November 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Fixes for tool shed functional tests.
by Bitbucket 29 Nov '12

29 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/607e9db258f2/ changeset: 607e9db258f2 user: greg date: 2012-11-29 18:42:04 summary: Fixes for tool shed functional tests. affected #: 4 files diff -r 60786207e48d952a69ccef95fd8fdc1740970923 -r 607e9db258f20ad47b8bb813508bd6a9056596b8 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,4 +1,5 @@ from base.twilltestcase import * +import ConfigParser class ShedTwillTestCase( TwillTestCase ): def setUp( self ): @@ -6,6 +7,7 @@ self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' ) self.history_id = None self.hgweb_config_manager = None + self.hgweb_config_dir = os.environ.get( 'TEST_HG_WEB_CONFIG_DIR' ) self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' ) self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) @@ -108,8 +110,8 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def delete_files_from_repository( self, repository, filenames=[], strings_displayed=[ 'were deleted from the repository' ], strings_not_displayed=[] ): files_to_delete = [] - basepath = self.get_repository_base_path_from_browse_page( repository ) - repository_files = self.get_repository_file_list( repository, basepath ) + basepath = self.get_repo_path( repository ) + repository_files = self.get_repository_file_list( base_path=basepath, current_path=None ) # Verify that the files to delete actually exist in the repository. for filename in repository_files: if filename in filenames: @@ -133,14 +135,15 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_file_contents( self, repository, filename, filepath=None, strings_displayed=[], strings_not_displayed=[] ): '''Find a file in the repository and display the contents.''' - basepath = self.get_repository_base_path_from_browse_page( repository ) + basepath = self.get_repo_path( repository ) repository_file_list = [] - relative_path = filename - if filepath is not None: - relative_path = os.path.join( filepath, filename ) - repository_file_list = self.get_repository_file_list( repository, basepath ) - assert relative_path in repository_file_list, 'File %s not found in the repository under %s.' % ( filename, filepath ) - url = '/repository/get_file_contents?file_path=%s' % os.path.join( basepath, relative_path ).replace( '/', '%2f' ) + if filepath: + relative_path = os.path.join( basepath, filepath ) + else: + relative_path = basepath + repository_file_list = self.get_repository_file_list( base_path=relative_path, current_path=None ) + assert filename in repository_file_list, 'File %s not found in the repository under %s.' % ( filename, relative_path ) + url = '/repository/get_file_contents?file_path=%s' % os.path.join( relative_path, filename ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) def edit_repository_categories( self, repository, categories_to_add=[], categories_to_remove=[], restore_original=True ): @@ -196,27 +199,27 @@ def get_latest_repository_metadata_for_repository( self, repository ): # TODO: This will not work as expected. Fix it. return repository.metadata_revisions[ 0 ] - def get_repository_base_path_from_browse_page( self, repository ): - '''Get the base path from the javascript dynatree parameters. This must be updated if the browse feature is altered.''' - self.visit_url( '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) ) - html = self.last_page() - found_file = None - basepath = None - search = re.search( 'data: { folder_path: "([^"]+)" },', html ) - if search is not None: - basepath = search.group( 1 ) - return basepath - def get_repository_file_list( self, repository, base_path, current_path=None ): - ''' - Recursively load repository folder contents and append them to a list. Similar to os.walk, - but via /repository/open_folder. - ''' + def get_repo_path( self, repository ): + # An entry in the hgweb.config file looks something like: repos/test/mira_assembler = database/community_files/000/repo_123 + lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) + hgweb_config = "%s/hgweb.config" % self.hgweb_config_dir + if not os.path.exists( hgweb_config ): + raise Exception( "Required file hgweb.config does not exist in directory %s" % self.hgweb_config_dir ) + config = ConfigParser.ConfigParser() + config.read( hgweb_config ) + for option in config.options( "paths" ): + if option == lhs: + return config.get( "paths", option ) + raise Exception( "Entry for repository %s missing in %s/hgweb.config file." % ( lhs, self.hgweb_config_dir ) ) + def get_repository_file_list( self, base_path, current_path=None ): + '''Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder.''' if current_path is None: - full_path = base_path + request_param_path = base_path else: - full_path = os.path.join( base_path, current_path ) + request_param_path = os.path.join( base_path, current_path ) + #request_param_path = request_param_path.replace( '/', '%2f' ) # Get the current folder's contents. - url = '/repository/open_folder?folder_path=%s' % full_path.replace( '/', '%2f' ) + url = '/repository/open_folder?folder_path=%s' % request_param_path self.visit_url( url ) file_list = from_json_string( self.last_page() ) returned_file_list = [] @@ -228,10 +231,10 @@ # This is a folder. Get the contents of the folder and append it to the list, # prefixed with the path relative to the repository root, if any. if current_path is None: - returned_file_list.extend( self.get_repository_file_list( repository, base_path, file_dict[ 'title' ] ) ) + returned_file_list.extend( self.get_repository_file_list( base_path=base_path, current_path=file_dict[ 'title' ] ) ) else: sub_path = os.path.join( current_path, file_dict[ 'title' ] ) - returned_file_list.extend( self.get_repository_file_list( repository, base_path, sub_path ) ) + returned_file_list.extend( self.get_repository_file_list( base_path=base_path, current_path=sub_path ) ) else: # This is a regular file, prefix the filename with the current path and append it to the list. if current_path is not None: diff -r 60786207e48d952a69ccef95fd8fdc1740970923 -r 607e9db258f20ad47b8bb813508bd6a9056596b8 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 @@ -15,7 +15,7 @@ repository_description = "Galaxy's filtering tool" repository_long_description = "Long description of Galaxy's filtering tool" -class TestCreateRepository( ShedTwillTestCase ): +class TestBasicRepositoryFeatures( ShedTwillTestCase ): def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" @@ -89,9 +89,13 @@ strings_displayed=[ 'has been marked as not deprecated', 'Mark as deprecated' ], set_deprecated=False ) def test_0045_display_repository_tip_file( self ): - '''Display the contents of a file in the repository tip revision''' + '''Display the contents of filtering.xml in the repository tip revision''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) - self.display_repository_file_contents( repository, filename='filtering.xml', strings_displayed=[ '1.1.0' ] ) + self.display_repository_file_contents( repository=repository, + filename='filtering.xml', + filepath=None, + strings_displayed=[ '1.1.0' ], + strings_not_displayed=[] ) def test_0050_upload_filtering_txt_file( self ): '''Upload filtering.txt file associated with tool version 1.1.0.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) @@ -105,7 +109,11 @@ '''Upload filtering test data.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, 'filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) - self.display_repository_file_contents( repository, filename='1.bed', filepath='test-data' ) + self.display_repository_file_contents( repository=repository, + filename='1.bed', + filepath='test-data', + strings_displayed=[], + strings_not_displayed=[] ) self.check_repository_metadata( repository, tip_only=True ) def test_0060_upload_filtering_2_2_0( self ): '''Upload filtering version 2.2.0''' diff -r 60786207e48d952a69ccef95fd8fdc1740970923 -r 607e9db258f20ad47b8bb813508bd6a9056596b8 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -0,0 +1,19 @@ +from tool_shed.base.twilltestcase import * +from tool_shed.base.test_db_util import * + +admin_user = None +admin_user_private_role = None +admin_email = 'test(a)bx.psu.edu' +admin_username = 'admin-user' + +regular_user = None +regular_user_private_role = None +regular_email = 'test-1(a)bx.psu.edu' +regular_username = 'user1' + +repository_name = 'freebayes' +repository_description = "Galaxy's freebayes tool" +repository_long_description = "Long description of Galaxy's freebayes tool" + +class TestRepositoryWithToolDependencies( ShedTwillTestCase ): + pass \ No newline at end of file diff -r 60786207e48d952a69ccef95fd8fdc1740970923 -r 607e9db258f20ad47b8bb813508bd6a9056596b8 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -6,6 +6,10 @@ cwd = os.getcwd() tool_shed_home_directory = os.path.join( cwd, 'test', 'tool_shed' ) default_tool_shed_test_file_dir = os.path.join( tool_shed_home_directory, 'test_data' ) +# Here's the directory where everything happens. Temporary directories are created within this directory to contain +# the hgweb.config file, the database, new repositories, etc. Since the tool shed browses repository contents via HTTP, +# the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters. +tool_shed_test_tmp_dir = os.path.join( tool_shed_home_directory, 'tmp' ) new_path = [ os.path.join( cwd, "lib" ) ] new_path.extend( sys.path[1:] ) sys.path = new_path @@ -31,7 +35,6 @@ import galaxy.webapps.community.app from galaxy.webapps.community.app import UniverseApplication from galaxy.webapps.community import buildapp -#from galaxy.webapps.community.util.hgweb_config import * import nose.core import nose.config @@ -81,6 +84,8 @@ use_distributed_object_store = os.environ.get( 'TOOL_SHED_USE_DISTRIBUTED_OBJECT_STORE', False ) if start_server: + if not os.path.isdir( tool_shed_test_tmp_dir ): + os.mkdir( tool_shed_test_tmp_dir ) psu_production = False tool_shed_test_proxy_port = None if 'TOOL_SHED_TEST_PSU_PRODUCTION' in os.environ: @@ -102,7 +107,8 @@ if not nginx_upload_store: raise Exception( 'Set TOOL_SHED_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' ) file_path = tempfile.mkdtemp( dir=base_file_path ) - new_file_path = tempfile.mkdtemp( dir=base_new_file_path ) + new_repos_path = tempfile.mkdtemp( dir=base_new_file_path ) + hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) kwargs = dict( database_engine_option_pool_size = '10', database_engine_option_max_overflow = '20', database_engine_option_strategy = 'threadlocal', @@ -113,16 +119,17 @@ if 'TOOL_SHED_TEST_DBPATH' in os.environ: db_path = os.environ[ 'TOOL_SHED_TEST_DBPATH' ] else: - tempdir = tempfile.mkdtemp() + tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) db_path = os.path.join( tempdir, 'database' ) file_path = os.path.join( db_path, 'files' ) - new_file_path = os.path.join( db_path, 'tmp' ) + hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) if 'TOOL_SHED_TEST_DBURI' in os.environ: database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] else: database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) kwargs = {} - for dir in file_path, new_file_path: + for dir in tool_shed_test_tmp_dir: try: os.makedirs( dir ) except OSError: @@ -130,6 +137,11 @@ print "Database connection:", 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 + # ---- Build Application -------------------------------------------------- app = None if start_server: @@ -150,7 +162,7 @@ database_connection = database_connection, database_engine_option_pool_size = '10', file_path = file_path, - new_file_path = new_file_path, + new_file_path = new_repos_path, tool_path=tool_path, datatype_converters_config_file = 'datatype_converters_conf.xml.sample', tool_parse_help = False, @@ -163,9 +175,8 @@ admin_users = 'test(a)bx.psu.edu', global_conf = global_conf, running_functional_tests = True, - hgweb_config_dir = new_file_path, + hgweb_config_dir = hgweb_config_dir, **kwargs ) -# app.hgweb_config_manager = HgWebConfigManager() log.info( "Embedded Universe application started" ) @@ -254,20 +265,14 @@ app.shutdown() app = None log.info( "Embedded Universe application stopped" ) - try: - if os.path.exists( tempdir ) and 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: - log.info( "Cleaning up temporary files in %s" % tempdir ) - shutil.rmtree( tempdir ) - except: - pass - if psu_production and 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: - for dir in ( file_path, new_file_path ): - try: + if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: + try: + for dir in [ tool_shed_test_tmp_dir ]: if os.path.exists( dir ): - log.info( 'Cleaning up temporary files in %s' % dir ) + log.info( "Cleaning up temporary files in %s" % dir ) shutil.rmtree( dir ) - except: - pass + except: + pass if success: return 0 else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Added more functional tests for basic tool shed repository features.
by Bitbucket 28 Nov '12

28 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e291341d0127/ changeset: e291341d0127 user: inithello date: 2012-11-28 21:21:23 summary: Added more functional tests for basic tool shed repository features. affected #: 9 files diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -77,7 +77,7 @@ elif file_data not in ( '', None ): uploaded_file = file_data.file uploaded_file_name = uploaded_file.name - uploaded_file_filename = file_data.filename + uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file or uploaded_directory: ok = True diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -39,7 +39,7 @@ sa_session.flush() def refresh( obj ): sa_session.refresh( obj ) -def get_repository_by_name( name, owner_username ): +def get_repository_by_name_and_owner( name, owner_username ): owner = get_user_by_name( owner_username ) repository = sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.name==name ) \ diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -5,6 +5,7 @@ # Security helper self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' ) self.history_id = None + self.hgweb_config_manager = None self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' ) self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) @@ -29,18 +30,67 @@ if strings_not_displayed: for string in strings_not_displayed: self.check_string_not_in_page( string ) - def check_for_tool_metadata(self, repository, changeset_revision, tool_id, strings_displayed=[], strings_not_displayed=[] ): - url = '/repository/view_tool_metadata?repository_id=%s&changeset_revision=%s&tool_id=%s' % \ - ( self.security.encode_id( repository.id ), changeset_revision, tool_id ) - self.visit_url( url ) - self.check_for_strings( strings_displayed, strings_not_displayed ) - def check_for_valid_tools( self, repository ): - self.manage_repository( repository ) - self.check_page_for_string( 'Valid tools' ) + def check_for_valid_tools( self, repository, strings_displayed=[], strings_not_displayed=[] ): + strings_displayed.append( 'Valid tools' ) + self.manage_repository( repository, strings_displayed, strings_not_displayed ) + def check_metadata_in_repository_changelog( self, repository, metadata_count ): + self.check_repository_changelog( repository ) + self.check_string_count_in_page( 'Repository metadata is associated with this change set.', metadata_count ) def check_repository_changelog( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def check_repository_metadata( self, repository, tip_only=True ): + assert self.tip_has_metadata( repository, tip_only ), \ + 'Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s.' % \ + ( self.get_repository_tip( repository ), ', '.join( self.get_repository_metadata_revisions( repository ) ) ) + def check_repository_tools( self, repository, include_invalid=False ): + ''' + Loop through each repository_metadata dict in the repository object. + For each of these, check for a tools attribute, and load the tool metadata + page if it exists, then display that tool's page. + ''' + tool_list, invalid_tool_list = self.get_tools_from_repository_metadata( repository, include_invalid=include_invalid ) + for valid_tool_dict in tool_list: + changeset_revision = valid_tool_dict[ 'changeset_revision' ] + for tool in valid_tool_dict[ 'tools' ]: + metadata_strings_displayed = [ tool[ 'guid' ], + tool[ 'version' ], + tool[ 'id' ], + tool[ 'name' ], + tool[ 'description' ], + changeset_revision ] + url = '/repository/view_tool_metadata?repository_id=%s&changeset_revision=%s&tool_id=%s' % \ + ( self.security.encode_id( repository.id ), changeset_revision, tool[ 'id' ] ) + self.visit_url( url ) + self.check_for_strings( metadata_strings_displayed ) + self.load_display_tool_page( repository, tool_xml_path=tool[ 'tool_config' ], + changeset_revision=changeset_revision, + strings_displayed=[ '%s (version %s)' % ( tool[ 'name' ], tool[ 'version' ] ) ], + strings_not_displayed=[] ) + if include_invalid and invalid_tool_list: + for invalid_tool_dict in invalid_tool_list: + for tool in invalid_tool_dict[ 'tools' ]: + tool_path = '%s/%s' % ( self.get_repository_filesystem_path( repository ), tool ) + self.load_display_tool_page( repository, + tool_xml_path=tool_path, + changeset_revision=changeset_revision, + strings_displayed=[ 'properly loaded' ], + strings_not_displayed=[] ) + def check_string_count_in_page( self, pattern, min_count, max_count=None ): + """Checks the number of 'pattern' occurrences in the current browser page""" + page = self.last_page() + pattern_count = page.count( pattern ) + if max_count is None: + max_count = min_count + # The number of occurrences of pattern in the page should be between min_count + # and max_count, so show error if pattern_count is less than min_count or greater + # than max_count. + if pattern_count < min_count or pattern_count > max_count: + fname = self.write_temp_file( page ) + errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % \ + ( pattern_count, pattern, min_count, max_count, fname ) + raise AssertionError( errmsg ) def create_category( self, category_name, category_description ): self.visit_url( '/admin/manage_categories?operation=create' ) tc.fv( "1", "name", category_name ) @@ -56,10 +106,43 @@ tc.fv( "1", "category_id", "+%s" % category ) tc.submit( "create_repository_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def delete_files_from_repository( self, repository, filenames=[], strings_displayed=[ 'were deleted from the repository' ], strings_not_displayed=[] ): + files_to_delete = [] + basepath = self.get_repository_base_path_from_browse_page( repository ) + repository_files = self.get_repository_file_list( repository, basepath ) + # Verify that the files to delete actually exist in the repository. + for filename in repository_files: + if filename in filenames: + files_to_delete.append( os.path.join( basepath, filename ) ) + self.browse_repository( repository ) + # Twill sets hidden form fields to read-only by default. We need to write to this field. + form = tc.browser.get_form( 'select_files_to_delete' ) + form.find_control( "selected_files_to_delete" ).readonly = False + tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) ) + tc.submit( 'select_files_to_delete_button' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_readme_file( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): + if changeset_revision is None: + changeset_revision = self.get_repository_tip( repository ) + repository_id = self.security.encode_id( repository.id ) + self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): url = '/repos/%s/%s' % ( owner_name, repository_name ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_repository_file_contents( self, repository, filename, filepath=None, strings_displayed=[], strings_not_displayed=[] ): + '''Find a file in the repository and display the contents.''' + basepath = self.get_repository_base_path_from_browse_page( repository ) + repository_file_list = [] + relative_path = filename + if filepath is not None: + relative_path = os.path.join( filepath, filename ) + repository_file_list = self.get_repository_file_list( repository, basepath ) + assert relative_path in repository_file_list, 'File %s not found in the repository under %s.' % ( filename, filepath ) + url = '/repository/get_file_contents?file_path=%s' % os.path.join( basepath, relative_path ).replace( '/', '%2f' ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def edit_repository_categories( self, repository, categories_to_add=[], categories_to_remove=[], restore_original=True ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -67,10 +150,10 @@ strings_not_displayed = [] for category in categories_to_add: tc.fv( "2", "category_id", '+%s' % category) - strings_displayed.append( "selected>%s</option>" % category ) + strings_displayed.append( "selected>%s" % category ) for category in categories_to_remove: tc.fv( "2", "category_id", '-%s' % category) - strings_not_displayed.append( "selected>%s</option>" % category ) + strings_not_displayed.append( "selected>%s" % category ) tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) if restore_original: @@ -78,22 +161,22 @@ strings_not_displayed = [] for category in categories_to_remove: tc.fv( "2", "category_id", '+%s' % category) - strings_displayed.append( "selected>%s</option>" % category ) + strings_displayed.append( "selected>%s" % category ) for category in categories_to_add: tc.fv( "2", "category_id", '-%s' % category) - strings_not_displayed.append( "selected>%s</option>" % category ) + strings_not_displayed.append( "selected>%s" % category ) tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def edit_repository_information( self, repository, **kwargs ): + def edit_repository_information( self, repository, **kwd ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) strings_displayed = [] strings_not_displayed = [] for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: - if input_elem_name in kwargs: - tc.fv( "1", input_elem_name, kwargs[ input_elem_name ] ) - strings_displayed.append( self.escape_html( kwargs[ input_elem_name ] ) ) + if input_elem_name in kwd: + tc.fv( "1", input_elem_name, kwd[ input_elem_name ] ) + strings_displayed.append( self.escape_html( kwd[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) strings_displayed = [] @@ -102,19 +185,84 @@ strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) - def escape_html( self, string ): + def escape_html( self, string, unescape=False ): html_entities = [ ('&', 'X' ), ( "'", ''' ), ( '"', '"' ) ] for character, replacement in html_entities: - string = string.replace( character, replacement ) + if unescape: + string = string.replace( replacement, character ) + else: + string = string.replace( character, replacement ) return string def get_latest_repository_metadata_for_repository( self, repository ): + # TODO: This will not work as expected. Fix it. return repository.metadata_revisions[ 0 ] - def get_readme( self, repository, strings_displayed=[], strings_not_displayed=[] ): - repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) - changeset_revision = repository_metadata.changeset_revision - repository_id = self.security.encode_id( repository.id ) - self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) ) - self.check_for_strings( strings_displayed, strings_not_displayed ) + def get_repository_base_path_from_browse_page( self, repository ): + '''Get the base path from the javascript dynatree parameters. This must be updated if the browse feature is altered.''' + self.visit_url( '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) ) + html = self.last_page() + found_file = None + basepath = None + search = re.search( 'data: { folder_path: "([^"]+)" },', html ) + if search is not None: + basepath = search.group( 1 ) + return basepath + def get_repository_file_list( self, repository, base_path, current_path=None ): + ''' + Recursively load repository folder contents and append them to a list. Similar to os.walk, + but via /repository/open_folder. + ''' + if current_path is None: + full_path = base_path + else: + full_path = os.path.join( base_path, current_path ) + # Get the current folder's contents. + url = '/repository/open_folder?folder_path=%s' % full_path.replace( '/', '%2f' ) + self.visit_url( url ) + file_list = from_json_string( self.last_page() ) + returned_file_list = [] + if current_path is not None: + returned_file_list.append( current_path ) + # Loop through the json dict returned by /repository/open_folder. + for file_dict in file_list: + if file_dict[ 'isFolder' ]: + # This is a folder. Get the contents of the folder and append it to the list, + # prefixed with the path relative to the repository root, if any. + if current_path is None: + returned_file_list.extend( self.get_repository_file_list( repository, base_path, file_dict[ 'title' ] ) ) + else: + sub_path = os.path.join( current_path, file_dict[ 'title' ] ) + returned_file_list.extend( self.get_repository_file_list( repository, base_path, sub_path ) ) + else: + # This is a regular file, prefix the filename with the current path and append it to the list. + if current_path is not None: + returned_file_list.append( os.path.join( current_path, file_dict[ 'title' ] ) ) + else: + returned_file_list.append( file_dict[ 'title' ] ) + return returned_file_list + def get_repository_metadata( self, repository ): + return [ metadata_revision for metadata_revision in repository.metadata_revisions ] + def get_repository_metadata_revisions( self, repository ): + return [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] + def get_repository_tip( self, repository ): + self.browse_repository( repository ) + html = self.last_page() + revision_regex = re.search( 'revision ([0-9a-f]+) $repository tip$', html ) + if revision_regex is not None: + return revision_regex.group( 1 ) + return None + def get_repository_filesystem_path( self, repository ): + repo_subdirectory = '%03d' % int( repository.id / 1000 ) + return os.path.join( 'database', 'community_files', repo_subdirectory, 'repo_%d' % repository.id ) + def get_tools_from_repository_metadata( self, repository, include_invalid=False ): + '''Get a list of valid and (optionally) invalid tool dicts from the repository metadata.''' + valid_tools = [] + invalid_tools = [] + for repository_metadata in repository.metadata_revisions: + if 'tools' in repository_metadata.metadata: + valid_tools.append( dict( tools=repository_metadata.metadata[ 'tools' ], changeset_revision=repository_metadata.changeset_revision ) ) + if include_invalid and 'invalid_tools' in repository_metadata.metadata: + invalid_tools.append( dict( tools=repository_metadata.metadata[ 'invalid_tools' ], changeset_revision=repository_metadata.changeset_revision ) ) + return valid_tools, invalid_tools def grant_write_access( self, repository, usernames=[], strings_displayed=[], strings_not_displayed=[] ): self.manage_repository( repository ) tc.fv( "3", "allow_push", '-Select one' ) @@ -122,10 +270,8 @@ tc.fv( "3", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def load_display_tool_page( self, repository, tool_xml_filename, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): + def load_display_tool_page( self, repository, tool_xml_path, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) - repo_subdirectory = '%03d' % int( repository.id / 1000 ) - tool_xml_path = '%2f'.join( [ 'database', 'community_files', repo_subdirectory, 'repo_%d' % repository.id, tool_xml_filename ] ) url = '/repository/display_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ ( repository_id, tool_xml_path, changeset_revision ) self.visit_url( url ) @@ -134,20 +280,37 @@ url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def set_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): + def revoke_write_access( self, repository, username ): + url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ + ( self.security.encode_id( repository.id ), username ) + self.visit_url( url ) + def set_repository_deprecated( self, repository, set_deprecated=True, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/deprecate?id=%s&mark_deprecated=%s' % ( self.security.encode_id( repository.id ), set_deprecated ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def set_repository_malicious( self, repository, set_malicious=True, strings_displayed=[], strings_not_displayed=[] ): self.manage_repository( repository ) - tc.fv( "malicious", "malicious", True ) + tc.fv( "malicious", "malicious", set_malicious ) tc.submit( "malicious_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def unset_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): - self.manage_repository( repository ) - tc.fv( "malicious", "malicious", False ) - tc.submit( "malicious_button" ) - self.check_for_strings( strings_displayed, strings_not_displayed ) - def upload( self, repository, filename, strings_displayed=[], strings_not_displayed=[], **kwargs ): + def tip_has_metadata( self, repository, tip_only=True ): + tip = self.get_repository_tip( repository ) + changeset_revisions = [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] + if tip_only: + return len( changeset_revisions ) == 1 and tip in changeset_revisions + return tip in changeset_revisions + def upload_file( self, + repository, + filename, + valid_tools_only=True, + strings_displayed=[], + strings_not_displayed=[], + **kwd ): self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) - for key in kwargs: - tc.fv( "1", key, kwargs[ key ] ) + if valid_tools_only: + strings_displayed.append( "has been successfully uploaded to the repository." ) + for key in kwd: + tc.fv( "1", key, kwd[ key ] ) tc.formfile( "1", "file_data", self.get_filename( filename ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 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 @@ -11,14 +11,14 @@ regular_email = 'test-1(a)bx.psu.edu' regular_username = 'user1' -repository_name = 'filter' -repository_description = "Galaxy's filter tool" -repository_long_description = "Long description of Galaxy's filter tool" +repository_name = 'filtering' +repository_description = "Galaxy's filtering tool" +repository_long_description = "Long description of Galaxy's filtering tool" class TestCreateRepository( ShedTwillTestCase ): def test_0000_initiate_users( self ): - """Create necessary users and login as an admin user.""" + """Create necessary user accounts and login as an admin user.""" self.login( email=regular_email, username=regular_username ) regular_user = get_user( regular_email ) assert regular_user is not None, 'Problem retrieving user with email %s from the database' % regular_email @@ -29,60 +29,117 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_categories( self ): - """Create a category""" + """Create categories""" self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) self.create_category( 'Text Analysis', 'Tools for analyzing text' ) def test_0010_create_repository( self ): - """Create a repository""" - strings_displayed = [ '<div class="toolFormTitle">Repository %s</div>' % "'%s'" % repository_name, \ + """Create the filtering repository""" + strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 'Repository %s has been created' % "'%s'" % repository_name ] - self.create_repository( repository_name, repository_description, \ - repository_long_description=repository_long_description, \ - categories=[ 'Text Manipulation' ], \ + self.create_repository( repository_name, + repository_description, + repository_long_description=repository_long_description, + categories=[ 'Text Manipulation' ], strings_displayed=strings_displayed ) def test_0015_edit_repository( self ): """Edit the repository name, description, and long description""" - repository = get_repository_by_name( repository_name, admin_username ) - new_name = "renamed_filter" - new_description = "Edited filter tool" + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + new_name = "renamed_filtering" + new_description = "Edited filtering tool" new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) def test_0020_change_repository_category( self ): - """Change the category of a repository""" - repository = get_repository_by_name( repository_name, admin_username ) + """Change the categories associated with the filtering repository""" + repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) -# def test_0025_grant_write_access( self ): -# '''Grant write access to another user''' -# repository = get_repository_by_name( repository_name, admin_username ) -# self.grant_write_access( repository, usernames=[ regular_username ] ) - def test_0030_upload_tarball( self ): + def test_0025_grant_write_access( self ): + '''Grant write access to another user''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.grant_write_access( repository, usernames=[ regular_username ] ) + self.revoke_write_access( repository, regular_username ) + def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" - repository = get_repository_by_name( repository_name, admin_username ) - self.upload( repository, - 'filtering_1.1.0.tar', - strings_displayed=[ "has been successfully uploaded to the repository." ], - commit_message="Uploaded filtering 1.1.0" ) + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) + def test_0035_verify_repository( self ): + '''Display basic repository pages''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + latest_changeset_revision = self.get_repository_tip( repository ) + self.check_for_valid_tools( repository, strings_displayed=[ 'Filter1' ] ) + self.check_metadata_in_repository_changelog( repository, metadata_count=1 ) + self.check_repository_tools( repository ) + self.check_repository_metadata( repository, tip_only=False ) + self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) + self.display_repository_clone_page( admin_username, + repository_name, + strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) + def test_0040_alter_repository_states( self ): + '''Test toggling the malicious and deprecated repository flags.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) + self.set_repository_malicious( repository, + set_malicious=False, + strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) + self.set_repository_deprecated( repository, + strings_displayed=[ 'has been marked as deprecated', 'Mark as not deprecated' ] ) + self.manage_repository( repository, + strings_displayed=[ 'This repository has been marked as deprecated' ], + strings_not_displayed=[ 'Upload files', 'Reset all repository metadata' ] ) + self.set_repository_deprecated( repository, + strings_displayed=[ 'has been marked as not deprecated', 'Mark as deprecated' ], + set_deprecated=False ) + def test_0045_display_repository_tip_file( self ): + '''Display the contents of a file in the repository tip revision''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.display_repository_file_contents( repository, filename='filtering.xml', strings_displayed=[ '1.1.0' ] ) + def test_0050_upload_filtering_txt_file( self ): + '''Upload filtering.txt file associated with tool version 1.1.0.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, + 'filtering.txt', + commit_message="Uploaded filtering.txt", + uncompress_file='No', + remove_repo_files_not_in_tar='No' ) + self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + def test_0055_upload_filtering_test_data( self ): + '''Upload filtering test data.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) + self.display_repository_file_contents( repository, filename='1.bed', filepath='test-data' ) + self.check_repository_metadata( repository, tip_only=True ) + def test_0060_upload_filtering_2_2_0( self ): + '''Upload filtering version 2.2.0''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, + 'filtering_2.2.0.tar', + commit_message="Uploaded filtering 2.2.0", + remove_repo_files_not_in_tar='No' ) + def test_0065_verify_filtering_repository( self ): + '''Verify the new tool versions and repository metadata.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.check_for_valid_tools( repository ) - latest_repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) - changeset_revision = latest_repository_metadata.changeset_revision - self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) - self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) - self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) - self.load_display_tool_page( repository, tool_xml_filename='filtering.xml', \ - changeset_revision=changeset_revision, \ - strings_displayed=[ 'Filter (version 1.1.0)', "c1=='chr1'" ], \ - strings_not_displayed=[] ) - tool = latest_repository_metadata.metadata[ 'tools' ][0] - metadata_strings_displayed = [ tool[ 'guid' ], tool[ 'version' ], tool[ 'id' ], tool[ 'name' ], tool[ 'description' ], changeset_revision ] - self.check_for_tool_metadata( repository, changeset_revision, 'Filter1', strings_displayed=metadata_strings_displayed ) - def test_0035_repository_browse_page( self ): - '''Visit the repository browse page''' - repository = get_repository_by_name( repository_name, admin_username ) - self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) - def test_0040_visit_clone_url_via_hgweb( self ): - '''Visit the repository clone URL via hgweb''' - repository = get_repository_by_name( repository_name, admin_username ) - latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) - self.display_repository_clone_page( admin_username, \ - repository_name, \ - strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision.changeset_revision ] ) + strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) + self.manage_repository( repository, strings_displayed=strings_displayed ) + self.check_metadata_in_repository_changelog( repository, metadata_count=2 ) + self.check_repository_tools( repository, include_invalid=False ) + self.check_repository_metadata( repository, tip_only=False ) + def test_0070_upload_readme_txt_file( self ): + '''Upload readme.txt file associated with tool version 2.2.0.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) + self.display_readme_file( repository, strings_displayed=[ 'This is a readme file.' ] ) + # Verify that there is a different readme file for each metadata revision. + metadata_revisions = self.get_repository_metadata_revisions( repository ) + strings_to_check = [ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] + for key, metadata_revision in enumerate( metadata_revisions ): + # Metadata revisions are in order newest to oldest at this point. + self.display_readme_file( repository, metadata_revision, strings_not_displayed=[ strings_to_check[ key ] ] ) + def test_0075_delete_readme_txt_file( self ): + '''Delete the readme.txt file.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) + self.check_metadata_in_repository_changelog( repository, metadata_count=2 ) + # Deleting a readme file for a specific revision should make the repository fall back + # to a previous revision's readme file, if one exists. + # TODO: All readme files should be displayed. + self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -31,6 +31,7 @@ import galaxy.webapps.community.app from galaxy.webapps.community.app import UniverseApplication from galaxy.webapps.community import buildapp +#from galaxy.webapps.community.util.hgweb_config import * import nose.core import nose.config @@ -164,6 +165,8 @@ running_functional_tests = True, hgweb_config_dir = new_file_path, **kwargs ) +# app.hgweb_config_manager = HgWebConfigManager() + log.info( "Embedded Universe application started" ) # ---- Run webserver ------------------------------------------------------ diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering.txt --- /dev/null +++ b/test/tool_shed/test_data/filtering.txt @@ -0,0 +1,1 @@ +Readme file for filtering 1.1.0 diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering_2.2.0.tar Binary file test/tool_shed/test_data/filtering_2.2.0.tar has changed diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering_test_data.tar Binary file test/tool_shed/test_data/filtering_test_data.tar has changed diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/readme.txt --- /dev/null +++ b/test/tool_shed/test_data/readme.txt @@ -0,0 +1,1 @@ +This is a readme file. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: scatterplot: add header discovery from first dataset line; fix animation; better hover info; fix column selection; pack scripts
by Bitbucket 28 Nov '12

28 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4eaa644dd478/ changeset: 4eaa644dd478 user: carlfeberhard date: 2012-11-28 16:45:01 summary: scatterplot: add header discovery from first dataset line; fix animation; better hover info; fix column selection; pack scripts affected #: 15 files diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -187,7 +187,6 @@ when the dataset is not yet indexed and hence using data would be slow because indexes need to be created. """ - # Dataset check. msg = self.check_dataset_state( trans, dataset ) if msg: diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -1322,4 +1322,3 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -793,9 +793,23 @@ hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) hda_dict = hda.get_api_value() hda_dict[ 'id' ] = dataset_id - if( hda_dict[ 'metadata_column_names' ] == None - and hasattr( hda.datatype, 'column_names' ) ): - hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names + + if( ( hda_dict[ 'metadata_column_names' ] == None ) + and ( hasattr( hda.datatype, 'column_names' ) ) ): + hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names + + # try to get the first line (assuming it's a header) + #TODO: doesn't belong here + try: + with open( hda.file_name ) as infile: + for index, line in enumerate( infile ): + if 'comment_lines' not in hda_dict: + hda_dict[ 'comment_lines' ] = [] + hda_dict[ 'comment_lines' ].append( line ) + if index >= 3: + break + except Exception, exc: + log.error( str( exc ) ) history_id = trans.security.encode_id( hda.history.id ) diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js @@ -67,8 +67,9 @@ //logger : console, className : 'scatterplot-control-form', - dataLoadDelay : 500, - dataLoadSize : 3001, + //NOTE: should include time needed to render + dataLoadDelay : 4000, + dataLoadSize : 5000, loadingIndicatorImage : 'loading_small_white_bg.gif', fetchMsg : 'Fetching data...', @@ -107,6 +108,16 @@ } this.log( '\t dataset:', this.dataset ); + // attempt to get possible headers from the data's first line + if( this.dataset.comment_lines && this.dataset.comment_lines.length ){ + //TODO:?? + var firstLine = this.dataset.comment_lines[0], + possibleHeaders = firstLine.split( '\t' ); + if( possibleHeaders.length === this.dataset.metadata_column_types.length ){ + this.possibleHeaders = possibleHeaders; + } + } + // passed from mako helper //TODO: integrate to galaxyPaths //TODO: ?? seems like data loader section would be better @@ -194,16 +205,24 @@ // controls for which columns are used to plot datapoints (and ids/additional info to attach if desired) var view = this, allColumns = [], - numericColumns = []; - + numericColumns = [], + usePossibleHeaders = ( this.possibleHeaders && this.$dataControl )? + ( this.$dataControl.find( '#first-line-header-checkbox' ).is( ':checked' ) ):( false ); + // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) _.each( this.dataset.metadata_column_types, function( type, index ){ // use a 1 based index in names/values within the form (will be dec. when parsed out) var oneBasedIndex = index + 1, - // label with the name if available (fall back on 'column <index>') + // default name is 'column <index>'... name = 'column ' + oneBasedIndex; + + // ...but label with the name if available... if( view.dataset.metadata_column_names ){ name = view.dataset.metadata_column_names[ index ]; + + // ...or, use the first line as headers if the user wants + } else if( usePossibleHeaders ){ + name = view.possibleHeaders[ index ]; } // cache all columns here @@ -218,11 +237,17 @@ // render the html var $dataControl = this.$el.find( '.tab-pane#data-control' ); - $dataControl.append( ScatterplotControlForm.templates.dataControl({ + $dataControl.html( ScatterplotControlForm.templates.dataControl({ allColumns : allColumns, - numericColumns : numericColumns + numericColumns : numericColumns, + possibleHeaders : ( this.possibleHeaders )?( this.possibleHeaders.join( ', ' ) ):( '' ), + usePossibleHeaders : usePossibleHeaders })); + if( !this.dataset.metadata_column_names && this.possibleHeaders ){ + $dataControl.find( '#first-line-header' ).show(); + } + // preset to column selectors if they were passed in the config in the query string $dataControl.find( '#X-select' ).val( this.chartConfig.xColumn ); $dataControl.find( '#Y-select' ).val( this.chartConfig.yColumn ); @@ -288,6 +313,7 @@ // ------------------------------------------------------------------------- EVENTS events : { 'change #include-id-checkbox' : 'toggleThirdColumnSelector', + 'change #first-line-header-checkbox' : 'rerenderDataControl', 'click #data-control #render-button' : 'renderChart', 'click #chart-control #render-button' : 'changeChartSettings' }, @@ -296,6 +322,10 @@ // show/hide the id selector on the data settings panel this.$el.find( 'select[name="ID"]' ).parent().toggle(); }, + + rerenderDataControl : function(){ + this.$dataControl = this._render_dataControl(); + }, showLoadingIndicator : function( message, callback ){ // display the loading indicator over the tab panels if hidden, update message (if passed) @@ -577,10 +607,8 @@ settings.yLabel = ( chartSettingsYLabel === 'Y' )? ( colSelections.Y.colName ):( chartSettingsYLabel ); - settings.animDuration = 10; - if( this.$chartControl.find( '#animDuration.checkbox-input' ).is( ':checked' ) ){ - settings.animDuration = 500; - } + settings.animDuration = ( this.$chartControl.find( '#animate-chart' ).is( ':checked' ) )? + ( this.chart.defaults.animDuration ):( 0 ); this.log( '\t chartSettings:', settings ); return settings; diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/packed/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js @@ -1,1 +1,1 @@ -var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],d=[];_.each(this.dataset.metadata_column_types,function(h,f){var g=f+1,e="column "+g;if(b.dataset.metadata_column_names){e=b.dataset.metadata_column_names[f]}a.push({index:g,name:e});if(h==="int"||h==="float"){d.push({index:g,name:e})}});var c=this.$el.find(".tab-pane#data-control");c.append(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:d}));c.find("#X-select").val(this.chartConfig.xColumn);c.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){c.find("#include-id-checkbox").attr("checked",true).trigger("change");c.find("#ID-select").val(this.chartConfig.idColumn)}return c},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=10;if(this.$chartControl.find("#animDuration.checkbox-input").is(":checked")){c.animDuration=500}this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file +var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/packed/templates/compiled/template-visualization-chartControl.js --- a/static/scripts/packed/templates/compiled/template-visualization-chartControl.js +++ b/static/scripts/packed/templates/compiled/template-visualization-chartControl.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartControl"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(p,o){return' checked="true"'}i+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n\n <div id="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">';h=e.datapointSize;if(h){c=h.call(m,{hash:{}})}else{c=m.datapointSize;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id="animDuration" class="form-input checkbox-input">\n <label for="animated">Animate graph transitions?: </label>\n <input type="checkbox" id="animated"\n class="checkbox control"';c=m.animDuration;c=e["if"].call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+=' />\n <p class="form-help help-text-small">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id="width" class="form-input numeric-slider-input">\n <label for="width">Graph width: </label>\n <div class="slider-output">';h=e.width;if(h){c=h.call(m,{hash:{}})}else{c=m.width;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="height" class="form-input numeric-slider-input">\n <label for="height">Graph height: </label>\n <div class="slider-output">';h=e.height;if(h){c=h.call(m,{hash:{}})}else{c=m.height;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="';h=e.xLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.xLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <div id="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="';h=e.yLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.yLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />';return i})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartControl"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(p,o){return' checked="true"'}i+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n\n <div id="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">';h=e.datapointSize;if(h){c=h.call(m,{hash:{}})}else{c=m.datapointSize;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id="animDuration" class="form-input checkbox-input">\n <label for="animate-chart">Animate chart transitions?: </label>\n <input type="checkbox" id="animate-chart"\n class="checkbox control"';c=m.animDuration;c=e["if"].call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+=' />\n <p class="form-help help-text-small">\n Uncheck this to disable the animations used on the chart\n </p>\n </div>\n\n <div id="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">';h=e.width;if(h){c=h.call(m,{hash:{}})}else{c=m.width;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n </div>\n\n <div id="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">';h=e.height;if(h){c=h.call(m,{hash:{}})}else{c=m.height;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n </div>\n\n <div id="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="';h=e.xLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.xLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <div id="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="';h=e.yLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.yLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />';return i})})(); \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/packed/templates/compiled/template-visualization-dataControl.js --- a/static/scripts/packed/templates/compiled/template-visualization-dataControl.js +++ b/static/scripts/packed/templates/compiled/template-visualization-dataControl.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-dataControl"]=b(function(g,m,f,l,k){f=f||g.helpers;var i="",d,h="function",j=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}function c(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}function n(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}i+="<p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n ";i+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=m.numericColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(1,e,k)});if(d||d===0){i+=d}i+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=m.numericColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(3,c,k)});if(d||d===0){i+=d}i+="\n </select>\n </div>\n\n ";i+='\n <div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="ID" id="ID-select">\n ';d=m.allColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(5,n,k)});if(d||d===0){i+=d}i+='\n </select>\n </div>\n\n <input id="render-button" type="button" value="Draw" />\n <div class="clear"></div>';return i})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-dataControl"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,q=this;function e(v,u){var s="",t,r;s+='\n <option value="';r=f.index;if(r){t=r.call(v,{hash:{}})}else{t=v.index;t=typeof t===h?t():t}s+=k(t)+'">';r=f.name;if(r){t=r.call(v,{hash:{}})}else{t=v.name;t=typeof t===h?t():t}s+=k(t)+"</option>\n ";return s}function c(v,u){var s="",t,r;s+='\n <option value="';r=f.index;if(r){t=r.call(v,{hash:{}})}else{t=v.index;t=typeof t===h?t():t}s+=k(t)+'">';r=f.name;if(r){t=r.call(v,{hash:{}})}else{t=v.name;t=typeof t===h?t():t}s+=k(t)+"</option>\n ";return s}function p(v,u){var s="",t,r;s+='\n <option value="';r=f.index;if(r){t=r.call(v,{hash:{}})}else{t=v.index;t=typeof t===h?t():t}s+=k(t)+'">';r=f.name;if(r){t=r.call(v,{hash:{}})}else{t=v.name;t=typeof t===h?t():t}s+=k(t)+"</option>\n ";return s}function o(s,r){return'checked="true"'}j+="<p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n ";j+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:q.noop,fn:q.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:q.noop,fn:q.program(3,c,l)});if(d||d===0){j+=d}j+="\n </select>\n </div>\n\n ";j+='\n <div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="ID" id="ID-select">\n ';d=n.allColumns;d=f.each.call(n,d,{hash:{},inverse:q.noop,fn:q.program(5,p,l)});if(d||d===0){j+=d}j+="\n </select>\n </div>\n\n ";j+='\n <div id="first-line-header" style="display: none;">\n <p>Possible headers: ';i=f.possibleHeaders;if(i){d=i.call(n,{hash:{}})}else{d=n.possibleHeaders;d=typeof d===h?d():d}j+=k(d)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ';d=n.usePossibleHeaders;d=f["if"].call(n,d,{hash:{},inverse:q.noop,fn:q.program(7,o,l)});if(d||d===0){j+=d}j+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />\n <div class="clear"></div>';return j})})(); \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/packed/utils/LazyDataLoader.js --- a/static/scripts/packed/utils/LazyDataLoader.js +++ b/static/scripts/packed/utils/LazyDataLoader.js @@ -1,1 +1,1 @@ -function LazyDataLoader(c){var a=this,d="loaded.new",b="complete";ERROR_EVENT="error";jQuery.extend(a,LoggableMixin);jQuery.extend(a,{total:undefined,url:undefined,currentIntervalId:undefined,data:[],delay:500,start:0,size:1000,initialize:function(e){jQuery.extend(a,e);if(e.hasOwnProperty("initialize")){e.initialize.call(a,e)}this.log(this+" initialized:",a)},buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})},ajaxErrorFn:function(g,e,f){},load:function(h){this.log(this+".load");if(!a.url){throw (a+" requires a url")}if(this.total===null){this.log("\t total is null (will load all)")}else{this.log("\t total:",this.total)}var g=a.size;if((a.total!==null)&&(a.total<a.size)){g=a.total}a.log(a+"\t beginning recursion");f(a.start,g);function f(k,j){a.log(a+".loadHelper, start:",k,"size:",j);var i=a.buildUrl(k,j);a.log("\t url:",i);jQuery.ajax({url:a.buildUrl(k,j),dataType:"json",error:function(n,l,m){a.log("\t ajax error, status:",l,"error:",m);if(a.currentIntervalId){clearInterval(a.currentIntervalId)}$(a).trigger(ERROR_EVENT,[l,m]);a.ajaxErrorFn(n,l,m)},success:function(l){a.log("\t ajax success, response:",l,"next:",m,"remainder:",n);if(l!==null){a.data.push(l);$(a).trigger(d,[l,k,j]);var m=k+j,n=a.size;if(a.total!==null){n=Math.min(a.total-m,a.size)}a.log("\t next recursion, start:",m,"size:",n);if(a.total===null||n>0){a.currentIntervalId=setTimeout(function(){f(m,n)},a.delay);a.log("\t currentIntervalId:",a.currentIntervalId)}else{e()}}else{e()}}})}function e(){a.log(a+".loadHelper, has finished:",a.data);$(a).trigger(b,[a.data,a.total]);if(h){h(a.data)}}},toString:function(){return"LazyDataLoader"}});a.initialize(c);return a}; \ No newline at end of file +function LazyDataLoader(c){var a=this,d="loaded.new",b="complete";ERROR_EVENT="error";jQuery.extend(a,LoggableMixin);jQuery.extend(a,{total:undefined,url:undefined,currentIntervalId:undefined,data:[],delay:4000,start:0,size:4000,initialize:function(e){jQuery.extend(a,e);if(e.hasOwnProperty("initialize")){e.initialize.call(a,e)}this.log(this+" initialized:",a)},buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})},ajaxErrorFn:function(g,e,f){},load:function(h){this.log(this+".load");if(!a.url){throw (a+" requires a url")}if(this.total===null){this.log("\t total is null (will load all)")}else{this.log("\t total:",this.total)}var g=a.size;if((a.total!==null)&&(a.total<a.size)){g=a.total}a.log(a+"\t beginning recursion");f(a.start,g);function f(k,j){a.log(a+".loadHelper, start:",k,"size:",j);var i=a.buildUrl(k,j);a.log("\t url:",i);jQuery.ajax({url:a.buildUrl(k,j),dataType:"json",error:function(n,l,m){a.log("\t ajax error, status:",l,"error:",m);if(a.currentIntervalId){clearInterval(a.currentIntervalId)}$(a).trigger(ERROR_EVENT,[l,m]);a.ajaxErrorFn(n,l,m)},success:function(l){a.log("\t ajax success, response:",l,"next:",m,"remainder:",n);if(l!==null){a.data.push(l);$(a).trigger(d,[l,k,j]);var m=k+j,n=a.size;if(a.total!==null){n=Math.min(a.total-m,a.size)}a.log("\t next recursion, start:",m,"size:",n);if(a.total===null||n>0){a.currentIntervalId=setTimeout(function(){f(m,n)},a.delay);a.log("\t currentIntervalId:",a.currentIntervalId)}else{e()}}else{e()}}})}function e(){a.log(a+".loadHelper, has finished:",a.data);$(a).trigger(b,[a.data,a.total]);if(h){h(a.data)}}},toString:function(){return"LazyDataLoader"}});a.initialize(c);return a}; \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -function TwoVarScatterplot(d){var b=10,f=7,e=10,c=8,a=5;this.log=function(){if(this.debugging&&console&&console.debug){var g=Array.prototype.slice.call(arguments);g.unshift(this.toString());console.debug.apply(console,g)}};this.log("new TwoVarScatterplot:",d);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:400,height:400,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,d);this.log("intial config:",this.config);this.updateConfig=function(g,h){_.extend(this.config,g);this.log(this+".updateConfig:",this.config)};this.toString=function(){return this.config.id};this.translateStr=function(g,h){return"translate("+g+","+h+")"};this.rotateStr=function(h,g,i){return"rotate("+h+","+g+","+i+")"};this.adjustChartDimensions=function(j,h,g,i){j=j||0;h=h||0;g=g||0;i=i||0;this.svg.attr("width",this.config.width+(this.config.marginRight+h)+(this.config.marginLeft+i)).attr("height",this.config.height+(this.config.marginTop+j)+(this.config.marginBottom+g)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+i,this.config.marginTop+j))};this.preprocessData=function(i,h,g){return(i.length>this.config.maxDataPoints)?(i.slice(0,this.config.maxDataPoints)):(i)};this.findMinMaxes=function(g,i,h){this.xMin=this.config.xMin||(h)?(h[0].min):(d3.min(g));this.xMax=this.config.xMax||(h)?(h[0].max):(d3.max(g));this.yMin=this.config.yMin||(h)?(h[1].min):(d3.min(i));this.yMax=this.config.yMax||(h)?(h[1].max):(d3.max(i))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);var g=d3.max(_.map([this.xMin,this.xMax],function(h){return(String(h)).length}));if(g>=a){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.log("this.config.xLabel:",this.config.xLabel);this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var g=this.yAxis.selectAll("text").filter(function(k,j){return j!==0});this.log("yTickLabels:",g);this.yLongestLabel=d3.max(g[0].map(function(k,j){return(d3.select(k).text()).length}))||0;var h=b+(this.yLongestLabel*f)+c+e;this.config.yAxisLabelBumpX=-(h-e);if(this.config.marginLeft<h){var i=(h)-this.config.marginLeft;i=(i<0)?(0):(i);this.adjustChartDimensions(0,0,0,i)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(g){};this.glyphFinalState=function(g){};this.glyphExitState=function(g){};this.renderDatapoints=function(g,j,h){this.log(this+".renderDatapoints",arguments);var i=0;this.datapoints=this.addDatapoints(g,j,h,".glyph");this.datapoints.exit().each(function(){i+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(i," glyphs removed")};this.addDatapoints=function(k,i,g,j){this.log(this+".addDatapoints",arguments);var n=this,m=0,o=function(q,p){return n.xScale(k[p])},h=function(q,p){return n.yScale(i[p])};var l=this.content.selectAll(j);this.log("existing datapoints:",l);l=l.data(k);m=0;l.enter().append("svg:circle").each(function(){m+=1}).classed("glyph",true).attr("cx",o).attr("cy",h).attr("r",0);this.log(m," new glyphs created");m=0;l.transition().duration(this.config.animDuration).each(function(){m+=1}).attr("cx",o).attr("cy",h).attr("r",n.config.datapointSize);this.log(m," existing glyphs transitioned");if(g){l.attr("data",function(q,p){return(g[p])})}l.attr("svg:title",function(q,p){return((g)?(g[p]+": "):(""))+k[p]+", "+i[p]});l.on("mouseover",function(r,p){var q=d3.select(this);q.style("fill","red").style("fill-opacity",1);n.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",q.attr("cx")).attr("y1",q.attr("cy")).attr("x2",0).attr("y2",q.attr("cy")).classed("hoverline",true);n.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",q.attr("cx")).attr("y1",q.attr("cy")).attr("x2",q.attr("cx")).attr("y2",n.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return l};this.render=function(i,j){this.log(this+".render",arguments);this.log("\t config:",this.config);var g=i[0],k=i[1],h=(i.length>2)?(i[2]):(undefined);g=this.preprocessData(g);k=this.preprocessData(k);this.log("xCol len",g.length,"yCol len",k.length);this.findMinMaxes(g,k,j);this.setUpScales();if(!this.svg){this.svg=d3.select("svg").attr("class","chart")}if(!this.content){this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id)}this.adjustChartDimensions();if(!this.xAxis){this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis")}if(!this.xAxisLabel){this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label")}if(!this.yAxis){this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis")}if(!this.yAxisLabel){this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label")}this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(g,k,h)}}; \ No newline at end of file +function TwoVarScatterplot(d){var b=10,f=7,e=10,c=8,a=5;this.log=function(){if(this.debugging&&console&&console.debug){var g=Array.prototype.slice.call(arguments);g.unshift(this.toString());console.debug.apply(console,g)}};this.log("new TwoVarScatterplot:",d);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-40,width:400,height:400,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,d);this.log("intial config:",this.config);this.updateConfig=function(g,h){_.extend(this.config,g);this.log(this+".updateConfig:",this.config)};this.toString=function(){return this.config.id};this.translateStr=function(g,h){return"translate("+g+","+h+")"};this.rotateStr=function(h,g,i){return"rotate("+h+","+g+","+i+")"};this.adjustChartDimensions=function(j,h,g,i){j=j||0;h=h||0;g=g||0;i=i||0;this.svg.attr("width",this.config.width+(this.config.marginRight+h)+(this.config.marginLeft+i)).attr("height",this.config.height+(this.config.marginTop+j)+(this.config.marginBottom+g)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+i,this.config.marginTop+j))};this.preprocessData=function(i,h,g){return(i.length>this.config.maxDataPoints)?(i.slice(0,this.config.maxDataPoints)):(i)};this.findMinMaxes=function(g,i,h){this.xMin=this.config.xMin||(h)?(h[0].min):(d3.min(g));this.xMax=this.config.xMax||(h)?(h[0].max):(d3.max(g));this.yMin=this.config.yMin||(h)?(h[1].min):(d3.min(i));this.yMax=this.config.yMax||(h)?(h[1].max):(d3.max(i))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);var g=d3.max(_.map([this.xMin,this.xMax],function(h){return(String(h)).length}));if(g>=a){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.log("this.config.xLabel:",this.config.xLabel);this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var g=this.yAxis.selectAll("text").filter(function(k,j){return j!==0});this.log("yTickLabels:",g);this.yLongestLabel=d3.max(g[0].map(function(k,j){return(d3.select(k).text()).length}))||0;var h=b+(this.yLongestLabel*f)+c+e;this.config.yAxisLabelBumpX=-(h-e);if(this.config.marginLeft<h){var i=(h)-this.config.marginLeft;i=(i<0)?(0):(i);this.adjustChartDimensions(0,0,0,i)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.renderDatapoints=function(g,n,j){this.log(this+".renderDatapoints",arguments);var k=0,m=this,i=function(p,o){return m.xScale(g[o])},h=function(p,o){return m.yScale(n[o])};var l=this.content.selectAll(".glyph").data(g);k=0;l.enter().append("svg:circle").each(function(){k+=1}).classed("glyph",true).attr("cx",0).attr("cy",this.config.height).attr("r",0);this.log(k," new glyphs created");k=0;l.transition().duration(this.config.animDuration).each(function(){k+=1}).attr("cx",i).attr("cy",h).attr("r",m.config.datapointSize);this.log(k," existing glyphs transitioned");l.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed");this._addDatapointEventhandlers(l,g,n,j)};this._addDatapointEventhandlers=function(j,g,k,h){var i=this;j.on("mouseover",function(o,l){var n=d3.select(this);n.style("fill","red").style("fill-opacity",1);i.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",n.attr("cx")-i.config.datapointSize).attr("y1",n.attr("cy")).attr("x2",0).attr("y2",n.attr("cy")).classed("hoverline",true);if(n.attr("cy")<i.config.height){i.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",n.attr("cx")).attr("y1",n.attr("cy")+i.config.datapointSize).attr("x2",n.attr("cx")).attr("y2",i.config.height).classed("hoverline",true)}var m=$(this).offset();i.datapointInfoBox=i.infoBox(m.top,m.left,i.infoHtml(g[l],k[l],(h)?(h[l]):(undefined)));$("body").append(i.datapointInfoBox)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);i.content.selectAll(".hoverline").remove();if(i.datapointInfoBox){i.datapointInfoBox.remove()}})},this.render=function(i,j){this.log(this+".render",arguments);this.log("\t config:",this.config);var g=i[0],k=i[1],h=(i.length>2)?(i[2]):(undefined);g=this.preprocessData(g);k=this.preprocessData(k);this.log("xCol len",g.length,"yCol len",k.length);this.findMinMaxes(g,k,j);this.setUpScales();if(!this.svg){this.svg=d3.select("svg").attr("class","chart")}if(!this.content){this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id)}this.adjustChartDimensions();if(!this.xAxis){this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis")}if(!this.xAxisLabel){this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label")}if(!this.yAxis){this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis")}if(!this.yAxisLabel){this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label")}this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(g,k,h)};this.infoHtml=function(g,j,i){var h=$("<div/>");if(i){$("<div/>").text(i).css("font-weight","bold").appendTo(h)}$("<div/>").text(g).appendTo(h);$("<div/>").text(j).appendTo(h);return h.html()};this.infoBox=function(l,k,i,h,g){h=h||0;g=g||20;var j=$("<div />").addClass("chart-info-box").css({position:"absolute",top:l+h,left:k+g});j.html(i);return j}}; \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/templates/compiled/template-visualization-chartControl.js --- a/static/scripts/templates/compiled/template-visualization-chartControl.js +++ b/static/scripts/templates/compiled/template-visualization-chartControl.js @@ -13,19 +13,19 @@ foundHelper = helpers.datapointSize; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"animDuration\" class=\"form-input checkbox-input\">\n <label for=\"animated\">Animate graph transitions?: </label>\n <input type=\"checkbox\" id=\"animated\"\n class=\"checkbox control\""; + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"animDuration\" class=\"form-input checkbox-input\">\n <label for=\"animate-chart\">Animate chart transitions?: </label>\n <input type=\"checkbox\" id=\"animate-chart\"\n class=\"checkbox control\""; stack1 = depth0.animDuration; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += " />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Graph width: </label>\n <div class=\"slider-output\">"; + buffer += " />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the chart\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Chart width: </label>\n <div class=\"slider-output\">"; foundHelper = helpers.width; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Graph height: </label>\n <div class=\"slider-output\">"; + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including chart margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Chart height: </label>\n <div class=\"slider-output\">"; foundHelper = helpers.height; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including chart margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; foundHelper = helpers.xLabel; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.xLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/templates/compiled/template-visualization-dataControl.js --- a/static/scripts/templates/compiled/template-visualization-dataControl.js +++ b/static/scripts/templates/compiled/template-visualization-dataControl.js @@ -2,7 +2,7 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-visualization-dataControl'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; function program1(depth0,data) { @@ -46,6 +46,11 @@ buffer += escapeExpression(stack1) + "</option>\n "; return buffer;} +function program7(depth0,data) { + + + return "checked=\"true\"";} + buffer += "<p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n "; buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; stack1 = depth0.numericColumns; @@ -60,6 +65,15 @@ stack1 = depth0.allColumns; stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>"; + buffer += "\n </select>\n </div>\n\n "; + buffer += "\n <div id=\"first-line-header\" style=\"display: none;\">\n <p>Possible headers: "; + foundHelper = helpers.possibleHeaders; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.possibleHeaders; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n </p>\n <label for=\"first-line-header-checkbox\">Use the above as column headers?</label>\n <input type=\"checkbox\" name=\"include-id\" id=\"first-line-header-checkbox\"\n "; + stack1 = depth0.usePossibleHeaders; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "/>\n <p class=\"help-text-small\">\n It looks like Galaxy couldn't get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>"; return buffer;}); })(); \ No newline at end of file diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -90,6 +90,19 @@ </select></div> + {{! if we're using generic column selection names ('column 1') - allow the user to use the first line }} + <div id="first-line-header" style="display: none;"> + <p>Possible headers: {{ possibleHeaders }} + </p> + <label for="first-line-header-checkbox">Use the above as column headers?</label> + <input type="checkbox" name="include-id" id="first-line-header-checkbox" + {{#if usePossibleHeaders }}checked="true"{{/if}}/> + <p class="help-text-small"> + It looks like Galaxy couldn't get proper column headers for this data. + Would you like to use the column headers above as column names to select columns? + </p> + </div> + <input id="render-button" type="button" value="Draw" /><div class="clear"></div></script> @@ -112,29 +125,29 @@ </div><div id="animDuration" class="form-input checkbox-input"> - <label for="animated">Animate graph transitions?: </label> - <input type="checkbox" id="animated" + <label for="animate-chart">Animate chart transitions?: </label> + <input type="checkbox" id="animate-chart" class="checkbox control"{{#if animDuration}} checked="true"{{/if}} /><p class="form-help help-text-small"> - Uncheck this to disable the animations used on the graph + Uncheck this to disable the animations used on the chart </p></div><div id="width" class="form-input numeric-slider-input"> - <label for="width">Graph width: </label> + <label for="width">Chart width: </label><div class="slider-output">{{width}}</div><div class="slider"></div><p class="form-help help-text-small"> - (not including graph margins and axes) + (not including chart margins and axes) </p></div><div id="height" class="form-input numeric-slider-input"> - <label for="height">Graph height: </label> + <label for="height">Chart height: </label><div class="slider-output">{{height}}</div><div class="slider"></div><p class="form-help help-text-small"> - (not including graph margins and axes) + (not including chart margins and axes) </p></div> diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/utils/LazyDataLoader.js --- a/static/scripts/utils/LazyDataLoader.js +++ b/static/scripts/utils/LazyDataLoader.js @@ -81,11 +81,11 @@ // it's the responsibility of the code using this to combine them properly data : [], // ms btwn recursive loads - delay : 500, + delay : 4000, // starting line, element, whatever start : 0, // size to fetch per load - size : 1000, + size : 4000, // loader init func: extends loader with config and calls config.init if there //@param {object} config : object containing variables to override (or additional) diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -90,7 +90,7 @@ xNumTicks : 10, yNumTicks : 10, xAxisLabelBumpY : 40, - yAxisLabelBumpX : -35, + yAxisLabelBumpX : -40, width : 400, height : 400, //TODO: anyway to make this a sub-obj? @@ -304,75 +304,37 @@ }; // ........................................................ data points - //TODO: these to config ...somehow - //TODO: use these in renderDatapoints ...somehow - this.glyphEnterState = function( d3Elem ){ - - }; - this.glyphFinalState = function( d3Elem ){ - - }; - this.glyphExitState = function( d3Elem ){ - - }; - - // initial render or complete re-render (REPLACE datapoints) this.renderDatapoints = function( xCol, yCol, ids ){ this.log( this + '.renderDatapoints', arguments ); - var count = 0; - - this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); - - // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM - this.datapoints.exit() - .each( function(){ count += 1; } ) - .transition().duration( this.config.animDuration ) - .attr( "cy", this.config.height ) - .attr( "r", 0 ) - .remove(); - this.log( count, ' glyphs removed' ); - - //this.log( this.datapoints.length, ' glyphs in the graph' ); - }; - - // adding points to existing - this.addDatapoints = function( newXCol, newYCol, ids, selectorForExisting ){ - this.log( this + '.addDatapoints', arguments ); - // ADD datapoints to plot that's already rendered - // if selectorForExisting === undefined (as in not passed), addDatapoints won't update existing - // pass in the class ( '.glyph' ) to update exising datapoints - var plot = this, - count = 0, + var count = 0, + plot = this, xPosFn = function( d, i ){ //if( d ){ this.log( 'x.data:', newXCol[ i ], 'plotted:', plot.xScale( newXCol[ i ] ) ); } - return plot.xScale( newXCol[ i ] ); + return plot.xScale( xCol[ i ] ); }, yPosFn = function( d, i ){ //if( d ){ this.log( 'y.data:', newYCol[ i ], 'plotted:', plot.yScale( newYCol[ i ] ) ); } - return plot.yScale( newYCol[ i ] ); + return plot.yScale( yCol[ i ] ); }; - - // select all existing glyphs and compare to incoming data - // enter() will yield those glyphs that need to be added - var newDatapoints = this.content.selectAll( selectorForExisting ); - this.log( 'existing datapoints:', newDatapoints ); - newDatapoints = newDatapoints.data( newXCol ); - - // enter - new data to be added as glyphs: give them a 'entry' position and style + + //this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); + var datapoints = this.content.selectAll( '.glyph' ).data( xCol ); + + // enter - NEW data to be added as glyphs: give them a 'entry' position and style count = 0; - newDatapoints.enter() + datapoints.enter() .append( 'svg:circle' ) .each( function(){ count += 1; } ) .classed( "glyph", true ) - .attr( "cx", xPosFn ) - .attr( "cy", yPosFn ) + .attr( "cx", 0 ) + .attr( "cy", this.config.height ) // start all bubbles small... .attr( "r", 0 ); this.log( count, ' new glyphs created' ); - // for all existing glyphs and those that need to be added: transition anim to final state + // for all EXISTING glyphs and those that need to be added: transition anim to final state count = 0; - newDatapoints + datapoints // ...animate to final position .transition().duration( this.config.animDuration ) .each( function(){ count += 1; } ) @@ -381,18 +343,22 @@ .attr( "r", plot.config.datapointSize ); this.log( count, ' existing glyphs transitioned' ); - // attach ids - if( ids ){ - newDatapoints.attr( 'data', function( d, i ){ return ( ids[ i ] ); } ); - } + // events + // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM + datapoints.exit() + .each( function(){ count += 1; } ) + .transition().duration( this.config.animDuration ) + .attr( "cy", this.config.height ) + .attr( "r", 0 ) + .remove(); + this.log( count, ' glyphs removed' ); - // titles - newDatapoints.attr( 'svg:title', function( d, i ){ - return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; - }); - - // events - newDatapoints + this._addDatapointEventhandlers( datapoints, xCol, yCol, ids ); + }; + + this._addDatapointEventhandlers = function( datapoints, xCol, yCol, ids ){ + var plot = this; + datapoints //TODO: remove magic numbers .on( 'mouseover', function( d, i ){ var datapoint = d3.select( this ); @@ -404,36 +370,42 @@ plot.content.append( 'line' ) .attr( 'stroke', 'red' ) .attr( 'stroke-width', 1 ) - .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) - .attr( 'x2', 0 ).attr( 'y2', datapoint.attr( 'cy' ) ) - .classed( 'hoverline', true ); - plot.content.append( 'line' ) - .attr( 'stroke', 'red' ) - .attr( 'stroke-width', 1 ) - .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) - .attr( 'x2', datapoint.attr( 'cx' ) ).attr( 'y2', plot.config.height ) + // start not at center, but at the edge of the circle - to prevent mouseover thrashing + .attr( 'x1', datapoint.attr( 'cx' ) - plot.config.datapointSize ) + .attr( 'y1', datapoint.attr( 'cy' ) ) + .attr( 'x2', 0 ) + .attr( 'y2', datapoint.attr( 'cy' ) ) .classed( 'hoverline', true ); - //var datapointWindowPos = $( this ).position(); - //var datapointWindowPos = $( this ).offset(); - //window.dot = this; - ////this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left + datapoint.attr( 'r' ), - //this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left, - // newXCol[ i ], newYCol[ i ], ( ids )?( ids[ i ] ):( undefined ) ); - //$( 'body' ).append( this.popup ); + // if the vertical hoverline + if( datapoint.attr( 'cy' ) < plot.config.height ){ + plot.content.append( 'line' ) + .attr( 'stroke', 'red' ) + .attr( 'stroke-width', 1 ) + .attr( 'x1', datapoint.attr( 'cx' ) ) + .attr( 'y1', datapoint.attr( 'cy' ) + plot.config.datapointSize ) + .attr( 'x2', datapoint.attr( 'cx' ) ) + .attr( 'y2', plot.config.height ) + .classed( 'hoverline', true ); + } + + var datapointWindowPos = $( this ).offset(); + plot.datapointInfoBox = plot.infoBox( + datapointWindowPos.top, datapointWindowPos.left, + plot.infoHtml( xCol[ i ], yCol[ i ], ( ids )?( ids[ i ] ):( undefined ) ) + ); + $( 'body' ).append( plot.datapointInfoBox ); }) .on( 'mouseout', function(){ d3.select( this ) .style( 'fill', 'black' ) .style( 'fill-opacity', 0.2 ); - d3.selectAll( '.hoverline' ).remove(); - //if( this.popup ){ - // this.popup.remove(); - //} + plot.content.selectAll( '.hoverline' ).remove(); + if( plot.datapointInfoBox ){ + plot.datapointInfoBox.remove(); + } }); - - return newDatapoints; - }; + }, this.render = function( columnData, meta ){ this.log( this + '.render', arguments ); @@ -457,7 +429,7 @@ //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); - // build the svg dom infrastructure + // find (or build if it doesn't exist) the svg dom infrastructure if( !this.svg ){ this.svg = d3.select( 'svg' ).attr( "class", "chart" ); } if( !this.content ){ this.content = this.svg.append( "svg:g" ).attr( "class", "content" ).attr( 'id', this.config.id ); @@ -485,6 +457,32 @@ this.renderGrid(); this.renderDatapoints( xCol, yCol, ids ); }; + + this.infoHtml = function( x, y, id ){ + var retDiv = $( '<div/>' ); + if( id ){ + $( '<div/>' ).text( id ).css( 'font-weight', 'bold' ).appendTo( retDiv ); + } + $( '<div/>' ).text( x ).appendTo( retDiv ); + $( '<div/>' ).text( y ).appendTo( retDiv ); + return retDiv.html(); + }; + + //TODO: html for now + this.infoBox = function( top, left, html, adjTop, adjLeft ){ + adjTop = adjTop || 0; + adjLeft = adjLeft || 20; + var infoBox = $( '<div />' ) + .addClass( 'chart-info-box' ) + .css({ + 'position' : 'absolute', + 'top' : top + adjTop, + 'left' : left + adjLeft + }); + infoBox.html( html ); + return infoBox; + }; + } //============================================================================== diff -r 3c4696f6af0d9c6c7885568c1fee02df53849322 -r 4eaa644dd47877c40ee7090d56379998d7aecafa templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -26,6 +26,7 @@ padding : 8px; background-color: #ebd9b2; margin-bottom: 16px; + overflow: auto; } #chart-header .subtitle { @@ -182,12 +183,11 @@ } /* -------------------------------------------- info box */ -.zero-dimensions { - width: 0; - height: 0; - border-top: 8px solid transparent; - border-bottom: 8px solid transparent; - border-right: 8px solid grey; +.chart-info-box { + border-radius: 4px; + padding: 4px; + background-color: white; + border: 1px solid black; } </style> @@ -255,63 +255,3 @@ </div><div id="scatterplot" class="scatterplot-control-form"></div></%def> - - -<script type="text/javascript"> -function make_abs_box( top, left, x, y, id ){ - var ARROW_SIZE = 8, - ARROW_COLOR = 'grey', - DIST_TO_POINT = 4, - halfArrowSize = ARROW_SIZE / 2; - - var boxContainer = $( '<div />' ) - .attr( 'id', 'abs-box-container' ) - // top left arrow - .css({ - 'position' : 'absolute', - 'top' : top - halfArrowSize, - 'left' : left + ARROW_SIZE + DIST_TO_POINT, - 'background-color': 'transparent', - }); - window.boxContainer = boxContainer; - - var arrowLeft = $( '<div />' ) - .attr( 'id', 'abs-box-arrow' ) - .addClass( 'zero-dimensions' ) - .css({ - 'border-top' : ARROW_SIZE + 'px solid transparent', - 'border-bottom' : ARROW_SIZE + 'px solid transparent', - 'border-right' : ARROW_SIZE + 'px solid ' + ARROW_COLOR, - }); - boxContainer.append( arrowLeft ); - window.arrow = arrowLeft; - - console.debug( 'arrow height:', arrowLeft.height() ); - var boxInfo = $( '<div />' ) - .attr( 'id', 'abs-box' ) - .css({ - 'position' : 'relative', - //TODO: 4 here is the border-radius - 'top' : -( 2 * ARROW_SIZE + 6 ), - 'left' : ARROW_SIZE, - 'border' : '2px solid grey', - 'border-radius' : '4px', - 'padding' : '4px', - 'background-color': 'white', - 'box-shadow' : '4px 4px 4px black' - }); - - // remove - if( id ){ - $( '<div />' ).addClass( 'abs-box-id' ).css( 'font-weight', 'bold' ).text( id ).appendTo( boxInfo ); - } - $( '<div />' ).addClass( 'abs-box-x' ).text( x ).appendTo( boxInfo ); - $( '<div />' ).addClass( 'abs-box-y' ).text( y ).appendTo( boxInfo ); - boxContainer.append( boxInfo ); - boxContainer.append( '<div style="clear:both"></div>' ); - window.boxInfo = boxContainer; - - //console.debug( boxContainer ); - return boxContainer; -} -</script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix check_galaxy for recent framework changes.
by Bitbucket 27 Nov '12

27 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3c4696f6af0d/ changeset: 3c4696f6af0d user: natefoo date: 2012-11-27 21:57:05 summary: Fix check_galaxy for recent framework changes. affected #: 1 file diff -r 51ffca8538ff769f54f379d6e070494fc2c14833 -r 3c4696f6af0d9c6c7885568c1fee02df53849322 contrib/nagios/check_galaxy.py --- a/contrib/nagios/check_galaxy.py +++ b/contrib/nagios/check_galaxy.py @@ -4,7 +4,7 @@ via the check_galaxy.sh script in Galaxy's cron/ directory. """ -import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt +import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt, json from user import home import warnings @@ -63,13 +63,6 @@ username = args[1] password = args[2] -if server.endswith(".g2.bx.psu.edu"): - if debug: - print "Checking a PSU Galaxy server, using maint file" - maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0] -else: - maint = None - new_history = False for o, a in opts: if o == "-n": @@ -95,13 +88,12 @@ def __init__(self): self.server = server - self.maint = maint self.tool = None self.tool_opts = None - self.id = None - self.status = None + self._hda_id = None + self._hda_state = None + self._history_id = None self.check_file = None - self.hid = None self.cookie_jar = os.path.join( var_dir, "cookie_jar" ) dprint("cookie jar path: %s" % self.cookie_jar) if not os.access(self.cookie_jar, os.R_OK): @@ -116,19 +108,14 @@ def reset(self): self.tool = None self.tool_opts = None - self.id = None - self.status = None + self._hda_id = None + self._hda_state = None + self._history_id = None self.check_file = None - self.delete_datasets() - self.get("/root/history") - p = didParser() - p.feed(tc.browser.get_html()) - if len(p.dids) > 0: - print "Remaining datasets ids:", " ".join( p.dids ) - raise Exception, "History still contains datasets after attempting to delete them" if new_history: self.get("/history/delete_current") tc.save_cookies(self.cookie_jar) + self.delete_datasets() def check_redir(self, url): try: @@ -143,25 +130,9 @@ dprint( "%s is not returning redirect (302): %s" % (url, e) ) code = tc.browser.get_code() if code == 502: - is_maint = self.check_maint() - if is_maint: - dprint( "Galaxy is down, but a maint file was found, so not sending alert" ) - sys.exit(0) - else: - print "Galaxy is down (code 502)" - sys.exit(1) - return(False) - - # checks for a maint file - def check_maint(self): - if self.maint is None: - #dprint( "Warning: unable to check maint file for %s" % self.server ) - return(False) - try: - self.get(self.maint) - return(True) - except twill.errors.TwillAssertionError, e: - return(False) + print "Galaxy is down (code 502)" + sys.exit(1) + return False def login(self, user, pw): self.get("/user/login") @@ -210,15 +181,64 @@ tc.submit("runtool_btn") tc.code(200) + @property + def history_id(self): + if self._history_id is None: + self.get('/api/histories') + self._history_id = json.loads(tc.browser.get_html())[0]['id'] + return self._history_id + + @property + def history_contents(self): + self.get('/api/histories/%s/contents' % self.history_id) + return json.loads(tc.browser.get_html()) + + @property + def hda_id(self): + if self._hda_id is None: + self.set_top_hda() + return self._hda_id + + @property + def hda_state(self): + if self._hda_state is None: + self.set_top_hda() + return self._hda_state + + def set_top_hda(self): + self.get(self.history_contents[-1]['url']) + hda = json.loads(tc.browser.get_html()) + self._hda_id = hda['id'] + self._hda_state = hda['state'] + + @property + def undeleted_hdas(self): + rval = [] + for item in self.history_contents: + self.get(item['url']) + hda = json.loads(tc.browser.get_html()) + if hda['deleted'] == False: + rval.append(hda) + return rval + + @property + def history_state(self): + self.get('/api/histories/%s' % self.history_id) + return json.loads(tc.browser.get_html())['state'] + + @property + def history_state_terminal(self): + if self.history_state not in ['queued', 'running', 'paused']: + return True + return False + def wait(self): sleep_amount = 1 count = 0 maxiter = 16 while count < maxiter: count += 1 - self.get("/root/history") - page = tc.browser.get_html() - if page.find( '' ) > -1: + if not self.history_state_terminal: time.sleep( sleep_amount ) sleep_amount += 1 else: @@ -226,20 +246,14 @@ if count == maxiter: raise Exception, "Tool never finished" - def check_status(self): - self.get("/root/history") - p = historyParser() - p.feed(tc.browser.get_html()) - if p.status != "ok": - self.get("/datasets/%s/stderr" % p.id) + def check_state(self): + if self.hda_state != "ok": + self.get("/datasets/%s/stderr" % self.hda_id) print tc.browser.get_html() - raise Exception, "HDA %s NOT OK: %s" % (p.id, p.status) - self.id = p.id - self.status = p.status - #return((p.id, p.status)) + raise Exception, "HDA %s NOT OK: %s" % (self.hda_id, self.hda_state) def diff(self): - self.get("/datasets/%s/display?to_ext=%s" % (self.id, self.tool_opts.get('out_format', 'fasta'))) + self.get("/datasets/%s/display?to_ext=%s" % (self.hda_id, self.tool_opts.get('out_format', 'fasta'))) data = tc.browser.get_html() tmp = tempfile.mkstemp() dprint("tmp file: %s" % tmp[1]) @@ -256,12 +270,12 @@ os.remove(tmp[1]) def delete_datasets(self): - self.get("/root/history") - p = didParser() - p.feed(tc.browser.get_html()) - dids = p.dids - for did in dids: - self.get("/datasets/%s/delete" % did) + for hda in self.undeleted_hdas: + self.get('/datasets/%s/delete' % hda['id']) + hdas = [hda['id'] for hda in self.undeleted_hdas] + if hdas: + print "Remaining datasets ids:", " ".join(hdas) + raise Exception, "History still contains datasets after attempting to delete them" def check_if_logged_in(self): self.get("/user?cntrller=user") @@ -294,33 +308,6 @@ elif data == "User with that email already exists": self.already_exists = True -class historyParser(htmllib.HTMLParser): - def __init__(self): - htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) - self.status = None - self.id = None - def start_div(self, attrs): - # find the top history item - for i in attrs: - if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"): - self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1] - dprint("status: %s" % self.status) - if i[0] == "id" and i[1].startswith("historyItem-"): - self.id = i[1].rsplit("historyItem-", 1)[1] - dprint("id: %s" % self.id) - if self.status is not None: - self.reset() - -class didParser(htmllib.HTMLParser): - def __init__(self): - htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) - self.dids = [] - def start_div(self, attrs): - for i in attrs: - if i[0] == "id" and i[1].startswith("historyItemContainer-"): - self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] ) - dprint("got a dataset id: %s" % self.dids[-1]) - class loggedinParser(htmllib.HTMLParser): def __init__(self): htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) @@ -379,15 +366,9 @@ b.runtool() b.wait() - b.check_status() + b.check_state() b.diff() b.delete_datasets() - # by this point, everything else has succeeded. there should be no maint. - is_maint = b.check_maint() - if is_maint: - print "Galaxy is up and fully functional, but a maint file is in place." - sys.exit(1) - print "OK" sys.exit(0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fixed error when granting write access to a repository.
by Bitbucket 27 Nov '12

27 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/51ffca8538ff/ changeset: 51ffca8538ff user: inithello date: 2012-11-27 19:53:17 summary: Fixed error when granting write access to a repository. affected #: 1 file diff -r 2aae11d62620b6c839b513d68a06d2cc57c5fa21 -r 51ffca8538ff769f54f379d6e070494fc2c14833 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -143,7 +143,7 @@ if username not in allow_push: allow_push.append( username ) allow_push = '%s\n' % ','.join( allow_push ) - repo = hg.repository( ui.ui(), path=self.repo_path ) + repo = hg.repository( ui.ui(), path=self.repo_path( app ) ) # Why doesn't the following work? #repo.ui.setconfig( 'web', 'allow_push', allow_push ) lines = repo.opener( 'hgrc', 'rb' ).readlines() 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: natefoo: Split job limits on ' = ' rather than '='.
by Bitbucket 27 Nov '12

27 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2aae11d62620/ changeset: 2aae11d62620 user: natefoo date: 2012-11-27 19:50:54 summary: Split job limits on ' = ' rather than '='. affected #: 1 file diff -r 4a95ae9a26d96f0dc9a0fe3b083a2c7b99b0466b -r 2aae11d62620b6c839b513d68a06d2cc57c5fa21 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -224,8 +224,8 @@ try: job_limits = global_conf_parser.items( 'galaxy:job_limits' ) for k, v in job_limits: - # ConfigParser considers the first colon to be the delimiter, undo this behavior - more_k, v = v.split('=', 1) + # Since the URL contains a colon and possibly an equals sign, consider ' = ' the delimiter + more_k, v = v.split(' = ', 1) k = '%s:%s' % (k, more_k.strip()) v = v.strip().rsplit(None, 1) v[1] = int(v[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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commit/galaxy-central: natefoo: Handle invalid job ids in the drmaa runner.
by Bitbucket 27 Nov '12

27 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a95ae9a26d9/ changeset: 4a95ae9a26d9 user: natefoo date: 2012-11-27 18:18:08 summary: Handle invalid job ids in the drmaa runner. affected #: 1 file diff -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff -r 4a95ae9a26d96f0dc9a0fe3b083a2c7b99b0466b lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -293,6 +293,7 @@ galaxy_job_id = drm_job_state.job_wrapper.job_id old_state = drm_job_state.old_state try: + assert job_id not in ( None, 'None' ), 'Invalid job id: %s' % job_id state = self.ds.jobStatus( job_id ) # InternalException was reported to be necessary on some DRMs, but # this could cause failures to be detected as completion! Please @@ -308,7 +309,7 @@ continue except Exception, e: # so we don't kill the monitor thread - log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) ) + log.exception("(%s/%s) Unable to check job status: %s" % ( galaxy_job_id, job_id, str( e ) ) ) log.warning("(%s/%s) job will now be errored" % ( galaxy_job_id, job_id ) ) drm_job_state.fail_message = "Cluster could not complete job" self.work_queue.put( ( 'fail', drm_job_state ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: scatterplot: renaming/re-organization pass; layout change to vertical tabs and inclusion of chart under tabs; pack scripts
by Bitbucket 27 Nov '12

27 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9bf411ee2476/ changeset: 9bf411ee2476 user: carlfeberhard date: 2012-11-27 17:19:32 summary: scatterplot: renaming/re-organization pass; layout change to vertical tabs and inclusion of chart under tabs; pack scripts affected #: 19 files diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/mvc/visualizations/scatterplotControlForm.js --- /dev/null +++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js @@ -0,0 +1,602 @@ +/* ============================================================================= +todo: + I'd like to move the svg creation out of the splot constr. to: + allow adding splots to an existing canvas + allow mult. splots sharing a canvas + + + outside this: + BUG: setting width, height in plot controls doesn't re-interpolate data locations!! + BUG?: get metadata_column_names (from datatype if necessary) + BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' + + wire label setters, anim setter + + TwoVarScatterplot: + ??: maybe better to do this with a canvas... + save as visualization + to seperate file? + remove underscore dependencies + add interface to change values (seperate)? + download svg -> base64 encode + incorporate glyphs, glyph state renderers + + ScatterplotSettingsForm: + some css bug that lowers the width of settings form when plot-controls tab is open + causes chart to shift + what can be abstracted/reused for other graphs? + avoid direct manipulation of this.plot + allow option to put plot into seperate tab of interface (for small multiples) + + provide callback in view to load data incrementally - for large sets + paginate + handle rerender + use endpoint (here and on the server (fileptr)) + fetch (new?) data + handle rerender + use d3.TSV? + render warning on long data (> maxDataPoints) + adjust endpoint + + selectable list of preset column comparisons (rnaseq etc.) + how to know what sort of Tabular the data is? + smarter about headers + validate columns selection (here or server) + + set stats column names by selected columns + move chart into tabbed area... + + Scatterplot.mako: + multiple plots on one page (small multiples) + ?? ensure svg styles thru d3 or css? + d3: configable (easily) + css: standard - better maintenance + ? override at config + +============================================================================= */ +/** + * Scatterplot control UI as a backbone view + * handles: + * getting the desired data + * configuring the plot display + * showing (general) statistics + * + * initialize attributes REQUIRES a dataset and an apiDatasetsURL + */ +var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ + //logger : console, + className : 'scatterplot-control-form', + + dataLoadDelay : 500, + dataLoadSize : 3001, + + loadingIndicatorImage : 'loading_small_white_bg.gif', + fetchMsg : 'Fetching data...', + renderMsg : 'Rendering...', + + initialize : function( attributes ){ + this.log( this + '.initialize, attributes:', attributes ); + + this.dataset = null; + this.chartConfig = null; + this.chart = null; + this.loader = null; + + // set up refs to the four tab areas + this.$dataControl = null; + this.$chartControl = null; + this.$statsDisplay = null; + this.$chartDisplay = null; + + this.dataFetch = null; + + this.initializeFromAttributes( attributes ); + this.initializeChart( attributes ); + this.initializeDataLoader( attributes ); + }, + + initializeFromAttributes : function( attributes ){ + // required settings: ensure certain vars we need are passed in attributes + if( !attributes || !attributes.dataset ){ + throw( "ScatterplotView requires a dataset" ); + } else { + this.dataset = attributes.dataset; + } + if( jQuery.type( this.dataset.metadata_column_types ) === 'string' ){ + this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); + } + this.log( '\t dataset:', this.dataset ); + + // passed from mako helper + //TODO: integrate to galaxyPaths + //TODO: ?? seems like data loader section would be better + if( !attributes.apiDatasetsURL ){ + throw( "ScatterplotView requires a apiDatasetsURL" ); + } else { + this.dataURL = attributes.apiDatasetsURL + '/' + this.dataset.id + '?'; + } + this.log( '\t dataURL:', this.dataURL ); + }, + + initializeChart : function( attributes ){ + // set up the basic chart infrastructure and config (if any) + this.chartConfig = attributes.chartConfig || {}; + //if( this.logger ){ this.chartConfig.debugging = true; } + this.log( '\t initial chartConfig:', this.chartConfig ); + + this.chart = new TwoVarScatterplot( this.chartConfig ); + //TODO: remove 2nd ref, use this.chart.config + this.chartConfig = this.chart.config; + }, + + initializeDataLoader : function( attributes ){ + // set up data loader + var view = this; + this.loader = new LazyDataLoader({ + //logger : ( this.logger )?( this.logger ):( null ), + // we'll generate this when columns are chosen + url : null, + start : attributes.start || 0, + //NOTE: metadata_data_lines can be null (so we won't know the total) + total : attributes.total || this.dataset.metadata_data_lines, + delay : this.dataLoadDelay, + size : this.dataLoadSize, + + buildUrl : function( start, size ){ + // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params + return this.url + '&' + jQuery.param({ + start_val: start, + max_vals: size + }); + } + }); + $( this.loader ).bind( 'error', function( event, status, error ){ + view.log( 'ERROR:', status, error ); + alert( 'ERROR fetching data:\n' + status + '\n' + error ); + view.hideLoadingIndicator(); + }); + }, + + // ------------------------------------------------------------------------- CONTROLS RENDERING + render : function(){ + this.log( this + '.render' ); + + // render the tab controls, areas and loading indicator + this.$el.append( ScatterplotControlForm.templates.mainLayout({ + loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage, + message : '' + })); + + // render the tab content + this.$dataControl = this._render_dataControl(); + this.$chartControl = this._render_chartControl(); + this.$statsDisplay = this.$el.find( '.tab-pane#stats-display' ); + this.$chartDisplay = this._render_chartDisplay(); + + // auto render if given both x, y column choices in query for page + //TODO:?? add autoRender=1 to query maybe? + if( this.chartConfig.xColumn && this.chartConfig.yColumn ){ + this.renderChart(); + } + + // set up behaviours + this.$el.find( '.tooltip' ).tooltip(); + + // uncomment any of the following to have that tab show on initial load (for testing) + //this.$el.find( 'ul.nav' ).find( 'a[href="#data-control"]' ).tab( 'show' ); + //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-control"]' ).tab( 'show' ); + //this.$el.find( 'ul.nav' ).find( 'a[href="#stats-display"]' ).tab( 'show' ); + //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' ); + return this; + }, + + _render_dataControl : function(){ + // controls for which columns are used to plot datapoints (and ids/additional info to attach if desired) + var view = this, + allColumns = [], + numericColumns = []; + + // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) + _.each( this.dataset.metadata_column_types, function( type, index ){ + // use a 1 based index in names/values within the form (will be dec. when parsed out) + var oneBasedIndex = index + 1, + // label with the name if available (fall back on 'column <index>') + name = 'column ' + oneBasedIndex; + if( view.dataset.metadata_column_names ){ + name = view.dataset.metadata_column_names[ index ]; + } + + // cache all columns here + allColumns.push({ index: oneBasedIndex, name: name }); + + // filter numeric columns to their own list + if( type === 'int' || type === 'float' ){ + numericColumns.push({ index: oneBasedIndex, name: name }); + } + }); + //TODO: other vals: max_vals, start_val, pagination (chart-settings) + + // render the html + var $dataControl = this.$el.find( '.tab-pane#data-control' ); + $dataControl.append( ScatterplotControlForm.templates.dataControl({ + allColumns : allColumns, + numericColumns : numericColumns + })); + + // preset to column selectors if they were passed in the config in the query string + $dataControl.find( '#X-select' ).val( this.chartConfig.xColumn ); + $dataControl.find( '#Y-select' ).val( this.chartConfig.yColumn ); + if( this.chartConfig.idColumn !== undefined ){ + $dataControl.find( '#include-id-checkbox' ) + .attr( 'checked', true ).trigger( 'change' ); + $dataControl.find( '#ID-select' ).val( this.chartConfig.idColumn ); + } + + return $dataControl; + }, + + _render_chartControl : function(){ + // tab content to control how the chart is rendered (data glyph size, chart size, etc.) + var view = this, + $chartControl = this.$el.find( '.tab-pane#chart-control' ), + // limits for controls (by control/chartConfig id) + //TODO: move into TwoVarScatterplot + controlRanges = { + 'datapointSize' : { min: 2, max: 10, step: 1 }, + 'width' : { min: 200, max: 800, step: 20 }, + 'height' : { min: 200, max: 800, step: 20 } + }; + + // render the html + $chartControl.append( ScatterplotControlForm.templates.chartControl( this.chartConfig ) ); + + // set up behaviours, js on sliders + $chartControl.find( '.numeric-slider-input' ).each( function(){ + var $this = $( this ), + $output = $this.find( '.slider-output' ), + $slider = $this.find( '.slider' ), + id = $this.attr( 'id' ); + //chartControl.log( 'slider set up', 'this:', $this, 'slider:', $slider, 'id', id ); + + // what to do when the slider changes: update display and update chartConfig + //TODO: move out of loop + function onSliderChange(){ + var $this = $( this ), + newValue = $this.slider( 'value' ); + //chartControl.log( 'slider change', 'this:', $this, 'output:', $output, 'value', newValue ); + $output.text( newValue ); + //chartControl.chartConfig[ id ] = newValue; + } + + $slider.slider( _.extend( controlRanges[ id ], { + value : view.chartConfig[ id ], + change : onSliderChange, + slide : onSliderChange + })); + }); + + return $chartControl; + }, + + _render_chartDisplay : function(){ + // render the tab content where the chart is displayed (but not the chart itself) + var $chartDisplay = this.$el.find( '.tab-pane#chart-display' ); + $chartDisplay.append( ScatterplotControlForm.templates.chartDisplay( this.chartConfig ) ); + return $chartDisplay; + }, + + // ------------------------------------------------------------------------- EVENTS + events : { + 'change #include-id-checkbox' : 'toggleThirdColumnSelector', + 'click #data-control #render-button' : 'renderChart', + 'click #chart-control #render-button' : 'changeChartSettings' + }, + + toggleThirdColumnSelector : function(){ + // show/hide the id selector on the data settings panel + this.$el.find( 'select[name="ID"]' ).parent().toggle(); + }, + + showLoadingIndicator : function( message, callback ){ + // display the loading indicator over the tab panels if hidden, update message (if passed) + message = message || ''; + var indicator = this.$el.find( 'div#loading-indicator' ); + messageBox = indicator.find( '.loading-message' ); + + if( indicator.is( ':visible' ) ){ + if( message ){ + messageBox.fadeOut( 'fast', function(){ + messageBox.text( message ); + messageBox.fadeIn( 'fast', callback ); + }); + } else { + callback(); + } + + } else { + if( message ){ messageBox.text( message ); } + indicator.fadeIn( 'fast', callback ); + } + }, + + hideLoadingIndicator : function( callback ){ + this.$el.find( 'div#loading-indicator' ).fadeOut( 'fast', callback ); + }, + + // ------------------------------------------------------------------------- CHART/STATS RENDERING + renderChart : function(){ + // fetch the data, (re-)render the chart + this.log( this + '.renderChart' ); + + //TODO: separate data fetch + + // this is a complete re-render, so clear the prev. data + this.data = null; + this.meta = null; + + // update the chartConfig (here and chart) using chart settings + //TODO: separate and improve (used in changeChartSettings too) + _.extend( this.chartConfig, this.getChartSettings() ); + this.log( '\t chartConfig:', this.chartConfig ); + this.chart.updateConfig( this.chartConfig, false ); + + // build the url with the current data settings + this.loader.url = this.dataURL + '&' + jQuery.param( this.getDataSettings() ); + this.log( '\t loader: total lines:', this.loader.total, ' url:', this.loader.url ); + + // bind the new data event to: aggregate data, update the chart and stats with new data + var view = this; + $( this.loader ).bind( 'loaded.new', function( event, response ){ + view.log( view + ' loaded.new', response ); + + // aggregate data and meta + view.postProcessDataFetchResponse( response ); + view.log( '\t postprocessed data:', view.data ); + view.log( '\t postprocessed meta:', view.meta ); + + // update the chart and stats + view.showLoadingIndicator( view.renderMsg, function(){ + view.chart.render( view.data, view.meta ); + view.renderStats( view.data, view.meta ); + view.hideLoadingIndicator(); + }); + }); + // when all data loaded - unbind (or we'll start doubling event handlers) + $( this.loader ).bind( 'complete', function( event, data ){ + view.log( view + ' complete', data ); + $( view.loader ).unbind(); + }); + + // begin loading the data, switch to the chart display tab + view.showLoadingIndicator( view.fetchMsg, function(){ + view.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' ); + view.loader.load(); + }); + }, + + renderStats : function(){ + this.log( this + '.renderStats' ); + // render the stats table in the stats panel + //TODO: there's a better way + this.$statsDisplay.html( ScatterplotControlForm.templates.statsDisplay({ + stats: [ + { name: 'Count', xval: this.meta[0].count, yval: this.meta[1].count }, + { name: 'Min', xval: this.meta[0].min, yval: this.meta[1].min }, + { name: 'Max', xval: this.meta[0].max, yval: this.meta[1].max }, + { name: 'Sum', xval: this.meta[0].sum, yval: this.meta[1].sum }, + { name: 'Mean', xval: this.meta[0].mean, yval: this.meta[1].mean }, + { name: 'Median', xval: this.meta[0].median, yval: this.meta[1].median } + ] + })); + }, + + changeChartSettings : function(){ + // re-render the chart with new chart settings and OLD data + var view = this; + newChartSettings = this.getChartSettings(); + + // update the chart config from the chartSettings panel controls + _.extend( this.chartConfig, newChartSettings ); + this.log( 'this.chartConfig:', this.chartConfig ); + this.chart.updateConfig( this.chartConfig, false ); + + // if there's current data, call chart.render with it (no data fetch) + if( view.data && view.meta ){ + view.showLoadingIndicator( view.renderMsg, function(){ + view.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' ); + view.chart.render( view.data, view.meta ); + view.hideLoadingIndicator(); + }); + + // no current data, call renderChart instead (which will fetch data) + } else { + this.renderChart(); + } + }, + + // ------------------------------------------------------------------------- DATA AGGREGATION + postProcessDataFetchResponse : function( response ){ + // the loader only returns new data - it's up to this to munge the fetches together properly + //TODO: we're now storing data in two places: loader and here + // can't we reduce incoming data into loader.data[0]? are there concurrency problems? + this.postProcessData( response.data ); + this.postProcessMeta( response.meta ); + }, + + postProcessData : function( newData ){ + // stack the column data on top of each other into this.data + //this.log( this + '.postProcessData:', newData ); + var view = this; + + // if we already have data: aggregate + if( view.data ){ + _.each( newData, function( newColData, colIndex ){ + //view.log( colIndex + ' data:', newColData ); + //TODO??: time, space efficiency of this? + view.data[ colIndex ] = view.data[ colIndex ].concat( newColData ); + }); + + // otherwise: assign (first load) + } else { + view.data = newData; + } + }, + + postProcessMeta : function( newMeta ){ + // munge the meta data (stats) from the server fetches together + //pre: this.data must be preprocessed (needed for medians) + //this.log( this + '.postProcessMeta:', newMeta ); + var view = this, + colTypes = this.dataset.metadata_column_types; + + // if we already have meta: aggregate + if( view.meta ){ + _.each( newMeta, function( newColMeta, colIndex ){ + var colMeta = view.meta[ colIndex ], + colType = colTypes[ colIndex ]; + //view.log( '\t ' + colIndex + ' postprocessing meta:', newColMeta ); + //view.log( colIndex + ' old meta:', + // 'min:', colMeta.min, + // 'max:', colMeta.max, + // 'sum:', colMeta.sum, + // 'mean:', colMeta.mean, + // 'median:', colMeta.median + //); + + //!TODO: at what point are we getting int/float overflow on these?! + //??: need to be null safe? + colMeta.count += ( newColMeta.count )?( newColMeta.count ):( 0 ); + //view.log( colIndex, 'count:', colMeta.count ); + + if( ( colType === 'int' ) || ( colType === 'float' ) ){ + //view.log( colIndex + ' incoming meta:', + // 'min:', newColMeta.min, + // 'max:', newColMeta.max, + // 'sum:', newColMeta.sum, + // 'mean:', newColMeta.mean, + // 'median:', newColMeta.median + //); + + colMeta.min = Math.min( newColMeta.min, colMeta.min ); + colMeta.max = Math.max( newColMeta.max, colMeta.max ); + colMeta.sum = newColMeta.sum + colMeta.sum; + colMeta.mean = ( colMeta.count )?( colMeta.sum / colMeta.count ):( null ); + + // median's a pain bc of sorting (requires the data as well) + var sortedCol = view.data[ colIndex ].slice().sort(), + middleIndex = Math.floor( sortedCol.length / 2 ); + + if( sortedCol.length % 2 === 0 ){ + colMeta.median = ( ( sortedCol[ middleIndex ] + sortedCol[( middleIndex + 1 )] ) / 2 ); + + } else { + colMeta.median = sortedCol[ middleIndex ]; + } + + //view.log( colIndex + ' new meta:', + // 'min:', colMeta.min, + // 'max:', colMeta.max, + // 'sum:', colMeta.sum, + // 'mean:', colMeta.mean, + // 'median:', colMeta.median + //); + } + }); + + // otherwise: assign (first load) + } else { + view.meta = newMeta; + //view.log( '\t meta (first load):', view.meta ); + } + }, + + // ------------------------------------------------------------------------- GET DATA/CHART SETTINGS + getDataSettings : function(){ + // parse the column values for both indeces (for the data fetch) and names (for the chart) + var columnSelections = this.getColumnSelections(), + columns = []; + this.log( '\t columnSelections:', columnSelections ); + + //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string + + // get column indices for params, include the desired ID column (if any) + //NOTE: these are presented in human-readable 1 base index (to match the data.peek) - adjust + columns = [ + columnSelections.X.colIndex - 1, + columnSelections.Y.colIndex - 1 + ]; + if( this.$dataControl.find( '#include-id-checkbox' ).attr( 'checked' ) ){ + columns.push( columnSelections.ID.colIndex - 1 ); + } + //TODO: other vals: max, start, page + + var params = { + data_type : 'raw_data', + columns : '[' + columns + ']' + }; + this.log( '\t data settings (url params):', params ); + return params; + }, + + getColumnSelections : function(){ + // gets the current user-selected values for which columns to fetch from the data settings panel + // returns a map: { column-select name (eg. X) : { colIndex : column-selector val, + // colName : selected option text }, ... } + var selections = {}; + this.$dataControl.find( 'div.column-select select' ).each( function(){ + var $this = $( this ), + val = $this.val(); + selections[ $this.attr( 'name' ) ] = { + colIndex : val, + colName : $this.children( '[value="' + val + '"]' ).text() + }; + }); + return selections; + }, + + getChartSettings : function(){ + // gets the user-selected chartConfig from the chart settings panel + var settings = {}, + colSelections = this.getColumnSelections(); + //this.log( 'colSelections:', colSelections ); + + //TODO: simplify with keys and loop + settings.datapointSize = this.$chartControl.find( '#datapointSize.numeric-slider-input' ) + .find( '.slider' ).slider( 'value' ); + settings.width = this.$chartControl.find( '#width.numeric-slider-input' ) + .find( '.slider' ).slider( 'value' ); + settings.height = this.$chartControl.find( '#height.numeric-slider-input' ) + .find( '.slider' ).slider( 'value' ); + + // update axes labels using chartSettings inputs (if not at defaults), otherwise the selects' colName + //TODO: a little confusing + var chartSettingsXLabel = this.$chartControl.find( 'input#X-axis-label' ).val(), + chartSettingsYLabel = this.$chartControl.find( 'input#Y-axis-label' ).val(); + settings.xLabel = ( chartSettingsXLabel === 'X' )? + ( colSelections.X.colName ):( chartSettingsXLabel ); + settings.yLabel = ( chartSettingsYLabel === 'Y' )? + ( colSelections.Y.colName ):( chartSettingsYLabel ); + + settings.animDuration = 10; + if( this.$chartControl.find( '#animDuration.checkbox-input' ).is( ':checked' ) ){ + settings.animDuration = 500; + } + + this.log( '\t chartSettings:', settings ); + return settings; + }, + + toString : function(){ + return 'ScatterplotControlForm(' + (( this.dataset )?( this.dataset.id ):( '' )) + ')'; + } +}); + +ScatterplotControlForm.templates = { + mainLayout : Handlebars.templates[ 'template-visualization-scatterplotControlForm' ], + dataControl : Handlebars.templates[ 'template-visualization-dataControl' ], + chartControl : Handlebars.templates[ 'template-visualization-chartControl' ], + statsDisplay : Handlebars.templates[ 'template-visualization-statsDisplay' ], + chartDisplay : Handlebars.templates[ 'template-visualization-chartDisplay' ] +}; + +//============================================================================== diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/mvc/visualizations/scatterplotControlForm.js --- /dev/null +++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js @@ -0,0 +1,1 @@ +var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find(".tooltip").tooltip();return this},_render_dataControl:function(){var b=this,a=[],d=[];_.each(this.dataset.metadata_column_types,function(h,f){var g=f+1,e="column "+g;if(b.dataset.metadata_column_names){e=b.dataset.metadata_column_names[f]}a.push({index:g,name:e});if(h==="int"||h==="float"){d.push({index:g,name:e})}});var c=this.$el.find(".tab-pane#data-control");c.append(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:d}));c.find("#X-select").val(this.chartConfig.xColumn);c.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){c.find("#include-id-checkbox").attr("checked",true).trigger("change");c.find("#ID-select").val(this.chartConfig.idColumn)}return c},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=10;if(this.$chartControl.find("#animDuration.checkbox-input").is(":checked")){c.animDuration=500}this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/templates/compiled/template-visualization-chartControl.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-chartControl.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartControl"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(p,o){return' checked="true"'}i+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n\n <div id="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">';h=e.datapointSize;if(h){c=h.call(m,{hash:{}})}else{c=m.datapointSize;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id="animDuration" class="form-input checkbox-input">\n <label for="animated">Animate graph transitions?: </label>\n <input type="checkbox" id="animated"\n class="checkbox control"';c=m.animDuration;c=e["if"].call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+=' />\n <p class="form-help help-text-small">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id="width" class="form-input numeric-slider-input">\n <label for="width">Graph width: </label>\n <div class="slider-output">';h=e.width;if(h){c=h.call(m,{hash:{}})}else{c=m.width;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="height" class="form-input numeric-slider-input">\n <label for="height">Graph height: </label>\n <div class="slider-output">';h=e.height;if(h){c=h.call(m,{hash:{}})}else{c=m.height;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="';h=e.xLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.xLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <div id="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="';h=e.yLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.yLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />';return i})})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/templates/compiled/template-visualization-chartDisplay.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-chartDisplay.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartDisplay"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<svg width="';g=d.width;if(g){c=g.call(l,{hash:{}})}else{c=l.width;c=typeof c===f?c():c}h+=i(c)+'" height="';g=d.height;if(g){c=g.call(l,{hash:{}})}else{c=l.height;c=typeof c===f?c():c}h+=i(c)+'"></svg>';return h})})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/templates/compiled/template-visualization-dataControl.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-dataControl.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-dataControl"]=b(function(g,m,f,l,k){f=f||g.helpers;var i="",d,h="function",j=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}function c(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}function n(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=j(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=j(r)+"</option>\n ";return q}i+="<p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n ";i+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=m.numericColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(1,e,k)});if(d||d===0){i+=d}i+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=m.numericColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(3,c,k)});if(d||d===0){i+=d}i+="\n </select>\n </div>\n\n ";i+='\n <div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="ID" id="ID-select">\n ';d=m.allColumns;d=f.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(5,n,k)});if(d||d===0){i+=d}i+='\n </select>\n </div>\n\n <input id="render-button" type="button" value="Draw" />\n <div class="clear"></div>';return i})})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function c(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function o(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}j+='\n\n<ul class="nav nav-tabs">\n <li class="active"><a data-toggle="tab" href="#data-settings">Data Controls</a></li>\n <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li>\n <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li>\n <li><a data-toggle="tab" href="#chart">Chart</a></li>\n</ul>\n\n';j+='\n<div class="tab-content">\n<div id="data-settings" class="tab-pane active">\n\n <p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n \n ';j+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)});if(d||d===0){j+=d}j+="\n </select>\n </div>\n \n ";j+='\n <div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="ID" id="ID-select">\n ';d=n.allColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n \n <input id="render-button" type="button" value="Draw" />\n <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" />\n <div class="clear"></div>\n</div>\n\n<div id="chart-settings" class="tab-pane">\n</div>\n\n<div id="chart-stats" class="tab-pane">\n</div>\n</div>';j+="\n\n";j+='\n<div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';i=f.loadingIndicatorImagePath;if(i){d=i.call(n,{hash:{}})}else{d=n.loadingIndicatorImagePath;d=typeof d===h?d():d}j+=k(d)+'" />\n <span class="loading-message">';i=f.message;if(i){d=i.call(n,{hash:{}})}else{d=n.message;d=typeof d===h?d():d}j+=k(d)+"</span>\n</div>";return j})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='\n\n<div class="scatterplot-container chart-container tabbable tabs-left">\n ';h+='\n <ul class="nav nav-tabs">\n ';h+='\n <li class="active"><a href="#data-control" data-toggle="tab" class="tooltip"\n title="Use this tab to change which data are used">Data Controls</a></li>\n <li><a href="#chart-control" data-toggle="tab" class="tooltip"\n title="Use this tab to change how the chart is drawn">Chart Controls</a></li>\n <li><a href="#stats-display" data-toggle="tab" class="tooltip"\n title="This tab will display overall statistics for your data">Statistics</a></li>\n <li><a href="#chart-display" data-toggle="tab" class="tooltip"\n title="This tab will display the chart">Chart</a>\n ';h+='\n <div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';g=d.loadingIndicatorImagePath;if(g){c=g.call(l,{hash:{}})}else{c=l.loadingIndicatorImagePath;c=typeof c===f?c():c}h+=i(c)+'" />\n <span class="loading-message">';g=d.message;if(g){c=g.call(l,{hash:{}})}else{c=l.message;c=typeof c===f?c():c}h+=i(c)+"</span>\n </div>\n </li>\n </ul>\n\n ";h+='\n <div class="tab-content">\n ';h+='\n <div id="data-control" class="tab-pane active">\n ';h+="\n </div>\n \n ";h+='\n <div id="chart-control" class="tab-pane">\n ';h+="\n </div>\n\n ";h+='\n <div id="stats-display" class="tab-pane">\n ';h+="\n </div>\n\n ";h+='\n <div id="chart-display" class="tab-pane">\n ';h+="\n </div>\n\n </div>";h+="\n</div>";return h})})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/templates/compiled/template-visualization-statsDisplay.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-statsDisplay.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-statsDisplay"]=b(function(f,l,e,k,j){e=e||f.helpers;var h="",c,g="function",i=this.escapeExpression,m=this;function d(r,q){var o="",p,n;o+="\n <tr><td>";n=e.name;if(n){p=n.call(r,{hash:{}})}else{p=r.name;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.xval;if(n){p=n.call(r,{hash:{}})}else{p=r.xval;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.yval;if(n){p=n.call(r,{hash:{}})}else{p=r.yval;p=typeof p===g?p():p}o+=i(p)+"</td></tr>\n </tr>\n ";return o}h+='<p class="help-text">By column:</p>\n <table id="chart-stats-table">\n <thead><th></th><th>X</th><th>Y</th></thead>\n ';c=l.stats;c=e.each.call(l,c,{hash:{},inverse:m.noop,fn:m.program(1,d,j)});if(c||c===0){h+=c}h+="\n </table>";return h})})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","../templates/compiled/template-visualization-scatterplotControlForm","../templates/compiled/template-visualization-statsTable","../templates/compiled/template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../libs/jquery/jquery-ui"],function(){function a(f){var d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(i,j){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart");this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id);this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.adjustChartDimensions=function(l,j,i,k){l=l||0;j=j||0;i=i||0;k=k||0;this.svg.attr("width",this.config.width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.preprocessData=function(k,j,i){return(k.length>this.config.maxDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=function(i,k,j){this.xMin=this.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=this.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=this.config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=this.config.yMax||(j)?(j[1].max):(d3.max(k))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var i=this.yAxis.selectAll("text").filter(function(m,l){return l!==0});this.yLongestLabel=d3.max(i[0].map(function(m,l){return(d3.select(m).text()).length}))||0;var j=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(j-g);if(this.config.marginLeft<j){var k=(j)-this.config.marginLeft;k=(k<0)?(0):(k);this.adjustChartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l,j){this.log(this+".renderDatapoints",arguments);var k=0;this.datapoints=this.addDatapoints(i,l,j,".glyph");this.datapoints.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed")};this.addDatapoints=function(m,k,i,l){this.log(this+".addDatapoints",arguments);var p=this,o=0,q=function(s,r){return p.xScale(m[r])},j=function(s,r){return p.yScale(k[r])};var n=this.content.selectAll(l);this.log("existing datapoints:",n);n=n.data(m);o=0;n.enter().append("svg:circle").each(function(){o+=1}).classed("glyph",true).attr("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=0;n.transition().duration(this.config.animDuration).each(function(){o+=1}).attr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseover",function(t,r){var s=d3.select(this);s.style("fill","red").style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",0).attr("y2",s.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",s.attr("cx")).attr("y2",p.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};this.render=function(k,l){this.log(this+".render",arguments);var i=k[0],m=k[1],j=(k.length>2)?(k[2]):(undefined);i=this.preprocessData(i);m=this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);this.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m,j)}}var b=BaseView.extend(LoggableMixin).extend({className:"scatterplot-settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_large_white_bg.gif",initialize:function(c){this.log(this+".initialize, attributes:",c);this.dataset=null;this.chartConfig=null;this.plot=null;this.loader=null;this.$statsPanel=null;this.$chartSettingsPanel=null;this.$dataSettingsPanel=null;this.dataFetch=null;this.initializeFromAttributes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFromAttributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.dataset);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=c.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig=c.chartConfig||{};if(this.logger){this.chartConfig.debugging=true}this.log("initial chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig);this.chartConfig=this.plot.config},initializeDataLoader:function(d){var c=this;this.loader=new LazyDataLoader({logger:(this.logger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){var c=this,d={config:this.chartConfig,allColumns:[],numericColumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e="column "+(f+1);if(c.dataset.metadata_column_names){e=c.dataset.metadata_column_names[f]}if(g==="int"||g==="float"){d.numericColumns.push({index:(f+1),name:e})}d.allColumns.push({index:(f+1),name:e})});this.$el.append(b.templates.form(d));this.$dataSettingsPanel=this.$el.find(".tab-pane#data-settings");this.$chartSettingsPanel=this._render_chartSettings();this.$statsPanel=this.$el.find(".tab-pane#chart-stats");this.$dataSettingsPanel.find("#X-select").val(this.chartConfig.xColumn);this.$dataSettingsPanel.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked",true).trigger("change");this.$dataSettingsPanel.find("#ID-select").val(this.chartConfig.idColumn)}if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderPlot()}return this},isColumnNumeric:function(c){if((c>=0)&&(c<this.dataset.metadata_column_types.length)){var d=this.dataset.metadata_column_types[c];return(d==="int"||d==="float")}return false},_render_chartSettings:function(){var c=this,d=this.$el.find(".tab-pane#chart-settings"),e={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings(this.chartConfig));d.find(".numeric-slider-input").each(function(){var h=$(this),g=h.find(".slider-output"),i=h.find(".slider"),j=h.attr("id");function f(){var l=$(this),k=l.slider("value");g.text(k)}i.slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-settings #render-button":"renderPlot","click #chart-settings #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(d,e){d=d||"";var c=this.$el.find("div#loading-indicator");messageBox=c.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:function(){var c=this;c.data=null;c.meta=null;_.extend(this.chartConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rendering...",function(){c.$el.find("ul.nav").find('a[href="#chart-stats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data...",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=this;newGraphSettings=this.getGraphSettings();this.log("newGraphSettings:",newGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.postProcessMeta(c.meta)},postProcessData:function(d){var c=this;if(c.data){_.each(d,function(f,e){c.data[e]=c.data[e].concat(f)})}else{c.data=d}},postProcessMeta:function(e){var c=this,d=this.dataset.metadata_column_types;if(c.meta){_.each(e,function(g,f){var k=c.meta[f],i=d[f];c.log(f+" postprocessing meta:",g);k.count+=(g.count)?(g.count):(0);c.log(f,"count:",k.count);if((i==="int")||(i==="float")){k.min=Math.min(g.min,k.min);k.max=Math.max(g.max,k.max);k.sum=g.sum+k.sum;k.mean=(k.count)?(k.sum/k.count):(null);var h=c.data[f].slice().sort(),j=Math.floor(h.length/2);if(h.length%2===0){k.median=((h[j]+h[(j+1)])/2)}else{k.median=h[j]}}})}else{c.meta=e;c.log("initial meta:",c.meta)}},getDataSettings:function(){var d=this.getColumnSelections(),c=[];this.log("columnSelections:",d);c=[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e={data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},getColumnSelections:function(){var c={};this.$dataSettingsPanel.find("div.column-select select").each(function(){var d=$(this),e=parseInt(d.val(),10)-1;c[d.attr("name")]={colIndex:e,colName:d.children('[value="'+e+'"]').text()}});return c},getGraphSettings:function(){var e={},f=this.getColumnSelections();e.datapointSize=this.$chartSettingsPanel.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");e.width=this.$chartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slider("value");e.height=this.$chartSettingsPanel.find("#height.numeric-slider-input").find(".slider").slider("value");var d=this.$chartSettingsPanel.find("input#X-axis-label").val(),c=this.$chartSettingsPanel.find("input#Y-axis-label").val();e.xLabel=(d==="X")?(f.X.colName):(d);e.yLabel=(c==="Y")?(f.Y.colName):(c);e.animDuration=10;if(this.$chartSettingsPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration=500}this.log("graphSettings:",e);return e},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});b.templates={form:Handlebars.templates["template-visualization-scatterplotControlForm"],statsTable:Handlebars.templates["template-visualization-statsTable"],chartSettings:Handlebars.templates["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +function TwoVarScatterplot(d){var b=10,f=7,e=10,c=8,a=5;this.log=function(){if(this.debugging&&console&&console.debug){var g=Array.prototype.slice.call(arguments);g.unshift(this.toString());console.debug.apply(console,g)}};this.log("new TwoVarScatterplot:",d);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:400,height:400,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,d);this.log("intial config:",this.config);this.updateConfig=function(g,h){_.extend(this.config,g);this.log(this+".updateConfig:",this.config)};this.toString=function(){return this.config.id};this.translateStr=function(g,h){return"translate("+g+","+h+")"};this.rotateStr=function(h,g,i){return"rotate("+h+","+g+","+i+")"};this.adjustChartDimensions=function(j,h,g,i){j=j||0;h=h||0;g=g||0;i=i||0;this.svg.attr("width",this.config.width+(this.config.marginRight+h)+(this.config.marginLeft+i)).attr("height",this.config.height+(this.config.marginTop+j)+(this.config.marginBottom+g)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+i,this.config.marginTop+j))};this.preprocessData=function(i,h,g){return(i.length>this.config.maxDataPoints)?(i.slice(0,this.config.maxDataPoints)):(i)};this.findMinMaxes=function(g,i,h){this.xMin=this.config.xMin||(h)?(h[0].min):(d3.min(g));this.xMax=this.config.xMax||(h)?(h[0].max):(d3.max(g));this.yMin=this.config.yMin||(h)?(h[1].min):(d3.min(i));this.yMax=this.config.yMax||(h)?(h[1].max):(d3.max(i))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);var g=d3.max(_.map([this.xMin,this.xMax],function(h){return(String(h)).length}));if(g>=a){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.log("this.config.xLabel:",this.config.xLabel);this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var g=this.yAxis.selectAll("text").filter(function(k,j){return j!==0});this.log("yTickLabels:",g);this.yLongestLabel=d3.max(g[0].map(function(k,j){return(d3.select(k).text()).length}))||0;var h=b+(this.yLongestLabel*f)+c+e;this.config.yAxisLabelBumpX=-(h-e);if(this.config.marginLeft<h){var i=(h)-this.config.marginLeft;i=(i<0)?(0):(i);this.adjustChartDimensions(0,0,0,i)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(g){};this.glyphFinalState=function(g){};this.glyphExitState=function(g){};this.renderDatapoints=function(g,j,h){this.log(this+".renderDatapoints",arguments);var i=0;this.datapoints=this.addDatapoints(g,j,h,".glyph");this.datapoints.exit().each(function(){i+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(i," glyphs removed")};this.addDatapoints=function(k,i,g,j){this.log(this+".addDatapoints",arguments);var n=this,m=0,o=function(q,p){return n.xScale(k[p])},h=function(q,p){return n.yScale(i[p])};var l=this.content.selectAll(j);this.log("existing datapoints:",l);l=l.data(k);m=0;l.enter().append("svg:circle").each(function(){m+=1}).classed("glyph",true).attr("cx",o).attr("cy",h).attr("r",0);this.log(m," new glyphs created");m=0;l.transition().duration(this.config.animDuration).each(function(){m+=1}).attr("cx",o).attr("cy",h).attr("r",n.config.datapointSize);this.log(m," existing glyphs transitioned");if(g){l.attr("data",function(q,p){return(g[p])})}l.attr("svg:title",function(q,p){return((g)?(g[p]+": "):(""))+k[p]+", "+i[p]});l.on("mouseover",function(r,p){var q=d3.select(this);q.style("fill","red").style("fill-opacity",1);n.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",q.attr("cx")).attr("y1",q.attr("cy")).attr("x2",0).attr("y2",q.attr("cy")).classed("hoverline",true);n.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",q.attr("cx")).attr("y1",q.attr("cy")).attr("x2",q.attr("cx")).attr("y2",n.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return l};this.render=function(i,j){this.log(this+".render",arguments);this.log("\t config:",this.config);var g=i[0],k=i[1],h=(i.length>2)?(i[2]):(undefined);g=this.preprocessData(g);k=this.preprocessData(k);this.log("xCol len",g.length,"yCol len",k.length);this.findMinMaxes(g,k,j);this.setUpScales();if(!this.svg){this.svg=d3.select("svg").attr("class","chart")}if(!this.content){this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id)}this.adjustChartDimensions();if(!this.xAxis){this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis")}if(!this.xAxisLabel){this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label")}if(!this.yAxis){this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis")}if(!this.yAxisLabel){this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label")}this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(g,k,h)}}; \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-chartControl.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-chartControl.js @@ -0,0 +1,38 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-chartControl'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + + return " checked=\"true\"";} + + buffer += "<p class=\"help-text\">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.datapointSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"animDuration\" class=\"form-input checkbox-input\">\n <label for=\"animated\">Animate graph transitions?: </label>\n <input type=\"checkbox\" id=\"animated\"\n class=\"checkbox control\""; + stack1 = depth0.animDuration; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Graph width: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.width; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Graph height: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.height; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; + foundHelper = helpers.xLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <div id=\"Y-axis-label\" class=\"text-input form-input\">\n <label for=\"Y-axis-label\">Re-label the Y axis: </label>\n <input type=\"text\" name=\"Y-axis-label\" id=\"Y-axis-label\" value=\""; + foundHelper = helpers.yLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />"; + return buffer;}); +})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-chartDisplay.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-chartDisplay.js @@ -0,0 +1,18 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-chartDisplay'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + buffer += "<svg width=\""; + foundHelper = helpers.width; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" height=\""; + foundHelper = helpers.height; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></svg>"; + return buffer;}); +})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-chartSettings.js --- a/static/scripts/templates/compiled/template-visualization-chartSettings.js +++ /dev/null @@ -1,38 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-visualization-chartSettings'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; - -function program1(depth0,data) { - - - return " checked=\"true\"";} - - buffer += "<p class=\"help-text\">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; - foundHelper = helpers.datapointSize; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"animDuration\" class=\"form-input checkbox-input\">\n <label for=\"animated\">Animate graph transitions?: </label>\n <input type=\"checkbox\" id=\"animated\"\n class=\"checkbox control\""; - stack1 = depth0.animDuration; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += " />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Graph width: </label>\n <div class=\"slider-output\">"; - foundHelper = helpers.width; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Graph height: </label>\n <div class=\"slider-output\">"; - foundHelper = helpers.height; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; - foundHelper = helpers.xLabel; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.xLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <div id=\"Y-axis-label\" class=\"text-input form-input\">\n <label for=\"Y-axis-label\">Re-label the Y axis: </label>\n <input type=\"text\" name=\"Y-axis-label\" id=\"Y-axis-label\" value=\""; - foundHelper = helpers.yLabel; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.yLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />"; - return buffer;}); -})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-dataControl.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-dataControl.js @@ -0,0 +1,65 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-dataControl'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + + buffer += "<p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n\n "; + buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n <div class=\"column-select\">\n <label for=\"Y-select\">Data column for Y: </label>\n <select name=\"Y\" id=\"Y-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n\n "; + buffer += "\n <div id=\"include-id\">\n <label for=\"include-id-checkbox\">Include a third column as data point IDs?</label>\n <input type=\"checkbox\" name=\"include-id\" id=\"include-id-checkbox\" />\n <p class=\"help-text-small\">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class=\"column-select\" style=\"display: none\">\n <label for=\"ID-select\">Data column for IDs: </label>\n <select name=\"ID\" id=\"ID-select\">\n "; + stack1 = depth0.allColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js @@ -2,75 +2,30 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-visualization-scatterplotControlForm'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <option value=\""; - foundHelper = helpers.index; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</option>\n "; - return buffer;} -function program3(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <option value=\""; - foundHelper = helpers.index; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</option>\n "; - return buffer;} - -function program5(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <option value=\""; - foundHelper = helpers.index; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</option>\n "; - return buffer;} - - buffer += "\n\n<ul class=\"nav nav-tabs\">\n <li class=\"active\"><a data-toggle=\"tab\" href=\"#data-settings\">Data Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-settings\">Plot Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-stats\">Statistics</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart\">Chart</a></li>\n</ul>\n\n"; - buffer += "\n<div class=\"tab-content\">\n<div id=\"data-settings\" class=\"tab-pane active\">\n\n <p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n "; - buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; - stack1 = depth0.numericColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n <div class=\"column-select\">\n <label for=\"Y-select\">Data column for Y: </label>\n <select name=\"Y\" id=\"Y-select\">\n "; - stack1 = depth0.numericColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n \n "; - buffer += "\n <div id=\"include-id\">\n <label for=\"include-id-checkbox\">Include a third column as data point IDs?</label>\n <input type=\"checkbox\" name=\"include-id\" id=\"include-id-checkbox\" />\n <p class=\"help-text-small\">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class=\"column-select\" style=\"display: none\">\n <label for=\"ID-select\">Data column for IDs: </label>\n <select name=\"ID\" id=\"ID-select\">\n "; - stack1 = depth0.allColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <input id=\"save-button\" type=\"button\" value=\"Download Plot as SVG\" style=\"display: none;\" />\n <div class=\"clear\"></div>\n</div>\n\n<div id=\"chart-settings\" class=\"tab-pane\">\n</div>\n\n<div id=\"chart-stats\" class=\"tab-pane\">\n</div>\n</div>"; - buffer += "\n\n"; - buffer += "\n<div id=\"loading-indicator\" style=\"display: none;\">\n <img class=\"loading-img\" src=\""; + buffer += "\n\n<div class=\"scatterplot-container chart-container tabbable tabs-left\">\n "; + buffer += "\n <ul class=\"nav nav-tabs\">\n "; + buffer += "\n <li class=\"active\"><a href=\"#data-control\" data-toggle=\"tab\" class=\"tooltip\"\n title=\"Use this tab to change which data are used\">Data Controls</a></li>\n <li><a href=\"#chart-control\" data-toggle=\"tab\" class=\"tooltip\"\n title=\"Use this tab to change how the chart is drawn\">Chart Controls</a></li>\n <li><a href=\"#stats-display\" data-toggle=\"tab\" class=\"tooltip\"\n title=\"This tab will display overall statistics for your data\">Statistics</a></li>\n <li><a href=\"#chart-display\" data-toggle=\"tab\" class=\"tooltip\"\n title=\"This tab will display the chart\">Chart</a>\n "; + buffer += "\n <div id=\"loading-indicator\" style=\"display: none;\">\n <img class=\"loading-img\" src=\""; foundHelper = helpers.loadingIndicatorImagePath; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.loadingIndicatorImagePath; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\">"; + buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\">"; foundHelper = helpers.message; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</span>\n</div>"; + buffer += escapeExpression(stack1) + "</span>\n </div>\n </li>\n </ul>\n\n "; + buffer += "\n <div class=\"tab-content\">\n "; + buffer += "\n <div id=\"data-control\" class=\"tab-pane active\">\n "; + buffer += "\n </div>\n \n "; + buffer += "\n <div id=\"chart-control\" class=\"tab-pane\">\n "; + buffer += "\n </div>\n\n "; + buffer += "\n <div id=\"stats-display\" class=\"tab-pane\">\n "; + buffer += "\n </div>\n\n "; + buffer += "\n <div id=\"chart-display\" class=\"tab-pane\">\n "; + buffer += "\n </div>\n\n </div>"; + buffer += "\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-statsDisplay.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-statsDisplay.js @@ -0,0 +1,31 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-statsDisplay'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <tr><td>"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.xval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.yval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td></tr>\n </tr>\n "; + return buffer;} + + buffer += "<p class=\"help-text\">By column:</p>\n <table id=\"chart-stats-table\">\n <thead><th></th><th>X</th><th>Y</th></thead>\n "; + stack1 = depth0.stats; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </table>"; + return buffer;}); +})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/compiled/template-visualization-statsTable.js --- a/static/scripts/templates/compiled/template-visualization-statsTable.js +++ /dev/null @@ -1,31 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-visualization-statsTable'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; - -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <tr><td>"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</td><td>"; - foundHelper = helpers.xval; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.xval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</td><td>"; - foundHelper = helpers.yval; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.yval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</td></tr>\n </tr>\n "; - return buffer;} - - buffer += "<p class=\"help-text\">By column:</p>\n <table id=\"chart-stats-table\">\n <thead><th></th><th>X</th><th>Y</th></thead>\n "; - stack1 = depth0.stats; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </table>"; - return buffer;}); -})(); \ No newline at end of file diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -1,22 +1,59 @@ <script type="text/template" class="template-visualization" id="template-visualization-scatterplotControlForm"> -{{! main controls }} +{{! main layout }} -<ul class="nav nav-tabs"> - <li class="active"><a data-toggle="tab" href="#data-settings">Data Controls</a></li> - <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li> - <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li> - <li><a data-toggle="tab" href="#chart">Chart</a></li> -</ul> +<div class="scatterplot-container chart-container tabbable tabs-left"> + {{! tab buttons/headers using Bootstrap }} + <ul class="nav nav-tabs"> + {{! start with the data controls as the displayed tab }} + <li class="active"><a href="#data-control" data-toggle="tab" class="tooltip" + title="Use this tab to change which data are used">Data Controls</a></li> + <li><a href="#chart-control" data-toggle="tab" class="tooltip" + title="Use this tab to change how the chart is drawn">Chart Controls</a></li> + <li><a href="#stats-display" data-toggle="tab" class="tooltip" + title="This tab will display overall statistics for your data">Statistics</a></li> + <li><a href="#chart-display" data-toggle="tab" class="tooltip" + title="This tab will display the chart">Chart</a> + {{! loading indicator - initially hidden }} + <div id="loading-indicator" style="display: none;"> + <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> + <span class="loading-message">{{message}}</span> + </div> + </li> + </ul> -{{! data settings }} -<div class="tab-content"> -<div id="data-settings" class="tab-pane active"> + {{! data form, chart config form, stats, and chart all get their own tab }} + <div class="tab-content"> + {{! ---------------------------- tab for data settings form }} + <div id="data-control" class="tab-pane active"> + {{! rendered separately }} + </div> + + {{! ---------------------------- tab for chart graphics control form }} + <div id="chart-control" class="tab-pane"> + {{! rendered separately }} + </div> + + {{! ---------------------------- tab for data statistics }} + <div id="stats-display" class="tab-pane"> + {{! rendered separately }} + </div> + + {{! ---------------------------- tab for actual chart }} + <div id="chart-display" class="tab-pane"> + {{! chart rendered separately }} + </div> + + </div>{{! end .tab-content }} +</div>{{! end .chart-control }} +</script> + +<script type="text/template" class="template-visualization" id="template-visualization-dataControl"><p class="help-text"> Use the following controls to change the data used by the chart. Use the 'Draw' button to render (or re-render) the chart with the current settings. </p> - + {{! column selector containers }} <div class="column-select"><label for="X-select">Data column for X: </label> @@ -34,7 +71,7 @@ {{/each}} </select></div> - + {{! optional id column }} <div id="include-id"><label for="include-id-checkbox">Include a third column as data point IDs?</label> @@ -52,47 +89,19 @@ {{/each}} </select></div> - + <input id="render-button" type="button" value="Draw" /> - <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" /><div class="clear"></div> -</div> - -<div id="chart-settings" class="tab-pane"> -</div> - -<div id="chart-stats" class="tab-pane"> -</div> -</div>{{! class="tab-content" }} - -{{! loading indicator - initially hidden }} -<div id="loading-indicator" style="display: none;"> - <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> - <span class="loading-message">{{message}}</span> -</div> - </script> -<script type="text/template" class="template-visualization" id="template-visualization-statsTable"> - <p class="help-text">By column:</p> - <table id="chart-stats-table"> - <thead><th></th><th>X</th><th>Y</th></thead> - {{#each stats}} - <tr><td>{{name}}</td><td>{{xval}}</td><td>{{yval}}</td></tr> - </tr> - {{/each}} - </table> -</script> - -<script type="text/template" class="template-visualization" id="template-visualization-chartSettings"> - +<script type="text/template" class="template-visualization" id="template-visualization-chartControl"><p class="help-text"> Use the following controls to how the chart is displayed. The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys. Move the focus between controls by using the tab or shift+tab keys on your keyboard. Use the 'Draw' button to render (or re-render) the chart with the current settings. </p> - + <div id="datapointSize" class="form-input numeric-slider-input"><label for="datapointSize">Size of data point: </label><div class="slider-output">{{datapointSize}}</div> @@ -143,3 +152,18 @@ <input id="render-button" type="button" value="Draw" /></script> + +<script type="text/template" class="template-visualization" id="template-visualization-statsDisplay"> + <p class="help-text">By column:</p> + <table id="chart-stats-table"> + <thead><th></th><th>X</th><th>Y</th></thead> + {{#each stats}} + <tr><td>{{name}}</td><td>{{xval}}</td><td>{{yval}}</td></tr> + </tr> + {{/each}} + </table> +</script> + +<script type="text/template" class="template-visualization" id="template-visualization-chartDisplay"> + <svg width="{{width}}" height="{{height}}"></svg> +</script> diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/utils/LazyDataLoader.js --- a/static/scripts/utils/LazyDataLoader.js +++ b/static/scripts/utils/LazyDataLoader.js @@ -1,3 +1,4 @@ +//============================================================================== /* TODO: ?? superclass dataloader, subclass lazydataloader?? @@ -213,3 +214,5 @@ loader.initialize( config ); return loader; } + +//============================================================================== diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,18 +1,3 @@ -define([ - "../libs/underscore", - - "../mvc/base-mvc", - "../utils/LazyDataLoader", - "../templates/compiled/template-visualization-scatterplotControlForm", - "../templates/compiled/template-visualization-statsTable", - "../templates/compiled/template-visualization-chartSettings", - - "../libs/d3", - - "../libs/bootstrap", - "../libs/jquery/jquery-ui" -], function(){ - /* ============================================================================= todo: outside this: @@ -106,8 +91,8 @@ yNumTicks : 10, xAxisLabelBumpY : 40, yAxisLabelBumpX : -35, - width : 500, - height : 500, + width : 400, + height : 400, //TODO: anyway to make this a sub-obj? marginTop : 50, marginRight : 50, @@ -123,11 +108,14 @@ yLabel : "Y" }; this.config = _.extend( {}, this.defaults, config ); + this.log( 'intial config:', this.config ); this.updateConfig = function( newConfig, rerender ){ // setter for chart config //TODO: validate here _.extend( this.config, newConfig ); + this.log( this + '.updateConfig:', this.config ); + //TODO: implement rerender flag }; // ........................................................ helpers @@ -143,20 +131,6 @@ }; // ........................................................ initial element creation - //NOTE: called on new - this.svg = d3.select( this.config.containerSelector ) - .append( "svg:svg" ).attr( "class", "chart" ); - - this.content = this.svg.append( "svg:g" ).attr( "class", "content" ).attr( 'id', this.config.id ); - - this.xAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ); - this.xAxisLabel = this.xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ); - - this.yAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ); - this.yAxisLabel = this.yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ); - - //this.log( 'built svg:', d3.selectAll( 'svg' ) ); - this.adjustChartDimensions = function( top, right, bottom, left ){ //this.log( this + '.adjustChartDimensions', arguments ); top = top || 0; @@ -186,8 +160,8 @@ return ( data.length > this.config.maxDataPoints )? ( data.slice( 0, this.config.maxDataPoints ) ): ( data ); }; - this.setUpDomains = function( xCol, yCol, meta ){ - //this.log( this + '.setUpDomains', arguments ); + this.findMinMaxes = function( xCol, yCol, meta ){ + //this.log( this + '.findMinMaxes', arguments ); // configuration takes priority, otherwise meta (from the server) if passed, last-resort: compute it here this.xMin = this.config.xMin || ( meta )?( meta[0].min ):( d3.min( xCol ) ); this.xMax = this.config.xMax || ( meta )?( meta[0].max ):( d3.max( xCol ) ); @@ -220,22 +194,22 @@ .call( this.xAxisFn ); //this.log( 'xAxis:', this.xAxis ); - this.xLongestLabel = d3.max( _.map( [ this.xMin, this.xMax ], + //TODO: adjust ticks when tick labels are long - move odds down and extend tick line + // (for now) hide them + var xLongestTickLabel = d3.max( _.map( [ this.xMin, this.xMax ], function( number ){ return ( String( number ) ).length; } ) ); - //this.log( 'xLongestLabel:', this.xLongestLabel ); - - if( this.xLongestLabel >= X_LABEL_TOO_LONG_AT ){ - //TODO: adjust ticks when tick labels are long - move odds down and extend tick line - // (for now) hide them + //this.log( 'xLongestTickLabel:', xLongestTickLabel ); + if( xLongestTickLabel >= X_LABEL_TOO_LONG_AT ){ this.xAxis.selectAll( 'g' ).filter( ':nth-child(odd)' ).style( 'display', 'none' ); } + this.log( 'this.config.xLabel:', this.config.xLabel ); this.xAxisLabel// = xAxis.select( 'text#x-axis-label' ) .attr( 'x', this.config.width / 2 ) .attr( 'y', this.config.xAxisLabelBumpY ) .attr( 'text-anchor', 'middle' ) .text( this.config.xLabel ); - //this.log( 'xAxisLabel:', this.xAxisLabel ); + this.log( 'xAxisLabel:', this.xAxisLabel ); }; this.setUpYAxis = function(){ @@ -248,9 +222,10 @@ .call( this.yAxisFn ); //this.log( 'yAxis:', this.yAxis ); + // a too complicated section for increasing the left margin when tick labels are long // get the tick labels for the y axis var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); - //this.log( 'yTickLabels:', yTickLabels ); + this.log( 'yTickLabels:', yTickLabels ); // get the longest label length (or 0 if no labels) this.yLongestLabel = d3.max( @@ -412,7 +387,7 @@ } // titles - newDatapoints.attr( 'title', function( d, i ){ + newDatapoints.attr( 'svg:title', function( d, i ){ return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; }); @@ -462,6 +437,9 @@ this.render = function( columnData, meta ){ this.log( this + '.render', arguments ); + this.log( '\t config:', this.config ); + + // prepare the data //pre: columns passed are numeric //pre: at least two columns are passed //assume: first column is x, second column is y, any remaining aren't used @@ -475,12 +453,32 @@ yCol = this.preprocessData( yCol ); this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); - this.setUpDomains( xCol, yCol, meta ); + this.findMinMaxes( xCol, yCol, meta ); //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + this.setUpScales(); + + // build the svg dom infrastructure + if( !this.svg ){ this.svg = d3.select( 'svg' ).attr( "class", "chart" ); } + if( !this.content ){ + this.content = this.svg.append( "svg:g" ).attr( "class", "content" ).attr( 'id', this.config.id ); + } + //this.log( 'svg:', this.svg ); + //this.log( 'content:', this.content ); + + this.adjustChartDimensions(); - this.setUpScales(); - this.adjustChartDimensions(); - + if( !this.xAxis ){ this.xAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ); } + if( !this.xAxisLabel ){ + this.xAxisLabel = this.xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ); + } + //this.log( 'xAxis:', this.xAxis, 'xAxisLabel:', this.xAxisLabel ); + + if( !this.yAxis ){ this.yAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ); } + if( !this.yAxisLabel ){ + this.yAxisLabel = this.yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ); + } + //this.log( 'yAxis:', this.yAxis, 'yAxisLabel:', this.yAxisLabel ); + this.setUpXAxis(); this.setUpYAxis(); @@ -490,510 +488,3 @@ } //============================================================================== -/** - * Scatterplot control UI as a backbone view - * handles: - * getting the desired data - * configuring the plot display - * showing (general) statistics - * - * initialize attributes REQUIRES a dataset and an apiDatasetsURL - */ -var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ - //logger : console, - className : 'scatterplot-settings-form', - - dataLoadDelay : 500, - dataLoadSize : 3001, - - loadingIndicatorImage : 'loading_large_white_bg.gif', - - initialize : function( attributes ){ - this.log( this + '.initialize, attributes:', attributes ); - - this.dataset = null; - this.chartConfig = null; - this.plot = null; - this.loader = null; - - this.$statsPanel = null; - this.$chartSettingsPanel = null; - this.$dataSettingsPanel = null; - this.dataFetch = null; - - this.initializeFromAttributes( attributes ); - this.initializeChart( attributes ); - this.initializeDataLoader( attributes ); - }, - - initializeFromAttributes : function( attributes ){ - // required settings: ensure certain vars we need are passed in attributes - if( !attributes || !attributes.dataset ){ - throw( "ScatterplotView requires a dataset" ); - } else { - this.dataset = attributes.dataset; - } - if( jQuery.type( this.dataset.metadata_column_types ) === 'string' ){ - this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); - } - this.log( 'dataset:', this.dataset ); - - // passed from mako helper - //TODO: integrate to galaxyPaths - if( !attributes.apiDatasetsURL ){ - throw( "ScatterplotView requires a apiDatasetsURL" ); - } else { - this.dataURL = attributes.apiDatasetsURL + '/' + this.dataset.id + '?'; - } - this.log( 'this.dataURL:', this.dataURL ); - }, - - initializeChart : function( attributes ){ - // set up the basic chart infrastructure and config (if any) - this.chartConfig = attributes.chartConfig || {}; - if( this.logger ){ this.chartConfig.debugging = true; } - this.log( 'initial chartConfig:', this.chartConfig ); - this.plot = new TwoVarScatterplot( this.chartConfig ); - this.chartConfig = this.plot.config; - }, - - initializeDataLoader : function( attributes ){ - // set up data loader - var view = this; - this.loader = new LazyDataLoader({ - logger : ( this.logger )?( this.logger ):( null ), - // we'll generate this when columns are chosen - url : null, - start : attributes.start || 0, - //NOTE: metadata_data_lines can be null (so we won't know the total) - total : attributes.total || this.dataset.metadata_data_lines, - delay : this.dataLoadDelay, - size : this.dataLoadSize, - - buildUrl : function( start, size ){ - // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params - return this.url + '&' + jQuery.param({ - start_val: start, - max_vals: size - }); - } - }); - $( this.loader ).bind( 'error', function( event, status, error ){ - view.log( 'ERROR:', status, error ); - alert( 'ERROR fetching data:\n' + status + '\n' + error ); - view.hideLoadingIndicator(); - }); - }, - - // ------------------------------------------------------------------------- CONTROLS RENDERING - render : function(){ - // render the data/chart control forms (but not the chart) - var view = this, - formData = { - config : this.chartConfig, - allColumns : [], - numericColumns : [], - loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage - }; - - //TODO: isNumericColumn - // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) - _.each( this.dataset.metadata_column_types, function( type, index ){ - // label with the name if available (fall back on 'column <index>') - var name = 'column ' + ( index + 1 ); - if( view.dataset.metadata_column_names ){ - name = view.dataset.metadata_column_names[ index ]; - } - - // filter numeric columns to their own list - if( type === 'int' || type === 'float' ){ - formData.numericColumns.push({ index: ( index + 1 ), name: name }); - } - formData.allColumns.push({ index: ( index + 1 ), name: name }); - }); - //TODO: other vals: max_vals, start_val, pagination (plot-settings) - - // render template and set up panels, store refs - this.$el.append( ScatterplotControlForm.templates.form( formData ) ); - - this.$dataSettingsPanel = this.$el.find( '.tab-pane#data-settings' ); - this.$chartSettingsPanel = this._render_chartSettings(); - this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); - - // preset to column selectors if they were passed in the config - this.$dataSettingsPanel.find( '#X-select' ).val( this.chartConfig.xColumn ); - this.$dataSettingsPanel.find( '#Y-select' ).val( this.chartConfig.yColumn ); - if( this.chartConfig.idColumn !== undefined ){ - this.$dataSettingsPanel.find( '#include-id-checkbox' ) - .attr( 'checked', true ).trigger( 'change' ); - this.$dataSettingsPanel.find( '#ID-select' ).val( this.chartConfig.idColumn ); - } - - //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); - - //TODO:?? add autoRender=1 to query maybe? - if( this.chartConfig.xColumn && this.chartConfig.yColumn ){ - this.renderPlot(); - } - return this; - }, - - //TODO: seems like a function of dataset or metadata - isColumnNumeric : function( index ){ - if( ( index >= 0 ) && ( index < this.dataset.metadata_column_types.length ) ){ - var columnType = this.dataset.metadata_column_types[ index ]; - return ( columnType === 'int' || columnType === 'float' ); - } - return false; - }, - - _render_chartSettings : function(){ - // chart settings panel - var chartControl = this, - $chartSettingsPanel = this.$el.find( '.tab-pane#chart-settings' ), - // limits for controls (by control/chartConfig id) - //TODO: move into TwoVarScatterplot - controlRanges = { - 'datapointSize' : { min: 2, max: 10, step: 1 }, - 'width' : { min: 200, max: 800, step: 20 }, - 'height' : { min: 200, max: 800, step: 20 } - }; - - // render the html - $chartSettingsPanel.append( ScatterplotControlForm.templates.chartSettings( this.chartConfig ) ); - - // set up js on sliders - $chartSettingsPanel.find( '.numeric-slider-input' ).each( function(){ - var $this = $( this ), - $output = $this.find( '.slider-output' ), - $slider = $this.find( '.slider' ), - id = $this.attr( 'id' ); - //chartControl.log( 'slider set up', 'this:', $this, 'slider:', $slider, 'id', id ); - - // what to do when the slider changes: update display and update chartConfig - function onSliderChange(){ - var $this = $( this ), - newValue = $this.slider( 'value' ); - //chartControl.log( 'slider change', 'this:', $this, 'output:', $output, 'value', newValue ); - $output.text( newValue ); - //chartControl.chartConfig[ id ] = newValue; - } - - $slider.slider( _.extend( controlRanges[ id ], { - value : chartControl.chartConfig[ id ], - change : onSliderChange, - slide : onSliderChange - })); - }); - - return $chartSettingsPanel; - }, - - // ------------------------------------------------------------------------- EVENTS - events : { - 'change #include-id-checkbox' : 'toggleThirdColumnSelector', - 'click #data-settings #render-button' : 'renderPlot', - 'click #chart-settings #render-button' : 'changeChartSettings' - }, - - toggleThirdColumnSelector : function(){ - // show/hide the id selector on the data settings panel - this.$el.find( 'select[name="ID"]' ).parent().toggle(); - }, - - showLoadingIndicator : function( message, callback ){ - // display the loading indicator over the tab panels if hidden, update message (if passed) - message = message || ''; - var indicator = this.$el.find( 'div#loading-indicator' ); - messageBox = indicator.find( '.loading-message' ); - - if( indicator.is( ':visible' ) ){ - if( message ){ - messageBox.fadeOut( 'fast', function(){ - messageBox.text( message ); - messageBox.fadeIn( 'fast', callback ); - }); - } else { - callback(); - } - - } else { - if( message ){ messageBox.text( message ); } - indicator.fadeIn( 'fast', callback ); - } - }, - - hideLoadingIndicator : function( callback ){ - this.$el.find( 'div#loading-indicator' ).fadeOut( 'fast', callback ); - }, - - // ------------------------------------------------------------------------- GRAPH/STATS RENDERING - renderPlot : function(){ - // fetch the data, (re-)render the chart - //TODO: separate data fetch - var view = this; - - // this is a complete re-render, so clear the prev. data - view.data = null; - view.meta = null; - - // update the chartConfig (here and plot) using graph settings - //TODO: separate and improve (used in changeChartSettings too) - _.extend( this.chartConfig, this.getGraphSettings() ); - this.log( 'this.chartConfig:', this.chartConfig ); - this.plot.updateConfig( this.chartConfig, false ); - - // build the url with the current data settings - this.loader.url = this.dataURL + '&' + jQuery.param( this.getDataSettings() ); - this.log( 'this.loader, url:', this.loader.url, 'total:', this.loader.total ); - - // bind the new data event to: aggregate data, update the chart and stats with new data - $( this.loader ).bind( 'loaded.new', function( event, response ){ - view.log( view + ' loaded.new', response ); - - // aggregate data and meta - view.postProcessDataFetchResponse( response ); - view.log( 'postprocessed data:', view.data, 'meta:', view.meta ); - - // update the graph and stats - view.showLoadingIndicator( 'Rendering...', function(){ - view.$el.find( 'ul.nav' ).find( 'a[href="#chart-stats"]' ).tab( 'show' ); - - view.plot.render( view.data, view.meta ); - view.renderStats( view.data, view.meta ); - view.hideLoadingIndicator(); - }); - }); - // when all data loaded - unbind (or we'll start doubling event handlers) - $( this.loader ).bind( 'complete', function( event, data ){ - view.log( 'complete', data ); - $( view.loader ).unbind(); - }); - - // begin loading the data - view.showLoadingIndicator( 'Fetching data...', function(){ view.loader.load(); }); - }, - - renderStats : function(){ - // render the stats table in the stats panel - //TODO: there's a better way - this.$statsPanel.html( ScatterplotControlForm.templates.statsTable({ - stats: [ - { name: 'Count', xval: this.meta[0].count, yval: this.meta[1].count }, - { name: 'Min', xval: this.meta[0].min, yval: this.meta[1].min }, - { name: 'Max', xval: this.meta[0].max, yval: this.meta[1].max }, - { name: 'Sum', xval: this.meta[0].sum, yval: this.meta[1].sum }, - { name: 'Mean', xval: this.meta[0].mean, yval: this.meta[1].mean }, - { name: 'Median', xval: this.meta[0].median, yval: this.meta[1].median } - ] - })); - }, - - changeChartSettings : function(){ - // re-render the chart with new chart settings and OLD data - var view = this; - newGraphSettings = this.getGraphSettings(); - - // update the chart config from the chartSettings panel controls - this.log( 'newGraphSettings:', newGraphSettings ); - _.extend( this.chartConfig, newGraphSettings ); - this.log( 'this.chartConfig:', this.chartConfig ); - this.plot.updateConfig( this.chartConfig, false ); - - // if there's current data, call plot.render with it (no data fetch) - if( view.data && view.meta ){ - view.showLoadingIndicator( 'Rendering...', function(){ - view.plot.render( view.data, view.meta ); - view.hideLoadingIndicator(); - }); - - // no current data, call renderPlot instead (which will fetch data) - } else { - this.renderPlot(); - } - }, - - // ------------------------------------------------------------------------- DATA AGGREGATION - postProcessDataFetchResponse : function( response ){ - // the loader only returns new data - it's up to this to munge the fetches together properly - //TODO: we're now storing data in two places: loader and here - // can't we reduce incoming data into loader.data[0]? are there concurrency problems? - this.postProcessData( response.data ); - this.postProcessMeta( response.meta ); - }, - - postProcessData : function( newData ){ - // stack the column data on top of each other into this.data - var view = this; - - // if we already have data: aggregate - if( view.data ){ - _.each( newData, function( newColData, colIndex ){ - //view.log( colIndex + ' data:', newColData ); - //TODO??: time, space efficiency of this? - view.data[ colIndex ] = view.data[ colIndex ].concat( newColData ); - }); - - // otherwise: assign (first load) - } else { - view.data = newData; - } - }, - - postProcessMeta : function( newMeta ){ - // munge the meta data (stats) from the server fetches together - //pre: this.data must be preprocessed (needed for medians) - var view = this, - colTypes = this.dataset.metadata_column_types; - - // if we already have meta: aggregate - if( view.meta ){ - _.each( newMeta, function( newColMeta, colIndex ){ - var colMeta = view.meta[ colIndex ], - colType = colTypes[ colIndex ]; - view.log( colIndex + ' postprocessing meta:', newColMeta ); - //view.log( colIndex + ' old meta:', - // 'min:', colMeta.min, - // 'max:', colMeta.max, - // 'sum:', colMeta.sum, - // 'mean:', colMeta.mean, - // 'median:', colMeta.median - //); - - //!TODO: at what point are we getting int/float overflow on these?! - //??: need to be null safe? - colMeta.count += ( newColMeta.count )?( newColMeta.count ):( 0 ); - view.log( colIndex, 'count:', colMeta.count ); - - if( ( colType === 'int' ) || ( colType === 'float' ) ){ - //view.log( colIndex + ' incoming meta:', - // 'min:', newColMeta.min, - // 'max:', newColMeta.max, - // 'sum:', newColMeta.sum, - // 'mean:', newColMeta.mean, - // 'median:', newColMeta.median - //); - - colMeta.min = Math.min( newColMeta.min, colMeta.min ); - colMeta.max = Math.max( newColMeta.max, colMeta.max ); - colMeta.sum = newColMeta.sum + colMeta.sum; - colMeta.mean = ( colMeta.count )?( colMeta.sum / colMeta.count ):( null ); - - // median's a pain bc of sorting (requires the data as well) - var sortedCol = view.data[ colIndex ].slice().sort(), - middleIndex = Math.floor( sortedCol.length / 2 ); - - if( sortedCol.length % 2 === 0 ){ - colMeta.median = ( ( sortedCol[ middleIndex ] + sortedCol[( middleIndex + 1 )] ) / 2 ); - - } else { - colMeta.median = sortedCol[ middleIndex ]; - } - - //view.log( colIndex + ' new meta:', - // 'min:', colMeta.min, - // 'max:', colMeta.max, - // 'sum:', colMeta.sum, - // 'mean:', colMeta.mean, - // 'median:', colMeta.median - //); - } - }); - - // otherwise: assign (first load) - } else { - view.meta = newMeta; - view.log( 'initial meta:', view.meta ); - } - }, - - // ------------------------------------------------------------------------- GET DATA/GRAPH SETTINGS - getDataSettings : function(){ - // parse the column values for both indeces (for the data fetch) and names (for the graph) - var columnSelections = this.getColumnSelections(), - columns = []; - this.log( 'columnSelections:', columnSelections ); - - //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string - - // get column indices for params, include the desired ID column (if any) - columns = [ columnSelections.X.colIndex, columnSelections.Y.colIndex ]; - if( this.$dataSettingsPanel.find( '#include-id-checkbox' ).attr( 'checked' ) ){ - columns.push( columnSelections.ID.colIndex ); - } - - //TODO: other vals: max, start, page - - var params = { - data_type : 'raw_data', - columns : '[' + columns + ']' - }; - this.log( 'params:', params ); - return params; - }, - - getColumnSelections : function(){ - // gets the current user-selected values for which columns to fetch from the data settings panel - // returns a map: { column-select name (eg. X) : { colIndex : column-selector val, - // colName : selected option text }, ... } - var selections = {}; - this.$dataSettingsPanel.find( 'div.column-select select' ).each( function(){ - var $this = $( this ), - val = parseInt( $this.val(), 10 ) - 1; - selections[ $this.attr( 'name' ) ] = { - colIndex : val, - colName : $this.children( '[value="' + val + '"]' ).text() - }; - }); - return selections; - }, - - getGraphSettings : function(){ - // gets the user-selected chartConfig from the chart settings panel - var settings = {}, - colSelections = this.getColumnSelections(); - //this.log( 'colSelections:', colSelections ); - - //TODO: simplify with keys and loop - settings.datapointSize = this.$chartSettingsPanel.find( '#datapointSize.numeric-slider-input' ) - .find( '.slider' ).slider( 'value' ); - settings.width = this.$chartSettingsPanel.find( '#width.numeric-slider-input' ) - .find( '.slider' ).slider( 'value' ); - settings.height = this.$chartSettingsPanel.find( '#height.numeric-slider-input' ) - .find( '.slider' ).slider( 'value' ); - - // update axes labels using chartSettings inputs (if not at defaults), otherwise the selects' colName - //TODO: a little confusing - var chartSettingsXLabel = this.$chartSettingsPanel.find( 'input#X-axis-label' ).val(), - chartSettingsYLabel = this.$chartSettingsPanel.find( 'input#Y-axis-label' ).val(); - settings.xLabel = ( chartSettingsXLabel === 'X' )? - ( colSelections.X.colName ):( chartSettingsXLabel ); - settings.yLabel = ( chartSettingsYLabel === 'Y' )? - ( colSelections.Y.colName ):( chartSettingsYLabel ); - - settings.animDuration = 10; - if( this.$chartSettingsPanel.find( '#animDuration.checkbox-input' ).is( ':checked' ) ){ - settings.animDuration = 500; - } - - this.log( 'graphSettings:', settings ); - return settings; - }, - - toString : function(){ - return 'ScatterplotControlForm(' + (( this.dataset )?( this.dataset.id ):( '' )) + ')'; - } -}); - -ScatterplotControlForm.templates = { - form : Handlebars.templates[ 'template-visualization-scatterplotControlForm' ], - statsTable : Handlebars.templates[ 'template-visualization-statsTable' ], - chartSettings : Handlebars.templates[ 'template-visualization-chartSettings' ] -}; - -//============================================================================== -return { - LazyDataLoader : LazyDataLoader, - TwoVarScatterplot : TwoVarScatterplot, - ScatterplotControlForm : ScatterplotControlForm -};}); diff -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 -r 9bf411ee2476c21c4c3fce6a5bbabf508f7505ff templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -12,21 +12,7 @@ /*TODO: use/move into base.less*/ * { margin: 0px; padding: 0px; } -/* -------------------------------------------- layout */ -.column { - position:relative; - overflow: auto; -} - -.left-column { - float: left; - width: 40%; -} - -.right-column { - margin-left: 41%; -} - +/* -------------------------------------------- general layout */ div.tab-pane { padding: 8px; } @@ -39,6 +25,7 @@ #chart-header { padding : 8px; background-color: #ebd9b2; + margin-bottom: 16px; } #chart-header .subtitle { @@ -48,90 +35,98 @@ font-size: small; } -/* -------------------------------------------- all controls */ -#chart-settings-form { +/* -------------------------------------------- main layout */ +#scatterplot { /*from width + margin of chart?*/ - padding-top: 1em; } -#chart-settings-form input[type=button], -#chart-settings-form select { +.scatterplot-container .tab-pane { +} + +/* -------------------------------------------- all controls */ + +#scatterplot input[type=button], +#scatterplot select { width: 100%; max-width: 256px; margin-bottom: 8px; } -#chart-settings-form .help-text, -#chart-settings-form .help-text-small { +#scatterplot .help-text, +#scatterplot .help-text-small { color: grey; } -#chart-settings-form .help-text { +#scatterplot .help-text { padding-bottom: 16px; } -#chart-settings-form .help-text-small { +#scatterplot .help-text-small { padding: 4px; font-size: smaller; } -#chart-settings-form > * { +#scatterplot > * { } -#chart-settings-form input[value=Draw] { +#scatterplot input[value=Draw] { display: block; margin-top: 16px; } +#scatterplot .numeric-slider-input { + max-width: 70%; +} + /* -------------------------------------------- data controls */ /* -------------------------------------------- chart controls */ -#chart-settings .form-input { +#chart-control .form-input { /*display: table-row;*/ } -#chart-settings label { +#chart-control label { /*text-align: right;*/ margin-bottom: 8px; /*display: table-cell;*/ } -#chart-settings .slider { +#chart-control .slider { /*display: table-cell;*/ height: 8px; display: block; margin: 8px 0px 0px 8px; } -#chart-settings .slider-output { +#chart-control .slider-output { /*display: table-cell;*/ float: right; } -#chart-settings input[type="text"] { +#chart-control input[type="text"] { border: 1px solid lightgrey; } /* -------------------------------------------- statistics */ -#chart-stats table#chart-stats-table { +#stats-display table#chart-stats-table { width: 100%; } -#chart-stats #chart-stats-table th { +#stats-display #chart-stats-table th { width: 30%; padding: 4px; font-weight: bold; color: grey; } -#chart-stats #chart-stats-table td { +#stats-display #chart-stats-table td { border: solid lightgrey; border-width: 1px 0px 0px 1px; padding: 4px; } -#chart-stats #chart-stats-table td:nth-child(1) { +#stats-display #chart-stats-table td:nth-child(1) { border-width: 1px 0px 0px 0px; padding-right: 1em; text-align: right; @@ -141,19 +136,12 @@ /* -------------------------------------------- load indicators */ #loading-indicator { - z-index: 2; - position: absolute; - top: 0; - bottom: 0; - left: 0; - right: 0; - background-color: white; - padding: 32px 0 0 32px; + margin: 12px 0px 0px 8px; } -#chart-settings-form #loading-indicator .loading-message { - margin-left: 10px; +#scatterplot #loading-indicator .loading-message { font-style: italic; + font-size: smaller; color: grey; } @@ -208,18 +196,37 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "libs/require" )} +${h.js( + + "libs/underscore", + "libs/jquery/jquery-ui", + "libs/d3", + + "mvc/base-mvc", + "utils/LazyDataLoader", + "viz/scatterplot" +)} + +${h.templates( + "../../templates/compiled/template-visualization-scatterplotControlForm", + "../../templates/compiled/template-visualization-dataControl", + "../../templates/compiled/template-visualization-chartControl", + "../../templates/compiled/template-visualization-chartDisplay", + "../../templates/compiled/template-visualization-statsDisplay" +)} + +${h.js( + "mvc/visualizations/scatterplotControlForm", +)} <script type="text/javascript"> -require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", }); +$(function(){ -require([ "viz/scatterplot" ], function( scatterplot ){ - var hda = ${h.to_json_string( hda )}, historyID = '${historyID}', querySettings = ${h.to_json_string( kwargs )}, chartConfig = _.extend( querySettings, { - containerSelector : '#chart-holder', + containerSelector : '#chart', //TODO: move to ScatterplotControlForm.initialize marginTop : ( querySettings.marginTop > 20 )?( querySettings.marginTop ):( 20 ), @@ -229,18 +236,29 @@ }); //console.debug( querySettings ); - var settingsForm = new scatterplot.ScatterplotControlForm({ + var settingsForm = new ScatterplotControlForm({ dataset : hda, apiDatasetsURL : "${h.url_for( controller='/api/datasets' )}", - el : $( '#chart-settings-form' ), + el : $( '#scatterplot' ), chartConfig : chartConfig }).render(); }); +</script> +</%def> +<%def name="body()"> +  + <div id="chart-header" class="header"> + <h2 class="title">Scatterplot of '${hda['name']}'</h2> + <p class="subtitle">${hda['misc_info']}</p> + </div> + <div id="scatterplot" class="scatterplot-control-form"></div> +</%def> + +<script type="text/javascript"> function make_abs_box( top, left, x, y, id ){ - console.debug( top, left, x, y, id ); var ARROW_SIZE = 8, ARROW_COLOR = 'grey', DIST_TO_POINT = 4, @@ -296,26 +314,4 @@ //console.debug( boxContainer ); return boxContainer; } - - </script> -</%def> - -<%def name="body()"> -  - <div id="chart-header" class="header"> - <h2 class="title">Scatterplot of '${hda['name']}'</h2> - <p class="subtitle">${hda['misc_info']}</p> - </div> - <div class="outer-container"> -  - <div id="chart-settings-form" class="column left-column"></div> -  - <div class="column right-column"> - <div id="chart-holder" class="inner-container"></div> - </div> - <div style="clear: both;"></div> - </div> - <div id="test"></div> - -</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8143d7f7b944/ changeset: 8143d7f7b944 user: jgoecks date: 2012-11-27 00:26:42 summary: Remove debugging statement. affected #: 1 file diff -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e -r 8143d7f7b94449889c1d590a3d72a3d20de291e3 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -564,7 +564,6 @@ // HACK: use a simple string to separate the elements in the // response: (1) table body; (2) number of pages in table; and (3) message. var parsed_response_text = response_text.split("*****"); - console.log(parsed_response_text); // Update grid body and footer. $('#grid-table-body').html(parsed_response_text[0]); 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: jgoecks: Some grid framework fixes.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1c5aa1094c41/ changeset: 1c5aa1094c41 user: jgoecks date: 2012-11-27 00:25:52 summary: Some grid framework fixes. affected #: 5 files diff -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -20,6 +20,7 @@ title = "" exposed = True model_class = None + show_item_checkboxes = False template = "grid_base.mako" async_template = "grid_base_async.mako" use_async = False @@ -273,7 +274,8 @@ message = message, use_panels=self.use_panels, webapp=webapp, - show_item_checkboxes = ( kwargs.get( 'show_item_checkboxes', '' ) in ['True', 'true'] ), + show_item_checkboxes = ( self.show_item_checkboxes or + kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ] ), # Pass back kwargs so that grid template can set and use args without # grid explicitly having to pass them. kwargs=kwargs ) diff -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -91,6 +91,7 @@ return item.name # Grid definition. + show_item_checkboxes = True template = "/page/select_items_grid.mako" async_template = "/page/select_items_grid_async.mako" default_filter = { "deleted" : "False" , "sharing" : "All" } diff -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -564,10 +564,13 @@ // HACK: use a simple string to separate the elements in the // response: (1) table body; (2) number of pages in table; and (3) message. var parsed_response_text = response_text.split("*****"); + console.log(parsed_response_text); // Update grid body and footer. $('#grid-table-body').html(parsed_response_text[0]); - $('#grid-table-footer').html(parsed_response_text[1]); + // FIXME: this does not work at all; what's needed is a function + // that updates page links when number of pages changes. + //$('#grid-table-footer').html(parsed_response_text[1]); // Trigger custom event to indicate grid body has changed. $('#grid-table-body').trigger('update'); @@ -906,7 +909,7 @@ %> Page: % if min_page > 1: - <span class='page-link'><a href="${url( page=1 )}" page_num="1">1</a></span> ... + <span class='page-link' id="page-link-1"><a href="${url( page=1 )}" page_num="1">1</a></span> ... % endif %for page_index in range(min_page, max_page + 1): %if page_index == cur_page_num: @@ -918,7 +921,7 @@ %endfor %if max_page < num_pages: ... - <span class='page-link'><a href="${url( page=num_pages )}" page_num="${num_pages}">${num_pages}</a></span> + <span class='page-link' id="page-link-${num_pages}"><a href="${url( page=num_pages )}" page_num="${num_pages}">${num_pages}</a></span> %endif </span> diff -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e templates/page/select_items_grid.mako --- a/templates/page/select_items_grid.mako +++ b/templates/page/select_items_grid.mako @@ -1,7 +1,7 @@ ## Template generates a grid that enables user to select items. <%namespace file="../grid_base.mako" import="*" /> -${javascripts()} +${grid_javascripts()} ${stylesheets()} ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} diff -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a -r 1c5aa1094c417760f0c48225f5a3dd8b71245b0e templates/page/select_items_grid_async.mako --- a/templates/page/select_items_grid_async.mako +++ b/templates/page/select_items_grid_async.mako @@ -2,7 +2,7 @@ <%namespace file="/display_common.mako" import="render_message" /> ## Always show item checkboxes so that users can select items. -${render_grid_table_body_contents( grid, show_item_checkboxes=True )} +${render_grid_table_body_contents( grid, show_item_checkboxes=show_item_checkboxes )} ***** ${num_pages} ***** 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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