++ b/lib/tool_shed/dependencies/tag_attribute_handler.py @@ -0,0 +1,199 @@ +import copy +import logging + +log = logging.getLogger( __name__ ) + + +class TagAttributeHandler( object ): + + def __init__( self, app, rdd, unpopulate ): + self.app = app + self.altered = False + self.rdd = rdd + self.unpopulate = unpopulate + + def process_action_tag_set( self, elem, message ): + # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . + # <action> + # <repository name="package_readline_6_2" owner="devteam"> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_tag_set( self, elem, message ): + # <actions> + # <package name="libgtextutils" version="0.6"> + # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> + # </package> + from tool_shed.util import xml_util + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'package': + altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'action': + # <action type="set_environment_for_install"> + # <repository name="package_readline_6_2" owner="devteam""> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, + message=message ) + else: + # Inspect the sub elements of elem to locate all <repository> tags and + # populate them with toolshed and changeset_revision attributes if necessary. + altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): + # Inspect all entries in the <actions_group> tag set, skipping <actions> + # tag sets that define os and architecture attributes. We want to inspect + # only the last <actions> tag set contained within the <actions_group> tag + # set to see if a complex repository dependency is defined. + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions': + if skip_actions_tags: + # Skip all actions tags that include os or architecture attributes. + system = sub_elem.get( 'os' ) + architecture = sub_elem.get( 'architecture' ) + if system or architecture: + continue + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_config( self, root ): + error_message = '' + new_root = copy.deepcopy( root ) + if root.tag == 'tool_dependency': + for elem_index, elem in enumerate( root ): + altered = False + if elem.tag == 'package': + # <package name="eigen" version="2.0.17"> + altered, new_elem, error_message = \ + self.process_package_tag_set( elem=elem, + message=error_message ) + if altered: + if not self.altered: + self.altered = True + new_root[ elem_index ] = new_elem + else: + error_message = "Invalid tool_dependencies.xml file." + return self.altered, new_root, error_message + + def process_install_tag_set( self, elem, message ): + # <install version="1.0"> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions_group': + altered, new_sub_elem, error_message = \ + self.process_actions_group_tag_set( elem=sub_elem, + message=message, + skip_actions_tags=True ) + elif sub_elem.tag == 'actions': + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + else: + package_name = elem.get( 'name', '' ) + package_version = elem.get( 'version', '' ) + error_message += 'Version %s of the %s package cannot be installed because ' % \ + ( str( package_version ), str( package_name ) ) + error_message += 'the recipe for installing the package is missing either an ' + error_message += '<actions> tag set or an <actions_group> tag set.' + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_package_tag_set( self, elem, message ): + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'install': + altered, new_sub_elem, error_message = \ + self.process_install_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): + # We have a complex repository dependency. + altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, + elem_index=elem_index, + elem=elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + return altered, new_elem, message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -20,7 +20,7 @@ class RecipeTag( object ): """Abstract class that defines a standard format for handling recipe tags when installing packages.""" - def process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): raise "Unimplemented Method" diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -5,14 +5,10 @@ import shutil import tempfile from galaxy.datatypes import checkers -from galaxy.util import asbool -from galaxy.util.odict import odict -from galaxy.web import url_for -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util -from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util log = logging.getLogger( __name__ ) @@ -48,8 +44,8 @@ def check_file_contents_for_email_alerts( app ): """ - See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be - checked for inappropriate content. + See if any admin users have chosen to receive email alerts when a repository is updated. + If so, the file contents of the update must be checked for inappropriate content. """ sa_session = app.model.context.current admin_users = app.config.get( "admin_users", "" ).split( "," ) @@ -71,8 +67,9 @@ def get_change_lines_in_file_for_tag( tag, change_dict ): """ - The received change_dict is the jsonified version of the changes to a file in a changeset being pushed to the tool shed from the command line. - This method cleans and returns appropriate lines for inspection. + The received change_dict is the jsonified version of the changes to a file in a + changeset being pushed to the Tool Shed from the command line. This method cleans + and returns appropriate lines for inspection. """ cleaned_lines = [] data_list = change_dict.get( 'data', [] ) @@ -108,7 +105,9 @@ return upload_point def handle_bz2( repository, uploaded_file_name ): - fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, + dir=os.path.dirname( uploaded_file_name ), + text=False ) bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) while 1: try: @@ -125,22 +124,6 @@ bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def handle_complex_repository_dependency_elem( app, elem, sub_elem_index, sub_elem, sub_elem_altered, altered, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines - a complex repository dependency. - """ - # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> - revised, repository_elem, error_message = handle_repository_dependency_elem( app, sub_elem, unpopulate=unpopulate ) - if error_message: - error_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - if revised: - elem[ sub_elem_index ] = repository_elem - sub_elem_altered = True - if not altered: - altered = True - return altered, sub_elem_altered, elem, error_message - def handle_directory_changes( app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) @@ -218,20 +201,10 @@ admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed -def handle_missing_repository_attribute( elem ): - # <repository name="molecule_datatypes" owner="test" /> - error_message = '' - name = elem.get( 'name' ) - if not name: - error_message += 'The tag is missing the required name attribute. ' - owner = elem.get( 'owner' ) - if not owner: - error_message += 'The tag is missing the required owner attribute. ' - log.debug( error_message ) - return error_message - def handle_gzip( repository, uploaded_file_name ): - fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, + dir=os.path.dirname( uploaded_file_name ), + text=False ) gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) while 1: try: @@ -248,249 +221,6 @@ gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def handle_repository_dependencies_definition( app, repository_dependencies_config, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag. Populating will occur when a - dependency definition file is being uploaded to the repository, while depopulating will occur when the repository is being - exported. - """ - altered = False - # Make sure we're looking at a valid repository_dependencies.xml file. - tree, error_message = xml_util.parse_xml( repository_dependencies_config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - if root.tag == 'repositories': - for index, elem in enumerate( root ): - if elem.tag == 'repository': - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - revised, elem, error_message = handle_repository_dependency_elem( app, elem, unpopulate=unpopulate ) - if error_message: - error_message = 'The repository_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - return False, None, error_message - if revised: - root[ index ] = elem - if not altered: - altered = True - return altered, root, error_message - return False, None, error_message - -def handle_repository_dependency_elem( app, elem, unpopulate=False ): - """Populate or unpopulate repository tags.""" - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> - # <package name="xorg_macros" version="1.17.1" /> - # </repository> - error_message = '' - name = elem.get( 'name' ) - owner = elem.get( 'owner' ) - # The name and owner attributes are always required, so if either are missing, return the error message. - if not name or not owner: - error_message = handle_missing_repository_attribute( elem ) - return False, elem, error_message - revised = False - toolshed = elem.get( 'toolshed' ) - changeset_revision = elem.get( 'changeset_revision' ) - # Over a short period of time a bug existed which caused the prior_installation_required attribute - # to be set to False and included in the <repository> tag when a repository was exported along with - # its dependencies. The following will eliminate this problematic attribute upon import. - prior_installation_required = elem.get( 'prior_installation_required' ) - if prior_installation_required is not None and not asbool( prior_installation_required ): - del elem.attrib[ 'prior_installation_required' ] - sub_elems = [ child_elem for child_elem in list( elem ) ] - if len( sub_elems ) > 0: - # At this point, a <repository> tag will point only to a package. - # <package name="xorg_macros" version="1.17.1" /> - # Coerce the list to an odict(). - sub_elements = odict() - packages = [] - for sub_elem in sub_elems: - sub_elem_type = sub_elem.tag - sub_elem_name = sub_elem.get( 'name' ) - sub_elem_version = sub_elem.get( 'version' ) - if sub_elem_type and sub_elem_name and sub_elem_version: - packages.append( ( sub_elem_name, sub_elem_version ) ) - sub_elements[ 'packages' ] = packages - else: - # Set to None. - sub_elements = None - if unpopulate: - # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes from the - # <repository> tag. - if toolshed or changeset_revision: - attributes = odict() - attributes[ 'name' ] = name - attributes[ 'owner' ] = owner - prior_installation_required = elem.get( 'prior_installation_required' ) - if asbool( prior_installation_required ): - attributes[ 'prior_installation_required' ] = 'True' - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - revised = True - return revised, elem, error_message - # From here on we're populating the toolshed and changeset_revisions if necessary. - if not toolshed: - # Default the setting to the current tool shed. - toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) - elem.attrib[ 'toolshed' ] = toolshed - revised = True - if not changeset_revision: - # Populate the changeset_revision attribute with the latest installable metadata revision for the defined repository. - # We use the latest installable revision instead of the latest metadata revision to ensure that the contents of the - # revision are valid. - repository = suc.get_repository_by_name_and_owner( app, name, owner ) - if repository: - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo ) - if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: - elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision - revised = True - else: - error_message = 'Invalid latest installable changeset_revision %s ' % str( lastest_installable_changeset_revision ) - error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) - else: - error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) - return revised, elem, error_message - -def handle_repository_dependency_sub_elem( app, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes for each of the following tag sets. - <action type="set_environment_for_install"> - <action type="setup_r_environment"> - <action type="setup_ruby_environment"> - """ - error_message = '' - for repo_index, repo_elem in enumerate( action_elem ): - # Make sure to skip comments and tags that are not <repository>. - if repo_elem.tag == 'repository': - revised, repository_elem, message = handle_repository_dependency_elem( app, repo_elem, unpopulate=unpopulate ) - if message: - error_message += 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % message - if revised: - action_elem[ repo_index ] = repository_elem - package_altered = True - if not altered: - altered = True - if package_altered: - actions_elem[ action_index ] = action_elem - return package_altered, altered, actions_elem, error_message - -def handle_tool_dependencies_definition( app, tool_dependencies_config, unpopulate=False ): - """ - Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> - tag defined within a tool_dependencies.xml file. - """ - altered = False - error_message = '' - # Make sure we're looking at a valid tool_dependencies.xml file. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - if root.tag == 'tool_dependency': - package_altered = False - for root_index, root_elem in enumerate( root ): - # <package name="eigen" version="2.0.17"> - package_altered = False - if root_elem.tag == 'package': - for package_index, package_elem in enumerate( root_elem ): - if package_elem.tag == 'repository': - # We have a complex repository dependency. - altered, package_altered, root_elem, message = \ - handle_complex_repository_dependency_elem( app, - root_elem, - package_index, - package_elem, - package_altered, - altered, - unpopulate=unpopulate ) - if message: - error_message += message - if package_altered: - root[ root_index ] = root_elem - elif package_elem.tag == 'install': - # <install version="1.0"> - for actions_index, actions_elem in enumerate( package_elem ): - if actions_elem.tag == 'actions_group': - # Inspect all entries in the <actions_group> tag set, skipping <actions> - # tag sets that define os and architecture attributes. We want to inspect - # only the last <actions> tag set contained within the <actions_group> tag - # set to see if a complex repository dependency is defined. - for actions_group_index, actions_group_elem in enumerate( actions_elem ): - if actions_group_elem.tag == 'actions': - # Skip all actions tags that include os or architecture attributes. - system = actions_group_elem.get( 'os' ) - architecture = actions_group_elem.get( 'architecture' ) - if system or architecture: - continue - # ... - # <actions> - # <package name="libgtextutils" version="0.6"> - # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> - # </package> - # ... - for last_actions_index, last_actions_elem in enumerate( actions_group_elem ): - last_actions_package_altered = False - if last_actions_elem.tag == 'package': - last_actions_elem_package_elem_altered = False - for last_actions_elem_package_index, last_actions_elem_package_elem in enumerate( last_actions_elem ): - if last_actions_elem_package_elem.tag == 'repository': - # We have a complex repository dependency. - last_actions_package_altered, last_actions_elem_package_elem_altered, last_actions_elem, message = \ - handle_complex_repository_dependency_elem( app, - last_actions_elem, - last_actions_elem_package_index, - last_actions_elem_package_elem, - last_actions_elem_package_elem_altered, - last_actions_package_altered, - unpopulate=unpopulate ) - if not altered and last_actions_package_altered: - altered = True - if message: - error_message += message - if last_actions_elem_package_elem_altered: - actions_group_elem[ last_actions_index ] = last_actions_elem - else: - # Inspect the sub elements of last_actions_elem to locate all <repository> tags and - # populate them with toolshed and changeset_revision attributes if necessary. - last_actions_package_altered, altered, last_actions_elem, message = \ - handle_repository_dependency_sub_elem( app, - last_actions_package_altered, - altered, - actions_group_elem, - last_actions_index, - last_actions_elem, - unpopulate=unpopulate ) - if message: - error_message += message - elif actions_elem.tag == 'actions': - # We are not in an <actions_group> tag set, so we must be in an <actions> tag set. - for action_index, action_elem in enumerate( actions_elem ): - # Inspect the sub elements of last_actions_elem to locate all <repository> tags - # and populate them with toolshed and changeset_revision attributes if necessary. - package_altered, altered, actions_elem, message = \ - handle_repository_dependency_sub_elem( app, - package_altered, - altered, - actions_elem, - action_index, - action_elem, - unpopulate=unpopulate ) - if message: - error_message += message - else: - package_name = root_elem.get( 'name', '' ) - package_version = root_elem.get( 'version', '' ) - error_message += 'Version %s of the %s package cannot be installed because ' % \ - ( str( package_version ), str( package_name ) ) - error_message += 'the recipe for installing the package is missing either an ' - error_message += '<actions> tag set or an <actions_group> tag set.' - if package_altered: - package_elem[ actions_index ] = actions_elem - if package_altered: - root[ root_index ] = root_elem - return altered, root, error_message - return False, None, error_message - def repository_tag_is_valid( filename, line ): """ Checks changes made to <repository> tags in a dependency definition file being pushed to the diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -6,19 +6,19 @@ import threading from time import gmtime from time import strftime -import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util from galaxy import eggs from galaxy import web from galaxy.util.odict import odict +from tool_shed.dependencies import dependency_manager from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util - from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager eggs.require( 'mercurial' ) @@ -129,6 +129,8 @@ return repositories_archive, error_messages def generate_repository_archive( trans, work_dir, tool_shed_url, repository, changeset_revision, file_type ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=True ) file_type_str = get_file_type_str( changeset_revision, file_type ) file_name = '%s-%s' % ( repository.name, file_type_str ) return_code, error_message = archive_repository_revision( trans, ui, repository, work_dir, changeset_revision ) @@ -151,8 +153,7 @@ # See if we have a repository dependencies defined. if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, full_path, unpopulate=True ) + altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) if error_message: return None, error_message if altered: @@ -160,8 +161,7 @@ shutil.move( tmp_filename, full_path ) elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = \ - commit_util.handle_tool_dependencies_definition( trans.app, full_path, unpopulate=True ) + altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) if error_message: return None, error_message if altered: diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -5,13 +5,14 @@ import tempfile import urllib from galaxy import util +from tool_shed.dependencies import dependency_manager from tool_shed.util import commit_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util -import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util log = logging.getLogger( __name__ ) @@ -267,6 +268,8 @@ def import_repository_archive( app, host, user, repository, repository_archive_dict ): """Import a repository archive contained within a repository capsule.""" + rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=False ) archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] @@ -303,9 +306,9 @@ for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( app, uploaded_file_name, unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message @@ -313,8 +316,9 @@ tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 test/tool_shed/functional/test_0470_tool_dependency_repository_type.py --- a/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py +++ b/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py @@ -169,7 +169,9 @@ commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', strings_displayed=[], strings_not_displayed=[] ) - assert len( package_x11_repository.metadata_revisions ) == 1, 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions' + assert len( package_x11_repository.metadata_revisions ) == 1, \ + 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d' % \ + len( package_x11_repository.metadata_revisions ) def test_0025_upload_updated_tool_dependency_to_package_emboss( self ): '''Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.''' @@ -189,7 +191,9 @@ commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', strings_displayed=[], strings_not_displayed=[] ) - assert len( package_emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + assert len( package_emboss_repository.metadata_revisions ) == 2, \ + 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d' % \ + len( package_emboss_repository.metadata_revisions ) def test_0030_upload_updated_tool_dependency_to_emboss_5_repository( self ): '''Upload a new tool_dependencies.xml to emboss_5_0470.''' 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: jmchilton: Fix for interpreter on version commands (when different from command interpreter).
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e832e4664714/ Changeset: e832e4664714 User: jmchilton Date: 2014-06-20 23:00:38 Summary: Fix for interpreter on version commands (when different from command interpreter). Thanks to Will Holtz for tracking down the problem and Peter Cock for submitting the patch. Affected #: 1 file diff -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 -r e832e466471403d54d788193c938f3c4d139142c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1264,7 +1264,7 @@ executable = self.version_string_cmd.split()[0] abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) command_line = self.version_string_cmd.replace(executable, abs_executable, 1) - self.version_string_cmd = self.interpreter + " " + command_line + self.version_string_cmd = version_cmd_interpreter + " " + command_line # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): 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: Charts: Fix last change
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c972ce1e3e88/ Changeset: c972ce1e3e88 User: guerler Date: 2014-06-20 09:37:10 Summary: Charts: Fix last change Affected #: 1 file diff -r bace76c0aa9b41aa32b793506794cb69e38cf44e -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -207,11 +207,11 @@ // add tooltip events boxes.selectAll('rect') .on('dblclick', function(d) { - d3.event.stopPropagation(); - var xLabel = self.categories.array.x[d.x]; - var yLabel = self.categories.array.y[d.y]; var url = self.chart.settings.get('url_template').trim(); if (url) { + d3.event.stopPropagation(); + var xLabel = self.categories.array.x[d.x]; + var yLabel = self.categories.array.y[d.y]; window.open(url.replace('__LABEL__', xLabel)); window.open(url.replace('__LABEL__', yLabel)); } 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: Charts: Connect data points with template url
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bace76c0aa9b/ Changeset: bace76c0aa9b User: guerler Date: 2014-06-20 09:28:41 Summary: Charts: Connect data points with template url Affected #: 3 files diff -r 5838c21c351afad135604337b94f11dc706fb9c8 -r bace76c0aa9b41aa32b793506794cb69e38cf44e config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" 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t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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Use __LABEL__ as placeholder.', + type : 'text', + init : '', + placeholder : 'http://someurl.com?id=__LABEL__' } } }); diff -r 5838c21c351afad135604337b94f11dc706fb9c8 -r bace76c0aa9b41aa32b793506794cb69e38cf44e config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -206,6 +206,16 @@ // add tooltip events boxes.selectAll('rect') + .on('dblclick', function(d) { + d3.event.stopPropagation(); + var xLabel = self.categories.array.x[d.x]; + var yLabel = self.categories.array.y[d.y]; + var url = self.chart.settings.get('url_template').trim(); + if (url) { + window.open(url.replace('__LABEL__', xLabel)); + window.open(url.replace('__LABEL__', yLabel)); + } + }) .on('mouseover', function(d) { self.tooltip.style('opacity', 0.9); self.tooltip .html(self._templateTooltip(d)) 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: Charts: Allow empty columns
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5838c21c351a/ Changeset: 5838c21c351a User: guerler Date: 2014-06-20 08:24:24 Summary: Charts: Allow empty columns Affected #: 5 files diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 5838c21c351afad135604337b94f11dc706fb9c8 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input 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n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var 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n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return 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Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}l.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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arguments.length?(o=e,t.x(e),m):o},m.y=function(e){return arguments.length?(u=e,t.y(e),m):u},m.clipEdge=function(e){return arguments.length?(l=e,m):l},m.color=function(n){return arguments.length?(s=e.utils.getColor(n),t.color(s),m):s},m.interpolate=function(e){return arguments.length?(p=e,m):p},m.defined=function(e){return arguments.length?(a=e,m):a},m.isArea=function(e){return arguments.length?(f=d3.functor(e),m):f},m},e.models.lineChart=function(){function N(m){return m.each(function(m){var x=d3.select(this),C=this,k=(a||parseInt(x.style("width"))||960)-o.left-o.right,L=(f||parseInt(x.style("height"))||400)-o.top-o.bottom;N.update=function(){x.call(N)},N.container=this,b.disabled=m.map(function(e){return!!e.disabled});if(!w){var A;w={};for(A in b)b[A]instanceof Array?w[A]=b[A].slice(0):w[A]=b[A]}if(!m||!m.length||!m.filter(function(e){return e.values.length}).length){var O=x.selectAll(".nv-noData").data([E]);return O.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;var 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 5838c21c351afad135604337b94f11dc706fb9c8 config/plugins/visualizations/charts/static/charts/others/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/config.js @@ -3,7 +3,7 @@ return $.extend(true, {}, config_default, { title : 'Heatmap', category : 'Others', - query_limit : 2000, + query_limit : 1000, library : 'Custom', tag : 'svg', keywords : 'small', diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 5838c21c351afad135604337b94f11dc706fb9c8 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -249,7 +249,7 @@ .style(this.options.style) .style({'font-size': xFontSize + 'px'}) .attr('transform', function(d) { - var y = -this.getBBox().height - 10; + var y = -this.getBBox().height - 15; var x = -xFontSize + boxWidth/2; return 'rotate(-90)translate(' + y + ',' + x + ')'; }); @@ -259,7 +259,8 @@ .attr('width', width) .attr('height', font_size + 3) .attr('y', height + margin.bottom - font_size - 3) - .attr('fill', this.options.debug_color); + .attr('fill', this.options.debug_color) + .attr('opacity', 0.7); // axis label this.gxAxisLabel = svg.append('text') @@ -316,7 +317,8 @@ .attr('width', font_size) .attr('height', height) .attr('x', -margin.left) - .attr('fill', this.options.debug_color); + .attr('fill', this.options.debug_color) + .attr('opacity', 0.7); // axis label this.gyAxisLabel = svg.append('text') @@ -349,9 +351,15 @@ var legendElementHeight = Math.max(legendSize * height / legendElements, font_size); var legendHeight = legendElements * legendElementHeight / 2; + // check number of legend elements + var data = d3.range(this.zMin, this.zMax, 2 * (this.zMax-this.zMin) / legendElements).reverse(); + if (data.length < 2) { + return; + } + // create legend elements var legend = this.svg.selectAll('.legend') - .data(d3.range(this.zMin, this.zMax, 2 * (this.zMax-this.zMin) / legendElements).reverse()) + .data(data) .enter().append('g') .attr('class', 'legend') .attr('transform', function(d, i) { diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 5838c21c351afad135604337b94f11dc706fb9c8 config/plugins/visualizations/charts/static/library/datasets.js --- a/config/plugins/visualizations/charts/static/library/datasets.js +++ b/config/plugins/visualizations/charts/static/library/datasets.js @@ -159,7 +159,7 @@ // check if column is in cache var block_id = this._block_id(request_dictionary, column); - if (this.cache[block_id] || column === 'auto') { + if (this.cache[block_id] || column === 'auto' || column === 'zero') { continue; } @@ -264,33 +264,44 @@ var column = group.columns[key]; // check if auto block is requested - if (column.index == 'auto') { - for (var j = 0; j < limit; j++) { - // get value dictionary - var value = group.values[j]; - - // add auto value - value[key] = parseInt(j) + start; - } - } else { - // get block - var block_id = this._block_id(request_dictionary, column.index); - var column_data = this.cache[block_id]; - - // go through column - for (var j = 0; j < limit; j++) { - // get value dictionary - var value = group.values[j]; - - // get/fix value - var v = column_data[j]; - if (isNaN(v) && !column.is_label) { - v = 0; + switch (column.index) { + case 'auto': + for (var j = 0; j < limit; j++) { + // get value dictionary + var value = group.values[j]; + + // add auto value + value[key] = parseInt(j) + start; } - - // add to dict - value[key] = v; - } + break; + case 'zero': + for (var j = 0; j < limit; j++) { + // get value dictionary + var value = group.values[j]; + + // add zero value + value[key] = 0; + } + break; + default: + // get block + var block_id = this._block_id(request_dictionary, column.index); + var column_data = this.cache[block_id]; + + // go through column + for (var j = 0; j < limit; j++) { + // get value dictionary + var value = group.values[j]; + + // get/fix value + var v = column_data[j]; + if (isNaN(v) && !column.is_label) { + v = 0; + } + + // add to dict + value[key] = v; + } } } } diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 5838c21c351afad135604337b94f11dc706fb9c8 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -149,6 +149,7 @@ var is_auto = column_definition.is_auto; var is_numeric = column_definition.is_numeric; var is_unique = column_definition.is_unique; + var is_zero = column_definition.is_zero; // configure columns var columns = []; @@ -164,6 +165,14 @@ }); } + // add zero selection column + if (is_zero) { + columns.push({ + 'label' : 'Column: None', + 'value' : 'zero' + }); + } + // meta data var meta = dataset.metadata_column_types; for (var key in meta) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Add a few more comments about dataset path rewriting in the dataset wrapper.
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cfa24d46767a/ Changeset: cfa24d46767a User: jmchilton Date: 2014-06-20 06:21:42 Summary: Add a few more comments about dataset path rewriting in the dataset wrapper. Affected #: 1 file diff -r d781366bc120787e201b73a4dd99b56282169d86 -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -209,13 +209,21 @@ def __getattr__( self, key ): if self.false_path is not None and key == 'file_name': + # Path to dataset was rewritten for this job. return self.false_path elif self.false_extra_files_path is not None and key == 'extra_files_path': + # Path to extra files was rewritten for this job. return self.false_extra_files_path elif key == 'extra_files_path': try: + # Assume it is an output and that this wrapper + # will be set with correct "files_path" for this + # job. return self.files_path except AttributeError: + # Otherwise, we have an input - delegate to model and + # object store to find the static location of this + # directory. try: return self.dataset.extra_files_path except exceptions.ObjectNotFound: 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: jmchilton: Improved (different at least) extra_files_path handling for dataset outputs.
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120/ Changeset: d781366bc120 User: jmchilton Date: 2014-06-20 06:07:21 Summary: Improved (different at least) extra_files_path handling for dataset outputs. $output.extra_files_path will now mimic $output.files_path behavior - writing these files to the working directory to have them copied over later. This is more correct when using outputs_to_working_directory, running jobs as the real user, running jobs through LWR/Pulsar, or when using the NestedObjectStore. This is less efficient the 90% of the time when none of these conditions hold. There is still an open issue that for inputs - $input.extra_files_path returns a non-exist path for DiskObjectStores but throws an error for NestedObjectStores. This behavior could be synchronized by this patch (https://gist.github.com/jmchilton/d05bcf02874762cdb829) - though I do not know if this is the intended behavior of NestedObjectStores. Affected #: 1 file diff -r 4eba60282f9d06ce6123478ea1bfa1f9ec741f45 -r d781366bc120787e201b73a4dd99b56282169d86 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -1,4 +1,5 @@ import pipes +from galaxy import exceptions from galaxy.util.none_like import NoneDataset from galaxy.util import odict @@ -211,6 +212,17 @@ return self.false_path elif self.false_extra_files_path is not None and key == 'extra_files_path': return self.false_extra_files_path + elif key == 'extra_files_path': + try: + return self.files_path + except AttributeError: + try: + return self.dataset.extra_files_path + except exceptions.ObjectNotFound: + # NestedObjectstore raises an error here + # instead of just returning a non-existent + # path like DiskObjectStore. + raise else: return getattr( self.dataset, key ) 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: greg: Fix for handling complex repository dependency definitions that contain recipes that include <package> tag sets that define dependencies needed only for compiling the dependent package.
by commits-noreply＠bitbucket.org 19 Jun '14

19 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4eba60282f9d/ Changeset: 4eba60282f9d User: greg Date: 2014-06-19 23:46:04 Summary: Fix for handling complex repository dependency definitions that contain recipes that include <package> tag sets that define dependencies needed only for compiling the dependent package. Affected #: 1 file diff -r d64ce44b0d0dc5fcf9978f6047fe78ef946165dc -r 4eba60282f9d06ce6123478ea1bfa1f9ec741f45 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -130,7 +130,6 @@ Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines a complex repository dependency. """ - # The received sub_elem looks something like the following: # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> revised, repository_elem, error_message = handle_repository_dependency_elem( app, sub_elem, unpopulate=unpopulate ) if error_message: @@ -432,22 +431,24 @@ for last_actions_index, last_actions_elem in enumerate( actions_group_elem ): last_actions_package_altered = False if last_actions_elem.tag == 'package': + last_actions_elem_package_elem_altered = False for last_actions_elem_package_index, last_actions_elem_package_elem in enumerate( last_actions_elem ): if last_actions_elem_package_elem.tag == 'repository': # We have a complex repository dependency. - altered, last_actions_package_altered, last_actions_elem, message = \ + last_actions_package_altered, last_actions_elem_package_elem_altered, last_actions_elem, message = \ handle_complex_repository_dependency_elem( app, last_actions_elem, last_actions_elem_package_index, last_actions_elem_package_elem, + last_actions_elem_package_elem_altered, last_actions_package_altered, - altered, unpopulate=unpopulate ) + if not altered and last_actions_package_altered: + altered = True if message: error_message += message - if last_actions_package_altered: - last_actions_elem[ last_actions_elem_package_index ] = last_actions_elem_package_elem - actions_group_elem[ last_actions_index ] = last_actions_elem + if last_actions_elem_package_elem_altered: + actions_group_elem[ last_actions_index ] = last_actions_elem else: # Inspect the sub elements of last_actions_elem to locate all <repository> tags and # populate them with toolshed and changeset_revision attributes if necessary. 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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