September 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

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

24 Sep '13

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

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commit/galaxy-central: guerler: Show dataset title in scratchbook frame header
by commits-noreply＠bitbucket.org 24 Sep '13

24 Sep '13

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

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commit/galaxy-central: guerler: Drag&drop multiple file upload: add status icon
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

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

1 0

commit/galaxy-central: natefoo: Merge stable branch, pack scripts.
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

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

1 0

commit/galaxy-central: natefoo: Remove unmaintained RGENETICS tools from Galaxy Main
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

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

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

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

1 0

commit/galaxy-central: guerler: Drag&drop multiple file upload: add status line, improve queueing, update select2
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

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

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ef6df129520/ Changeset: 4ef6df129520 User: carlfeberhard Date: 2013-09-23 21:23:38 Summary: Style: add proper alert macro for warning, add errormessagesmall; pack scripts Affected #: 10 files diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -82,6 +82,10 @@ this.$el.attr( 'id', 'historyItemContainer-' + id ); + //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide + // handle that here by removing previous view's tooltips + this.$el.find("[title]").tooltip( "destroy" ); + /** web controller urls for functions relating to this hda. * These are rendered from urlTemplates using the model data. */ this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() ); diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -166,6 +166,7 @@ success: function() { // FIXME: setting model attribute causes re-rendering, which is unnecessary. //self.$el.remove(); + self.model.set({ deleted: true }); } }); diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var 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a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var 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p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($("<button></button>").text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($('<button id="'+String(e).toLowerCase()+'"></button>').text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){$("#galaxy-upload-box").addClass("highlight")},event_mouseleave:function(d){$("#galaxy-upload-box").removeClass("highlight")},event_start:function(d,e,f){var g="#galaxy-upload-file-"+d;$("#galaxy-upload-box").append(this.template_file(g));$("#galaxy-upload-file-"+d).find(".title").html(e.name);this.event_progress(d,e,0);this.file_counter++;this.refresh()},event_progress:function(e,f,h){var g=$("#galaxy-upload-file-"+e);var d=parseInt(h);g.find(".progress").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,f){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(d,e,g){var f=$("#galaxy-upload-file-"+d);f.find(".progress-frame").addClass("failed");f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.file_counter--;this.refresh()},event_show:function(g){g.preventDefault();if(!Galaxy.currHistoryPanel){var f=this;window.setTimeout(function(){f.event_show(g)},200);return}if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template(),buttons:{Close:function(){f.modal.hide()}}});var d=Galaxy.currHistoryPanel.model.get("id");var f=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+d+"/contents",dragover:f.event_mouseover,dragleave:f.event_mouseleave,start:function(e,h,i){f.event_start(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box"></form>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="file corner-soft shadow"><div class="title"></div><div class="error"></div><div class="progress-frame corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){this.uploadbox.info().hide();var i="#upload-"+e;$(this.el).append(this.template_file(i));$(this.el).scrollTop($(this.el).prop("scrollHeight"));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);g.find("#extension").select2({placeholder:"Auto-detect",width:"copy",ajax:{url:"http://www.weighttraining.com/sm/search",dataType:"jsonp",quietMillis:100,data:function(j,k){return{types:["exercise"],limit:-1,term:j}},results:function(k,j){return{results:k.results.exercise}}},formatResult:function(j){return"<div class='select2-user-result'>"+j.term+"</div>"},formatSelection:function(j){return j.term},initSelection:function(j,l){var k=$(j).attr("data-init-text");l({term:k})}});var d=this;g.find(".remove").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.modal.enable("Upload");this.modal.enable("Reset")},event_initialize:function(d,e,g){this.button_show.number(g);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("")},event_error:function(d,e,g){var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.button_show.number("")},event_upload:function(){$(this.el).find(".panel-body").hide();$(this.el).find(".remove").each(function(){$(this).removeClass("fa-icon-trash");$(this).addClass("fa-icon-caret-down")});this.modal.disable("Upload");var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_reset:function(){var e=$(this.el).find(".panel");var d=this;e.fadeOut({complete:function(){e.remove();d.uploadbox.info().fadeIn()}});this.modal.disable("Upload");this.modal.disable("Reset");this.uploadbox.reset()},event_remove:function(e){var d=this;var f=this.get_upload_item(e);f.fadeOut({complete:function(){f.remove();d.uploadbox.remove(e);if($(d.el).find(".panel").length>0){d.modal.enable("Reset")}else{d.modal.disable("Reset");d.uploadbox.info().fadeIn()}if(d.uploadbox.length()>0){d.modal.enable("Upload")}else{d.modal.disable("Upload")}}})},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}}});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},});this.modal.disable("Upload");this.modal.disable("Reset")}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(d){return'<div id="'+d+'" class="upload-box"></div>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="remove fa-icon-trash"></div></div><div class="panel-body"><div class="menu"><span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.$el.find("[title]").tooltip("destroy");this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: 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\ No newline at end of file diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1245,9 +1245,10 @@ .errormessage .alert-link,.warningmessage .alert-link,.donemessage .alert-link,.infomessage .alert-link,.errormessagesmall .alert-link,.warningmessagesmall .alert-link,.donemessagesmall .alert-link,.infomessagesmall .alert-link{font-weight:bold} .errormessage>p,.warningmessage>p,.donemessage>p,.infomessage>p,.errormessagesmall>p,.warningmessagesmall>p,.donemessagesmall>p,.infomessagesmall>p,.errormessage>ul,.warningmessage>ul,.donemessage>ul,.infomessage>ul,.errormessagesmall>ul,.warningmessagesmall>ul,.donemessagesmall>ul,.infomessagesmall>ul{margin-bottom:0} .errormessage>p+p,.warningmessage>p+p,.donemessage>p+p,.infomessage>p+p,.errormessagesmall>p+p,.warningmessagesmall>p+p,.donemessagesmall>p+p,.infomessagesmall>p+p{margin-top:5px} -.errormessage{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr{border-top-color:#c61913} -.errormessage .alert-link{color:#571d1b} -.warningmessage,.warningmessagesmall{background-image:url(warn_small.png)} +.errormessage,.errormessagesmall{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr,.errormessagesmall hr{border-top-color:#c61913} +.errormessage .alert-link,.errormessagesmall .alert-link{color:#571d1b} +.warningmessage,.warningmessagesmall{background-color:#fce1ba;border-color:#e28709;color:#80571e;background-image:url(warn_small.png)}.warningmessage hr,.warningmessagesmall hr{border-top-color:#c97908} +.warningmessage .alert-link,.warningmessagesmall .alert-link{color:#573b14} .donemessage,.donemessagesmall{background-color:#aff1af;border-color:#20b420;color:#295f29;background-image:url(ok_small.png)}.donemessage hr,.donemessagesmall hr{border-top-color:#1c9e1c} .donemessage .alert-link,.donemessagesmall .alert-link{color:#193b19} .infomessage,.infomessagesmall{background-color:#a6e4f7;border-color:#1197c0;color:#1f5566;background-image:url(info_small.png)}.infomessage hr,.infomessagesmall hr{border-top-color:#0f85a8} diff -r e70289bdc4144bd4f20ac5d76042570e1dff41cb -r 4ef6df129520040017cfd4a287cb01558c6af35f static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -759,28 +759,23 @@ background-position: 5px 5px; } -.errormessage { +.errormessage, .errormessagesmall { .alert-danger(); } .warningmessage, .warningmessagesmall { + .alert-warning(); background-image: url(warn_small.png); - //border-color: @warn_message_border; - //background-color: @warn_message_bg; } .donemessage, .donemessagesmall { .alert-success(); background-image: url(ok_small.png); - // border-color: @done_message_border; - // background-color: @done_message_bg; } .infomessage, .infomessagesmall { .alert-info(); background-image: url(info_small.png); - //border-color: @info_message_border; - //background-color: @info_message_bg; } .errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Update drmaa to 0.6
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e70289bdc414/ Changeset: e70289bdc414 User: natefoo Date: 2013-09-23 21:08:34 Summary: Update drmaa to 0.6 Affected #: 1 file diff -r 0c1ecb1f4190800abdb29b3a17fc2b9d8bd21eba -r e70289bdc4144bd4f20ac5d76042570e1dff41cb eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ boto = 2.5.2 decorator = 3.1.2 docutils = 0.7 -drmaa = 0.4b3 +drmaa = 0.6 elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 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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