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

commit/galaxy-central: dannon: Prevent galaxy session cookie from being accessed via script. We don't use it via js anywhere, only other cookies specifically set for dynatree/genetrack.
by Bitbucket 17 Sep '12

17 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dc749983abdf/ changeset: dc749983abdf user: dannon date: 2012-09-17 18:27:03 summary: Prevent galaxy session cookie from being accessed via script. We don't use it via js anywhere, only other cookies specifically set for dynatree/genetrack. affected #: 1 file diff -r 38015598badbfe47112bda3d6894a5a2c9bc9200 -r dc749983abdf243d6ff9a8295d917a2cec475771 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -347,6 +347,7 @@ tstamp = time.localtime ( time.time() + 3600 * 24 * age ) self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) self.response.cookies[name]['version'] = version + self.response.cookies[name]['httponly'] = True def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Sep '12

17 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c79b1228673a/ changeset: c79b1228673a user: james_taylor date: 2012-09-17 17:49:31 summary: trackster: starting to split tackster up and load using require.js affected #: 11 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/38015598badb/ changeset: 38015598badb user: james_taylor date: 2012-09-17 18:06:02 summary: trackster: merge affected #: 11 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster and sweepster fixes for vis framework refactoring.
by Bitbucket 16 Sep '12

16 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fe12d92febf9/ changeset: fe12d92febf9 user: jgoecks date: 2012-09-16 16:57:30 summary: Trackster and sweepster fixes for vis framework refactoring. affected #: 5 files diff -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 -r fe12d92febf99c19708ab5cb65a527366a2bece5 lib/galaxy/visualization/genome/data_providers.py --- a/lib/galaxy/visualization/genome/data_providers.py +++ b/lib/galaxy/visualization/genome/data_providers.py @@ -1186,6 +1186,12 @@ # Read first line in order to match chrom naming format. line = source.readline() + + # If line empty, assume file is empty and return empty iterator. + if len( line ) == 0: + return iter([]) + + # Determine chromosome naming format. dataset_chrom = line.split()[0] if not _chrom_naming_matches( chrom, dataset_chrom ): chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) diff -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 -r fe12d92febf99c19708ab5cb65a527366a2bece5 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -5,6 +5,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.web.controllers.library import LibraryListGrid from galaxy.visualization.genomes import decode_dbkey +from galaxy.visualization.genome.visual_analytics import get_dataset_job # # -- Grids -- diff -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 -r fe12d92febf99c19708ab5cb65a527366a2bece5 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -925,6 +925,9 @@ }, output.first().get('track_config')), track_obj = object_from_template(track_config, self, null); + // Track uses only raw data. + track_obj.data_manager.set('data_type', 'raw_data'); + // Set track block colors. track_obj.prefs.block_color = self.block_color; track_obj.prefs.reverse_strand_color = self.reverse_strand_color; diff -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 -r fe12d92febf99c19708ab5cb65a527366a2bece5 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -3843,8 +3843,8 @@ // Tool-execution specific post-draw init: - // Reset dataset state, wait time. - self.dataset_state_url = converted_datasets_state_url; + // Reset dataset check, wait time. + self.dataset_check_type = 'converted_datasets_state'; self.data_query_wait = DEFAULT_DATA_QUERY_WAIT; // Reset data URL when dataset indexing has completed/when not pending. @@ -3858,8 +3858,6 @@ $.when(ss_deferred.go()).then(function() { // Dataset is indexed, so use converted data. self.data_manager.set('data_type', 'data'); - self.dataset_check_type = 'converted_datasets_state'; - this.data_query_wait = 5000; }); // Reset post-draw actions function. diff -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 -r fe12d92febf99c19708ab5cb65a527366a2bece5 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -108,7 +108,7 @@ ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )} ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/sweepster", - "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider" )} + "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery-ui-1.8.23.custom.min" )} <script type="text/javascript"> var viz; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 15 Sep '12

15 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6243b992762c/ changeset: 6243b992762c user: jgoecks date: 2012-09-15 22:08:41 summary: Viz framework refactoring: remove tracks controller, moving code that handles data requests to the API and code that manages track browsers to visualization controller. affected #: 13 files diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -10,9 +10,6 @@ log = logging.getLogger( __name__ ) -def is_true ( a_str ): - return is_true == True or a_str in [ 'True', 'true', 'T', 't' ] - class DatasetsController( BaseAPIController, UsesVisualizationMixin ): @web.expose_api @@ -24,14 +21,11 @@ pass @web.expose_api - def show( self, trans, id, hda_ldda='hda', deleted='False', **kwd ): + def show( self, trans, id, hda_ldda='hda', data_type=None, **kwd ): """ GET /api/datasets/{encoded_dataset_id} Displays information about and/or content of a dataset. """ - - # Process arguments. - track_config = is_true( kwd.get( 'track_config', False ) ) # Get dataset. try: @@ -39,9 +33,18 @@ except Exception, e: return str( e ) - # Return info. - rval = None - if track_config: + # Use data type to return particular type of data. + if data_type == 'state': + rval = self._dataset_state( self, trans, dataset ) + elif data_type == 'converted_datasets_state': + rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ) ) + elif data_type == 'data': + rval = self._data( trans, dataset, **kwd ) + elif data_type == 'features': + rval = self._search_features( trans, dataset, kwd.get( 'query ' ) ) + elif data_type == 'raw_data': + rval = self._raw_data( trans, dataset, **kwd ) + elif data_type == 'track_config': rval = self.get_new_track_config( trans, dataset ) else: # Default: return dataset as API value. @@ -52,3 +55,172 @@ log.error( rval + ": %s" % str(e) ) trans.response.status = 500 return rval + + def _dataset_state( self, trans, dataset, **kwargs ): + """ Returns state of dataset. """ + + msg = self.check_dataset_state( trans, dataset ) + if not msg: + msg = messages.DATA + + return msg + + def _converted_datasets_state( self, trans, dataset, chrom=None ): + """ + Init-like method that returns state of dataset's converted datasets. Returns valid chroms + for that dataset as well. + """ + + msg = self.check_dataset_state( trans, dataset ) + if msg: + return msg + + # Get datasources and check for messages. + data_sources = self._get_datasources( trans, dataset ) + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + msg = get_highest_priority_msg( messages_list ) + if msg: + return msg + + # NOTE: finding valid chroms is prohibitive for large summary trees and is not currently used by + # the client. + valid_chroms = None + # Check for data in the genome window. + if data_sources.get( 'index' ): + tracks_dataset_type = data_sources['index']['name'] + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) + if not indexer.has_data( chrom ): + return messages.NO_DATA + #valid_chroms = indexer.valid_chroms() + else: + # Standalone data provider + standalone_provider = get_data_provider( data_sources['data_standalone']['name'] )( dataset ) + kwargs = {"stats": True} + if not standalone_provider.has_data( chrom ): + return messages.NO_DATA + #valid_chroms = standalone_provider.valid_chroms() + + # Have data if we get here + return { "status": messages.DATA, "valid_chroms": valid_chroms } + + def _search_features( self, trans, dataset, query ): + """ + Returns features, locations in dataset that match query. Format is a + list of features; each feature is a list itself: [name, location] + """ + if dataset.can_convert_to( "fli" ): + converted_dataset = dataset.get_converted_dataset( trans, "fli" ) + if converted_dataset: + data_provider = FeatureLocationIndexDataProvider( converted_dataset=converted_dataset ) + if data_provider: + return data_provider.get_data( query ) + + return [] + + + def _data( self, trans, dataset, chrom, low, high, start_val=0, max_vals=None, **kwargs ): + """ + Provides a block of data from a dataset. + """ + + # Parameter check. + if not chrom: + return messages.NO_DATA + + # Dataset check. + msg = self.check_dataset_state( trans, dataset ) + if msg: + return msg + + # Get datasources and check for messages. + data_sources = self._get_datasources( trans, dataset ) + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + return_message = get_highest_priority_msg( messages_list ) + if return_message: + return return_message + + extra_info = None + mode = kwargs.get( "mode", "Auto" ) + # Handle histogram mode uniquely for now: + if mode == "Coverage": + # Get summary using minimal cutoffs. + tracks_dataset_type = data_sources['index']['name'] + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) + summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 ) + if summary == "detail": + # Use maximum level of detail--2--to get summary data no matter the resolution. + summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) + frequencies, max_v, avg_v, delta = summary + return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + + if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": + # Only check for summary_tree if it's Auto mode (which is the default) + # + # Have to choose between indexer and data provider + tracks_dataset_type = data_sources['index']['name'] + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) + summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] ) + if summary is None: + return { 'dataset_type': tracks_dataset_type, 'data': None } + + if summary == "draw": + kwargs["no_detail"] = True # meh + extra_info = "no_detail" + elif summary != "detail": + frequencies, max_v, avg_v, delta = summary + return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + + # Get data provider. + if "data_standalone" in data_sources: + tracks_dataset_type = data_sources['data_standalone']['name'] + data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) + data_provider = data_provider_class( original_dataset=dataset ) + else: + tracks_dataset_type = data_sources['data']['name'] + data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) + data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) + + # Allow max_vals top be data provider set if not passed + if max_vals is None: + max_vals = data_provider.get_default_max_vals() + + # Get and return data from data_provider. + result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) + result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) + return result + + def _raw_data( self, trans, dataset, chrom, low, high, **kwargs ): + """ + Uses original (raw) dataset to return data. This method is useful + 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: + return msg + + low, high = int( low ), int( high ) + + # Return data. + data = None + # TODO: for raw data requests, map dataset type to provider using dict in data_providers.py + if isinstance( dataset.datatype, Gff ): + data = RawGFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'interval_index' + data[ 'extra_info' ] = None + elif isinstance( dataset.datatype, Bed ): + data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'interval_index' + data[ 'extra_info' ] = None + elif isinstance( dataset.datatype, Vcf ): + data = RawVcfDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'tabix' + data[ 'extra_info' ] = None + return data diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -450,7 +450,7 @@ session.add( vis_rev ) session.flush() encoded_id = trans.security.encode_id( vis.id ) - return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } + return { "vis_id": encoded_id, "url": url_for( action=vis.type, id=encoded_id ) } def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ /dev/null @@ -1,258 +0,0 @@ -""" -Support for constructing and viewing custom "track" browsers within Galaxy. -""" - -import re, pkg_resources -pkg_resources.require( "bx-python" ) - -from galaxy import model -from galaxy.util.json import to_json_string, from_json_string -from galaxy.web.base.controller import * -from galaxy.web.framework import simplejson -from galaxy.web.framework.helpers import time_ago, grids -from galaxy.util.bunch import Bunch -from galaxy.datatypes.interval import Gff, Bed -from galaxy.model import NoConverterException, ConverterDependencyException -from galaxy.visualization.genome.data_providers import * -from galaxy.visualization.genomes import decode_dbkey, Genomes -from galaxy.visualization.genome.visual_analytics import get_dataset_job - -class TracksController( BaseUIController, UsesVisualizationMixin, SharableMixin ): - """ - Controller for track browser interface. Handles building a new browser from - datasets in the current history, and display of the resulting browser. - """ - - @web.expose - @web.require_login() - def index( self, trans, **kwargs ): - config = {} - return trans.fill_template( "tracks/browser.mako", config=config, add_dataset=kwargs.get("dataset_id", None), \ - default_dbkey=kwargs.get("default_dbkey", None) ) - - @web.expose - @web.require_login() - def new_browser( self, trans, **kwargs ): - return trans.fill_template( "tracks/new_browser.mako", dbkeys=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), default_dbkey=kwargs.get("default_dbkey", None) ) - - @web.json - def save( self, trans, vis_json ): - """ - Save a visualization; if visualization does not have an ID, a new - visualization is created. Returns JSON of visualization. - """ - - # TODO: Need from_dict to convert json to Visualization object. - vis_config = from_json_string( vis_json ) - config = { - 'view': vis_config[ 'datasets' ], - 'bookmarks': vis_config[ 'bookmarks' ], - 'viewport': vis_config[ 'viewport' ] - } - type = vis_config[ 'type' ] - id = vis_config.get( 'id', None ) - title = vis_config[ 'title' ] - dbkey = vis_config[ 'dbkey' ] - annotation = vis_config.get( 'annotation', None ) - return self.save_visualization( trans, config, type, id, title, dbkey, annotation ) - - @web.expose - @web.require_login() - def browser(self, trans, id, **kwargs): - """ - Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`. - """ - vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) - viz_config = self.get_visualization_config( trans, vis ) - - new_dataset = kwargs.get("dataset_id", None) - if new_dataset is not None: - if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: - new_dataset = None # Already in browser, so don't add - return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) - - @web.json - def raw_data( self, trans, dataset_id, chrom, low, high, **kwargs ): - """ - Uses original (raw) dataset to return data. This method is useful - when the dataset is not yet indexed and hence using data would - be slow because indexes need to be created. - """ - - # Dataset check. - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - msg = self.check_dataset_state( trans, dataset ) - if msg: - return msg - - low, high = int( low ), int( high ) - - # Return data. - data = None - # TODO: for raw data requests, map dataset type to provider using dict in data_providers.py - if isinstance( dataset.datatype, Gff ): - data = RawGFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) - data[ 'dataset_type' ] = 'interval_index' - data[ 'extra_info' ] = None - elif isinstance( dataset.datatype, Bed ): - data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) - data[ 'dataset_type' ] = 'interval_index' - data[ 'extra_info' ] = None - elif isinstance( dataset.datatype, Vcf ): - data = RawVcfDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) - data[ 'dataset_type' ] = 'tabix' - data[ 'extra_info' ] = None - return data - - @web.json - def dataset_state( self, trans, dataset_id, **kwargs ): - """ Returns state of dataset. """ - - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - msg = self.check_dataset_state( trans, dataset ) - if not msg: - msg = messages.DATA - - return msg - - @web.json - def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None ): - """ - Init-like method that returns state of dataset's converted datasets. Returns valid chroms - for that dataset as well. - """ - # TODO: this code is copied from data() -- should refactor. - - # Dataset check. - if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - else: - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - msg = self.check_dataset_state( trans, dataset ) - if msg: - return msg - - # Get datasources and check for messages. - data_sources = self._get_datasources( trans, dataset ) - messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - msg = get_highest_priority_msg( messages_list ) - if msg: - return msg - - # NOTE: finding valid chroms is prohibitive for large summary trees and is not currently used by - # the client. - valid_chroms = None - # Check for data in the genome window. - if data_sources.get( 'index' ): - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) - if not indexer.has_data( chrom ): - return messages.NO_DATA - #valid_chroms = indexer.valid_chroms() - else: - # Standalone data provider - standalone_provider = get_data_provider( data_sources['data_standalone']['name'] )( dataset ) - kwargs = {"stats": True} - if not standalone_provider.has_data( chrom ): - return messages.NO_DATA - #valid_chroms = standalone_provider.valid_chroms() - - # Have data if we get here - return { "status": messages.DATA, "valid_chroms": valid_chroms } - - @web.json - def search_features( self, trans, hda_ldda, dataset_id, query ): - """ - Returns features, locations in dataset that match query. Format is a - list of features; each feature is a list itself: [name, location] - """ - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - if dataset.can_convert_to( "fli" ): - converted_dataset = dataset.get_converted_dataset( trans, "fli" ) - if converted_dataset: - data_provider = FeatureLocationIndexDataProvider( converted_dataset=converted_dataset ) - if data_provider: - return data_provider.get_data( query ) - - return [] - - @web.json - def data( self, trans, hda_ldda, dataset_id, chrom, low, high, start_val=0, max_vals=None, **kwargs ): - """ - Provides a block of data from a dataset. - """ - - # Parameter check. - if not chrom: - return messages.NO_DATA - - # Dataset check. - if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - else: - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - msg = self.check_dataset_state( trans, dataset ) - if msg: - return msg - - # Get datasources and check for messages. - data_sources = self._get_datasources( trans, dataset ) - messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - return_message = get_highest_priority_msg( messages_list ) - if return_message: - return return_message - - extra_info = None - mode = kwargs.get( "mode", "Auto" ) - # Handle histogram mode uniquely for now: - if mode == "Coverage": - # Get summary using minimal cutoffs. - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 ) - if summary == "detail": - # Use maximum level of detail--2--to get summary data no matter the resolution. - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) - frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } - - if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": - # Only check for summary_tree if it's Auto mode (which is the default) - # - # Have to choose between indexer and data provider - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] ) - if summary is None: - return { 'dataset_type': tracks_dataset_type, 'data': None } - - if summary == "draw": - kwargs["no_detail"] = True # meh - extra_info = "no_detail" - elif summary != "detail": - frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } - - # Get data provider. - if "data_standalone" in data_sources: - tracks_dataset_type = data_sources['data_standalone']['name'] - data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - data_provider = data_provider_class( original_dataset=dataset ) - else: - tracks_dataset_type = data_sources['data']['name'] - data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) - data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) - - # Allow max_vals top be data provider set if not passed - if max_vals is None: - max_vals = data_provider.get_default_max_vals() - - # Get and return data from data_provider. - result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) - result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) - return result diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -148,15 +148,9 @@ """ Returns dictionary used to create item link. """ - controller = "tracks" - if item.type == "trackster": - action = "browser" - elif item.type == "paramamonster": - action = "paramamonster" - elif item.type == "circster": - action = "circster" - elif item.type == "phyloviz": - # Support phyloviz + controller = "visualization" + action = item.type + if item.type == "phyloviz": controller = "phyloviz" action = "visualization" return dict( controller=controller, action=action, id=item.id ) @@ -679,6 +673,65 @@ help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) + # + # Visualizations. + # + + @web.expose + @web.require_login() + def new_browser( self, trans, **kwargs ): + """ + Provide info necessary for creating a new trackster browser. + """ + return trans.fill_template( "tracks/new_browser.mako", + dbkeys=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), + default_dbkey=kwargs.get("default_dbkey", None) ) + + @web.expose + @web.require_login() + def trackster(self, trans, id=None, **kwargs): + """ + Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`. + """ + + # Display new browser if no id provided. + if not id: + return trans.fill_template( "tracks/browser.mako", config={}, + add_dataset=kwargs.get("dataset_id", None), + default_dbkey=kwargs.get("default_dbkey", None) ) + + # Display saved visualization. + vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + viz_config = self.get_visualization_config( trans, vis ) + + # Get new dataset if specified. + new_dataset = kwargs.get("dataset_id", None) + if new_dataset is not None: + if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: + new_dataset = None # Already in browser, so don't add + return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) + + @web.json + def save_trackster( self, trans, vis_json ): + """ + Save a visualization; if visualization does not have an ID, a new + visualization is created. Returns JSON of visualization. + """ + + # TODO: Need from_dict to convert json to Visualization object. + vis_config = from_json_string( vis_json ) + config = { + 'view': vis_config[ 'datasets' ], + 'bookmarks': vis_config[ 'bookmarks' ], + 'viewport': vis_config[ 'viewport' ] + } + type = vis_config[ 'type' ] + id = vis_config.get( 'id', None ) + title = vis_config[ 'title' ] + dbkey = vis_config[ 'dbkey' ] + annotation = vis_config.get( 'annotation', None ) + return self.save_visualization( trans, config, type, id, title, dbkey, annotation ) + @web.expose def circster( self, trans, id, **kwargs ): """ diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -2974,12 +2974,10 @@ // // Attribute init. // - this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : default_data_url); + var url_base = datasets_url + '/' + obj_dict.dataset_id; + this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : url_base); this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); - this.dataset_check_url = ('converted_datasets_state_url' in obj_dict ? obj_dict.converted_datasets_state_url : converted_datasets_state_url); - this.feature_search_url = ('feature_search_url' in obj_dict ? obj_dict.feature_search_url : feature_search_url); - // A little ugly creating data manager right now due to transition to Backbone-based objects. var track = this, dataset = new Dataset({ @@ -2991,8 +2989,6 @@ new GenomeDataManager({ dataset: dataset, data_url: track.data_url, - dataset_state_url: track.dataset_check_url, - feature_search_url: track.feature_search_url, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset })); @@ -3312,9 +3308,12 @@ // Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. - var init_deferred = $.Deferred(); - $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, - function (result) { + var init_deferred = $.Deferred(), + params = { + hda_ldda: track.hda_ldda, + data_type: 'converted_datasets_state', + chrom: track.view.chrom} + $.getJSON(this.data_url, params, function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); track.tiles_div.text(DATA_ERROR); @@ -4320,8 +4319,10 @@ predraw_init: function() { var track = this; track.vertical_range = undefined; - return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: 0, high: track.view.max_high, - hda_ldda: track.hda_ldda, dataset_id: track.dataset_id }, function(result) { + return $.getJSON( track.data_url, + { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, + high: track.view.max_high, hda_ldda: track.hda_ldda, dataset_id: + track.dataset_id }, function(result) { track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -170,7 +170,6 @@ dataset: null, filters_manager: null, data_url: null, - dataset_state_url: null, feature_search_url: null, genome_wide_summary_data: null, data_mode_compatible: function(entry, mode) { return true; }, @@ -186,10 +185,11 @@ ready_deferred = $.Deferred(), ss_deferred = new ServerStateDeferred({ ajax_settings: { - url: this.get('dataset_state_url'), + url: this.get('data_url'), data: { dataset_id: dataset.id, - hda_ldda: dataset.get('hda_ldda') + hda_ldda: dataset.get('hda_ldda'), + data_type: 'state' }, dataType: "json" }, @@ -211,9 +211,10 @@ params = { query: query, dataset_id: dataset.id, - hda_ldda: dataset.get('hda_ldda') + hda_ldda: dataset.get('hda_ldda'), + data_type: 'features' }; - return $.getJSON(this.get('feature_search_url'), params); + return $.getJSON(this.get('data_url'), params); }, /** @@ -222,10 +223,11 @@ load_data: function(region, mode, resolution, extra_params) { // Setup data request params. var params = { + "data_type": "data", "chrom": region.get('chrom'), "low": region.get('start'), "high": region.get('end'), - "mode": mode, + "mode": mode, "resolution": resolution }, dataset = this.get('dataset'); @@ -743,7 +745,7 @@ var requests = []; $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { var data = { - 'track_config': true, + data_type: 'track_config', 'hda_ldda': 'hda' }, id = $(this).val(); diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -58,10 +58,7 @@ tool_url: '${h.url_for( controller="/api/tools" )}', history_url: '${h.url_for( controller="/api/histories" )}', - data_url: '${h.url_for( controller="/tracks", action="data" )}', - raw_data_url: '${h.url_for( controller="/tracks", action="raw_data" )}', - converted_datasets_state_url: '${h.url_for( controller="/tracks", action="converted_datasets_state" )}', - dataset_state_url: '${h.url_for( controller="/tracks", action="dataset_state" )}', + datasets_url: '${h.url_for( controller="/api/datasets" )}', sweepster_url: '${h.url_for( controller="/visualization", action="sweepster" )}', visualization_url: '${h.url_for( controller="/visualization", action="save" )}', }); diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -136,8 +136,8 @@ else: data_url = h.url_for( controller='visualization', action='list_tracks' ) trackster_urls[ 'hda-url' ] = data_url - trackster_urls[ 'action-url' ] = h.url_for( controller='tracks', action='browser', dataset_id=encoded_data_id ) - trackster_urls[ 'new-url' ] = h.url_for( controller='tracks', action='index', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) + trackster_urls[ 'action-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id ) + trackster_urls[ 'new-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) add_to_data( trackster_url=trackster_urls ) if trans.user: diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -235,8 +235,8 @@ data_url = h.url_for( controller='visualization', action='list_tracks' ) %><a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip trackster-add" - action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" - new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="View in Trackster"></a> + action-url="${h.url_for( controller='visualization', action='trackster', dataset_id=dataset_id)}" + new-url="${h.url_for( controller='visualization', action='trackster', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="View in Trackster"></a> %endif <% isPhylogenyData = isinstance(data.datatype, (Phyloxml, Nexus, Newick)) diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -77,7 +77,7 @@ $(".add-librarydataset").live("click", function() { var link = $(this); $.ajax({ - url: "/tracks/list_libraries", + url: "/visualization/list_libraries", error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, success: function(table_html) { show_modal( diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -23,13 +23,15 @@ <![endif]--> ${render_trackster_js_files()} +${h.js( "libs/jquery/jquery.autocomplete" )} + <script type="text/javascript"> // // Place URLs here so that url_for can be used to generate them. // galaxy_paths.set({ - visualization_url: "${h.url_for( action='save' )}" + visualization_url: "${h.url_for( action='save_trackster' )}" }); ${render_trackster_js_vars()} @@ -234,7 +236,7 @@ %if add_dataset is not None: $.ajax({ url: add_track_async_url + "/${add_dataset}", - data: { hda_ldda: 'hda', 'track_config': true }, + data: { hda_ldda: 'hda', data_type: 'track_config' }, dataType: "json", success: function(track_data) { view.add_drawable( object_from_template(track_data, view, view) ) } }); diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -18,11 +18,7 @@ <%def name="render_trackster_js_vars()"> var add_track_async_url = "${h.url_for( controller='/api/datasets' )}", add_datasets_url = "${h.url_for( controller='/visualization', action='list_current_history_datasets' )}", - default_data_url = "${h.url_for( controller='/tracks', action='data' )}", - raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", reference_url = "${h.url_for( controller='/api/genomes' )}", chrom_url = "${h.url_for( controller='/api/genomes' )}", - dataset_state_url = "${h.url_for( controller='/tracks', action='dataset_state' )}", - converted_datasets_state_url = "${h.url_for( controller='/tracks', action='converted_datasets_state' )}", - feature_search_url = "${h.url_for( controller='/tracks', action='search_features' )}"; + datasets_url = "${h.url_for( controller='/api/datasets' )}"; </%def> \ No newline at end of file diff -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 -r 6243b992762c3f90abda948e081d266ca63e1db0 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -98,7 +98,7 @@ ## Visualization menu. <% menu_options = [ - [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], + [_('New Visualization'), h.url_for( controller='/visualization', action='trackster' ) ], [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] ] tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) https://bitbucket.org/galaxy/galaxy-central/changeset/2f63df922488/ changeset: 2f63df922488 user: jgoecks date: 2012-09-15 23:06:36 summary: Bug fixes for changeset 6243b992762c that enable tools to be run in Trackster. Also add URL to all datasets and pack scripts. affected #: 19 files diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -7,6 +7,10 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.datatypes.interval import Gff, Bed +from galaxy.datatypes.tabular import Vcf +from galaxy.visualization.genome.data_providers import * +from galaxy.model import NoConverterException, ConverterDependencyException log = logging.getLogger( __name__ ) @@ -35,7 +39,7 @@ # Use data type to return particular type of data. if data_type == 'state': - rval = self._dataset_state( self, trans, dataset ) + rval = self._dataset_state( trans, dataset ) elif data_type == 'converted_datasets_state': rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ) ) elif data_type == 'data': diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -8,7 +8,9 @@ type: '', name: '', hda_ldda: 'hda' - } + }, + + urlRoot: galaxy_paths.get('datasets_url') }); var DatasetCollection = Backbone.Collection.extend({ diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/libs/require.js --- /dev/null +++ b/static/scripts/packed/libs/require.js @@ -0,0 +1,1 @@ +var requirejs,require,define;(function(global){var 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inCheckLoaded,Module,context,handlers,checkLoadedTimeoutId,config={waitSeconds:7,baseUrl:"./",paths:{},pkgs:{},shim:{}},registry={},undefEvents={},defQueue=[],defined={},urlFetched={},requireCounter=1,unnormalizedCounter=1,waitAry=[];function trimDots(ary){var i,part;for(i=0;ary[i];i+=1){part=ary[i];if(part==="."){ary.splice(i,1);i-=1}else{if(part===".."){if(i===1&&(ary[2]===".."||ary[0]==="..")){break}else{if(i>0){ary.splice(i-1,2);i-=2}}}}}}function normalize(name,baseName,applyMap){var pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(config.pkgs[baseName]){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=config.pkgs[(pkgName=name[0])];name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&(baseParts||starMap)&&map){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=map[baseParts.slice(0,j).join("/")];if(mapValue){mapValue=mapValue[nameSegment];if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&starMap[nameSegment]){foundStarMap=starMap[nameSegment];starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=config.paths[id];if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.undef(id);context.require([id]);return true}}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,index=name?name.indexOf("!"):-1,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}if(index!==-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=defined[prefix]}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return normalize(name,parentName,applyMap)})}else{normalizedName=normalize(name,parentName,applyMap)}}else{normalizedName=normalize(name,parentName,applyMap);url=context.nameToUrl(normalizedName)}}suffix=prefix&&!pluginModule&&!isNormalized?"_unnormalized"+(unnormalizedCounter+=1):"";return{prefix:prefix,name:normalizedName,parentMap:parentModuleMap,unnormalized:!!suffix,url:url,originalName:originalName,isDefine:isDefine,id:(prefix?prefix+"!"+normalizedName:normalizedName)+suffix}}function getModule(depMap){var id=depMap.id,mod=registry[id];if(!mod){mod=registry[id]=new context.Module(depMap)}return mod}function on(depMap,name,fn){var id=depMap.id,mod=registry[id];if(hasProp(defined,id)&&(!mod||mod.defineEmitComplete)){if(name==="defined"){fn(defined[id])}}else{getModule(depMap).on(name,fn)}}function onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=registry[id];if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}function makeRequire(mod,enableBuildCallback,altRequire){var relMap=mod&&mod.map,modRequire=makeContextModuleFunc(altRequire||context.require,relMap,enableBuildCallback);addRequireMethods(modRequire,context,relMap);modRequire.isBrowser=isBrowser;return modRequire}handlers={require:function(mod){return makeRequire(mod)},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){return(mod.exports=defined[mod.map.id]={})}},module:function(mod){return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){return(config.config&&config.config[mod.map.id])||{}},exports:defined[mod.map.id]})}};function removeWaiting(id){delete registry[id];each(waitAry,function(mod,i){if(mod.map.id===id){waitAry.splice(i,1);if(!mod.defined){context.waitCount-=1}return true}})}function findCycle(mod,traced,processed){var id=mod.map.id,depArray=mod.depMaps,foundModule;if(!mod.inited){return}if(traced[id]){return mod}traced[id]=true;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId];if(!depMod||processed[depId]||!depMod.inited||!depMod.enabled){return}return(foundModule=findCycle(depMod,traced,processed))});processed[id]=true;return foundModule}function forceExec(mod,traced,uninited){var id=mod.map.id,depArray=mod.depMaps;if(!mod.inited||!mod.map.isDefine){return}if(traced[id]){return defined[id]}traced[id]=mod;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId],value;if(handlers[depId]){return}if(depMod){if(!depMod.inited||!depMod.enabled){uninited[id]=true;return}value=forceExec(depMod,traced,uninited);if(!uninited[depId]){mod.defineDepById(depId,value)}}});mod.check(true);return defined[id]}function modCheck(mod){mod.check()}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)<new Date().getTime(),noLoads=[],stillLoading=false,needCycleCheck=true;if(inCheckLoaded){return}inCheckLoaded=true;eachProp(registry,function(mod){map=mod.map;modId=map.id;if(!mod.enabled){return}if(!mod.error){if(!mod.inited&&expired){if(hasPathFallback(modId)){usingPathFallback=true;stillLoading=true}else{noLoads.push(modId);removeScript(modId)}}else{if(!mod.inited&&mod.fetched&&map.isDefine){stillLoading=true;if(!map.prefix){return(needCycleCheck=false)}}}}});if(expired&&noLoads.length){err=makeError("timeout","Load timeout for modules: "+noLoads,null,noLoads);err.contextName=context.contextName;return onError(err)}if(needCycleCheck){each(waitAry,function(mod){if(mod.defined){return}var cycleMod=findCycle(mod,{},{}),traced={};if(cycleMod){forceExec(cycleMod,traced,{});eachProp(traced,modCheck)}});eachProp(registry,modCheck)}if((!expired||usingPathFallback)&&stillLoading){if((isBrowser||isWebWorker)&&!checkLoadedTimeoutId){checkLoadedTimeoutId=setTimeout(function(){checkLoadedTimeoutId=0;checkLoaded()},50)}}inCheckLoaded=false}Module=function(map){this.events=undefEvents[map.id]||{};this.map=map;this.shim=config.shim[map.id];this.depExports=[];this.depMaps=[];this.depMatched=[];this.pluginMaps={};this.depCount=0};Module.prototype={init:function(depMaps,factory,errback,options){options=options||{};if(this.inited){return}this.factory=factory;if(errback){this.on("error",errback)}else{if(this.events.error){errback=bind(this,function(err){this.emit("error",err)})}}this.depMaps=depMaps&&depMaps.slice(0);this.depMaps.rjsSkipMap=depMaps.rjsSkipMap;this.errback=errback;this.inited=true;this.ignore=options.ignore;if(options.enabled||this.enabled){this.enable()}else{this.check()}},defineDepById:function(id,depExports){var i;each(this.depMaps,function(map,index){if(map.id===id){i=index;return true}});return this.defineDep(i,depExports)},defineDep:function(i,depExports){if(!this.depMatched[i]){this.depMatched[i]=true;this.depCount-=1;this.depExports[i]=depExports}},fetch:function(){if(this.fetched){return}this.fetched=true;context.startTime=(new Date()).getTime();var map=this.map;if(this.shim){makeRequire(this,true)(this.shim.deps||[],bind(this,function(){return map.prefix?this.callPlugin():this.load()}))}else{return map.prefix?this.callPlugin():this.load()}},load:function(){var url=this.map.url;if(!urlFetched[url]){urlFetched[url]=true;context.load(this.map.id,url)}},check:function(silent){if(!this.enabled||this.enabling){return}var err,cjsModule,id=this.map.id,depExports=this.depExports,exports=this.exports,factory=this.factory;if(!this.inited){this.fetch()}else{if(this.error){this.emit("error",this.error)}else{if(!this.defining){this.defining=true;if(this.depCount<1&&!this.defined){if(isFunction(factory)){if(this.events.error){try{exports=context.execCb(id,factory,depExports,exports)}catch(e){err=e}}else{exports=context.execCb(id,factory,depExports,exports)}if(this.map.isDefine){cjsModule=this.module;if(cjsModule&&cjsModule.exports!==undefined&&cjsModule.exports!==this.exports){exports=cjsModule.exports}else{if(exports===undefined&&this.usingExports){exports=this.exports}}}if(err){err.requireMap=this.map;err.requireModules=[this.map.id];err.requireType="define";return onError((this.error=err))}}else{exports=factory}this.exports=exports;if(this.map.isDefine&&!this.ignore){defined[id]=exports;if(req.onResourceLoad){req.onResourceLoad(context,this.map,this.depMaps)}}delete registry[id];this.defined=true;context.waitCount-=1;if(context.waitCount===0){waitAry=[]}}this.defining=false;if(!silent){if(this.defined&&!this.defineEmitted){this.defineEmitted=true;this.emit("defined",this.exports);this.defineEmitComplete=true}}}}}},callPlugin:function(){var map=this.map,id=map.id,pluginMap=makeModuleMap(map.prefix,null,false,true);on(pluginMap,"defined",bind(this,function(plugin){var load,normalizedMap,normalizedMod,name=this.map.name,parentName=this.map.parentMap?this.map.parentMap.name:null;if(this.map.unnormalized){if(plugin.normalize){name=plugin.normalize(name,function(name){return normalize(name,parentName,true)})||""}normalizedMap=makeModuleMap(map.prefix+"!"+name,this.map.parentMap,false,true);on(normalizedMap,"defined",bind(this,function(value){this.init([],function(){return value},null,{enabled:true,ignore:true})}));normalizedMod=registry[normalizedMap.id];if(normalizedMod){if(this.events.error){normalizedMod.on("error",bind(this,function(err){this.emit("error",err)}))}normalizedMod.enable()}return}load=bind(this,function(value){this.init([],function(){return value},null,{enabled:true})});load.error=bind(this,function(err){this.inited=true;this.error=err;err.requireModules=[id];eachProp(registry,function(mod){if(mod.map.id.indexOf(id+"_unnormalized")===0){removeWaiting(mod.map.id)}});onError(err)});load.fromText=function(moduleName,text){var hasInteractive=useInteractive;if(hasInteractive){useInteractive=false}getModule(makeModuleMap(moduleName));req.exec(text);if(hasInteractive){useInteractive=true}context.completeLoad(moduleName)};plugin.load(map.name,makeRequire(map.parentMap,true,function(deps,cb,er){deps.rjsSkipMap=true;return context.require(deps,cb,er)}),load,config)}));context.enable(pluginMap,this);this.pluginMaps[pluginMap.id]=pluginMap},enable:function(){this.enabled=true;if(!this.waitPushed){waitAry.push(this);context.waitCount+=1;this.waitPushed=true}this.enabling=true;each(this.depMaps,bind(this,function(depMap,i){var id,mod,handler;if(typeof depMap==="string"){depMap=makeModuleMap(depMap,(this.map.isDefine?this.map:this.map.parentMap),false,!this.depMaps.rjsSkipMap);this.depMaps[i]=depMap;handler=handlers[depMap.id];if(handler){this.depExports[i]=handler(this);return}this.depCount+=1;on(depMap,"defined",bind(this,function(depExports){this.defineDep(i,depExports);this.check()}));if(this.errback){on(depMap,"error",this.errback)}}id=depMap.id;mod=registry[id];if(!handlers[id]&&mod&&!mod.enabled){context.enable(depMap,this)}}));eachProp(this.pluginMaps,bind(this,function(pluginMap){var mod=registry[pluginMap.id];if(mod&&!mod.enabled){context.enable(pluginMap,this)}}));this.enabling=false;this.check()},on:function(name,cb){var cbs=this.events[name];if(!cbs){cbs=this.events[name]=[]}cbs.push(cb)},emit:function(name,evt){each(this.events[name],function(cb){cb(evt)});if(name==="error"){delete this.events[name]}}};function callGetModule(args){getModule(makeModuleMap(args[0],null,true)).init(args[1],args[2])}function removeListener(node,func,name,ieName){if(node.detachEvent&&!isOpera){if(ieName){node.detachEvent(ieName,func)}}else{node.removeEventListener(name,func,false)}}function getScriptData(evt){var node=evt.currentTarget||evt.srcElement;removeListener(node,context.onScriptLoad,"load","onreadystatechange");removeListener(node,context.onScriptError,"error");return{node:node,id:node&&node.getAttribute("data-requiremodule")}}return(context={config:config,contextName:contextName,registry:registry,defined:defined,urlFetched:urlFetched,waitCount:0,defQueue:defQueue,Module:Module,makeModuleMap:makeModuleMap,configure:function(cfg){if(cfg.baseUrl){if(cfg.baseUrl.charAt(cfg.baseUrl.length-1)!=="/"){cfg.baseUrl+="/"}}var pkgs=config.pkgs,shim=config.shim,paths=config.paths,map=config.map;mixin(config,cfg,true);config.paths=mixin(paths,cfg.paths,true);if(cfg.map){config.map=mixin(map||{},cfg.map,true,true)}if(cfg.shim){eachProp(cfg.shim,function(value,id){if(isArray(value)){value={deps:value}}if(value.exports&&!value.exports.__buildReady){value.exports=context.makeShimExports(value.exports)}shim[id]=value});config.shim=shim}if(cfg.packages){each(cfg.packages,function(pkgObj){var location;pkgObj=typeof pkgObj==="string"?{name:pkgObj}:pkgObj;location=pkgObj.location;pkgs[pkgObj.name]={name:pkgObj.name,location:location||pkgObj.name,main:(pkgObj.main||"main").replace(currDirRegExp,"").replace(jsSuffixRegExp,"")}});config.pkgs=pkgs}eachProp(registry,function(mod,id){if(!mod.inited&&!mod.map.unnormalized){mod.map=makeModuleMap(id)}});if(cfg.deps||cfg.callback){context.require(cfg.deps||[],cfg.callback)}},makeShimExports:function(exports){var func;if(typeof exports==="string"){func=function(){return getGlobal(exports)};func.exports=exports;return func}else{return function(){return exports.apply(global,arguments)}}},requireDefined:function(id,relMap){return hasProp(defined,makeModuleMap(id,relMap,false,true).id)},requireSpecified:function(id,relMap){id=makeModuleMap(id,relMap,false,true).id;return hasProp(defined,id)||hasProp(registry,id)},require:function(deps,callback,errback,relMap){var moduleName,id,map,requireMod,args;if(typeof deps==="string"){if(isFunction(callback)){return onError(makeError("requireargs","Invalid require call"),errback)}if(req.get){return req.get(context,deps,callback)}moduleName=deps;relMap=callback;map=makeModuleMap(moduleName,relMap,false,true);id=map.id;if(!hasProp(defined,id)){return onError(makeError("notloaded",'Module name "'+id+'" has not been loaded yet for context: '+contextName))}return defined[id]}if(errback&&!isFunction(errback)){relMap=errback;errback=undefined}if(callback&&!isFunction(callback)){relMap=callback;callback=undefined}takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){return onError(makeError("mismatch","Mismatched anonymous define() module: "+args[args.length-1]))}else{callGetModule(args)}}requireMod=getModule(makeModuleMap(null,relMap));requireMod.init(deps,callback,errback,{enabled:true});checkLoaded();return context.require},undef:function(id){takeGlobalQueue();var map=makeModuleMap(id,null,true),mod=registry[id];delete defined[id];delete urlFetched[map.url];delete undefEvents[id];if(mod){if(mod.events.defined){undefEvents[id]=mod.events}removeWaiting(id)}},enable:function(depMap,parent){var mod=registry[depMap.id];if(mod){getModule(depMap).enable()}},completeLoad:function(moduleName){var found,args,mod,shim=config.shim[moduleName]||{},shExports=shim.exports&&shim.exports.exports;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){args[0]=moduleName;if(found){break}found=true}else{if(args[0]===moduleName){found=true}}callGetModule(args)}mod=registry[moduleName];if(!found&&!defined[moduleName]&&mod&&!mod.inited){if(config.enforceDefine&&(!shExports||!getGlobal(shExports))){if(hasPathFallback(moduleName)){return}else{return onError(makeError("nodefine","No define call for "+moduleName,null,[moduleName]))}}else{callGetModule([moduleName,(shim.deps||[]),shim.exports])}}checkLoaded()},toUrl:function(moduleNamePlusExt,relModuleMap){var index=moduleNamePlusExt.lastIndexOf("."),ext=null;if(index!==-1){ext=moduleNamePlusExt.substring(index,moduleNamePlusExt.length);moduleNamePlusExt=moduleNamePlusExt.substring(0,index)}return context.nameToUrl(normalize(moduleNamePlusExt,relModuleMap&&relModuleMap.id,true),ext)},nameToUrl:function(moduleName,ext){var paths,pkgs,pkg,pkgPath,syms,i,parentModule,url,parentPath;if(req.jsExtRegExp.test(moduleName)){url=moduleName+(ext||"")}else{paths=config.paths;pkgs=config.pkgs;syms=moduleName.split("/");for(i=syms.length;i>0;i-=1){parentModule=syms.slice(0,i).join("/");pkg=pkgs[parentModule];parentPath=paths[parentModule];if(parentPath){if(isArray(parentPath)){parentPath=parentPath[0]}syms.splice(0,i,parentPath);break}else{if(pkg){if(moduleName===pkg.name){pkgPath=pkg.location+"/"+pkg.main}else{pkgPath=pkg.location}syms.splice(0,i,pkgPath);break}}}url=syms.join("/");url+=(ext||(/\?/.test(url)?"":".js"));url=(url.charAt(0)==="/"||url.match(/^[\w\+\.\-]+:/)?"":config.baseUrl)+url}return config.urlArgs?url+((url.indexOf("?")===-1?"?":"&")+config.urlArgs):url},load:function(id,url){req.load(context,id,url)},execCb:function(name,callback,args,exports){return callback.apply(exports,args)},onScriptLoad:function(evt){if(evt.type==="load"||(readyRegExp.test((evt.currentTarget||evt.srcElement).readyState))){interactiveScript=null;var data=getScriptData(evt);context.completeLoad(data.id)}},onScriptError:function(evt){var data=getScriptData(evt);if(!hasPathFallback(data.id)){return onError(makeError("scripterror","Script error",evt,[data.id]))}}})}req=requirejs=function(deps,callback,errback,optional){var context,config,contextName=defContextName;if(!isArray(deps)&&typeof deps!=="string"){config=deps;if(isArray(callback)){deps=callback;callback=errback;errback=optional}else{deps=[]}}if(config&&config.context){contextName=config.context}context=contexts[contextName];if(!context){context=contexts[contextName]=req.s.newContext(contextName)}if(config){context.configure(config)}return context.require(deps,callback,errback)};req.config=function(config){return req(config)};if(!require){require=req}req.version=version;req.jsExtRegExp=/^\/|:|\?|\.js$/;req.isBrowser=isBrowser;s=req.s={contexts:contexts,newContext:newContext};req({});addRequireMethods(req);if(isBrowser){head=s.head=document.getElementsByTagName("head")[0];baseElement=document.getElementsByTagName("base")[0];if(baseElement){head=s.head=baseElement.parentNode}}req.onError=function(err){throw err};req.load=function(context,moduleName,url){var config=(context&&context.config)||{},node;if(isBrowser){node=config.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");node.type=config.scriptType||"text/javascript";node.charset="utf-8";node.async=true;node.setAttribute("data-requirecontext",context.contextName);node.setAttribute("data-requiremodule",moduleName);if(node.attachEvent&&!(node.attachEvent.toString&&node.attachEvent.toString().indexOf("[native code")<0)&&!isOpera){useInteractive=true;node.attachEvent("onreadystatechange",context.onScriptLoad)}else{node.addEventListener("load",context.onScriptLoad,false);node.addEventListener("error",context.onScriptError,false)}node.src=url;currentlyAddingScript=node;if(baseElement){head.insertBefore(node,baseElement)}else{head.appendChild(node)}currentlyAddingScript=null;return node}else{if(isWebWorker){importScripts(url);context.completeLoad(moduleName)}}};function getInteractiveScript(){if(interactiveScript&&interactiveScript.readyState==="interactive"){return interactiveScript}eachReverse(scripts(),function(script){if(script.readyState==="interactive"){return(interactiveScript=script)}});return interactiveScript}if(isBrowser){eachReverse(scripts(),function(script){if(!head){head=script.parentNode}dataMain=script.getAttribute("data-main");if(dataMain){if(!cfg.baseUrl){src=dataMain.split("/");mainScript=src.pop();subPath=src.length?src.join("/")+"/":"./";cfg.baseUrl=subPath;dataMain=mainScript}dataMain=dataMain.replace(jsSuffixRegExp,"");cfg.deps=cfg.deps?cfg.deps.concat(dataMain):[dataMain];return true}})}define=function(name,deps,callback){var node,context;if(typeof name!=="string"){callback=deps;deps=name;name=null}if(!isArray(deps)){callback=deps;deps=[]}if(!deps.length&&isFunction(callback)){if(callback.length){callback.toString().replace(commentRegExp,"").replace(cjsRequireRegExp,function(match,dep){deps.push(dep)});deps=(callback.length===1?["require"]:["require","exports","module"]).concat(deps)}}if(useInteractive){node=currentlyAddingScript||getInteractiveScript();if(node){if(!name){name=node.getAttribute("data-requiremodule")}context=contexts[node.getAttribute("data-requirecontext")]}}(context?context.defQueue:globalDefQueue).push([name,deps,callback])};define.amd={jQuery:true};req.exec=function(text){return eval(text)};req(cfg)}(this)); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -var Dataset=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda"}});var DatasetCollection=Backbone.Collection.extend({model:Dataset}); \ No newline at end of file +var Dataset=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda"},urlRoot:galaxy_paths.get("datasets_url")});var DatasetCollection=Backbone.Collection.extend({model:Dataset}); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -function linkHTMLTemplate(b,a){if(!b){return"<a></a>"}a=a||"a";var c=["<"+a];for(key in b){var d=b[key];if(d===""){continue}switch(key){case"text":continue;case"classes":key="class";d=(b.classes.join)?(b.classes.join(" ")):(b.classes);default:c.push([" ",key,'="',d,'"'].join(""))}}c.push(">");if("text" in b){c.push(b.text)}c.push("</"+a+">");return c.join("")}var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"))},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({logger:console,tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){this.log(this+".model:",this.model);var d=this.model.get("id"),c=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+d);var a=$("<div/>").attr("id","historyItem-"+d).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});var b=a.find("[popupmenu]");b.each(function(e,f){f=$(f);make_popupmenu(f)});this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display",}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display",});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a=(this.model.get("delete_url"))?({title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"}):({title:"Dataset is already deleted",icon_class:"delete",enabled:false});this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){this.log("model:",this.model.toJSON());return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_showParamsAndRerun())},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_showParamsAndRerun())},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));var b=$(this._render_showParamsAndRerun());if(this.model.get("for_editing")){this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});b.prepend(this.errButton.render().$el)}if(this.model.hasData()){b.prepend(this._render_downloadLinks())}a.append(b)},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_showParamsAndRerun())},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_showParamsAndRerun())},_render_body_failed_metadata:function(b){var c="An error occurred setting the metadata for this dataset.";if(this.model.isEditable()){var a=linkHTMLTemplate({text:"set it manually or retry auto-detection",href:this.model.get("edit_url"),target:"galaxy_main"});c+="You may be able to "+a+"."}b.append($(HistoryItemView.templates.warningMsg({warning:c})));this._render_body_ok(b)},_render_body_ok:function(h){h.append(this._render_hdaSummary());if(this.model.get("misc_info")){h.append($('<div class="info">Info: '+this.model.get("misc_info")+"</div>"))}if(this.model.hasData()){var c=$("<div/>");c.append(this._render_downloadLinks());c.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){c.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})));if(this.model.get("trackster_urls")){var a=this.model.get("trackster_urls");c.append($(linkHTMLTemplate({title:"View in Trackster",href:"javascript:void(0)",classes:["icon-button","tooltip","chart_curve","trackster-add"],"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]})))}if(this.model.get("retag_url")&&this.model.get("annotate_url")){var d=$('<div style="float: right;"></div>');d.append($(linkHTMLTemplate({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),classes:["icon-button","tooltip","tags"]})));d.append($(linkHTMLTemplate({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotation_url"),classes:["icon-button","tooltip","annotate"]})));c.append(d);c.append('<div style="clear: both"></div>');this.tagArea=$('<div class="tag-area" style="display: none">');this.tagArea.append("<strong>Tags:</strong>");this.tagElt=$('<div class="tag-elt"></div>');c.append(this.tagArea.append(this.tagElt));var e=$(('<div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none">'));this.annotationArea=e;e.append("<strong>Annotation:</strong>");this.annotationElem=$('<div id="'+this.model.get("id")+'-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div>');e.append(this.annotationElem);c.append(e)}}c.append('<div style="clear: both;"></div>');h.append(c);var i=$("<div/>");if(this.model.get("display_apps")){var j=this.model.get("display_apps"),b=$("<span/>");for(app_name in j){var g=j[app_name],f=app_name+" ";for(location_name in g){f+=linkHTMLTemplate({text:location_name,href:g[location_name].url,target:g[location_name].target})+" "}b.append(f)}i.append(b)}h.append(i)}else{if(this.model.get("for_editing")){h.append(this._render_showParamsAndRerun())}}h.append(this._render_peek())},_render_body:function(){var b=this.model.get("state"),c=this.model.get("for_editing");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_showParamsAndRerun:function(){var a=$("<div/>");this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});a.append(this.showParamsButton.render().$el);if(this.model.get("for_editing")){this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})})}return a},_render_downloadLinks:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('<div popupmenu="dataset-'+this.model.get("id")+'-popup"></div>');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("<a>Additional Files</a>");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$(('<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"></div>'));b.append(a);c.append(b);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this,".loadAndDisplayTags",b);var c=this.tagArea;var a=this.tagElt;if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){this.log("tag_elt_html:",d);a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this,".loadAndDisplayAnnotation",b);var d=this.annotationArea,c=this.annotationElem,a=this.model.get("ajax_set_annotation_url");this.log("annotationArea hidden:",d.is(":hidden"));this.log("annotationElem html:",c.html());if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});function createMockHistoryData(){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,undelete_url:"example.com/undelete",purge_url:"example.com/purge",unhide_url:"example.com/unhide",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>','<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>',"</table>"].join("")}};_.extend(mockHistory.data,{deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR,report_error_url:"example.com/report_err"}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})}; \ No newline at end of file +function linkHTMLTemplate(b,a){if(!b){return"<a></a>"}a=a||"a";var c=["<"+a];for(key in b){var d=b[key];if(d===""){continue}switch(key){case"text":continue;case"classes":key="class";d=(b.classes.join)?(b.classes.join(" ")):(b.classes);default:c.push([" ",key,'="',d,'"'].join(""))}}c.push(">");if("text" in b){c.push(b.text)}c.push("</"+a+">");return c.join("")}var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var d=this.model.get("id"),c=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+d);var a=$("<div/>").attr("id","historyItem-"+d).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});var b=a.find("[popupmenu]");b.each(function(e,f){f=$(f);make_popupmenu(f)});this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>"),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('<div popupmenu="dataset-'+this.model.get("id")+'-popup"></div>');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("<a>Additional Files</a>");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$(('<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"></div>'));b.append(a);c.append(b);return c},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$('<div style="float: right;"></div>'),a=this;_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.get("display_apps")){return null}var a=this.model.get("displayApps"),c=$("<div/>"),b=$("<span/>");this.log(this+"displayApps:",a);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});function createMockHistoryData(){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file (misc_info)",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,accessible:true,undelete_url:"",purge_url:"",unhide_url:"",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>','<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>',"</table>"].join("")}};_.extend(mockHistory.data,{notAccessible:_.extend(_.clone(mockHistory.data.template),{accessible:false}),deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true,delete_url:"",purge_url:"example.com/purge",undelete_url:"example.com/undelete"}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true,delete_url:""}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false,unhide_url:"example.com/unhide"}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR,report_error_url:"example.com/report_err"}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})}; \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({tagName:"a",className:"icon-button",hrefVoidFn:["javascript",":void(0)"].join(""),fadeSpeed:0,initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){var a=this.model.attributes.icon_class+"_disabled";if(!this.model.attributes.visible){this.$el.fadeOut(this.fadeSpeed)}if(this.model.attributes.enabled){if(this.$el.hasClass(a)){this.$el.removeClass(a)}this.$el.addClass(this.model.attributes.icon_class)}else{this.$el.removeClass(this.model.attributes.icon_class);this.$el.addClass(a)}if(this.model.attributes.isMenuButton){this.$el.addClass("menu-button")}else{this.$el.removeClass("menu-button")}this.$el.data("tooltip",false);this.$el.attr("data-original-title",null);this.$el.removeClass("tooltip");if(this.model.attributes.title){this.$el.attr("title",this.model.attributes.title).addClass("tooltip");this.$el.tooltip(this.model.attributes.tooltip_config)}this.$el.attr("id",(this.model.attributes.id)?(this.model.attributes.id):(null));this.$el.attr("target",(this.model.attributes.target)?(this.model.attributes.target):(null));this.$el.attr("href",(this.model.attributes.href&&!this.model.attributes.on_click)?(this.model.attributes.href):(this.hrefVoidFn));if(this.model.attributes.visible){this.$el.fadeIn(this.fadeSpeed)}return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){try{return this.localizedStrings[b]}catch(a){return b}},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){try{return this.localizedStrings[b]}catch(a){return b}},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)}; \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/require.js --- a/static/scripts/packed/require.js +++ /dev/null @@ -1,1 +0,0 @@ -var requirejs,require,define;(function(global){var req,s,head,baseElement,dataMain,src,interactiveScript,currentlyAddingScript,mainScript,subPath,version="2.0.6",commentRegExp=/(\/\*([\s\S]*?)\*\/|([^:]|^)\/\/(.*)$)/mg,cjsRequireRegExp=/[^.]\s*require\s*$\s*["']([^'"\s]+)["']\s*$/g,jsSuffixRegExp=/\.js$/,currDirRegExp=/^\.\//,op=Object.prototype,ostring=op.toString,hasOwn=op.hasOwnProperty,ap=Array.prototype,aps=ap.slice,apsp=ap.splice,isBrowser=!!(typeof window!=="undefined"&&navigator&&document),isWebWorker=!isBrowser&&typeof importScripts!=="undefined",readyRegExp=isBrowser&&navigator.platform==="PLAYSTATION 3"?/^complete$/:/^(complete|loaded)$/,defContextName="_",isOpera=typeof opera!=="undefined"&&opera.toString()==="[object Opera]",contexts={},cfg={},globalDefQueue=[],useInteractive=false;function isFunction(it){return ostring.call(it)==="[object Function]"}function isArray(it){return ostring.call(it)==="[object Array]"}function each(ary,func){if(ary){var i;for(i=0;i<ary.length;i+=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function eachReverse(ary,func){if(ary){var i;for(i=ary.length-1;i>-1;i-=1){if(ary[i]&&func(ary[i],i,ary)){break}}}}function hasProp(obj,prop){return hasOwn.call(obj,prop)}function eachProp(obj,func){var prop;for(prop in obj){if(obj.hasOwnProperty(prop)){if(func(obj[prop],prop)){break}}}}function mixin(target,source,force,deepStringMixin){if(source){eachProp(source,function(value,prop){if(force||!hasProp(target,prop)){if(deepStringMixin&&typeof value!=="string"){if(!target[prop]){target[prop]={}}mixin(target[prop],value,force,deepStringMixin)}else{target[prop]=value}}})}return target}function bind(obj,fn){return function(){return fn.apply(obj,arguments)}}function scripts(){return document.getElementsByTagName("script")}function getGlobal(value){if(!value){return value}var g=global;each(value.split("."),function(part){g=g[part]});return g}function makeContextModuleFunc(func,relMap,enableBuildCallback){return function(){var args=aps.call(arguments,0),lastArg;if(enableBuildCallback&&isFunction((lastArg=args[args.length-1]))){lastArg.__requireJsBuild=true}args.push(relMap);return func.apply(null,args)}}function addRequireMethods(req,context,relMap){each([["toUrl"],["undef"],["defined","requireDefined"],["specified","requireSpecified"]],function(item){var prop=item[1]||item[0];req[item[0]]=context?makeContextModuleFunc(context[prop],relMap):function(){var ctx=contexts[defContextName];return ctx[prop].apply(ctx,arguments)}})}function makeError(id,msg,err,requireModules){var e=new Error(msg+"\nhttp://requirejs.org/docs/errors.html#"+id);e.requireType=id;e.requireModules=requireModules;if(err){e.originalError=err}return e}if(typeof define!=="undefined"){return}if(typeof requirejs!=="undefined"){if(isFunction(requirejs)){return}cfg=requirejs;requirejs=undefined}if(typeof require!=="undefined"&&!isFunction(require)){cfg=require;require=undefined}function newContext(contextName){var inCheckLoaded,Module,context,handlers,checkLoadedTimeoutId,config={waitSeconds:7,baseUrl:"./",paths:{},pkgs:{},shim:{}},registry={},undefEvents={},defQueue=[],defined={},urlFetched={},requireCounter=1,unnormalizedCounter=1,waitAry=[];function trimDots(ary){var i,part;for(i=0;ary[i];i+=1){part=ary[i];if(part==="."){ary.splice(i,1);i-=1}else{if(part===".."){if(i===1&&(ary[2]===".."||ary[0]==="..")){break}else{if(i>0){ary.splice(i-1,2);i-=2}}}}}}function normalize(name,baseName,applyMap){var pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(config.pkgs[baseName]){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=config.pkgs[(pkgName=name[0])];name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&(baseParts||starMap)&&map){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=map[baseParts.slice(0,j).join("/")];if(mapValue){mapValue=mapValue[nameSegment];if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&starMap[nameSegment]){foundStarMap=starMap[nameSegment];starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=config.paths[id];if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.undef(id);context.require([id]);return true}}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,index=name?name.indexOf("!"):-1,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}if(index!==-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=defined[prefix]}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return normalize(name,parentName,applyMap)})}else{normalizedName=normalize(name,parentName,applyMap)}}else{normalizedName=normalize(name,parentName,applyMap);url=context.nameToUrl(normalizedName)}}suffix=prefix&&!pluginModule&&!isNormalized?"_unnormalized"+(unnormalizedCounter+=1):"";return{prefix:prefix,name:normalizedName,parentMap:parentModuleMap,unnormalized:!!suffix,url:url,originalName:originalName,isDefine:isDefine,id:(prefix?prefix+"!"+normalizedName:normalizedName)+suffix}}function getModule(depMap){var id=depMap.id,mod=registry[id];if(!mod){mod=registry[id]=new context.Module(depMap)}return mod}function on(depMap,name,fn){var id=depMap.id,mod=registry[id];if(hasProp(defined,id)&&(!mod||mod.defineEmitComplete)){if(name==="defined"){fn(defined[id])}}else{getModule(depMap).on(name,fn)}}function onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=registry[id];if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}function makeRequire(mod,enableBuildCallback,altRequire){var relMap=mod&&mod.map,modRequire=makeContextModuleFunc(altRequire||context.require,relMap,enableBuildCallback);addRequireMethods(modRequire,context,relMap);modRequire.isBrowser=isBrowser;return modRequire}handlers={require:function(mod){return makeRequire(mod)},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){return(mod.exports=defined[mod.map.id]={})}},module:function(mod){return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){return(config.config&&config.config[mod.map.id])||{}},exports:defined[mod.map.id]})}};function removeWaiting(id){delete registry[id];each(waitAry,function(mod,i){if(mod.map.id===id){waitAry.splice(i,1);if(!mod.defined){context.waitCount-=1}return true}})}function findCycle(mod,traced,processed){var id=mod.map.id,depArray=mod.depMaps,foundModule;if(!mod.inited){return}if(traced[id]){return mod}traced[id]=true;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId];if(!depMod||processed[depId]||!depMod.inited||!depMod.enabled){return}return(foundModule=findCycle(depMod,traced,processed))});processed[id]=true;return foundModule}function forceExec(mod,traced,uninited){var id=mod.map.id,depArray=mod.depMaps;if(!mod.inited||!mod.map.isDefine){return}if(traced[id]){return defined[id]}traced[id]=mod;each(depArray,function(depMap){var depId=depMap.id,depMod=registry[depId],value;if(handlers[depId]){return}if(depMod){if(!depMod.inited||!depMod.enabled){uninited[id]=true;return}value=forceExec(depMod,traced,uninited);if(!uninited[depId]){mod.defineDepById(depId,value)}}});mod.check(true);return defined[id]}function modCheck(mod){mod.check()}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)<new Date().getTime(),noLoads=[],stillLoading=false,needCycleCheck=true;if(inCheckLoaded){return}inCheckLoaded=true;eachProp(registry,function(mod){map=mod.map;modId=map.id;if(!mod.enabled){return}if(!mod.error){if(!mod.inited&&expired){if(hasPathFallback(modId)){usingPathFallback=true;stillLoading=true}else{noLoads.push(modId);removeScript(modId)}}else{if(!mod.inited&&mod.fetched&&map.isDefine){stillLoading=true;if(!map.prefix){return(needCycleCheck=false)}}}}});if(expired&&noLoads.length){err=makeError("timeout","Load timeout for modules: "+noLoads,null,noLoads);err.contextName=context.contextName;return onError(err)}if(needCycleCheck){each(waitAry,function(mod){if(mod.defined){return}var cycleMod=findCycle(mod,{},{}),traced={};if(cycleMod){forceExec(cycleMod,traced,{});eachProp(traced,modCheck)}});eachProp(registry,modCheck)}if((!expired||usingPathFallback)&&stillLoading){if((isBrowser||isWebWorker)&&!checkLoadedTimeoutId){checkLoadedTimeoutId=setTimeout(function(){checkLoadedTimeoutId=0;checkLoaded()},50)}}inCheckLoaded=false}Module=function(map){this.events=undefEvents[map.id]||{};this.map=map;this.shim=config.shim[map.id];this.depExports=[];this.depMaps=[];this.depMatched=[];this.pluginMaps={};this.depCount=0};Module.prototype={init:function(depMaps,factory,errback,options){options=options||{};if(this.inited){return}this.factory=factory;if(errback){this.on("error",errback)}else{if(this.events.error){errback=bind(this,function(err){this.emit("error",err)})}}this.depMaps=depMaps&&depMaps.slice(0);this.depMaps.rjsSkipMap=depMaps.rjsSkipMap;this.errback=errback;this.inited=true;this.ignore=options.ignore;if(options.enabled||this.enabled){this.enable()}else{this.check()}},defineDepById:function(id,depExports){var i;each(this.depMaps,function(map,index){if(map.id===id){i=index;return true}});return this.defineDep(i,depExports)},defineDep:function(i,depExports){if(!this.depMatched[i]){this.depMatched[i]=true;this.depCount-=1;this.depExports[i]=depExports}},fetch:function(){if(this.fetched){return}this.fetched=true;context.startTime=(new Date()).getTime();var map=this.map;if(this.shim){makeRequire(this,true)(this.shim.deps||[],bind(this,function(){return map.prefix?this.callPlugin():this.load()}))}else{return map.prefix?this.callPlugin():this.load()}},load:function(){var url=this.map.url;if(!urlFetched[url]){urlFetched[url]=true;context.load(this.map.id,url)}},check:function(silent){if(!this.enabled||this.enabling){return}var err,cjsModule,id=this.map.id,depExports=this.depExports,exports=this.exports,factory=this.factory;if(!this.inited){this.fetch()}else{if(this.error){this.emit("error",this.error)}else{if(!this.defining){this.defining=true;if(this.depCount<1&&!this.defined){if(isFunction(factory)){if(this.events.error){try{exports=context.execCb(id,factory,depExports,exports)}catch(e){err=e}}else{exports=context.execCb(id,factory,depExports,exports)}if(this.map.isDefine){cjsModule=this.module;if(cjsModule&&cjsModule.exports!==undefined&&cjsModule.exports!==this.exports){exports=cjsModule.exports}else{if(exports===undefined&&this.usingExports){exports=this.exports}}}if(err){err.requireMap=this.map;err.requireModules=[this.map.id];err.requireType="define";return onError((this.error=err))}}else{exports=factory}this.exports=exports;if(this.map.isDefine&&!this.ignore){defined[id]=exports;if(req.onResourceLoad){req.onResourceLoad(context,this.map,this.depMaps)}}delete registry[id];this.defined=true;context.waitCount-=1;if(context.waitCount===0){waitAry=[]}}this.defining=false;if(!silent){if(this.defined&&!this.defineEmitted){this.defineEmitted=true;this.emit("defined",this.exports);this.defineEmitComplete=true}}}}}},callPlugin:function(){var map=this.map,id=map.id,pluginMap=makeModuleMap(map.prefix,null,false,true);on(pluginMap,"defined",bind(this,function(plugin){var load,normalizedMap,normalizedMod,name=this.map.name,parentName=this.map.parentMap?this.map.parentMap.name:null;if(this.map.unnormalized){if(plugin.normalize){name=plugin.normalize(name,function(name){return normalize(name,parentName,true)})||""}normalizedMap=makeModuleMap(map.prefix+"!"+name,this.map.parentMap,false,true);on(normalizedMap,"defined",bind(this,function(value){this.init([],function(){return value},null,{enabled:true,ignore:true})}));normalizedMod=registry[normalizedMap.id];if(normalizedMod){if(this.events.error){normalizedMod.on("error",bind(this,function(err){this.emit("error",err)}))}normalizedMod.enable()}return}load=bind(this,function(value){this.init([],function(){return value},null,{enabled:true})});load.error=bind(this,function(err){this.inited=true;this.error=err;err.requireModules=[id];eachProp(registry,function(mod){if(mod.map.id.indexOf(id+"_unnormalized")===0){removeWaiting(mod.map.id)}});onError(err)});load.fromText=function(moduleName,text){var hasInteractive=useInteractive;if(hasInteractive){useInteractive=false}getModule(makeModuleMap(moduleName));req.exec(text);if(hasInteractive){useInteractive=true}context.completeLoad(moduleName)};plugin.load(map.name,makeRequire(map.parentMap,true,function(deps,cb,er){deps.rjsSkipMap=true;return context.require(deps,cb,er)}),load,config)}));context.enable(pluginMap,this);this.pluginMaps[pluginMap.id]=pluginMap},enable:function(){this.enabled=true;if(!this.waitPushed){waitAry.push(this);context.waitCount+=1;this.waitPushed=true}this.enabling=true;each(this.depMaps,bind(this,function(depMap,i){var id,mod,handler;if(typeof depMap==="string"){depMap=makeModuleMap(depMap,(this.map.isDefine?this.map:this.map.parentMap),false,!this.depMaps.rjsSkipMap);this.depMaps[i]=depMap;handler=handlers[depMap.id];if(handler){this.depExports[i]=handler(this);return}this.depCount+=1;on(depMap,"defined",bind(this,function(depExports){this.defineDep(i,depExports);this.check()}));if(this.errback){on(depMap,"error",this.errback)}}id=depMap.id;mod=registry[id];if(!handlers[id]&&mod&&!mod.enabled){context.enable(depMap,this)}}));eachProp(this.pluginMaps,bind(this,function(pluginMap){var mod=registry[pluginMap.id];if(mod&&!mod.enabled){context.enable(pluginMap,this)}}));this.enabling=false;this.check()},on:function(name,cb){var cbs=this.events[name];if(!cbs){cbs=this.events[name]=[]}cbs.push(cb)},emit:function(name,evt){each(this.events[name],function(cb){cb(evt)});if(name==="error"){delete this.events[name]}}};function callGetModule(args){getModule(makeModuleMap(args[0],null,true)).init(args[1],args[2])}function removeListener(node,func,name,ieName){if(node.detachEvent&&!isOpera){if(ieName){node.detachEvent(ieName,func)}}else{node.removeEventListener(name,func,false)}}function getScriptData(evt){var node=evt.currentTarget||evt.srcElement;removeListener(node,context.onScriptLoad,"load","onreadystatechange");removeListener(node,context.onScriptError,"error");return{node:node,id:node&&node.getAttribute("data-requiremodule")}}return(context={config:config,contextName:contextName,registry:registry,defined:defined,urlFetched:urlFetched,waitCount:0,defQueue:defQueue,Module:Module,makeModuleMap:makeModuleMap,configure:function(cfg){if(cfg.baseUrl){if(cfg.baseUrl.charAt(cfg.baseUrl.length-1)!=="/"){cfg.baseUrl+="/"}}var pkgs=config.pkgs,shim=config.shim,paths=config.paths,map=config.map;mixin(config,cfg,true);config.paths=mixin(paths,cfg.paths,true);if(cfg.map){config.map=mixin(map||{},cfg.map,true,true)}if(cfg.shim){eachProp(cfg.shim,function(value,id){if(isArray(value)){value={deps:value}}if(value.exports&&!value.exports.__buildReady){value.exports=context.makeShimExports(value.exports)}shim[id]=value});config.shim=shim}if(cfg.packages){each(cfg.packages,function(pkgObj){var location;pkgObj=typeof pkgObj==="string"?{name:pkgObj}:pkgObj;location=pkgObj.location;pkgs[pkgObj.name]={name:pkgObj.name,location:location||pkgObj.name,main:(pkgObj.main||"main").replace(currDirRegExp,"").replace(jsSuffixRegExp,"")}});config.pkgs=pkgs}eachProp(registry,function(mod,id){if(!mod.inited&&!mod.map.unnormalized){mod.map=makeModuleMap(id)}});if(cfg.deps||cfg.callback){context.require(cfg.deps||[],cfg.callback)}},makeShimExports:function(exports){var func;if(typeof exports==="string"){func=function(){return getGlobal(exports)};func.exports=exports;return func}else{return function(){return exports.apply(global,arguments)}}},requireDefined:function(id,relMap){return hasProp(defined,makeModuleMap(id,relMap,false,true).id)},requireSpecified:function(id,relMap){id=makeModuleMap(id,relMap,false,true).id;return hasProp(defined,id)||hasProp(registry,id)},require:function(deps,callback,errback,relMap){var moduleName,id,map,requireMod,args;if(typeof deps==="string"){if(isFunction(callback)){return onError(makeError("requireargs","Invalid require call"),errback)}if(req.get){return req.get(context,deps,callback)}moduleName=deps;relMap=callback;map=makeModuleMap(moduleName,relMap,false,true);id=map.id;if(!hasProp(defined,id)){return onError(makeError("notloaded",'Module name "'+id+'" has not been loaded yet for context: '+contextName))}return defined[id]}if(errback&&!isFunction(errback)){relMap=errback;errback=undefined}if(callback&&!isFunction(callback)){relMap=callback;callback=undefined}takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){return onError(makeError("mismatch","Mismatched anonymous define() module: "+args[args.length-1]))}else{callGetModule(args)}}requireMod=getModule(makeModuleMap(null,relMap));requireMod.init(deps,callback,errback,{enabled:true});checkLoaded();return context.require},undef:function(id){takeGlobalQueue();var map=makeModuleMap(id,null,true),mod=registry[id];delete defined[id];delete urlFetched[map.url];delete undefEvents[id];if(mod){if(mod.events.defined){undefEvents[id]=mod.events}removeWaiting(id)}},enable:function(depMap,parent){var mod=registry[depMap.id];if(mod){getModule(depMap).enable()}},completeLoad:function(moduleName){var found,args,mod,shim=config.shim[moduleName]||{},shExports=shim.exports&&shim.exports.exports;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){args[0]=moduleName;if(found){break}found=true}else{if(args[0]===moduleName){found=true}}callGetModule(args)}mod=registry[moduleName];if(!found&&!defined[moduleName]&&mod&&!mod.inited){if(config.enforceDefine&&(!shExports||!getGlobal(shExports))){if(hasPathFallback(moduleName)){return}else{return onError(makeError("nodefine","No define call for "+moduleName,null,[moduleName]))}}else{callGetModule([moduleName,(shim.deps||[]),shim.exports])}}checkLoaded()},toUrl:function(moduleNamePlusExt,relModuleMap){var index=moduleNamePlusExt.lastIndexOf("."),ext=null;if(index!==-1){ext=moduleNamePlusExt.substring(index,moduleNamePlusExt.length);moduleNamePlusExt=moduleNamePlusExt.substring(0,index)}return context.nameToUrl(normalize(moduleNamePlusExt,relModuleMap&&relModuleMap.id,true),ext)},nameToUrl:function(moduleName,ext){var paths,pkgs,pkg,pkgPath,syms,i,parentModule,url,parentPath;if(req.jsExtRegExp.test(moduleName)){url=moduleName+(ext||"")}else{paths=config.paths;pkgs=config.pkgs;syms=moduleName.split("/");for(i=syms.length;i>0;i-=1){parentModule=syms.slice(0,i).join("/");pkg=pkgs[parentModule];parentPath=paths[parentModule];if(parentPath){if(isArray(parentPath)){parentPath=parentPath[0]}syms.splice(0,i,parentPath);break}else{if(pkg){if(moduleName===pkg.name){pkgPath=pkg.location+"/"+pkg.main}else{pkgPath=pkg.location}syms.splice(0,i,pkgPath);break}}}url=syms.join("/");url+=(ext||(/\?/.test(url)?"":".js"));url=(url.charAt(0)==="/"||url.match(/^[\w\+\.\-]+:/)?"":config.baseUrl)+url}return 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b/static/scripts/packed/templates/compiled/helpers-common-templates.js @@ -1,1 +1,1 @@ -Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){c.buffer+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">Bler"+((c.enabled)?("</a>"):("</span>"));return a});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"}); \ No newline at end of file +Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){a+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">"+((c.enabled)?("</a>"):("</span>"));return a});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"}); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/templates/compiled/template-history-annotationArea.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-annotationArea.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-annotationArea"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='\n<div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>Annotation:</strong>\n <div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'-anotation-elt" class="annotation-elt tooltip editable-text"\n style="margin: 1px 0px 1px 0px" title="Edit dataset annotation">\n </div>\n</div>';return h})})(); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/templates/compiled/template-history-failedMetaData.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-failedMetaData.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(s,r){var p="",q,o;p+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';o=e.edit_url;if(o){q=o.call(s,{hash:{}})}else{q=s.edit_url;q=typeof q===g?q():q}p+=i(q)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return p}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/packed/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/packed/templates/compiled/template-history-hdaSummary.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <a href="';p=f.edit_url;if(p){r=p.call(t,{hash:{}})}else{r=t.edit_url;r=typeof r===h?r():r}q+=k(r)+'" target="galaxy_main">';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+"</a>\n";return q}function c(t,s){var q="",r,p;q+='\n <span class="';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+'">';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+"</span>\n";return q}i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\nformat: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\ndatabase:\n";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:o.program(3,c,l),fn:o.program(1,e,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=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 <a href="';q=f.edit_url;if(q){s=q.call(u,{hash:{}})}else{s=u.edit_url;s=typeof s===h?s():s}r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info">';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+"</div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n 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static/scripts/packed/templates/compiled/template-history-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/packed/templates/compiled/template-history-warning-messages.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,v){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}if(x||x===0){return x}else{return""}}function n(z,y){var w="",x;w+="\n This dataset has been deleted.\n ";x=z.undelete_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(3,m,y)});if(x||x===0){w+=x}w+="\n";return w}function m(A,z){var x="",y,w;x+='\n Click <a href="';w=q.undelete_url;if(w){y=w.call(A,{hash:{}})}else{y=A.undelete_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUndelete" id="historyItemUndeleter-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to undelete it\n ';y=A.purge_url;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(4,l,z)});if(y||y===0){x+=y}x+="\n ";return x}function l(A,z){var x="",y,w;x+='\n or <a href="';w=q.purge_url;if(w){y=w.call(A,{hash:{}})}else{y=A.purge_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemPurge" id="historyItemPurger-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return x}function j(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}else{x=z.warningmessagesmall;x=typeof 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x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}if(x||x===0){return x}else{return""}}function i(x,w){return"\n This dataset has been deleted and removed from disk.\n"}function f(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}if(x||x===0){return x}else{return""}}function u(z,y){var w="",x;w+="\n This dataset has been hidden.\n ";x=z.unhide_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(11,t,y)});if(x||x===0){w+=x}w+="\n";return w}function t(A,z){var x="",y,w;x+='\n Click <a href="';w=q.unhide_url;if(w){y=w.call(A,{hash:{}})}else{y=A.unhide_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUnhide" id="historyItemUnhider-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to unhide it\n ';return x}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,v)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(6,j,v)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,v)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/templates/compiled/template-iconButton.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-iconButton.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-iconButton"]=b(function(i,j,g,e,h){g=g||i.helpers;e=e||i.partials;var c="",f,d=this;c+="\n";f=d.invokePartial(e.iconButton,"iconButton",j,g,e);if(f||f===0){c+=f}return c})})(); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/templates/compiled/template-warningmessagesmall.js --- a/static/scripts/packed/templates/compiled/template-warningmessagesmall.js +++ b/static/scripts/packed/templates/compiled/template-warningmessagesmall.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-warningmessagesmall"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+=' \n <div class="warningmessagesmall"><strong>';g=d.warning;if(g){c=g.call(l,{hash:{}})}else{c=l.warning;c=typeof c===f?c():c}h+=i(c)+"</strong></div>";return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-warningmessagesmall"]=b(function(e,k,d,j,i){d=d||e.helpers;var h="",c,g,f="function";h+=' \n <div class="warningmessagesmall"><strong>';g=d.warning;if(g){c=g.call(k,{hash:{}})}else{c=k.warning;c=typeof c===f?c():c}if(c||c===0){h+=c}h+="</strong></div>";return h})})(); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus();Z.nav_input.autocomplete({source:function(af,ad){var ag=[],ae=$.map(Z.get_drawables(),function(ah){return ah.data_manager.search_features(af.term).success(function(ai){ag=ag.concat(ai)})});$.when.apply($,ae).done(function(){ad($.map(ag,function(ah){return{label:ah[0],value:ah[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom 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aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var 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ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: 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style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);this.feature_search_url=("feature_search_url" in ad?ad.feature_search_url:feature_search_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,feature_search_url:Z.feature_search_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){},get_drawables:function(){return this}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus();Z.nav_input.autocomplete({source:function(af,ad){var ag=[],ae=$.map(Z.get_drawables(),function(ah){return ah.data_manager.search_features(af.term).success(function(ai){ag=ag.concat(ai)})});$.when.apply($,ae).done(function(){ad($.map(ag,function(ah){return{label:ah[0],value:ah[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: 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Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+" ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(aa,Z,ab){o(ab,{drag_handle_class:"draghandle"});p.call(this,aa,Z,ab);this.dataset=new Dataset({id:ab.dataset_id,hda_ldda:ab.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ab?ab.data_query_wait:H);this.data_manager=("data_manager" in ab?ab.data_manager:new GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ab)||ab.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred(),ab={hda_ldda:aa.hda_ldda,data_type:this.dataset_check_type,chrom:aa.view.chrom};$.getJSON(this.dataset.url(),ab,function(ac){if(!ac||ac==="error"||ac.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ac.message){var ad=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ac.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ad)}}else{if(ac==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ac==="no data"||(ac.data!==undefined&&(ac.data===null||ac.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ac==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ac==="data"||ac.status==="data"){if(ac.valid_chroms){aa.valid_chroms=ac.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){},get_drawables:function(){return this}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_type","data");aa.dataset_check_type="converted_datasets_state";this.data_query_wait=5000});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.dataset.url(),{data_type:"data",stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.dataset=Z;this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ab.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -(function(){var f=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(t){return true}},go:function(){var w=$.Deferred(),v=this,y=v.get("ajax_settings"),x=v.get("success_fn"),u=v.get("interval"),t=function(){$.ajax(y).success(function(z){if(x(z)){w.resolve(z)}else{setTimeout(t,u)}})};t();return w}});var g=function(t){this.default_font=t!==undefined?t:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(g.prototype,{load_pattern:function(t,x){var u=this.patterns,v=this.dummy_context,w=new Image();w.src=galaxy_paths.attributes.image_path+x;w.onload=function(){u[t]=v.createPattern(w,"repeat")}},get_pattern:function(t){return this.patterns[t]},new_canvas:function(){var t=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(t)}t.manager=this;return t}});var p=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(t){this.clear()},get_elt:function(u){var v=this.attributes.obj_cache,w=this.attributes.key_ary,t=w.indexOf(u);if(t!==-1){if(v[u].stale){w.splice(t,1);delete v[u]}else{this.move_key_to_end(u,t)}}return v[u]},set_elt:function(u,w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=this.attributes.num_elements;if(!x[u]){if(y.length>=v){var t=y.shift();delete x[t]}y.push(u)}x[u]=w;return w},move_key_to_end:function(u,t){this.attributes.key_ary.splice(t,1);this.attributes.key_ary.push(u)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=p.extend({defaults:_.extend({},p.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,feature_search_url:null,genome_wide_summary_data:null,data_mode_compatible:function(t,u){return true},can_subset:function(t){return false}}),data_is_ready:function(){var v=this.get("dataset"),u=$.Deferred(),t=new f({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:v.id,hda_ldda:v.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(w){return w!=="pending"}});$.when(t.go()).then(function(w){u.resolve(w==="ok"||w==="data")});return u},search_features:function(t){var u=this.get("dataset"),v={query:t,dataset_id:u.id,hda_ldda:u.get("hda_ldda")};return $.getJSON(this.get("feature_search_url"),v)},load_data:function(B,A,u,z){var w={chrom:B.get("chrom"),low:B.get("start"),high:B.get("end"),mode:A,resolution:u},x=this.get("dataset");if(x){w.dataset_id=x.id;w.hda_ldda=x.get("hda_ldda")}$.extend(w,z);var C=this.get("filters_manager");if(C){var D=[];var t=C.filters;for(var y=0;y<t.length;y++){D.push(t[y].name)}w.filter_cols=JSON.stringify(D)}var v=this;return $.getJSON(this.get("data_url"),w,function(E){v.set_data(B,E)})},get_data:function(z,y,v,x){var A=this.get_elt(z);if(A&&(is_deferred(A)||this.get("data_mode_compatible")(A,y))){return A}var B=this.get("key_ary"),u=this.get("obj_cache"),C,t;for(var w=0;w<B.length;w++){C=B[w];t=new h({from_str:C});if(t.contains(z)){A=u[C];if(is_deferred(A)||(this.get("data_mode_compatible")(A,y)&&this.get("can_subset")(A))){this.move_key_to_end(C,w);return A}}}A=this.load_data(z,y,v,x);this.set_data(z,A);return A},set_data:function(u,t){this.set_elt(u,t)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(B,A,w,z,x){var D=this.get_elt(B);if(!(D&&this.get("data_mode_compatible")(D,A))){console.log("ERROR: no current data for: ",dataset,B.toString(),A,w,z);return}D.stale=true;var v=B.get("start");if(x===this.DEEP_DATA_REQ){$.extend(z,{start_val:D.data.length+1})}else{if(x===this.BROAD_DATA_REQ){v=(D.max_high?D.max_high:D.data[D.data.length-1][2])+1}}var C=B.copy().set("start",v);var u=this,y=this.load_data(C,A,w,z),t=$.Deferred();this.set_data(B,t);$.when(y).then(function(E){if(E.data){E.data=D.data.concat(E.data);if(E.max_low){E.max_low=D.max_low}if(E.message){E.message=E.message.replace(/[0-9]+/,E.data.length)}}u.set_data(B,E);t.resolve(E)});return t},get_elt:function(t){return p.prototype.get_elt.call(this,t.toString())},set_elt:function(u,t){return p.prototype.set_elt.call(this,u.toString(),t)}});var n=d.extend({load_data:function(t,w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,t,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var h=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(u){if(u.from_str){var w=u.from_str.split(":"),v=w[0],t=w[1].split("-");this.set({chrom:v,start:parseInt(t[0],10),end:parseInt(t[1],10)})}},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(A){var u=this.get("chrom"),z=A.get("chrom"),y=this.get("start"),w=A.get("start"),x=this.get("end"),v=A.get("end"),t;if(u&&z&&u!==z){return this.get("DIF_CHROMS")}if(y<w){if(x<w){t=this.get("BEFORE")}else{if(x<=v){t=this.get("OVERLAP_START")}else{t=this.get("CONTAINS")}}}else{if(y>v){t=this.get("AFTER")}else{if(x<=v){t=this.get("CONTAINED_BY")}else{t=this.get("OVERLAP_END")}}}return t},contains:function(t){return this.compute_overlap(t)===this.get("CONTAINS")},overlaps:function(t){return _.intersection([this.compute_overlap(t)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:h});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:h}]});var q=Backbone.Collection.extend({model:e});var b=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.flatten(_.map(this.get("data"),function(v){if(v.data.length!==0){return _.map(v.data,function(w){return w[1]})}else{return 0}}));this.set("max",_.max(t));this.set("min",_.min(t))}});var m=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.max(this.get("data"),function(v){if(!v||typeof v==="string"){return 0}return v[1]});this.attributes.max=(t&&typeof t!=="string"?t[1]:0)}});var s=Dataset.extend({initialize:function(t){this.set("id",t.dataset_id);var v=this.get("genome_wide_data");if(v){var u=(this.get("track_type")==="LineTrack"?b:m);this.set("genome_wide_data",new u(v))}}});var o=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:s}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:_.extend({},o.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(u){this.view=u.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(v){t.navigate(v)})},change_location:function(t){this.view.go_to(t)}});var j=function(t,v,u){$.ajax({url:t,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(w){show_modal("Select datasets for new tracks",w,{Cancel:function(){hide_modal()},Add:function(){var x=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var y,z=$(this).val();if($(this).attr("name")==="id"){y={hda_id:z}}else{y={ldda_id:z}}x[x.length]=$.ajax({url:v,data:y,dataType:"json"})});$.when.apply($,x).then(function(){var y=(arguments[0] instanceof Array?$.map(arguments,function(z){return z[0]}):[arguments[0]]);u(y)});hide_modal()}})}})};var r=(function(){if(typeof module!=="undefined"&&module.exports){return module.exports}else{if(typeof define==="function"&&define.amd){r={};define(function(){return r});return r}else{return window}}})();r.BrowserBookmark=e;r.BrowserBookmarkCollection=q;r.Cache=p;r.CanvasManager=g;r.Genome=c;r.GenomeDataManager=d;r.GenomeRegion=h;r.GenomeRegionCollection=l;r.GenomeVisualization=k;r.GenomeWideBigWigData=b;r.GenomeWideSummaryTreeData=m;r.ReferenceTrackDataManager=n;r.ServerStateDeferred=f;r.TrackBrowserRouter=i;r.TrackConfig=a;r.Visualization=o;r.add_datasets=j}).call(this); \ No newline at end of file +(function(){var f=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(t){return true}},go:function(){var w=$.Deferred(),v=this,y=v.get("ajax_settings"),x=v.get("success_fn"),u=v.get("interval"),t=function(){$.ajax(y).success(function(z){if(x(z)){w.resolve(z)}else{setTimeout(t,u)}})};t();return w}});var g=function(t){this.default_font=t!==undefined?t:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(g.prototype,{load_pattern:function(t,x){var u=this.patterns,v=this.dummy_context,w=new Image();w.src=galaxy_paths.attributes.image_path+x;w.onload=function(){u[t]=v.createPattern(w,"repeat")}},get_pattern:function(t){return this.patterns[t]},new_canvas:function(){var t=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(t)}t.manager=this;return t}});var p=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(t){this.clear()},get_elt:function(u){var v=this.attributes.obj_cache,w=this.attributes.key_ary,t=w.indexOf(u);if(t!==-1){if(v[u].stale){w.splice(t,1);delete v[u]}else{this.move_key_to_end(u,t)}}return v[u]},set_elt:function(u,w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=this.attributes.num_elements;if(!x[u]){if(y.length>=v){var t=y.shift();delete x[t]}y.push(u)}x[u]=w;return w},move_key_to_end:function(u,t){this.attributes.key_ary.splice(t,1);this.attributes.key_ary.push(u)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=p.extend({defaults:_.extend({},p.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",genome_wide_summary_data:null,data_mode_compatible:function(t,u){return true},can_subset:function(t){return false}}),data_is_ready:function(){var v=this.get("dataset"),u=$.Deferred(),t=new f({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:v.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(w){return w!=="pending"}});$.when(t.go()).then(function(w){u.resolve(w==="ok"||w==="data")});return u},search_features:function(t){var u=this.get("dataset"),v={query:t,dataset_id:u.id,hda_ldda:u.get("hda_ldda"),data_type:"features"};return $.getJSON(u.url(),v)},load_data:function(B,A,u,z){var w={data_type:this.get("data_type"),chrom:B.get("chrom"),low:B.get("start"),high:B.get("end"),mode:A,resolution:u},x=this.get("dataset");if(x){w.dataset_id=x.id;w.hda_ldda=x.get("hda_ldda")}$.extend(w,z);var C=this.get("filters_manager");if(C){var D=[];var t=C.filters;for(var y=0;y<t.length;y++){D.push(t[y].name)}w.filter_cols=JSON.stringify(D)}var v=this;return $.getJSON(x.url(),w,function(E){v.set_data(B,E)})},get_data:function(z,y,v,x){var A=this.get_elt(z);if(A&&(is_deferred(A)||this.get("data_mode_compatible")(A,y))){return A}var B=this.get("key_ary"),u=this.get("obj_cache"),C,t;for(var w=0;w<B.length;w++){C=B[w];t=new h({from_str:C});if(t.contains(z)){A=u[C];if(is_deferred(A)||(this.get("data_mode_compatible")(A,y)&&this.get("can_subset")(A))){this.move_key_to_end(C,w);return A}}}A=this.load_data(z,y,v,x);this.set_data(z,A);return A},set_data:function(u,t){this.set_elt(u,t)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(B,A,w,z,x){var D=this.get_elt(B);if(!(D&&this.get("data_mode_compatible")(D,A))){console.log("ERROR: no current data for: ",dataset,B.toString(),A,w,z);return}D.stale=true;var v=B.get("start");if(x===this.DEEP_DATA_REQ){$.extend(z,{start_val:D.data.length+1})}else{if(x===this.BROAD_DATA_REQ){v=(D.max_high?D.max_high:D.data[D.data.length-1][2])+1}}var C=B.copy().set("start",v);var u=this,y=this.load_data(C,A,w,z),t=$.Deferred();this.set_data(B,t);$.when(y).then(function(E){if(E.data){E.data=D.data.concat(E.data);if(E.max_low){E.max_low=D.max_low}if(E.message){E.message=E.message.replace(/[0-9]+/,E.data.length)}}u.set_data(B,E);t.resolve(E)});return t},get_elt:function(t){return p.prototype.get_elt.call(this,t.toString())},set_elt:function(u,t){return p.prototype.set_elt.call(this,u.toString(),t)}});var n=d.extend({load_data:function(t,w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,t,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var h=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(u){if(u.from_str){var w=u.from_str.split(":"),v=w[0],t=w[1].split("-");this.set({chrom:v,start:parseInt(t[0],10),end:parseInt(t[1],10)})}},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(A){var u=this.get("chrom"),z=A.get("chrom"),y=this.get("start"),w=A.get("start"),x=this.get("end"),v=A.get("end"),t;if(u&&z&&u!==z){return this.get("DIF_CHROMS")}if(y<w){if(x<w){t=this.get("BEFORE")}else{if(x<=v){t=this.get("OVERLAP_START")}else{t=this.get("CONTAINS")}}}else{if(y>v){t=this.get("AFTER")}else{if(x<=v){t=this.get("CONTAINED_BY")}else{t=this.get("OVERLAP_END")}}}return t},contains:function(t){return this.compute_overlap(t)===this.get("CONTAINS")},overlaps:function(t){return _.intersection([this.compute_overlap(t)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:h});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:h}]});var q=Backbone.Collection.extend({model:e});var b=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.flatten(_.map(this.get("data"),function(v){if(v.data.length!==0){return _.map(v.data,function(w){return w[1]})}else{return 0}}));this.set("max",_.max(t));this.set("min",_.min(t))}});var m=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.max(this.get("data"),function(v){if(!v||typeof v==="string"){return 0}return v[1]});this.attributes.max=(t&&typeof t!=="string"?t[1]:0)}});var s=Dataset.extend({initialize:function(t){this.set("id",t.dataset_id);var v=this.get("genome_wide_data");if(v){var u=(this.get("track_type")==="LineTrack"?b:m);this.set("genome_wide_data",new u(v))}}});var o=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:s}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:_.extend({},o.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(u){this.view=u.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(v){t.navigate(v)})},change_location:function(t){this.view.go_to(t)}});var j=function(t,v,u){$.ajax({url:t,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(w){show_modal("Select datasets for new tracks",w,{Cancel:function(){hide_modal()},Add:function(){var x=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var y={data_type:"track_config",hda_ldda:"hda"},z=$(this).val();if($(this).attr("name")!=="id"){y.hda_ldda="ldda"}x[x.length]=$.ajax({url:v+"/"+z,data:y,dataType:"json"})});$.when.apply($,x).then(function(){var y=(arguments[0] instanceof Array?$.map(arguments,function(z){return z[0]}):[arguments[0]]);u(y)});hide_modal()}})}})};var r=(function(){if(typeof module!=="undefined"&&module.exports){return module.exports}else{if(typeof define==="function"&&define.amd){r={};define(function(){return r});return r}else{return window}}})();r.BrowserBookmark=e;r.BrowserBookmarkCollection=q;r.Cache=p;r.CanvasManager=g;r.Genome=c;r.GenomeDataManager=d;r.GenomeRegion=h;r.GenomeRegionCollection=l;r.GenomeVisualization=k;r.GenomeWideBigWigData=b;r.GenomeWideSummaryTreeData=m;r.ReferenceTrackDataManager=n;r.ServerStateDeferred=f;r.TrackBrowserRouter=i;r.TrackConfig=a;r.Visualization=o;r.add_datasets=j}).call(this); \ No newline at end of file diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -2974,21 +2974,18 @@ // // Attribute init. // - var url_base = datasets_url + '/' + obj_dict.dataset_id; - this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : url_base); + this.dataset = new Dataset({ + id: obj_dict.dataset_id, + hda_ldda: obj_dict.hda_ldda + }); + this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); // A little ugly creating data manager right now due to transition to Backbone-based objects. - var track = this, - dataset = new Dataset({ - id: obj_dict.dataset_id, - hda_ldda: obj_dict.hda_ldda - }); this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : new GenomeDataManager({ - dataset: dataset, - data_url: track.data_url, + dataset: this.dataset, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset })); @@ -3311,9 +3308,9 @@ var init_deferred = $.Deferred(), params = { hda_ldda: track.hda_ldda, - data_type: 'converted_datasets_state', - chrom: track.view.chrom} - $.getJSON(this.data_url, params, function (result) { + data_type: this.dataset_check_type, + chrom: track.view.chrom }; + $.getJSON(this.dataset.url(), params, function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); track.tiles_div.text(DATA_ERROR); @@ -3829,11 +3826,10 @@ * Set up track to receive tool data. */ init_for_tool_data: function() { - // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- - // is ready. - this.data_manager.set('data_url', raw_data_url); + // Set up track to fetch raw data rather than converted data. + this.data_manager.set('data_type', 'raw_data'); this.data_query_wait = 1000; - this.dataset_check_url = dataset_state_url; + this.dataset_check_type = 'state'; // // Set up one-time, post-draw to clear tool execution settings. @@ -3860,8 +3856,10 @@ success_fn: function(result) { return result !== "pending"; } }); $.when(ss_deferred.go()).then(function() { - // Dataset is indexed, so use default data URL. - self.data_manager.set('data_url', default_data_url); + // Dataset is indexed, so use converted data. + self.data_manager.set('data_type', 'data'); + self.dataset_check_type = 'converted_datasets_state'; + this.data_query_wait = 5000; }); // Reset post-draw actions function. @@ -4319,7 +4317,7 @@ predraw_init: function() { var track = this; track.vertical_range = undefined; - return $.getJSON( track.data_url, + return $.getJSON( track.dataset.url(), { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, high: track.view.max_high, hda_ldda: track.hda_ldda, dataset_id: track.dataset_id }, function(result) { @@ -4541,6 +4539,7 @@ set_dataset: function(dataset) { this.dataset_id = dataset.get('id'); this.hda_ldda = dataset.get('hda_ldda'); + this.dataset = dataset; this.data_manager.set('dataset', dataset); }, diff -r 6243b992762c3f90abda948e081d266ca63e1db0 -r 2f63df92248894e78f9113fb79107fcbd6e12ff7 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -169,8 +169,7 @@ defaults: _.extend({}, Cache.prototype.defaults, { dataset: null, filters_manager: null, - data_url: null, - feature_search_url: null, + data_type: "data", genome_wide_summary_data: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } @@ -185,9 +184,8 @@ ready_deferred = $.Deferred(), ss_deferred = new ServerStateDeferred({ ajax_settings: { - url: this.get('data_url'), + url: this.get('dataset').url(), data: { - dataset_id: dataset.id, hda_ldda: dataset.get('hda_ldda'), data_type: 'state' }, @@ -214,7 +212,7 @@ hda_ldda: dataset.get('hda_ldda'), data_type: 'features' }; - return $.getJSON(this.get('data_url'), params); + return $.getJSON(dataset.url(), params); }, /** @@ -223,7 +221,7 @@ load_data: function(region, mode, resolution, extra_params) { // Setup data request params. var params = { - "data_type": "data", + "data_type": this.get('data_type'), "chrom": region.get('chrom'), "low": region.get('start'), "high": region.get('end'), @@ -253,7 +251,7 @@ // Do request. var manager = this; - return $.getJSON(this.get('data_url'), params, function (result) { + return $.getJSON(dataset.url(), params, function (result) { manager.set_data(region, result); }); }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Viz framework refactoring: move visualization view methods into base class and move chromosome/reference data methods to API.
by Bitbucket 14 Sep '12

14 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0d077bcf9ab7/ changeset: 0d077bcf9ab7 user: jgoecks date: 2012-09-14 23:57:07 summary: Viz framework refactoring: move visualization view methods into base class and move chromosome/reference data methods to API. affected #: 8 files diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 lib/galaxy/web/api/genomes.py --- a/lib/galaxy/web/api/genomes.py +++ b/lib/galaxy/web/api/genomes.py @@ -2,13 +2,16 @@ from galaxy.web.base.controller import BaseController, BaseAPIController from galaxy.util.bunch import Bunch +def is_true ( a_str ): + return is_true == True or a_str in [ 'True', 'true', 'T', 't' ] + class GenomesController( BaseAPIController ): """ RESTful controller for interactions with genome data. """ @web.expose_api - def index( self, trans, **kwds ): + def index( self, trans, **kwd ): """ GET /api/genomes: returns a list of installed genomes """ @@ -16,13 +19,23 @@ return [] @web.json - def show( self, trans, id, num=None, chrom=None, low=None ): + def show( self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ): """ GET /api/genomes/{id} Returns information about build <id> """ - return self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) + + # Process kwds. + reference = is_true( kwd.get( 'reference', False ) ) + + # Return info. + rval = None + if reference: + rval = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high, **kwd ) + else: + rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) + return rval @web.expose_api def create( self, trans, payload, **kwd ): diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -626,6 +626,29 @@ return visualization + def _get_datasources( self, trans, dataset ): + """ + Returns datasources for dataset; if datasources are not available + due to indexing, indexing is started. Return value is a dictionary + with entries of type + (<datasource_type> : {<datasource_name>, <indexing_message>}). + """ + track_type, data_sources = dataset.datatype.get_track_type() + data_sources_dict = {} + msg = None + for source_type, data_source in data_sources.iteritems(): + if source_type == "data_standalone": + # Nothing to do. + msg = None + else: + # Convert. + msg = self.convert_dataset( trans, dataset, data_source ) + + # Store msg. + data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } + + return data_sources_dict + class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -17,7 +17,7 @@ from galaxy.visualization.genomes import decode_dbkey, Genomes from galaxy.visualization.genome.visual_analytics import get_dataset_job -class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, SharableMixin ): +class TracksController( BaseUIController, UsesVisualizationMixin, SharableMixin ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. @@ -34,28 +34,6 @@ @web.require_login() def new_browser( self, trans, **kwargs ): return trans.fill_template( "tracks/new_browser.mako", dbkeys=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), default_dbkey=kwargs.get("default_dbkey", None) ) - - @web.json - def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): - if hda_id: - hda_ldda = "hda" - dataset_id = hda_id - elif ldda_id: - hda_ldda = "ldda" - dataset_id = ldda_id - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - - rows = [] - if isinstance( dataset.datatype, Bed ): - data = RawBedDataProvider( original_dataset=dataset ).get_iterator() - for i, line in enumerate( data ): - if ( i > 500 ): break - fields = line.split() - location = name = "%s:%s-%s" % ( fields[0], fields[1], fields[2] ) - if len( fields ) > 3: - name = fields[4] - rows.append( [location, name] ) - return { 'data': rows } @web.json def save( self, trans, vis_json ): @@ -92,14 +70,6 @@ if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: new_dataset = None # Already in browser, so don't add return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) - - @web.json - def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): - return self.app.genomes.chroms( trans, dbkey=dbkey, num=num, chrom=chrom, low=low ) - - @web.json - def reference( self, trans, dbkey, chrom, low, high, **kwargs ): - return self.app.genomes.reference( trans, dbkey, chrom, low, high, **kwargs ) @web.json def raw_data( self, trans, dataset_id, chrom, low, high, **kwargs ): @@ -137,9 +107,7 @@ @web.json def dataset_state( self, trans, dataset_id, **kwargs ): """ Returns state of dataset. """ - # TODO: this code is copied from data() -- should refactor. - - # Dataset check. + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self.check_dataset_state( trans, dataset ) if not msg: @@ -288,91 +256,3 @@ result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result - - @web.expose - def sweepster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ): - """ - Creates a sweepster visualization using the incoming parameters. If id is available, - get the visualization with the given id; otherwise, create a new visualization using - a given dataset and regions. - """ - # Need to create history if necessary in order to create tool form. - trans.get_history( create=True ) - - if id: - # Loading a shared visualization. - viz = self.get_visualization( trans, id ) - viz_config = self.get_visualization_config( trans, viz ) - dataset = self.get_dataset( trans, viz_config[ 'dataset_id' ] ) - else: - # Loading new visualization. - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - job = get_dataset_job( dataset ) - viz_config = { - 'dataset_id': dataset_id, - 'tool_id': job.tool_id, - 'regions': from_json_string( regions ) - } - - # Add tool, dataset attributes to config based on id. - tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] ) - viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True ) - viz_config[ 'dataset' ] = dataset.get_api_value() - - return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config ) - - @web.expose - def circster( self, trans, id, **kwargs ): - vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) - viz_config = self.get_visualization_config( trans, vis ) - - # Get genome info. - dbkey = viz_config[ 'dbkey' ] - chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) - genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } - - # Add genome-wide summary tree data to each track in viz. - tracks = viz_config[ 'tracks' ] - for track in tracks: - # Get dataset and indexed datatype. - dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - data_sources = self._get_datasources( trans, dataset ) - if 'data_standalone' in data_sources: - indexed_type = data_sources['data_standalone']['name'] - data_provider = get_data_provider( indexed_type )( dataset ) - else: - indexed_type = data_sources['index']['name'] - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } - - return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) - - # ----------------- - # Helper methods. - # ----------------- - - def _get_datasources( self, trans, dataset ): - """ - Returns datasources for dataset; if datasources are not available - due to indexing, indexing is started. Return value is a dictionary - with entries of type - (<datasource_type> : {<datasource_name>, <indexing_message>}). - """ - track_type, data_sources = dataset.datatype.get_track_type() - data_sources_dict = {} - msg = None - for source_type, data_source in data_sources.iteritems(): - if source_type == "data_standalone": - # Nothing to do. - msg = None - else: - # Convert. - msg = self.convert_dataset( trans, dataset, data_source ) - - # Store msg. - data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } - - return data_sources_dict \ No newline at end of file diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -232,6 +232,73 @@ _histories_grid = HistorySelectionGrid() _history_datasets_grid = HistoryDatasetsSelectionGrid() _tracks_grid = TracksterSelectionGrid() + + # + # -- Functions for listing visualizations. -- + # + + @web.expose + @web.require_login( "see all available libraries" ) + def list_libraries( self, trans, **kwargs ): + """List all libraries that can be used for selecting datasets.""" + + # Render the list view + return self._libraries_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see a library's datasets that can added to this visualization" ) + def list_library_datasets( self, trans, **kwargs ): + """List a library's datasets that can be added to a visualization.""" + + library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) + return trans.fill_template( '/tracks/library_datasets_select_grid.mako', + cntrller="library", + use_panels=False, + library=library, + created_ldda_ids='', + hidden_folder_ids='', + show_deleted=False, + comptypes=[], + current_user_roles=trans.get_current_user_roles(), + message='', + status="done" ) + + @web.expose + @web.require_login( "see all available histories" ) + def list_histories( self, trans, **kwargs ): + """List all histories that can be used for selecting datasets.""" + + # Render the list view + return self._histories_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see current history's datasets that can added to this visualization" ) + def list_current_history_datasets( self, trans, **kwargs ): + """ List a history's datasets that can be added to a visualization. """ + + kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id ) + kwargs[ 'show_item_checkboxes' ] = 'True' + return self.list_history_datasets( trans, **kwargs ) + + @web.expose + @web.require_login( "see a history's datasets that can added to this visualization" ) + def list_history_datasets( self, trans, **kwargs ): + """List a history's datasets that can be added to a visualization.""" + + # Render the list view + return self._history_datasets_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see all available datasets" ) + def list_datasets( self, trans, **kwargs ): + """List all datasets that can be added as tracks""" + + # Render the list view + return self._data_grid( trans, **kwargs ) + + @web.expose + def list_tracks( self, trans, **kwargs ): + return self._tracks_grid( trans, **kwargs ) @web.expose def list_published( self, trans, *args, **kwargs ): @@ -244,6 +311,38 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) + def list( self, trans, *args, **kwargs ): + # Handle operation + if 'operation' in kwargs and 'id' in kwargs: + session = trans.sa_session + operation = kwargs['operation'].lower() + ids = util.listify( kwargs['id'] ) + for id in ids: + item = session.query( model.Visualization ).get( trans.security.decode_id( id ) ) + if operation == "delete": + item.deleted = True + if operation == "share or publish": + return self.sharing( trans, **kwargs ) + session.flush() + + # Build list of visualizations shared with user. + shared_by_others = trans.sa_session \ + .query( model.VisualizationUserShareAssociation ) \ + .filter_by( user=trans.get_user() ) \ + .join( model.Visualization.table ) \ + .filter( model.Visualization.deleted == False ) \ + .order_by( desc( model.Visualization.update_time ) ) \ + .all() + + return trans.fill_template( "visualization/list.mako", grid=self._user_list_grid( trans, *args, **kwargs ), shared_by_others=shared_by_others ) + + + # + # -- Functions for operating on visualizations. -- + # + + @web.expose + @web.require_login( "use Galaxy visualizations", use_panels=True ) def index( self, trans, *args, **kwargs ): """ Lists user's saved visualizations. """ return self.list( trans, *args, **kwargs ) @@ -268,34 +367,7 @@ # Display the management page trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) return self.list( trans ) - - @web.expose - @web.require_login( "use Galaxy visualizations", use_panels=True ) - def list( self, trans, *args, **kwargs ): - # Handle operation - if 'operation' in kwargs and 'id' in kwargs: - session = trans.sa_session - operation = kwargs['operation'].lower() - ids = util.listify( kwargs['id'] ) - for id in ids: - item = session.query( model.Visualization ).get( trans.security.decode_id( id ) ) - if operation == "delete": - item.deleted = True - if operation == "share or publish": - return self.sharing( trans, **kwargs ) - session.flush() - # Build list of visualizations shared with user. - shared_by_others = trans.sa_session \ - .query( model.VisualizationUserShareAssociation ) \ - .filter_by( user=trans.get_user() ) \ - .join( model.Visualization.table ) \ - .filter( model.Visualization.deleted == False ) \ - .order_by( desc( model.Visualization.update_time ) ) \ - .all() - - return trans.fill_template( "visualization/list.mako", grid=self._user_list_grid( trans, *args, **kwargs ), shared_by_others=shared_by_others ) - @web.expose @web.require_login( "modify Galaxy visualizations" ) def set_slug_async( self, trans, id, new_slug ): @@ -608,68 +680,91 @@ template="visualization/create.mako" ) @web.expose - @web.require_login( "see all available libraries" ) - def list_libraries( self, trans, **kwargs ): - """List all libraries that can be used for selecting datasets.""" + def circster( self, trans, id, **kwargs ): + """ + Display a circster visualization. + """ + vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + viz_config = self.get_visualization_config( trans, vis ) - # Render the list view - return self._libraries_grid( trans, **kwargs ) + # Get genome info. + dbkey = viz_config[ 'dbkey' ] + chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) + genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } + + # Add genome-wide summary tree data to each track in viz. + tracks = viz_config[ 'tracks' ] + for track in tracks: + # Get dataset and indexed datatype. + dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) + data_sources = self._get_datasources( trans, dataset ) + if 'data_standalone' in data_sources: + indexed_type = data_sources['data_standalone']['name'] + data_provider = get_data_provider( indexed_type )( dataset ) + else: + indexed_type = data_sources['index']['name'] + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + # HACK: pass in additional params, which are only used for summary tree data, not BBI data. + track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } + + return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) @web.expose - @web.require_login( "see a library's datasets that can added to this visualization" ) - def list_library_datasets( self, trans, **kwargs ): - """List a library's datasets that can be added to a visualization.""" - - library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) - return trans.fill_template( '/tracks/library_datasets_select_grid.mako', - cntrller="library", - use_panels=False, - library=library, - created_ldda_ids='', - hidden_folder_ids='', - show_deleted=False, - comptypes=[], - current_user_roles=trans.get_current_user_roles(), - message='', - status="done" ) - - @web.expose - @web.require_login( "see all available histories" ) - def list_histories( self, trans, **kwargs ): - """List all histories that can be used for selecting datasets.""" - - # Render the list view - return self._histories_grid( trans, **kwargs ) - - @web.expose - @web.require_login( "see current history's datasets that can added to this visualization" ) - def list_current_history_datasets( self, trans, **kwargs ): - """ List a history's datasets that can be added to a visualization. """ - - kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id ) - kwargs[ 'show_item_checkboxes' ] = 'True' - return self.list_history_datasets( trans, **kwargs ) - - @web.expose - @web.require_login( "see a history's datasets that can added to this visualization" ) - def list_history_datasets( self, trans, **kwargs ): - """List a history's datasets that can be added to a visualization.""" + def sweepster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ): + """ + Displays a sweepster visualization using the incoming parameters. If id is available, + get the visualization with the given id; otherwise, create a new visualization using + a given dataset and regions. + """ + # Need to create history if necessary in order to create tool form. + trans.get_history( create=True ) - # Render the list view - return self._history_datasets_grid( trans, **kwargs ) - - @web.expose - @web.require_login( "see all available datasets" ) - def list_datasets( self, trans, **kwargs ): - """List all datasets that can be added as tracks""" - - # Render the list view - return self._data_grid( trans, **kwargs ) - - @web.expose - def list_tracks( self, trans, **kwargs ): - return self._tracks_grid( trans, **kwargs ) + if id: + # Loading a shared visualization. + viz = self.get_visualization( trans, id ) + viz_config = self.get_visualization_config( trans, viz ) + dataset = self.get_dataset( trans, viz_config[ 'dataset_id' ] ) + else: + # Loading new visualization. + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + job = get_dataset_job( dataset ) + viz_config = { + 'dataset_id': dataset_id, + 'tool_id': job.tool_id, + 'regions': from_json_string( regions ) + } + + # Add tool, dataset attributes to config based on id. + tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] ) + viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True ) + viz_config[ 'dataset' ] = dataset.get_api_value() + + return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config ) def get_item( self, trans, id ): return self.get_visualization( trans, id ) + + @web.json + def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): + if hda_id: + hda_ldda = "hda" + dataset_id = hda_id + elif ldda_id: + hda_ldda = "ldda" + dataset_id = ldda_id + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + + rows = [] + if isinstance( dataset.datatype, Bed ): + data = RawBedDataProvider( original_dataset=dataset ).get_iterator() + for i, line in enumerate( data ): + if ( i > 500 ): break + fields = line.split() + location = name = "%s:%s-%s" % ( fields[0], fields[1], fields[2] ) + if len( fields ) > 3: + name = fields[4] + rows.append( [location, name] ) + return { 'data': rows } diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -1320,13 +1320,12 @@ */ load_chroms: function(url_parms) { url_parms.num = MAX_CHROMS_SELECTABLE; - url_parms.dbkey = this.dbkey; var view = this, chrom_data = $.Deferred(); $.ajax({ - url: chrom_url, + url: chrom_url + "/" + this.dbkey, data: url_parms, dataType: "json", success: function (result) { @@ -4198,10 +4197,10 @@ this.content_div.css("background", "none"); this.content_div.css("min-height", "0px"); this.content_div.css("border", "none"); - this.data_url = reference_url; - this.data_url_extra_params = {dbkey: view.dbkey}; + this.data_url = reference_url + "/" + this.view.dbkey; + this.data_url_extra_params = {reference: true}; this.data_manager = new ReferenceTrackDataManager({ - data_url: reference_url + data_url: this.data_url }); this.hide_contents(); }; diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -62,8 +62,7 @@ raw_data_url: '${h.url_for( controller="/tracks", action="raw_data" )}', converted_datasets_state_url: '${h.url_for( controller="/tracks", action="converted_datasets_state" )}', dataset_state_url: '${h.url_for( controller="/tracks", action="dataset_state" )}', - sweepster_url: '${h.url_for( controller="/tracks", action="sweepster" )}', - + sweepster_url: '${h.url_for( controller="/visualization", action="sweepster" )}', visualization_url: '${h.url_for( controller="/visualization", action="save" )}', }); </script> diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -113,7 +113,7 @@ title: 'Circster', on_click: function() { // Add viz id dynamically so that newly saved visualizations work as well. - window.location = "${h.url_for( controller='tracks', action='circster' )}?id=" + view.vis_id; + window.location = "${h.url_for( controller='visualization', action='circster' )}?id=" + view.vis_id; } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { diff -r 81e32d70ee2daf03228752992b1765904f7e93fa -r 0d077bcf9ab71ea928fb832cf85a9f7f4f20b5f8 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -20,8 +20,8 @@ add_datasets_url = "${h.url_for( controller='/visualization', action='list_current_history_datasets' )}", default_data_url = "${h.url_for( controller='/tracks', action='data' )}", raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", - reference_url = "${h.url_for( controller='/tracks', action='reference' )}", - chrom_url = "${h.url_for( controller='/tracks', action='chroms' )}", + reference_url = "${h.url_for( controller='/api/genomes' )}", + chrom_url = "${h.url_for( controller='/api/genomes' )}", dataset_state_url = "${h.url_for( controller='/tracks', action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( controller='/tracks', action='converted_datasets_state' )}", feature_search_url = "${h.url_for( controller='/tracks', action='search_features' )}"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fixes for controller mixin hierarchy. Move track config response from tracks controller to API datasets controller.
by Bitbucket 14 Sep '12

14 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81e32d70ee2d/ changeset: 81e32d70ee2d user: jgoecks date: 2012-09-14 23:03:11 summary: Fixes for controller mixin hierarchy. Move track config response from tracks controller to API datasets controller. affected #: 9 files diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -10,10 +10,13 @@ log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesHistoryDatasetAssociationMixin ): +def is_true ( a_str ): + return is_true == True or a_str in [ 'True', 'true', 'T', 't' ] + +class DatasetsController( BaseAPIController, UsesVisualizationMixin ): @web.expose_api - def index( self, trans, hda_id, **kwd ): + def index( self, trans, **kwd ): """ GET /api/datasets Lists datasets. @@ -21,24 +24,31 @@ pass @web.expose_api - def show( self, trans, id, deleted='False', **kwd ): + def show( self, trans, id, hda_ldda='hda', deleted='False', **kwd ): """ GET /api/datasets/{encoded_dataset_id} Displays information about and/or content of a dataset. """ + + # Process arguments. + track_config = is_true( kwd.get( 'track_config', False ) ) - # Get HDA. + # Get dataset. try: - hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True ) + dataset = self.get_hda_or_ldda( trans, hda_ldda=hda_ldda, dataset_id=id ) except Exception, e: return str( e ) - - # Return information about HDA. + + # Return info. rval = None - try: - rval = hda.get_api_value() - except Exception, e: - rval = "Error in dataset API at listing contents" - log.error( rval + ": %s" % str(e) ) - trans.response.status = 500 + if track_config: + rval = self.get_new_track_config( trans, dataset ) + else: + # Default: return dataset as API value. + try: + rval = dataset.get_api_value() + except Exception, e: + rval = "Error in dataset API at listing contents" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 return rval diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -5,7 +5,7 @@ from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.genome.data_providers import * -class ToolsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin ): +class ToolsController( BaseAPIController, UsesVisualizationMixin ): """ RESTful controller for interactions with tools. """ diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -357,7 +357,8 @@ def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible ) -class UsesVisualizationMixin( SharableItemSecurityMixin, UsesLibraryMixinItems ): +class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, + UsesLibraryMixinItems ): """ Mixin for controllers that use Visualization objects. """ viz_types = [ "trackster", "circster" ] diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -273,7 +273,7 @@ _BaseHTMLProcessor.unknown_endtag( self, tag ) class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin, - UsesStoredWorkflowMixin, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ): + UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings ): _page_list = PageListGrid() _all_published_list = PageAllPublishedGrid() diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -36,19 +36,6 @@ return trans.fill_template( "tracks/new_browser.mako", dbkeys=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), default_dbkey=kwargs.get("default_dbkey", None) ) @web.json - def add_track_async(self, trans, hda_id=None, ldda_id=None): - # Get dataset. - if hda_id: - hda_ldda = "hda" - dataset_id = hda_id - elif ldda_id: - hda_ldda = "ldda" - dataset_id = ldda_id - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - - return self.get_new_track_config( trans, dataset ) - - @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): if hda_id: hda_ldda = "hda" diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -224,7 +224,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, - UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, + UsesVisualizationMixin, UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -742,15 +742,16 @@ "Add": function() { var requests = []; $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data, + var data = { + 'track_config': true, + 'hda_ldda': 'hda' + }, id = $(this).val(); - if ($(this).attr("name") === "id") { - data = { hda_id: id }; - } else { - data = { ldda_id: id}; + if ($(this).attr("name") !== "id") { + data['hda_ldda'] = 'ldda'; } requests[requests.length] = $.ajax({ - url: add_track_async_url, + url: add_track_async_url + "/" + id, data: data, dataType: "json" }); diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -233,8 +233,8 @@ %if add_dataset is not None: $.ajax({ - url: "${h.url_for( action='add_track_async' )}", - data: { hda_id: "${add_dataset}" }, + url: add_track_async_url + "/${add_dataset}", + data: { hda_ldda: 'hda', 'track_config': true }, dataType: "json", success: function(track_data) { view.add_drawable( object_from_template(track_data, view, view) ) } }); diff -r 034a27f9c6c687803b337024c526d9b42c6a25b2 -r 81e32d70ee2daf03228752992b1765904f7e93fa templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -16,7 +16,7 @@ ## Render a block of JavaScript that contains all necessary variables for Trackster. <%def name="render_trackster_js_vars()"> - var add_track_async_url = "${h.url_for( controller='/tracks', action='add_track_async' )}", + var add_track_async_url = "${h.url_for( controller='/api/datasets' )}", add_datasets_url = "${h.url_for( controller='/visualization', action='list_current_history_datasets' )}", default_data_url = "${h.url_for( controller='/tracks', action='data' )}", raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for fastq filter tests of paired_end boolean.
by Bitbucket 14 Sep '12

14 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/034a27f9c6c6/ changeset: 034a27f9c6c6 user: dan date: 2012-09-14 21:50:38 summary: Fix for fastq filter tests of paired_end boolean. affected #: 1 file diff -r be38ea1ed21376549a244cf29bb6d1b0bd73059f -r 034a27f9c6c687803b337024c526d9b42c6a25b2 tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml +++ b/tools/fastq/fastq_filter.xml @@ -111,7 +111,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -127,7 +127,7 @@ <param name="min_quality" value="-5"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -144,7 +144,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -161,7 +161,7 @@ <param name="min_quality" value="1"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -177,7 +177,7 @@ <param name="min_quality" value="-4"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -194,7 +194,7 @@ <param name="min_quality" value="1"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="1"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -210,7 +210,7 @@ <param name="min_quality" value="-5"/><param name="max_quality" value="61"/><param name="max_num_deviants" value="1"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="0"/><param name="right_column_offset" value="0"/> @@ -227,7 +227,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="1"/><param name="right_column_offset" value="1"/> @@ -243,7 +243,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_absolute"/><param name="left_column_offset" value="1"/><param name="right_column_offset" value="1"/> @@ -260,7 +260,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="False"/><param name="base_offset_type" value="offsets_percent"/><param name="left_column_offset" value="1.075"/><param name="right_column_offset" value="1.075"/> @@ -276,7 +276,7 @@ <param name="min_quality" value="0"/><param name="max_quality" value="0"/><param name="max_num_deviants" value="0"/> - <param name="paired_end" value="single_end"/> + <param name="paired_end" value="True"/><param name="base_offset_type" value="offsets_percent"/><param name="left_column_offset" value="1"/><param name="right_column_offset" value="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: dan: Fix for unit tests in galaxy.tools.deps
by Bitbucket 14 Sep '12

14 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be38ea1ed213/ changeset: be38ea1ed213 user: dan date: 2012-09-14 20:50:27 summary: Fix for unit tests in galaxy.tools.deps affected #: 1 file diff -r f8ea04e7bbff4acbc14f95e14fd6f955c307f906 -r be38ea1ed21376549a244cf29bb6d1b0bd73059f lib/galaxy/tools/deps/__init__.py --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -73,13 +73,14 @@ else: return None, None, None def _get_installed_dependency( self, installed_tool_dependencies, name, type, version=None ): - for installed_tool_dependency in installed_tool_dependencies: - if version: - if installed_tool_dependency.name==name and installed_tool_dependency.type==type and installed_tool_dependency.version==version: - return installed_tool_dependency - else: - if installed_tool_dependency.name==name and installed_tool_dependency.type==type: - return installed_tool_dependency + if installed_tool_dependencies: + for installed_tool_dependency in installed_tool_dependencies: + if version: + if installed_tool_dependency.name==name and installed_tool_dependency.type==type and installed_tool_dependency.version==version: + return installed_tool_dependency + else: + if installed_tool_dependency.name==name and installed_tool_dependency.type==type: + return installed_tool_dependency return None def _get_package_installed_dependency_path( self, installed_tool_dependency, base_path, name, version ): tool_shed_repository = installed_tool_dependency.tool_shed_repository Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 14 Sep '12

14 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bc56358a5c51/ changeset: bc56358a5c51 user: jgoecks date: 2012-09-14 20:40:53 summary: Visualization framework: (a) put summary tree back in tracks module because pickling requires it not move modules and (b) move grids from tracks controller to visualization controller. affected #: 14 files diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -14,7 +14,7 @@ import sys, fileinput, optparse from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.genome.summary import * +from galaxy.visualization.tracks.summary import * from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed from bx.interval_index_file import Indexes diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -15,7 +15,7 @@ import sys, fileinput, optparse from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.genome.summary import * +from galaxy.visualization.tracks.summary import * from bx.intervals.io import * from galaxy.datatypes.util.gff_util import * diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py @@ -14,7 +14,7 @@ pkg_resources.require( "pysam" ) from pysam import csamtools -from galaxy.visualization.genome.summary import * +from galaxy.visualization.tracks.summary import * def main(): parser = optparse.OptionParser() diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py @@ -9,7 +9,7 @@ import optparse import galaxy_utils.sequence.vcf -from galaxy.visualization.genome.summary import SummaryTree +from galaxy.visualization.tracks.summary import SummaryTree def main(): # Read options, args. diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/visualization/genome/data_providers.py --- a/lib/galaxy/visualization/genome/data_providers.py +++ b/lib/galaxy/visualization/genome/data_providers.py @@ -16,7 +16,7 @@ from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache -from galaxy.visualization.genome.summary import * +from galaxy.visualization.tracks.summary import * from galaxy.visualization.data_providers import BaseDataProvider import galaxy_utils.sequence.vcf from galaxy.datatypes.tabular import Tabular, Vcf diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/visualization/genome/summary.py --- a/lib/galaxy/visualization/genome/summary.py +++ /dev/null @@ -1,111 +0,0 @@ -''' -Summary tree data structure for feature aggregation across large genomic regions. -''' - -import sys, os -import cPickle - -# TODO: What are the performance implications of setting min level to 1? Data -# structure size and/or query speed? It would be nice to have level 1 data -# so that client does not have to compute it. -MIN_LEVEL = 2 - -class SummaryTree: - def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ): - self.chrom_blocks = {} - self.levels = levels - self.draw_cutoff = draw_cutoff - self.detail_cutoff = detail_cutoff - self.block_size = block_size - self.chrom_stats = {} - - def find_block( self, num, level ): - """ Returns block that num is in for level. """ - return ( num / self.block_size ** level ) - - def insert_range( self, chrom, start, end ): - """ Inserts a feature at chrom:start-end into the tree. """ - - # Get or set up chrom blocks. - if chrom in self.chrom_blocks: - blocks = self.chrom_blocks[ chrom ] - else: - blocks = self.chrom_blocks[ chrom ] = {} - self.chrom_stats[ chrom ] = {} - for level in range( MIN_LEVEL, self.levels + 1 ): - blocks[ level ] = {} - - # Insert feature into all matching blocks at all levels. - for level in range( MIN_LEVEL, self.levels + 1 ): - block_level = blocks[ level ] - starting_block = self.find_block( start, level ) - ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block + 1 ): - if block in block_level: - block_level[ block ] += 1 - else: - block_level[ block ] = 1 - - def finish( self ): - """ Compute stats for levels. """ - - for chrom, blocks in self.chrom_blocks.iteritems(): - for level in range( self.levels, MIN_LEVEL - 1, -1 ): - # Set level's stats. - max_val = max( blocks[ level ].values() ) - self.chrom_stats[ chrom ][ level ] = {} - self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level - self.chrom_stats[ chrom ][ level ][ "max" ] = max_val - self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] ) - - self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] ) - - def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ): - """ Queries tree for data. """ - - # Set cutoffs to self's attributes if not defined. - if draw_cutoff != 0: - draw_cutoff = self.draw_cutoff - if detail_cutoff != 0: - detail_cutoff = self.detail_cutoff - - # Get data. - if chrom in self.chrom_blocks: - stats = self.chrom_stats[ chrom ] - - # For backwards compatibility: - if "detail_level" in stats and level <= stats[ "detail_level" ]: - return "detail" - elif "draw_level" in stats and level <= stats[ "draw_level" ]: - return "draw" - - # If below draw, detail level, return string to denote this. - max = stats[ level ][ "max" ] - if max < detail_cutoff: - return "detail" - if max < draw_cutoff: - return "draw" - - # Return block data. - blocks = self.chrom_blocks[ chrom ] - results = [] - multiplier = self.block_size ** level - starting_block = self.find_block( start, level ) - ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block + 1 ): - val = 0 - if block in blocks[ level ]: - val = blocks[ level ][ block ] - results.append( ( block * multiplier, val ) ) - return results - - return None - - def write( self, filename ): - """ Writes tree to file. """ - self.finish() - cPickle.dump( self, open( filename, 'wb' ), 2 ) - -def summary_tree_from_file( filename ): - return cPickle.load( open( filename, "rb" ) ) - diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/visualization/tracks/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/tracks/__init__.py @@ -0,0 +1,1 @@ +""" Summary.py required to be in this module due to pickling. """ \ No newline at end of file diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/visualization/tracks/summary.py --- /dev/null +++ b/lib/galaxy/visualization/tracks/summary.py @@ -0,0 +1,111 @@ +''' +Summary tree data structure for feature aggregation across large genomic regions. +''' + +import sys, os +import cPickle + +# TODO: What are the performance implications of setting min level to 1? Data +# structure size and/or query speed? It would be nice to have level 1 data +# so that client does not have to compute it. +MIN_LEVEL = 2 + +class SummaryTree: + def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ): + self.chrom_blocks = {} + self.levels = levels + self.draw_cutoff = draw_cutoff + self.detail_cutoff = detail_cutoff + self.block_size = block_size + self.chrom_stats = {} + + def find_block( self, num, level ): + """ Returns block that num is in for level. """ + return ( num / self.block_size ** level ) + + def insert_range( self, chrom, start, end ): + """ Inserts a feature at chrom:start-end into the tree. """ + + # Get or set up chrom blocks. + if chrom in self.chrom_blocks: + blocks = self.chrom_blocks[ chrom ] + else: + blocks = self.chrom_blocks[ chrom ] = {} + self.chrom_stats[ chrom ] = {} + for level in range( MIN_LEVEL, self.levels + 1 ): + blocks[ level ] = {} + + # Insert feature into all matching blocks at all levels. + for level in range( MIN_LEVEL, self.levels + 1 ): + block_level = blocks[ level ] + starting_block = self.find_block( start, level ) + ending_block = self.find_block( end, level ) + for block in range( starting_block, ending_block + 1 ): + if block in block_level: + block_level[ block ] += 1 + else: + block_level[ block ] = 1 + + def finish( self ): + """ Compute stats for levels. """ + + for chrom, blocks in self.chrom_blocks.iteritems(): + for level in range( self.levels, MIN_LEVEL - 1, -1 ): + # Set level's stats. + max_val = max( blocks[ level ].values() ) + self.chrom_stats[ chrom ][ level ] = {} + self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level + self.chrom_stats[ chrom ][ level ][ "max" ] = max_val + self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] ) + + self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] ) + + def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ): + """ Queries tree for data. """ + + # Set cutoffs to self's attributes if not defined. + if draw_cutoff != 0: + draw_cutoff = self.draw_cutoff + if detail_cutoff != 0: + detail_cutoff = self.detail_cutoff + + # Get data. + if chrom in self.chrom_blocks: + stats = self.chrom_stats[ chrom ] + + # For backwards compatibility: + if "detail_level" in stats and level <= stats[ "detail_level" ]: + return "detail" + elif "draw_level" in stats and level <= stats[ "draw_level" ]: + return "draw" + + # If below draw, detail level, return string to denote this. + max = stats[ level ][ "max" ] + if max < detail_cutoff: + return "detail" + if max < draw_cutoff: + return "draw" + + # Return block data. + blocks = self.chrom_blocks[ chrom ] + results = [] + multiplier = self.block_size ** level + starting_block = self.find_block( start, level ) + ending_block = self.find_block( end, level ) + for block in range( starting_block, ending_block + 1 ): + val = 0 + if block in blocks[ level ]: + val = blocks[ level ][ block ] + results.append( ( block * multiplier, val ) ) + return results + + return None + + def write( self, filename ): + """ Writes tree to file. """ + self.finish() + cPickle.dump( self, open( filename, 'wb' ), 2 ) + +def summary_tree_from_file( filename ): + return cPickle.load( open( filename, "rb" ) ) + diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -8,7 +8,6 @@ from galaxy import model from galaxy.util.json import to_json_string, from_json_string from galaxy.web.base.controller import * -from galaxy.web.controllers.library import LibraryListGrid from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch @@ -16,152 +15,13 @@ from galaxy.model import NoConverterException, ConverterDependencyException from galaxy.visualization.genome.data_providers import * from galaxy.visualization.genomes import decode_dbkey, Genomes -from galaxy.visualization.genome.visual_analytics import get_dataset_job - - -class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, history ): - return history.get_display_name() - def get_link( self, trans, grid, history ): - # Provide link to list all datasets in history that have a given dbkey. - # Right now, only dbkey needs to be passed through, but pass through - # all for now since it's cleaner. - d = dict( action=grid.datasets_action, show_item_checkboxes=True ) - d[ grid.datasets_param ] = trans.security.encode_id( history.id ) - for filter, value in grid.cur_filter_dict.iteritems(): - d[ "f-" + filter ] = value - return d - -class DbKeyPlaceholderColumn( grids.GridColumn ): - """ Placeholder to keep track of dbkey. """ - def filter( self, trans, user, query, dbkey ): - return query - -class HistorySelectionGrid( grids.Grid ): - """ - Grid enables user to select a history, which is then used to display - datasets from the history. - """ - title = "Add Track: Select History" - model_class = model.History - template='/tracks/history_select_grid.mako' - default_sort_key = "-update_time" - datasets_action = 'list_history_datasets' - datasets_param = "f-history" - columns = [ - NameColumn( "History Name", key="name", filterable="standard" ), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago, visible=False ), - DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) - ] - num_rows_per_page = 10 - use_async = True - use_paging = True - def apply_query_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False, deleted=False, importing=False ) - -class LibrarySelectionGrid( LibraryListGrid ): - """ - Grid enables user to select a Library, which is then used to display - datasets from the history. - """ - title = "Add Track: Select Library" - template='/tracks/history_select_grid.mako' - model_class = model.Library - datasets_action = 'list_library_datasets' - datasets_param = "f-library" - columns = [ - NameColumn( "Library Name", key="name", filterable="standard" ) - ] - num_rows_per_page = 10 - use_async = True - use_paging = True - -class DbKeyColumn( grids.GridColumn ): - """ Column for filtering by and displaying dataset dbkey. """ - def filter( self, trans, user, query, dbkey ): - """ Filter by dbkey; datasets without a dbkey are returned as well. """ - # use raw SQL b/c metadata is a BLOB - dbkey_user, dbkey = decode_dbkey( dbkey ) - dbkey = dbkey.replace("'", "\\'") - return query.filter( or_( \ - or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ - or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ - ) - ) - -class HistoryColumn( grids.GridColumn ): - """ Column for filtering by history id. """ - def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==trans.security.decode_id(history_id) ) - -class HistoryDatasetsSelectionGrid( grids.Grid ): - # Grid definition. - available_tracks = None - title = "Add Datasets" - template = "tracks/history_datasets_select_grid.mako" - model_class = model.HistoryDatasetAssociation - default_filter = { "deleted" : "False" , "shared" : "All" } - default_sort_key = "-hid" - use_async = True - use_paging = False - columns = [ - grids.GridColumn( "Id", key="hid" ), - grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), - grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ), - HistoryColumn( "History", key="history", visible=False ), - DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False ) - ] - columns.append( - grids.MulticolFilterColumn( "Search name and filetype", cols_to_filter=[ columns[1], columns[2] ], - key="free-text-search", visible=False, filterable="standard" ) - ) - - def get_current_item( self, trans, **kwargs ): - """ - Current item for grid is the history being queried. This is a bit - of hack since current_item typically means the current item in the grid. - """ - return model.History.get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) - def build_initial_query( self, trans, **kwargs ): - return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) - def apply_query_filter( self, trans, query, **kwargs ): - if self.available_tracks is None: - self.available_tracks = trans.app.datatypes_registry.get_available_tracks() - return query.filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \ - .filter( model.Dataset.state == model.Dataset.states.OK ) \ - .filter( model.HistoryDatasetAssociation.deleted == False ) \ - .filter( model.HistoryDatasetAssociation.visible == True ) - -class TracksterSelectionGrid( grids.Grid ): - # Grid definition. - title = "Insert into visualization" - template = "/tracks/add_to_viz.mako" - async_template = "/page/select_items_grid_async.mako" - model_class = model.Visualization - default_sort_key = "-update_time" - use_async = True - use_paging = False - columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ), - grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) - ] - - def build_initial_query( self, trans, **kwargs ): - return trans.sa_session.query( self.model_class ).filter( self.model_class.deleted == False ) - def apply_query_filter( self, trans, query, **kwargs ): - return query.filter( self.model_class.user_id == trans.user.id ) +from galaxy.visualization.genome.visual_analytics import get_dataset_job class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, SharableMixin ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. """ - - libraries_grid = LibrarySelectionGrid() - histories_grid = HistorySelectionGrid() - history_datasets_grid = HistoryDatasetsSelectionGrid() - tracks_grid = TracksterSelectionGrid() @web.expose @web.require_login() @@ -441,70 +301,7 @@ result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result - - @web.expose - @web.require_login( "see all available libraries" ) - def list_libraries( self, trans, **kwargs ): - """List all libraries that can be used for selecting datasets.""" - - # Render the list view - return self.libraries_grid( trans, **kwargs ) - - @web.expose - @web.require_login( "see a library's datasets that can added to this visualization" ) - def list_library_datasets( self, trans, **kwargs ): - """List a library's datasets that can be added to a visualization.""" - - library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) - return trans.fill_template( '/tracks/library_datasets_select_grid.mako', - cntrller="library", - use_panels=False, - library=library, - created_ldda_ids='', - hidden_folder_ids='', - show_deleted=False, - comptypes=[], - current_user_roles=trans.get_current_user_roles(), - message='', - status="done" ) - - @web.expose - @web.require_login( "see all available histories" ) - def list_histories( self, trans, **kwargs ): - """List all histories that can be used for selecting datasets.""" - - # Render the list view - return self.histories_grid( trans, **kwargs ) - - @web.expose - @web.require_login( "see current history's datasets that can added to this visualization" ) - def list_current_history_datasets( self, trans, **kwargs ): - """ List a history's datasets that can be added to a visualization. """ - - kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id ) - kwargs[ 'show_item_checkboxes' ] = 'True' - return self.list_history_datasets( trans, **kwargs ) - - @web.expose - @web.require_login( "see a history's datasets that can added to this visualization" ) - def list_history_datasets( self, trans, **kwargs ): - """List a history's datasets that can be added to a visualization.""" - - # Render the list view - return self.history_datasets_grid( trans, **kwargs ) - - @web.expose - @web.require_login( "see all available datasets" ) - def list_datasets( self, trans, **kwargs ): - """List all datasets that can be added as tracks""" - - # Render the list view - return self.data_grid( trans, **kwargs ) - - @web.expose - def list_tracks( self, trans, **kwargs ): - return self.tracks_grid( trans, **kwargs ) - + @web.expose def sweepster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ): """ diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -3,6 +3,145 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, grids, iff from galaxy.util.sanitize_html import sanitize_html +from galaxy.web.controllers.library import LibraryListGrid +from galaxy.visualization.genomes import decode_dbkey + +# +# -- Grids -- +# + +class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, history ): + return history.get_display_name() + def get_link( self, trans, grid, history ): + # Provide link to list all datasets in history that have a given dbkey. + # Right now, only dbkey needs to be passed through, but pass through + # all for now since it's cleaner. + d = dict( action=grid.datasets_action, show_item_checkboxes=True ) + d[ grid.datasets_param ] = trans.security.encode_id( history.id ) + for filter, value in grid.cur_filter_dict.iteritems(): + d[ "f-" + filter ] = value + return d + +class DbKeyPlaceholderColumn( grids.GridColumn ): + """ Placeholder to keep track of dbkey. """ + def filter( self, trans, user, query, dbkey ): + return query + +class HistorySelectionGrid( grids.Grid ): + """ + Grid enables user to select a history, which is then used to display + datasets from the history. + """ + title = "Add Track: Select History" + model_class = model.History + template='/tracks/history_select_grid.mako' + default_sort_key = "-update_time" + datasets_action = 'list_history_datasets' + datasets_param = "f-history" + columns = [ + NameColumn( "History Name", key="name", filterable="standard" ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago, visible=False ), + DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) + ] + num_rows_per_page = 10 + use_async = True + use_paging = True + def apply_query_filter( self, trans, query, **kwargs ): + return query.filter_by( user=trans.user, purged=False, deleted=False, importing=False ) + +class LibrarySelectionGrid( LibraryListGrid ): + """ + Grid enables user to select a Library, which is then used to display + datasets from the history. + """ + title = "Add Track: Select Library" + template='/tracks/history_select_grid.mako' + model_class = model.Library + datasets_action = 'list_library_datasets' + datasets_param = "f-library" + columns = [ + NameColumn( "Library Name", key="name", filterable="standard" ) + ] + num_rows_per_page = 10 + use_async = True + use_paging = True + +class DbKeyColumn( grids.GridColumn ): + """ Column for filtering by and displaying dataset dbkey. """ + def filter( self, trans, user, query, dbkey ): + """ Filter by dbkey; datasets without a dbkey are returned as well. """ + # use raw SQL b/c metadata is a BLOB + dbkey_user, dbkey = decode_dbkey( dbkey ) + dbkey = dbkey.replace("'", "\\'") + return query.filter( or_( \ + or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ + or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ + ) + ) + +class HistoryColumn( grids.GridColumn ): + """ Column for filtering by history id. """ + def filter( self, trans, user, query, history_id ): + return query.filter( model.History.id==trans.security.decode_id(history_id) ) + +class HistoryDatasetsSelectionGrid( grids.Grid ): + # Grid definition. + available_tracks = None + title = "Add Datasets" + template = "tracks/history_datasets_select_grid.mako" + model_class = model.HistoryDatasetAssociation + default_filter = { "deleted" : "False" , "shared" : "All" } + default_sort_key = "-hid" + use_async = True + use_paging = False + columns = [ + grids.GridColumn( "Id", key="hid" ), + grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), + grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ), + HistoryColumn( "History", key="history", visible=False ), + DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False ) + ] + columns.append( + grids.MulticolFilterColumn( "Search name and filetype", cols_to_filter=[ columns[1], columns[2] ], + key="free-text-search", visible=False, filterable="standard" ) + ) + + def get_current_item( self, trans, **kwargs ): + """ + Current item for grid is the history being queried. This is a bit + of hack since current_item typically means the current item in the grid. + """ + return model.History.get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) + def build_initial_query( self, trans, **kwargs ): + return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) + def apply_query_filter( self, trans, query, **kwargs ): + if self.available_tracks is None: + self.available_tracks = trans.app.datatypes_registry.get_available_tracks() + return query.filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \ + .filter( model.Dataset.state == model.Dataset.states.OK ) \ + .filter( model.HistoryDatasetAssociation.deleted == False ) \ + .filter( model.HistoryDatasetAssociation.visible == True ) + +class TracksterSelectionGrid( grids.Grid ): + # Grid definition. + title = "Insert into visualization" + template = "/tracks/add_to_viz.mako" + async_template = "/page/select_items_grid_async.mako" + model_class = model.Visualization + default_sort_key = "-update_time" + use_async = True + use_paging = False + columns = [ + grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ), + grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) + ] + + def build_initial_query( self, trans, **kwargs ): + return trans.sa_session.query( self.model_class ).filter( self.model_class.deleted == False ) + def apply_query_filter( self, trans, query, **kwargs ): + return query.filter( self.model_class.user_id == trans.user.id ) class VisualizationListGrid( grids.Grid ): def get_url_args( item ): @@ -89,6 +228,10 @@ UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() + _libraries_grid = LibrarySelectionGrid() + _histories_grid = HistorySelectionGrid() + _history_datasets_grid = HistoryDatasetsSelectionGrid() + _tracks_grid = TracksterSelectionGrid() @web.expose def list_published( self, trans, *args, **kwargs ): @@ -464,6 +607,69 @@ help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) + @web.expose + @web.require_login( "see all available libraries" ) + def list_libraries( self, trans, **kwargs ): + """List all libraries that can be used for selecting datasets.""" + + # Render the list view + return self._libraries_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see a library's datasets that can added to this visualization" ) + def list_library_datasets( self, trans, **kwargs ): + """List a library's datasets that can be added to a visualization.""" + + library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) + return trans.fill_template( '/tracks/library_datasets_select_grid.mako', + cntrller="library", + use_panels=False, + library=library, + created_ldda_ids='', + hidden_folder_ids='', + show_deleted=False, + comptypes=[], + current_user_roles=trans.get_current_user_roles(), + message='', + status="done" ) + + @web.expose + @web.require_login( "see all available histories" ) + def list_histories( self, trans, **kwargs ): + """List all histories that can be used for selecting datasets.""" + + # Render the list view + return self._histories_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see current history's datasets that can added to this visualization" ) + def list_current_history_datasets( self, trans, **kwargs ): + """ List a history's datasets that can be added to a visualization. """ + + kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id ) + kwargs[ 'show_item_checkboxes' ] = 'True' + return self.list_history_datasets( trans, **kwargs ) + + @web.expose + @web.require_login( "see a history's datasets that can added to this visualization" ) + def list_history_datasets( self, trans, **kwargs ): + """List a history's datasets that can be added to a visualization.""" + + # Render the list view + return self._history_datasets_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see all available datasets" ) + def list_datasets( self, trans, **kwargs ): + """List all datasets that can be added as tracks""" + + # Render the list view + return self._data_grid( trans, **kwargs ) + + @web.expose + def list_tracks( self, trans, **kwargs ): + return self._tracks_grid( trans, **kwargs ) + def get_item( self, trans, id ): return self.get_visualization( trans, id ) diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -131,10 +131,10 @@ # do these need _localized_ dbkeys? trackster_urls = {} if hda.dbkey != '?': - data_url = h.url_for( controller='tracks', action='list_tracks', dbkey=hda.dbkey ) + data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=hda.dbkey ) data_url = hda.replace( 'dbkey', 'f-dbkey' ) else: - data_url = h.url_for( controller='tracks', action='list_tracks' ) + data_url = h.url_for( controller='visualization', action='list_tracks' ) trackster_urls[ 'hda-url' ] = data_url trackster_urls[ 'action-url' ] = h.url_for( controller='tracks', action='browser', dataset_id=encoded_data_id ) trackster_urls[ 'new-url' ] = h.url_for( controller='tracks', action='index', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -229,10 +229,10 @@ %if data.ext in app.datatypes_registry.get_available_tracks(): <% if data.dbkey != '?': - data_url = h.url_for( controller='tracks', action='list_tracks', dbkey=data.dbkey ) + data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=data.dbkey ) data_url = data_url.replace( 'dbkey', 'f-dbkey' ) else: - data_url = h.url_for( controller='tracks', action='list_tracks' ) + data_url = h.url_for( controller='visualization', action='list_tracks' ) %><a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip trackster-add" action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -51,7 +51,7 @@ var add_bookmarks = function() { show_modal( "Select dataset for new bookmarks", "progress" ); $.ajax({ - url: "${h.url_for( action='list_histories' )}", + url: "${h.url_for( controller='visualization', action='list_histories' )}", data: { "f-dbkey": view.dbkey }, error: function() { alert( "Grid failed" ); }, success: function(table_html) { diff -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 -r bc56358a5c51512f98c09a88c31a7b445e8160e0 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -17,7 +17,7 @@ ## Render a block of JavaScript that contains all necessary variables for Trackster. <%def name="render_trackster_js_vars()"> var add_track_async_url = "${h.url_for( controller='/tracks', action='add_track_async' )}", - add_datasets_url = "${h.url_for( controller='/tracks', action='list_current_history_datasets' )}", + add_datasets_url = "${h.url_for( controller='/visualization', action='list_current_history_datasets' )}", default_data_url = "${h.url_for( controller='/tracks', action='data' )}", raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", reference_url = "${h.url_for( controller='/tracks', action='reference' )}", https://bitbucket.org/galaxy/galaxy-central/changeset/f8ea04e7bbff/ changeset: f8ea04e7bbff user: jgoecks date: 2012-09-14 20:42:11 summary: Summary tree documentation update. affected #: 1 file diff -r bc56358a5c51512f98c09a88c31a7b445e8160e0 -r f8ea04e7bbff4acbc14f95e14fd6f955c307f906 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -1,5 +1,5 @@ ''' -Summary tree data structure for feature aggregation across large genomic regions. +This module cannot be moved due to the use of pickling. ''' import sys, os @@ -11,6 +11,9 @@ MIN_LEVEL = 2 class SummaryTree: + ''' + Summary tree data structure for feature aggregation across large genomic regions. + ''' def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ): self.chrom_blocks = {} self.levels = levels Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by Bitbucket 14 Sep '12

14 Sep '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6eae334427ce/ changeset: 6eae334427ce user: jgoecks date: 2012-09-14 17:11:04 summary: Add column data provider. affected #: 1 file diff -r a5f93d5b509835c9e4a29ba793c6406cb3a63ca2 -r 6eae334427ce58f209a53eb7833c5b442f797040 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -18,24 +18,30 @@ from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * import galaxy_utils.sequence.vcf -from galaxy.datatypes.tabular import Vcf +from galaxy.datatypes.tabular import Tabular, Vcf from galaxy.datatypes.interval import Interval, Bed, Gff, Gtf, ENCODEPeak, ChromatinInteractions from pysam import csamtools, ctabix ERROR_MAX_VALS = "Only the first %i %s in this region are displayed." -# Return None instead of NaN to pass jQuery 1.4's strict JSON +# +# Utility functions. +# + def float_nan(n): + ''' + Return None instead of NaN to pass jQuery 1.4's strict JSON + ''' if n != n: # NaN != NaN return None else: return float(n) def get_bounds( reads, start_pos_index, end_pos_index ): - """ + ''' Returns the minimum and maximum position for a set of reads. - """ + ''' max_low = sys.maxint max_high = -sys.maxint for read in reads: @@ -60,6 +66,50 @@ def _chrom_naming_matches( chrom1, chrom2 ): return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) + +class ColumnDataProvider( object ): + """ Data provider for columnar data """ + + def __init__( self, original_dataset ): + # Compatibility check. + if not isinstance( original_dataset.datatype, Tabular ): + raise Exception( "Data provider can only be used with tabular data" ) + + # Attribute init. + self.original_dataset = original_dataset + + def get_data( self, cols, start_val=0, max_vals=sys.maxint ): + """ + Returns data from specified columns in dataset. Format is list of lists + where each list is a line of data. + """ + + def cast_val( val, type ): + """ Cast value based on type. """ + if type == 'int': + try: val = int( val ) + except: pass + elif type == 'float': + try: val = float( val ) + except: pass + return val + + data = [] + f = open( self.original_dataset.file_name ) + for count, line in enumerate( f ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + + fields = line.split() + data.append( [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) for c in cols ] ) + + f.close() + + return data + class FeatureLocationIndexDataProvider( object ): ''' https://bitbucket.org/galaxy/galaxy-central/changeset/586506caaad4/ changeset: 586506caaad4 user: jgoecks date: 2012-09-14 18:14:15 summary: Codify data providers framework by adding and using a base provider. affected #: 2 files diff -r 6eae334427ce58f209a53eb7833c5b442f797040 -r 586506caaad452c533493e5db8f26a362fb61280 lib/galaxy/visualization/data_providers.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers.py @@ -0,0 +1,93 @@ +import sys + +class BaseDataProvider( object ): + """ + Base class for data providers. Data providers (a) read and package data from datasets; + and (b) write subsets of data to new datasets. + """ + + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None, + error_max_vals="Only the first %i values are returned." ): + """ Create basic data provider. """ + self.converted_dataset = converted_dataset + self.original_dataset = original_dataset + self.dependencies = dependencies + self.error_max_vals = error_max_vals + + def has_data( self, **kwargs ): + """ + Returns true if dataset has data in the specified genome window, false + otherwise. + """ + raise Exception( "Unimplemented Function" ) + + def get_iterator( self, **kwargs ): + """ + Returns an iterator that provides data in the region chrom:start-end + """ + raise Exception( "Unimplemented Function" ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Process data from an iterator to a format that can be provided to client. + """ + raise Exception( "Unimplemented Function" ) + + def get_data( self, start_val=0, max_vals=sys.maxint, **kwargs ): + """ + Returns data as specified by kwargs. start_val is the first element to + return and max_vals indicates the number of values to return. + + Return value must be a dictionary with the following attributes: + dataset_type, data + """ + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + def write_data_to_file( self, filename, **kwargs ): + """ + Write data in region defined by chrom, start, and end to a file. + """ + raise Exception( "Unimplemented Function" ) + +class ColumnDataProvider( BaseDataProvider ): + """ Data provider for columnar data """ + + def __init__( self, original_dataset ): + # Compatibility check. + if not isinstance( original_dataset.datatype, Tabular ): + raise Exception( "Data provider can only be used with tabular data" ) + + # Attribute init. + self.original_dataset = original_dataset + + def get_data( self, cols, start_val=0, max_vals=sys.maxint ): + """ + Returns data from specified columns in dataset. Format is list of lists + where each list is a line of data. + """ + + def cast_val( val, type ): + """ Cast value based on type. """ + if type == 'int': + try: val = int( val ) + except: pass + elif type == 'float': + try: val = float( val ) + except: pass + return val + + data = [] + f = open( self.original_dataset.file_name ) + for count, line in enumerate( f ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + + fields = line.split() + data.append( [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) for c in cols ] ) + + f.close() + + return data diff -r 6eae334427ce58f209a53eb7833c5b442f797040 -r 586506caaad452c533493e5db8f26a362fb61280 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -1,5 +1,5 @@ """ -Data providers for tracks visualizations. +Data providers for genome visualizations. """ import os, sys @@ -17,14 +17,13 @@ from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * +from galaxy.visualization.data_providers import BaseDataProvider import galaxy_utils.sequence.vcf from galaxy.datatypes.tabular import Tabular, Vcf from galaxy.datatypes.interval import Interval, Bed, Gff, Gtf, ENCODEPeak, ChromatinInteractions from pysam import csamtools, ctabix -ERROR_MAX_VALS = "Only the first %i %s in this region are displayed." - # # Utility functions. # @@ -66,54 +65,10 @@ def _chrom_naming_matches( chrom1, chrom2 ): return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) - -class ColumnDataProvider( object ): - """ Data provider for columnar data """ - - def __init__( self, original_dataset ): - # Compatibility check. - if not isinstance( original_dataset.datatype, Tabular ): - raise Exception( "Data provider can only be used with tabular data" ) - - # Attribute init. - self.original_dataset = original_dataset - - def get_data( self, cols, start_val=0, max_vals=sys.maxint ): - """ - Returns data from specified columns in dataset. Format is list of lists - where each list is a line of data. - """ - - def cast_val( val, type ): - """ Cast value based on type. """ - if type == 'int': - try: val = int( val ) - except: pass - elif type == 'float': - try: val = float( val ) - except: pass - return val - - data = [] - f = open( self.original_dataset.file_name ) - for count, line in enumerate( f ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) - break - - fields = line.split() - data.append( [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) for c in cols ] ) - - f.close() - - return data - -class FeatureLocationIndexDataProvider( object ): - ''' - - ''' +class FeatureLocationIndexDataProvider( BaseDataProvider ): + """ + Reads/writes/queries feature location index (FLI) datasets. + """ def __init__( self, converted_dataset ): self.converted_dataset = converted_dataset @@ -155,7 +110,7 @@ textloc_file.close() return result -class TracksDataProvider( object ): +class TracksDataProvider( BaseDataProvider ): """ Base class for tracks data providers. """ """ @@ -167,11 +122,12 @@ """ col_name_data_attr_mapping = {} - def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): - """ Create basic data provider. """ - self.converted_dataset = converted_dataset - self.original_dataset = original_dataset - self.dependencies = dependencies + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None, + error_max_vals="Only the first %i %s in this region are displayed." ): + super( TracksDataProvider, self ).__init__( converted_dataset=converted_dataset, + original_dataset=original_dataset, + dependencies=dependencies, + error_max_vals=error_max_vals ) def write_data_to_file( self, regions, filename ): """ @@ -429,7 +385,7 @@ if count < start_val: continue if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) + message = self.error_max_vals % ( max_vals, "features" ) break feature = line.split() @@ -502,7 +458,7 @@ if count < start_val: continue if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) + message = self.error_max_vals % ( max_vals, "features" ) break # TODO: can we use column metadata to fill out payload? # TODO: use function to set payload data @@ -656,7 +612,7 @@ if count < start_val: continue if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) + message = self.error_max_vals % ( max_vals, "features" ) break feature = line.split() @@ -927,7 +883,7 @@ if count < start_val: continue if ( count - start_val - unmapped ) >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "reads" ) + message = self.error_max_vals % ( max_vals, "reads" ) break # If not mapped, skip read. @@ -1198,7 +1154,7 @@ if count < start_val: continue if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) + message = self.error_max_vals % ( max_vals, "features" ) break source.seek( offset ) # TODO: can we use column metadata to fill out payload? @@ -1260,7 +1216,7 @@ if count < start_val: continue if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "reads" ) + message = self.error_max_vals % ( max_vals, "reads" ) break payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) @@ -1302,7 +1258,7 @@ if count < start_val: continue if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "reads" ) + message = self.error_max_vals % ( max_vals, "reads" ) break feature = GFFFeature( None, intervals=intervals ) @@ -1348,7 +1304,7 @@ if count < start_val: continue if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) + message = self.error_max_vals % ( max_vals, "features" ) break feature = line.split() @@ -1440,7 +1396,7 @@ if count < start_val: continue if max_vals and count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "interactions" ) + message = self.error_max_vals % ( max_vals, "interactions" ) break feature = line.split() https://bitbucket.org/galaxy/galaxy-central/changeset/6805c477d616/ changeset: 6805c477d616 user: jgoecks date: 2012-09-14 18:23:03 summary: Rename tracks package to genome to reflect that code is used for all genome browsers, not just trackster. affected #: 16 files diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -14,7 +14,7 @@ import sys, fileinput, optparse from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * +from galaxy.visualization.genome.summary import * from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed from bx.interval_index_file import Indexes diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -15,7 +15,7 @@ import sys, fileinput, optparse from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * +from galaxy.visualization.genome.summary import * from bx.intervals.io import * from galaxy.datatypes.util.gff_util import * diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py @@ -14,7 +14,7 @@ pkg_resources.require( "pysam" ) from pysam import csamtools -from galaxy.visualization.tracks.summary import * +from galaxy.visualization.genome.summary import * def main(): parser = optparse.OptionParser() diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py @@ -9,7 +9,7 @@ import optparse import galaxy_utils.sequence.vcf -from galaxy.visualization.tracks.summary import SummaryTree +from galaxy.visualization.genome.summary import SummaryTree def main(): # Read options, args. diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -35,7 +35,7 @@ from galaxy.util.shed_util import * from galaxy.web import url_for -from galaxy.visualization.tracks.visual_analytics import TracksterConfig +from galaxy.visualization.genome.visual_analytics import TracksterConfig log = logging.getLogger( __name__ ) diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/genome/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/genome/__init__.py @@ -0,0 +1,3 @@ +""" +Code for Galaxy genome visualizations. +""" \ No newline at end of file diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/genome/data_providers.py --- /dev/null +++ b/lib/galaxy/visualization/genome/data_providers.py @@ -0,0 +1,1557 @@ +""" +Data providers for genome visualizations. +""" + +import os, sys +from math import ceil, log +import pkg_resources +pkg_resources.require( "bx-python" ) +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) +pkg_resources.require( "numpy" ) +import numpy +from galaxy.datatypes.util.gff_util import * +from galaxy.util.json import from_json_string +from bx.interval_index_file import Indexes +from bx.bbi.bigwig_file import BigWigFile +from galaxy.util.lrucache import LRUCache +from galaxy.visualization.genome.summary import * +from galaxy.visualization.data_providers import BaseDataProvider +import galaxy_utils.sequence.vcf +from galaxy.datatypes.tabular import Tabular, Vcf +from galaxy.datatypes.interval import Interval, Bed, Gff, Gtf, ENCODEPeak, ChromatinInteractions + +from pysam import csamtools, ctabix + +# +# Utility functions. +# + +def float_nan(n): + ''' + Return None instead of NaN to pass jQuery 1.4's strict JSON + ''' + if n != n: # NaN != NaN + return None + else: + return float(n) + +def get_bounds( reads, start_pos_index, end_pos_index ): + ''' + Returns the minimum and maximum position for a set of reads. + ''' + max_low = sys.maxint + max_high = -sys.maxint + for read in reads: + if read[ start_pos_index ] < max_low: + max_low = read[ start_pos_index ] + if read[ end_pos_index ] > max_high: + max_high = read[ end_pos_index ] + return max_low, max_high + +def _convert_between_ucsc_and_ensemble_naming( chrom ): + ''' + Convert between UCSC chromosome ('chr1') naming conventions and Ensembl + naming conventions ('1') + ''' + if chrom.startswith( 'chr' ): + # Convert from UCSC to Ensembl + return chrom[ 3: ] + else: + # Convert from Ensembl to UCSC + return 'chr' + chrom + +def _chrom_naming_matches( chrom1, chrom2 ): + return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) + +class FeatureLocationIndexDataProvider( BaseDataProvider ): + """ + Reads/writes/queries feature location index (FLI) datasets. + """ + + def __init__( self, converted_dataset ): + self.converted_dataset = converted_dataset + + def get_data( self, query ): + # Init. + textloc_file = open( self.converted_dataset.file_name, 'r' ) + line_len = int( textloc_file.readline() ) + file_len = os.path.getsize( self.converted_dataset.file_name ) + query = query.lower() + + # Find query in file using binary search. + low = 0 + high = file_len / line_len + while low < high: + mid = ( low + high ) // 2 + position = mid * line_len + textloc_file.seek( position ) + + # Compare line with query and update low, high. + line = textloc_file.readline() + if line < query: + low = mid + 1 + else: + high = mid + + position = low * line_len + + # At right point in file, generate hits. + result = [] + while True: + line = textloc_file.readline() + if not line.startswith( query ): + break + if line[ -1: ] == '\n': + line = line[ :-1 ] + result.append( line.split()[1:] ) + + textloc_file.close() + return result + +class GenomeDataProvider( BaseDataProvider ): + """ Base class for genome data providers. """ + + """ + Mapping from column name to payload data; this mapping is used to create + filters. Key is column name, value is a dict with mandatory key 'index' and + optional key 'name'. E.g. this defines column 4 + + col_name_data_attr_mapping = {4 : { index: 5, name: 'Score' } } + """ + col_name_data_attr_mapping = {} + + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None, + error_max_vals="Only the first %i %s in this region are displayed." ): + super( GenomeDataProvider, self ).__init__( converted_dataset=converted_dataset, + original_dataset=original_dataset, + dependencies=dependencies, + error_max_vals=error_max_vals ) + + def write_data_to_file( self, regions, filename ): + """ + Write data in region defined by chrom, start, and end to a file. + """ + raise Exception( "Unimplemented Function" ) + + def valid_chroms( self ): + """ + Returns chroms/contigs that the dataset contains + """ + return None # by default + + def has_data( self, chrom, start, end, **kwargs ): + """ + Returns true if dataset has data in the specified genome window, false + otherwise. + """ + raise Exception( "Unimplemented Function" ) + + def get_iterator( self, chrom, start, end ): + """ + Returns an iterator that provides data in the region chrom:start-end + """ + raise Exception( "Unimplemented Function" ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Process data from an iterator to a format that can be provided to client. + """ + raise Exception( "Unimplemented Function" ) + + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): + """ + Returns data in region defined by chrom, start, and end. start_val and + max_vals are used to denote the data to return: start_val is the first element to + return and max_vals indicates the number of values to return. + + Return value must be a dictionary with the following attributes: + dataset_type, data + """ + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def get_genome_data( self, chroms_info, **kwargs ): + """ + Returns data for complete genome. + """ + dataset_summary = [] + for chrom_info in chroms_info[ 'chrom_info' ]: + summary = self.get_data( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], **kwargs ) + dataset_summary.append( summary ) + + return dataset_summary + + def get_filters( self ): + """ + Returns filters for provider's data. Return value is a list of + filters; each filter is a dictionary with the keys 'name', 'index', 'type'. + NOTE: This method uses the original dataset's datatype and metadata to + create the filters. + """ + # Get column names. + try: + column_names = self.original_dataset.datatype.column_names + except AttributeError: + try: + column_names = range( self.original_dataset.metadata.columns ) + except: # Give up + return [] + + # Dataset must have column types; if not, cannot create filters. + try: + column_types = self.original_dataset.metadata.column_types + except AttributeError: + return [] + + # Create and return filters. + filters = [] + if self.original_dataset.metadata.viz_filter_cols: + for viz_col_index in self.original_dataset.metadata.viz_filter_cols: + # Some columns are optional, so can't assume that a filter + # column is in dataset. + if viz_col_index >= len( column_names ): + continue; + col_name = column_names[ viz_col_index ] + # Make sure that column has a mapped index. If not, do not add filter. + try: + attrs = self.col_name_data_attr_mapping[ col_name ] + except KeyError: + continue + filters.append( + { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ + 'index' : attrs[ 'index' ] } ) + return filters + + def get_default_max_vals( self ): + return 5000 + +# +# -- Base mixins and providers -- +# + +class FilterableMixin: + def get_filters( self ): + """ Returns a dataset's filters. """ + + # is_ functions taken from Tabular.set_meta + def is_int( column_text ): + try: + int( column_text ) + return True + except: + return False + def is_float( column_text ): + try: + float( column_text ) + return True + except: + if column_text.strip().lower() == 'na': + return True #na is special cased to be a float + return False + + # + # Get filters. + # TODOs: + # (a) might be useful to move this into each datatype's set_meta method; + # (b) could look at first N lines to ensure GTF attribute types are consistent. + # + filters = [] + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + if isinstance( self.original_dataset.datatype, Gff ): + # Can filter by score and GTF attributes. + filters = [ { 'name': 'Score', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c6' } ] + filter_col += 1 + if isinstance( self.original_dataset.datatype, Gtf ): + # Create filters based on dataset metadata. + for name, a_type in self.original_dataset.metadata.attribute_types.items(): + if a_type in [ 'int', 'float' ]: + filters.append( + { 'name': name, + 'type': 'number', + 'index': filter_col, + 'tool_id': 'gff_filter_by_attribute', + 'tool_exp_name': name } ) + filter_col += 1 + + ''' + # Old code: use first line in dataset to find attributes. + for i, line in enumerate( open(self.original_dataset.file_name) ): + if not line.startswith('#'): + # Look at first line for attributes and types. + attributes = parse_gff_attributes( line.split('\t')[8] ) + for attr, value in attributes.items(): + # Get attribute type. + if is_int( value ): + attr_type = 'int' + elif is_float( value ): + attr_type = 'float' + else: + attr_type = 'str' + # Add to filters. + if attr_type is not 'str': + filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) + filter_col += 1 + break + ''' + elif isinstance( self.original_dataset.datatype, Bed ): + # Can filter by score column only. + filters = [ { 'name': 'Score', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c5' + } ] + + return filters + + +class TabixDataProvider( FilterableMixin, GenomeDataProvider ): + """ + Tabix index data provider for the Galaxy track browser. + """ + + col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } + + def get_iterator( self, chrom, start, end ): + start, end = int(start), int(end) + if end >= (2<<29): + end = (2<<29 - 1) # Tabix-enforced maximum + + bgzip_fname = self.dependencies['bgzip'].file_name + + tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + + # If chrom not in data, try alternative. + if chrom not in tabix.contigs: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + + return tabix.fetch(reference=chrom, start=start, end=end) + + def write_data_to_file( self, regions, filename ): + out = open( filename, "w" ) + + for region in regions: + # Write data in region. + chrom = region.chrom + start = region.start + end = region.end + iterator = self.get_iterator( chrom, start, end ) + for line in iterator: + out.write( "%s\n" % line ) + + out.close() + +# +# -- Interval data providers -- +# + +class IntervalDataProvider( GenomeDataProvider ): + """ + Processes BED data from native format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise Exception( "Unimplemented Function" ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <strand> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + # Subtract one b/c columns are 1-based but indices are 0-based. + col_fn = lambda col: None if col is None else col - 1 + start_col = self.original_dataset.metadata.startCol - 1 + end_col = self.original_dataset.metadata.endCol - 1 + strand_col = col_fn( self.original_dataset.metadata.strandCol ) + name_col = col_fn( self.original_dataset.metadata.nameCol ) + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + + feature = line.split() + length = len(feature) + # Unique id is just a hash of the line + payload = [ hash(line), int( feature[start_col] ), int( feature [end_col] ) ] + + if no_detail: + rval.append( payload ) + continue + + # Name, strand. + if name_col: + payload.append( feature[name_col] ) + if strand_col: + # Put empty name as placeholder. + if not name_col: payload.append( "" ) + payload.append( feature[strand_col] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + try: + payload.append( float( feature[4] ) ) + except: + payload.append( feature[4] ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, regions, filename ): + raise Exception( "Unimplemented Function" ) + +class IntervalTabixDataProvider( TabixDataProvider, IntervalDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + + +# +# -- BED data providers -- +# + +class BedDataProvider( GenomeDataProvider ): + """ + Processes BED data from native format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise Exception( "Unimplemented Method" ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>, + # <thick_end>, <blocks> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + # TODO: can we use column metadata to fill out payload? + # TODO: use function to set payload data + + feature = line.split() + length = len(feature) + # Unique id is just a hash of the line + payload = [ hash(line), int(feature[1]), int(feature[2]) ] + + if no_detail: + rval.append( payload ) + continue + + # Name, strand, thick start, thick end. + if length >= 4: + payload.append(feature[3]) + if length >= 6: + payload.append(feature[5]) + if length >= 8: + payload.append(int(feature[6])) + payload.append(int(feature[7])) + + # Blocks. + if length >= 12: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip( block_sizes, block_starts ) + payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + # If dataset doesn't have name/strand/thick start/thick end/blocks, + # add placeholders. There should be 8 entries if all attributes + # are present. + payload.extend( [ None for i in range( 8 - len( payload ) ) ] ) + + try: + payload.append( float( feature[4] ) ) + except: + payload.append( feature[4] ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, regions, filename ): + out = open( filename, "w" ) + + for region in regions: + # Write data in region. + chrom = region.chrom + start = region.start + end = region.end + iterator = self.get_iterator( chrom, start, end ) + for line in iterator: + out.write( "%s\n" % line ) + + out.close() + +class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + +class RawBedDataProvider( BedDataProvider ): + """ + Provide data from BED file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom=None, start=None, end=None ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + if line.startswith( "track" ) or line.startswith( "browser" ): + continue + feature = line.split() + feature_chrom = feature[0] + feature_start = int( feature[1] ) + feature_end = int( feature[2] ) + if ( chrom is not None and feature_chrom != chrom ) \ + or ( start is not None and feature_start > end ) \ + or ( end is not None and feature_end < start ): + continue + yield line + + return line_filter_iter() + +# +# -- VCF data providers -- +# + +class VcfDataProvider( GenomeDataProvider ): + """ + Abstract class that processes VCF data from native format to payload format. + + Payload format: TODO + """ + + col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Returns a dict with the following attributes: + data - a list of variants with the format + [<guid>, <start>, <end>, <name>, cigar, seq] + + message - error/informative message + """ + rval = [] + message = None + + def get_mapping( ref, alt ): + """ + Returns ( offset, new_seq, cigar ) tuple that defines mapping of + alt to ref. Cigar format is an array of [ op_index, length ] pairs + where op_index is the 0-based index into the string "MIDNSHP=X" + """ + + cig_ops = "MIDNSHP=X" + + ref_len = len( ref ) + alt_len = len( alt ) + + # Substitutions? + if ref_len == alt_len: + return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ] + + # Deletions? + alt_in_ref_index = ref.find( alt ) + if alt_in_ref_index != -1: + return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ] + + # Insertions? + ref_in_alt_index = alt.find( ref ) + if ref_in_alt_index != -1: + return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] + + # Pack data. + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + + feature = line.split() + start = int( feature[1] ) - 1 + ref = feature[3] + alts = feature[4] + + # HACK? alts == '.' --> monomorphism. + if alts == '.': + alts = ref + + # Pack variants. + for alt in alts.split(","): + offset, new_seq, cigar = get_mapping( ref, alt ) + start += offset + end = start + len( new_seq ) + + # Pack line. + payload = [ + hash( line ), + start, + end, + # ID: + feature[2], + cigar, + # TODO? VCF does not have strand, so default to positive. + "+", + new_seq, + None if feature[5] == '.' else float( feature[5] ) + ] + rval.append(payload) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, regions, filename ): + out = open( filename, "w" ) + + for region in regions: + # Write data in region. + chrom = region.chrom + start = region.start + end = region.end + iterator = self.get_iterator( chrom, start, end ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() + +class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): + """ + Provides data from a VCF file indexed via tabix. + """ + pass + +class RawVcfDataProvider( VcfDataProvider ): + """ + Provide data from VCF file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + if line.startswith("#"): + continue + variant = line.split() + variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ] + variant_start = int( variant_start ) + longest_alt = -1 + for alt in alts: + if len( alt ) > longest_alt: + longest_alt = len( alt ) + variant_end = variant_start + abs( len( ref ) - longest_alt ) + if variant_chrom != chrom or variant_start > end or variant_end < start: + continue + yield line + + return line_filter_iter() + +class SummaryTreeDataProvider( GenomeDataProvider ): + """ + Summary tree data provider for the Galaxy track browser. + """ + + CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance + + def valid_chroms( self ): + st = summary_tree_from_file( self.converted_dataset.file_name ) + return st.chrom_blocks.keys() + + def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None ): + """ + Returns summary tree data for a given genomic region. + """ + filename = self.converted_dataset.file_name + st = self.CACHE[filename] + if st is None: + st = summary_tree_from_file( self.converted_dataset.file_name ) + self.CACHE[filename] = st + + # Look for chrom in tree using both naming conventions. + if chrom not in st.chrom_blocks: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + if chrom not in st.chrom_blocks: + return None + + # Get or compute level. + if level: + level = int( level ) + elif resolution: + resolution = max( 1, ceil( float( resolution ) ) ) + level = ceil( log( resolution, st.block_size ) ) - 1 + level = int( max( level, 0 ) ) + else: + # Either level or resolution is required. + return None + + if level <= 1: + return "detail" + + # Use level to get results. + stats = st.chrom_stats[ chrom ] + results = st.query( chrom, int(start), int(end), level, detail_cutoff=detail_cutoff, draw_cutoff=draw_cutoff ) + if results == "detail" or results == "draw": + return results + else: + return results, stats[ level ][ "max" ], stats[ level ]["avg" ], stats[ level ][ "delta" ] + + def has_data( self, chrom ): + """ + Returns true if dataset has data for this chrom + """ + + # Get summary tree. + filename = self.converted_dataset.file_name + st = self.CACHE[filename] + if st is None: + st = summary_tree_from_file( self.converted_dataset.file_name ) + self.CACHE[filename] = st + + # Check for data. + return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None) + +class BamDataProvider( GenomeDataProvider, FilterableMixin ): + """ + Provides access to intervals from a sorted indexed BAM file. Position data + is reported in 1-based, closed format, i.e. SAM/BAM format. + """ + + def get_filters( self ): + """ + Returns filters for dataset. + """ + # HACK: first 7 fields are for drawing, so start filter column index at 7. + filter_col = 7 + filters = [] + filters.append( { 'name': 'Mapping Quality', + 'type': 'number', + 'index': filter_col + } ) + return filters + + + def write_data_to_file( self, regions, filename ): + """ + Write reads in regions to file. + """ + + # Open current BAM file using index. + bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', \ + index_filename=self.converted_dataset.file_name ) + + # TODO: write headers as well? + new_bamfile = csamtools.Samfile( template=bamfile, filename=filename, mode='wb' ) + + for region in regions: + # Write data from region. + chrom = region.chrom + start = region.start + end = region.end + + try: + data = bamfile.fetch(start=start, end=end, reference=chrom) + except ValueError, e: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: + return None + + # Write reads in region. + for i, read in enumerate( data ): + new_bamfile.write( read ) + + # Cleanup. + new_bamfile.close() + bamfile.close() + + def get_iterator( self, chrom, start, end ): + """ + Returns an iterator that provides data in the region chrom:start-end + """ + start, end = int(start), int(end) + orig_data_filename = self.original_dataset.file_name + index_filename = self.converted_dataset.file_name + + # Attempt to open the BAM file with index + bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) + try: + data = bamfile.fetch(start=start, end=end, reference=chrom) + except ValueError, e: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: + return None + return data + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Returns a dict with the following attributes: + data - a list of reads with the format + [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] + where <read_1> has the format + [<start>, <end>, <cigar>, <strand>, <read_seq>] + and <read_2> has the format + [<start>, <end>, <cigar>, <strand>, <read_seq>] + Field 7 is empty so that mapq scores' location matches that in single-end reads. + For single-end reads, read has format: + [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>, <mapq_score>] + + NOTE: read end and sequence data are not valid for reads outside of + requested region and should not be used. + + max_low - lowest coordinate for the returned reads + max_high - highest coordinate for the returned reads + message - error/informative message + """ + # No iterator indicates no reads. + if iterator is None: + return { 'data': [], 'message': None } + + # Decode strand from read flag. + def decode_strand( read_flag, mask ): + strand_flag = ( read_flag & mask == 0 ) + if strand_flag: + return "+" + else: + return "-" + + # Encode reads as list of lists. + results = [] + paired_pending = {} + unmapped = 0 + message = None + for count, read in enumerate( iterator ): + if count < start_val: + continue + if ( count - start_val - unmapped ) >= max_vals: + message = self.error_max_vals % ( max_vals, "reads" ) + break + + # If not mapped, skip read. + is_mapped = ( read.flag & 0x0004 == 0 ) + if not is_mapped: + unmapped += 1 + continue + + qname = read.qname + seq = read.seq + strand = decode_strand( read.flag, 0x0010 ) + if read.cigar is not None: + read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length + else: + read_len = len(seq) # If no cigar, just use sequence length + + if read.is_proper_pair: + if qname in paired_pending: # one in dict is always first + pair = paired_pending[qname] + results.append( [ "%i_%s" % ( pair['start'], qname ), + pair['start'], + read.pos + read_len, + qname, + [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], + [ read.pos, read.pos + read_len, read.cigar, strand, seq ], + None, [ pair['mapq'], read.mapq ] + ] ) + del paired_pending[qname] + else: + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, + 'rlen': read_len, 'strand': strand, 'cigar': read.cigar, 'mapq': read.mapq } + else: + results.append( [ "%i_%s" % ( read.pos, qname ), + read.pos, read.pos + read_len, qname, + read.cigar, strand, read.seq, read.mapq ] ) + + # Take care of reads whose mates are out of range. + # TODO: count paired reads when adhering to max_vals? + for qname, read in paired_pending.iteritems(): + if read['mate_start'] < read['start']: + # Mate is before read. + read_start = read['mate_start'] + read_end = read['end'] + # Make read_1 start=end so that length is 0 b/c we don't know + # read length. + r1 = [ read['mate_start'], read['mate_start'] ] + r2 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] + else: + # Mate is after read. + read_start = read['start'] + # Make read_2 start=end so that length is 0 b/c we don't know + # read length. Hence, end of read is start of read_2. + read_end = read['mate_start'] + r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] + r2 = [ read['mate_start'], read['mate_start'] ] + + results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) + + # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data. + # bamfile.close() + + max_low, max_high = get_bounds( results, 1, 2 ) + + return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } + +class SamDataProvider( BamDataProvider ): + + def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): + """ Create SamDataProvider. """ + + # HACK: to use BamDataProvider, original dataset must be BAM and + # converted dataset must be BAI. Use BAI from BAM metadata. + if converted_dataset: + self.converted_dataset = converted_dataset.metadata.bam_index + self.original_dataset = converted_dataset + self.dependencies = dependencies + +class BBIDataProvider( GenomeDataProvider ): + """ + BBI data provider for the Galaxy track browser. + """ + def valid_chroms( self ): + # No way to return this info as of now + return None + + def has_data( self, chrom ): + f, bbi = self._get_dataset() + all_dat = bbi.query(chrom, 0, 2147483647, 1) + f.close() + return all_dat is not None + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + # Bigwig can be a standalone bigwig file, in which case we use + # original_dataset, or coming from wig->bigwig conversion in + # which we use converted_dataset + f, bbi = self._get_dataset() + + # If stats requested, compute overall summary data for the range + # start:endbut no reduced data. This is currently used by client + # to determine the default range. + if 'stats' in kwargs: + summary = bbi.summarize( chrom, start, end, 1 ) + f.close() + + min = 0 + max = 0 + mean = 0 + sd = 0 + if summary is not None: + # Does the summary contain any defined values? + valid_count = summary.valid_count[0] + if summary.valid_count > 0: + # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower + # bounds that contain ~95% of the data. + mean = summary.sum_data[0] / valid_count + var = summary.sum_squares[0] - mean + if valid_count > 1: + var /= valid_count - 1 + sd = numpy.sqrt( var ) + min = summary.min_val[0] + max = summary.max_val[0] + + return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) ) + + # Sample from region using approximately this many samples. + N = 1000 + + def summarize_region( bbi, chrom, start, end, num_points ): + ''' + Returns results from summarizing a region using num_points. + NOTE: num_points cannot be greater than end - start or BBI + will return None for all positions.s + ''' + result = [] + + # Get summary; this samples at intervals of length + # (end - start)/num_points -- i.e. drops any fractional component + # of interval length. + summary = bbi.summarize( chrom, start, end, num_points ) + if summary: + #mean = summary.sum_data / summary.valid_count + + ## Standard deviation by bin, not yet used + ## var = summary.sum_squares - mean + ## var /= minimum( valid_count - 1, 1 ) + ## sd = sqrt( var ) + + pos = start + step_size = (end - start) / num_points + + for i in range( num_points ): + result.append( (pos, float_nan( summary.sum_data[i] / summary.valid_count[i] ) ) ) + pos += step_size + + return result + + # Approach is different depending on region size. + if end - start < N: + # Get values for individual bases in region, including start and end. + # To do this, need to increase end to next base and request number of points. + num_points = end - start + 1 + end += 1 + else: + # + # The goal is to sample the region between start and end uniformly + # using ~N data points. The challenge is that the size of sampled + # intervals rarely is full bases, so sampling using N points will + # leave the end of the region unsampled due to remainders for each + # interval. To recitify this, a new N is calculated based on the + # step size that covers as much of the region as possible. + # + # However, this still leaves some of the region unsampled. This + # could be addressed by repeatedly sampling remainder using a + # smaller and smaller step_size, but that would require iteratively + # going to BBI, which could be time consuming. + # + + # Start with N samples. + num_points = N + step_size = ( end - start ) / num_points + # Add additional points to sample in the remainder not covered by + # the initial N samples. + remainder_start = start + step_size * num_points + additional_points = ( end - remainder_start ) / step_size + num_points += additional_points + + result = summarize_region( bbi, chrom, start, end, num_points ) + + # Cleanup and return. + f.close() + return { 'data': result } + +class BigBedDataProvider( BBIDataProvider ): + def _get_dataset( self ): + # Nothing converts to bigBed so we don't consider converted dataset + f = open( self.original_dataset.file_name ) + return f, BigBedFile(file=f) + +class BigWigDataProvider ( BBIDataProvider ): + """ + Provides data from BigWig files; position data is reported in 1-based + coordinate system, i.e. wiggle format. + """ + def _get_dataset( self ): + if self.converted_dataset is not None: + f = open( self.converted_dataset.file_name ) + else: + f = open( self.original_dataset.file_name ) + return f, BigWigFile(file=f) + +class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): + """ + Interval index files used only for GFF files. + """ + col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } + + def write_data_to_file( self, regions, filename ): + source = open( self.original_dataset.file_name ) + index = Indexes( self.converted_dataset.file_name ) + out = open( filename, 'w' ) + + for region in regions: + # Write data from region. + chrom = region.chrom + start = region.start + end = region.end + for start, end, offset in index.find(chrom, start, end): + source.seek( offset ) + + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + for interval in feature.intervals: + out.write( '\t'.join( interval.fields ) + '\n' ) + + out.close() + + def get_iterator( self, chrom, start, end ): + """ + Returns an array with values: (a) source file and (b) an iterator that + provides data in the region chrom:start-end + """ + start, end = int(start), int(end) + source = open( self.original_dataset.file_name ) + index = Indexes( self.converted_dataset.file_name ) + + if chrom not in index.indexes: + # Try alternative naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + + return index.find(chrom, start, end) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + results = [] + message = None + source = open( self.original_dataset.file_name ) + + # + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, + # <thick_end>, <blocks> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + for count, val in enumerate( iterator ): + start, end, offset = val[0], val[1], val[2] + if count < start_val: + continue + if count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + source.seek( offset ) + # TODO: can we use column metadata to fill out payload? + + # GFF dataset. + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + payload = package_gff_feature( feature, no_detail, filter_cols ) + payload.insert( 0, offset ) + + results.append( payload ) + + return { 'data': results, 'message': message } + +class RawGFFDataProvider( GenomeDataProvider ): + """ + Provide data from GFF file that has not been indexed. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + """ + Returns an iterator that provides data in the region chrom:start-end as well as + a file offset. + """ + source = open( self.original_dataset.file_name ) + + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + + def features_in_region_iter(): + offset = 0 + for feature in GFFReaderWrapper( source, fix_strand=True ): + # Only provide features that are in region. + feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) + if feature.chrom == chrom and feature_end > start and feature_start < end: + yield feature, offset + offset += feature.raw_size + + return features_in_region_iter() + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Process data from an iterator to a format that can be provided to client. + """ + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + results = [] + message = None + + for count, ( feature, offset ) in enumerate( iterator ): + if count < start_val: + continue + if count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "reads" ) + break + + payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) + payload.insert( 0, offset ) + results.append( payload ) + + + return { 'data': results, 'message': message } + +class GtfTabixDataProvider( TabixDataProvider ): + """ + Returns data from GTF datasets that are indexed via tabix. + """ + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + # Loop through lines and group by transcript_id; each group is a feature. + + # TODO: extend this code or use code in gff_util to process GFF/3 as well + # and then create a generic GFFDataProvider that can be used with both + # raw and tabix datasets. + features = {} + for count, line in enumerate( iterator ): + line_attrs = parse_gff_attributes( line.split('\t')[8] ) + transcript_id = line_attrs[ 'transcript_id' ] + if transcript_id in features: + feature = features[ transcript_id ] + else: + feature = [] + features[ transcript_id ] = feature + feature.append( GFFInterval( None, line.split( '\t') ) ) + + # Process data. + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + results = [] + message = None + + for count, intervals in enumerate( features.values() ): + if count < start_val: + continue + if count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "reads" ) + break + + feature = GFFFeature( None, intervals=intervals ) + payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) + payload.insert( 0, feature.intervals[ 0 ].attributes[ 'transcript_id' ] ) + results.append( payload ) + + return { 'data': results, 'message': message } + +# +# -- ENCODE Peak data providers. +# + +class ENCODEPeakDataProvider( GenomeDataProvider ): + """ + Abstract class that processes ENCODEPeak data from native format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise "Unimplemented Method" + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + + ## FIXMEs: + # (1) should be able to unify some of this code with BedDataProvider.process_data + # (2) are optional number of parameters supported? + + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>, + # <thick_end>, <blocks> ] + # + # First three entries are mandatory, others are optional. + # + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "features" ) + break + + feature = line.split() + length = len( feature ) + + # Feature initialization. + payload = [ + # GUID is just a hash of the line + hash( line ), + # Add start, end. + int( feature[1] ), + int( feature[2] ) + ] + + if no_detail: + rval.append( payload ) + continue + + # Extend with additional data. + payload.extend( [ + # Add name, strand. + feature[3], + feature[5], + # Thick start, end are feature start, end for now. + int( feature[1] ), + int( feature[2] ), + # No blocks. + None, + # Filtering data: Score, signalValue, pValue, qValue. + float( feature[4] ), + float( feature[6] ), + float( feature[7] ), + float( feature[8] ) + ] ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + +class ENCODEPeakTabixDataProvider( TabixDataProvider, ENCODEPeakDataProvider ): + """ + Provides data from an ENCODEPeak dataset indexed via tabix. + """ + + def get_filters( self ): + """ + Returns filters for dataset. + """ + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + filters = [] + filters.append( { 'name': 'Score', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c6' } ) + filter_col += 1 + filters.append( { 'name': 'Signal Value', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c7' } ) + filter_col += 1 + filters.append( { 'name': 'pValue', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c8' } ) + filter_col += 1 + filters.append( { 'name': 'qValue', + 'type': 'number', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c9' } ) + return filters + +# +# -- ChromatinInteraction data providers -- +# +class ChromatinInteractionsDataProvider( GenomeDataProvider ): + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + + rval = [] + message = None + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = self.error_max_vals % ( max_vals, "interactions" ) + break + + feature = line.split() + length = len( feature ) + + s1 = int( feature[1] ), + e1 = int( feature[2] ), + c = feature[3], + s2 = int( feature[4] ), + e2 = int( feature[5] ), + v = float( feature[6] ) + + # Feature initialization. + payload = [ + # GUID is just a hash of the line + hash( line ), + # Add start1, end1, chr2, start2, end2, value. + s1, e1, c, s2, e2, v + ] + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def get_default_max_vals( self ): + return 50000; + +class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): + def get_iterator( self, chrom, start, end ): + """ + """ + # Modify start as needed to get earlier interactions with start region. + start = max( 0, int( start) - 1000000 ) + def filter( iter ): + for line in iter: + feature = line.split() + s1 = int( feature[1] ), + e1 = int( feature[2] ), + c = feature[3] + s2 = int( feature[4] ), + e2 = int( feature[5] ), + if ( ( c == chrom ) and ( s1 < end and e1 > start ) and ( s2 < end and e2 > start ) ): + yield line + return filter( TabixDataProvider.get_iterator( self, chrom, start, end ) ) + +# +# -- Helper methods. -- +# + +# Mapping from dataset type name to a class that can fetch data from a file of that +# type. First key is converted dataset type; if result is another dict, second key +# is original dataset type. TODO: This needs to be more flexible. +dataset_type_name_to_data_provider = { + "tabix": { + Vcf: VcfTabixDataProvider, + Bed: BedTabixDataProvider, + Gtf: GtfTabixDataProvider, + ENCODEPeak: ENCODEPeakTabixDataProvider, + Interval: IntervalTabixDataProvider, + ChromatinInteractions: ChromatinInteractionsTabixDataProvider, + "default" : TabixDataProvider + }, + "interval_index": IntervalIndexDataProvider, + "bai": BamDataProvider, + "bam": SamDataProvider, + "summary_tree": SummaryTreeDataProvider, + "bigwig": BigWigDataProvider, + "bigbed": BigBedDataProvider +} + +def get_data_provider( name=None, original_dataset=None ): + """ + Returns data provider class by name and/or original dataset. + """ + data_provider = None + if name: + value = dataset_type_name_to_data_provider[ name ] + if isinstance( value, dict ): + # Get converter by dataset extension; if there is no data provider, + # get the default. + data_provider = value.get( original_dataset.datatype.__class__, value.get( "default" ) ) + else: + data_provider = value + elif original_dataset: + # Look up data provider from datatype's informaton. + try: + # Get data provider mapping and data provider for 'data'. If + # provider available, use it; otherwise use generic provider. + _ , data_provider_mapping = original_dataset.datatype.get_track_type() + if 'data_standalone' in data_provider_mapping: + data_provider_name = data_provider_mapping[ 'data_standalone' ] + else: + data_provider_name = data_provider_mapping[ 'data' ] + if data_provider_name: + data_provider = get_data_provider( name=data_provider_name, original_dataset=original_dataset ) + else: + data_provider = GenomeDataProvider + except: + pass + return data_provider + +def package_gff_feature( feature, no_detail=False, filter_cols=[] ): + """ Package a GFF feature in an array for data providers. """ + feature = convert_gff_coords_to_bed( feature ) + + # No detail means only start, end. + if no_detail: + return [ feature.start, feature.end ] + + # Return full feature. + payload = [ feature.start, + feature.end, + feature.name(), + feature.strand, + # No notion of thick start, end in GFF, so make everything + # thick. + feature.start, + feature.end + ] + + # HACK: ignore interval with name 'transcript' from feature. + # Cufflinks puts this interval in each of its transcripts, + # and they mess up trackster by covering the feature's blocks. + # This interval will always be a feature's first interval, + # and the GFF's third column is its feature name. + feature_intervals = feature.intervals + if feature.intervals[0].fields[2] == 'transcript': + feature_intervals = feature.intervals[1:] + # Add blocks. + block_sizes = [ (interval.end - interval.start ) for interval in feature_intervals ] + block_starts = [ ( interval.start - feature.start ) for interval in feature_intervals ] + blocks = zip( block_sizes, block_starts ) + payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) + + # Add filter data to payload. + for col in filter_cols: + if col == "Score": + if feature.score == 'nan': + payload.append( feature.score ) + else: + try: + f = float( feature.score ) + payload.append( f ) + except: + payload.append( feature.score ) + elif col in feature.attributes: + if feature.attributes[col] == 'nan': + payload.append( feature.attributes[col] ) + else: + try: + f = float( feature.attributes[col] ) + payload.append( f ) + except: + payload.append( feature.attributes[col] ) + else: + # Dummy value. + payload.append( 0 ) + return payload diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/genome/summary.py --- /dev/null +++ b/lib/galaxy/visualization/genome/summary.py @@ -0,0 +1,111 @@ +''' +Summary tree data structure for feature aggregation across large genomic regions. +''' + +import sys, os +import cPickle + +# TODO: What are the performance implications of setting min level to 1? Data +# structure size and/or query speed? It would be nice to have level 1 data +# so that client does not have to compute it. +MIN_LEVEL = 2 + +class SummaryTree: + def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ): + self.chrom_blocks = {} + self.levels = levels + self.draw_cutoff = draw_cutoff + self.detail_cutoff = detail_cutoff + self.block_size = block_size + self.chrom_stats = {} + + def find_block( self, num, level ): + """ Returns block that num is in for level. """ + return ( num / self.block_size ** level ) + + def insert_range( self, chrom, start, end ): + """ Inserts a feature at chrom:start-end into the tree. """ + + # Get or set up chrom blocks. + if chrom in self.chrom_blocks: + blocks = self.chrom_blocks[ chrom ] + else: + blocks = self.chrom_blocks[ chrom ] = {} + self.chrom_stats[ chrom ] = {} + for level in range( MIN_LEVEL, self.levels + 1 ): + blocks[ level ] = {} + + # Insert feature into all matching blocks at all levels. + for level in range( MIN_LEVEL, self.levels + 1 ): + block_level = blocks[ level ] + starting_block = self.find_block( start, level ) + ending_block = self.find_block( end, level ) + for block in range( starting_block, ending_block + 1 ): + if block in block_level: + block_level[ block ] += 1 + else: + block_level[ block ] = 1 + + def finish( self ): + """ Compute stats for levels. """ + + for chrom, blocks in self.chrom_blocks.iteritems(): + for level in range( self.levels, MIN_LEVEL - 1, -1 ): + # Set level's stats. + max_val = max( blocks[ level ].values() ) + self.chrom_stats[ chrom ][ level ] = {} + self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level + self.chrom_stats[ chrom ][ level ][ "max" ] = max_val + self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] ) + + self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] ) + + def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ): + """ Queries tree for data. """ + + # Set cutoffs to self's attributes if not defined. + if draw_cutoff != 0: + draw_cutoff = self.draw_cutoff + if detail_cutoff != 0: + detail_cutoff = self.detail_cutoff + + # Get data. + if chrom in self.chrom_blocks: + stats = self.chrom_stats[ chrom ] + + # For backwards compatibility: + if "detail_level" in stats and level <= stats[ "detail_level" ]: + return "detail" + elif "draw_level" in stats and level <= stats[ "draw_level" ]: + return "draw" + + # If below draw, detail level, return string to denote this. + max = stats[ level ][ "max" ] + if max < detail_cutoff: + return "detail" + if max < draw_cutoff: + return "draw" + + # Return block data. + blocks = self.chrom_blocks[ chrom ] + results = [] + multiplier = self.block_size ** level + starting_block = self.find_block( start, level ) + ending_block = self.find_block( end, level ) + for block in range( starting_block, ending_block + 1 ): + val = 0 + if block in blocks[ level ]: + val = blocks[ level ][ block ] + results.append( ( block * multiplier, val ) ) + return results + + return None + + def write( self, filename ): + """ Writes tree to file. """ + self.finish() + cPickle.dump( self, open( filename, 'wb' ), 2 ) + +def summary_tree_from_file( filename ): + return cPickle.load( open( filename, "rb" ) ) + diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/genome/visual_analytics.py --- /dev/null +++ b/lib/galaxy/visualization/genome/visual_analytics.py @@ -0,0 +1,80 @@ +import urllib + +from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter +from galaxy.tools.parameters.dynamic_options import DynamicOptions + +class TracksterConfig: + """ Trackster configuration encapsulation. """ + + def __init__( self, actions ): + self.actions = actions + + @staticmethod + def parse( root ): + actions = [] + for action_elt in root.findall( "action" ): + actions.append( SetParamAction.parse( action_elt ) ) + return TracksterConfig( actions ) + +class SetParamAction: + """ Set parameter action. """ + + def __init__( self, name, output_name ): + self.name = name + self.output_name = output_name + + @staticmethod + def parse( elt ): + """ Parse action from element. """ + return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + +def get_dataset_job( hda ): + # Get dataset's job. + job = None + for job_output_assoc in hda.creating_job_associations: + job = job_output_assoc.job + break + return job + +def get_tool_def( trans, hda ): + """ Returns definition of an interactive tool for an HDA. """ + + job = get_dataset_job( hda ) + # TODO: could use this assertion to provide more information. + # assert job is not None, 'Requested job has not been loaded.' + if not job: + return None + tool = trans.app.toolbox.get_tool( job.tool_id ) + # TODO: could use this assertion to provide more information. + # assert tool is not None, 'Requested tool has not been loaded.' + if not tool: + return None + + # Tool must have a Trackster configuration. + if not tool.trackster_conf: + return None + + # Get list of tool parameters that can be interactively modified. + tool_params = [] + tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) + tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) + for name, input in tool.inputs.items(): + if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter: + param_dict = { 'name' : name, 'label' : input.label, \ + 'value' : tool_param_values.get( name, input.value ), \ + 'type' : 'number', 'init_value' : input.value, + 'html' : urllib.quote( input.get_html() ) } + if input.min: + param_dict['min'] = input.min + if input.max: + param_dict['max'] = input.max + tool_params.append( param_dict ) + elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: + tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ + 'value' : tool_param_values.get( name, None ), \ + 'html' : urllib.quote( input.get_html() ) } ) + + # If tool has parameters that can be interactively modified, return tool. + if len( tool_params ) != 0: + return { 'name' : tool.name, 'params' : tool_params } + return None \ No newline at end of file diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/tracks/__init__.py --- a/lib/galaxy/visualization/tracks/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -""" -Package for track style visualization using the trackster UI. -""" \ No newline at end of file diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ /dev/null @@ -1,1557 +0,0 @@ -""" -Data providers for genome visualizations. -""" - -import os, sys -from math import ceil, log -import pkg_resources -pkg_resources.require( "bx-python" ) -if sys.version_info[:2] == (2, 4): - pkg_resources.require( "ctypes" ) -pkg_resources.require( "pysam" ) -pkg_resources.require( "numpy" ) -import numpy -from galaxy.datatypes.util.gff_util import * -from galaxy.util.json import from_json_string -from bx.interval_index_file import Indexes -from bx.bbi.bigwig_file import BigWigFile -from galaxy.util.lrucache import LRUCache -from galaxy.visualization.tracks.summary import * -from galaxy.visualization.data_providers import BaseDataProvider -import galaxy_utils.sequence.vcf -from galaxy.datatypes.tabular import Tabular, Vcf -from galaxy.datatypes.interval import Interval, Bed, Gff, Gtf, ENCODEPeak, ChromatinInteractions - -from pysam import csamtools, ctabix - -# -# Utility functions. -# - -def float_nan(n): - ''' - Return None instead of NaN to pass jQuery 1.4's strict JSON - ''' - if n != n: # NaN != NaN - return None - else: - return float(n) - -def get_bounds( reads, start_pos_index, end_pos_index ): - ''' - Returns the minimum and maximum position for a set of reads. - ''' - max_low = sys.maxint - max_high = -sys.maxint - for read in reads: - if read[ start_pos_index ] < max_low: - max_low = read[ start_pos_index ] - if read[ end_pos_index ] > max_high: - max_high = read[ end_pos_index ] - return max_low, max_high - -def _convert_between_ucsc_and_ensemble_naming( chrom ): - ''' - Convert between UCSC chromosome ('chr1') naming conventions and Ensembl - naming conventions ('1') - ''' - if chrom.startswith( 'chr' ): - # Convert from UCSC to Ensembl - return chrom[ 3: ] - else: - # Convert from Ensembl to UCSC - return 'chr' + chrom - -def _chrom_naming_matches( chrom1, chrom2 ): - return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) - -class FeatureLocationIndexDataProvider( BaseDataProvider ): - """ - Reads/writes/queries feature location index (FLI) datasets. - """ - - def __init__( self, converted_dataset ): - self.converted_dataset = converted_dataset - - def get_data( self, query ): - # Init. - textloc_file = open( self.converted_dataset.file_name, 'r' ) - line_len = int( textloc_file.readline() ) - file_len = os.path.getsize( self.converted_dataset.file_name ) - query = query.lower() - - # Find query in file using binary search. - low = 0 - high = file_len / line_len - while low < high: - mid = ( low + high ) // 2 - position = mid * line_len - textloc_file.seek( position ) - - # Compare line with query and update low, high. - line = textloc_file.readline() - if line < query: - low = mid + 1 - else: - high = mid - - position = low * line_len - - # At right point in file, generate hits. - result = [] - while True: - line = textloc_file.readline() - if not line.startswith( query ): - break - if line[ -1: ] == '\n': - line = line[ :-1 ] - result.append( line.split()[1:] ) - - textloc_file.close() - return result - -class TracksDataProvider( BaseDataProvider ): - """ Base class for tracks data providers. """ - - """ - Mapping from column name to payload data; this mapping is used to create - filters. Key is column name, value is a dict with mandatory key 'index' and - optional key 'name'. E.g. this defines column 4 - - col_name_data_attr_mapping = {4 : { index: 5, name: 'Score' } } - """ - col_name_data_attr_mapping = {} - - def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None, - error_max_vals="Only the first %i %s in this region are displayed." ): - super( TracksDataProvider, self ).__init__( converted_dataset=converted_dataset, - original_dataset=original_dataset, - dependencies=dependencies, - error_max_vals=error_max_vals ) - - def write_data_to_file( self, regions, filename ): - """ - Write data in region defined by chrom, start, and end to a file. - """ - raise Exception( "Unimplemented Function" ) - - def valid_chroms( self ): - """ - Returns chroms/contigs that the dataset contains - """ - return None # by default - - def has_data( self, chrom, start, end, **kwargs ): - """ - Returns true if dataset has data in the specified genome window, false - otherwise. - """ - raise Exception( "Unimplemented Function" ) - - def get_iterator( self, chrom, start, end ): - """ - Returns an iterator that provides data in the region chrom:start-end - """ - raise Exception( "Unimplemented Function" ) - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Process data from an iterator to a format that can be provided to client. - """ - raise Exception( "Unimplemented Function" ) - - def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): - """ - Returns data in region defined by chrom, start, and end. start_val and - max_vals are used to denote the data to return: start_val is the first element to - return and max_vals indicates the number of values to return. - - Return value must be a dictionary with the following attributes: - dataset_type, data - """ - iterator = self.get_iterator( chrom, start, end ) - return self.process_data( iterator, start_val, max_vals, **kwargs ) - - def get_genome_data( self, chroms_info, **kwargs ): - """ - Returns data for complete genome. - """ - dataset_summary = [] - for chrom_info in chroms_info[ 'chrom_info' ]: - summary = self.get_data( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], **kwargs ) - dataset_summary.append( summary ) - - return dataset_summary - - def get_filters( self ): - """ - Returns filters for provider's data. Return value is a list of - filters; each filter is a dictionary with the keys 'name', 'index', 'type'. - NOTE: This method uses the original dataset's datatype and metadata to - create the filters. - """ - # Get column names. - try: - column_names = self.original_dataset.datatype.column_names - except AttributeError: - try: - column_names = range( self.original_dataset.metadata.columns ) - except: # Give up - return [] - - # Dataset must have column types; if not, cannot create filters. - try: - column_types = self.original_dataset.metadata.column_types - except AttributeError: - return [] - - # Create and return filters. - filters = [] - if self.original_dataset.metadata.viz_filter_cols: - for viz_col_index in self.original_dataset.metadata.viz_filter_cols: - # Some columns are optional, so can't assume that a filter - # column is in dataset. - if viz_col_index >= len( column_names ): - continue; - col_name = column_names[ viz_col_index ] - # Make sure that column has a mapped index. If not, do not add filter. - try: - attrs = self.col_name_data_attr_mapping[ col_name ] - except KeyError: - continue - filters.append( - { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ - 'index' : attrs[ 'index' ] } ) - return filters - - def get_default_max_vals( self ): - return 5000 - -# -# -- Base mixins and providers -- -# - -class FilterableMixin: - def get_filters( self ): - """ Returns a dataset's filters. """ - - # is_ functions taken from Tabular.set_meta - def is_int( column_text ): - try: - int( column_text ) - return True - except: - return False - def is_float( column_text ): - try: - float( column_text ) - return True - except: - if column_text.strip().lower() == 'na': - return True #na is special cased to be a float - return False - - # - # Get filters. - # TODOs: - # (a) might be useful to move this into each datatype's set_meta method; - # (b) could look at first N lines to ensure GTF attribute types are consistent. - # - filters = [] - # HACK: first 8 fields are for drawing, so start filter column index at 9. - filter_col = 8 - if isinstance( self.original_dataset.datatype, Gff ): - # Can filter by score and GTF attributes. - filters = [ { 'name': 'Score', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c6' } ] - filter_col += 1 - if isinstance( self.original_dataset.datatype, Gtf ): - # Create filters based on dataset metadata. - for name, a_type in self.original_dataset.metadata.attribute_types.items(): - if a_type in [ 'int', 'float' ]: - filters.append( - { 'name': name, - 'type': 'number', - 'index': filter_col, - 'tool_id': 'gff_filter_by_attribute', - 'tool_exp_name': name } ) - filter_col += 1 - - ''' - # Old code: use first line in dataset to find attributes. - for i, line in enumerate( open(self.original_dataset.file_name) ): - if not line.startswith('#'): - # Look at first line for attributes and types. - attributes = parse_gff_attributes( line.split('\t')[8] ) - for attr, value in attributes.items(): - # Get attribute type. - if is_int( value ): - attr_type = 'int' - elif is_float( value ): - attr_type = 'float' - else: - attr_type = 'str' - # Add to filters. - if attr_type is not 'str': - filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) - filter_col += 1 - break - ''' - elif isinstance( self.original_dataset.datatype, Bed ): - # Can filter by score column only. - filters = [ { 'name': 'Score', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c5' - } ] - - return filters - - -class TabixDataProvider( FilterableMixin, TracksDataProvider ): - """ - Tabix index data provider for the Galaxy track browser. - """ - - col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - - def get_iterator( self, chrom, start, end ): - start, end = int(start), int(end) - if end >= (2<<29): - end = (2<<29 - 1) # Tabix-enforced maximum - - bgzip_fname = self.dependencies['bgzip'].file_name - - tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) - - # If chrom not in data, try alternative. - if chrom not in tabix.contigs: - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - - return tabix.fetch(reference=chrom, start=start, end=end) - - def write_data_to_file( self, regions, filename ): - out = open( filename, "w" ) - - for region in regions: - # Write data in region. - chrom = region.chrom - start = region.start - end = region.end - iterator = self.get_iterator( chrom, start, end ) - for line in iterator: - out.write( "%s\n" % line ) - - out.close() - -# -# -- Interval data providers -- -# - -class IntervalDataProvider( TracksDataProvider ): - """ - Processes BED data from native format to payload format. - - Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] - """ - - def get_iterator( self, chrom, start, end ): - raise Exception( "Unimplemented Function" ) - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Provides - """ - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <strand> ] - # - # First three entries are mandatory, others are optional. - # - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - rval = [] - message = None - # Subtract one b/c columns are 1-based but indices are 0-based. - col_fn = lambda col: None if col is None else col - 1 - start_col = self.original_dataset.metadata.startCol - 1 - end_col = self.original_dataset.metadata.endCol - 1 - strand_col = col_fn( self.original_dataset.metadata.strandCol ) - name_col = col_fn( self.original_dataset.metadata.nameCol ) - for count, line in enumerate( iterator ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) - break - - feature = line.split() - length = len(feature) - # Unique id is just a hash of the line - payload = [ hash(line), int( feature[start_col] ), int( feature [end_col] ) ] - - if no_detail: - rval.append( payload ) - continue - - # Name, strand. - if name_col: - payload.append( feature[name_col] ) - if strand_col: - # Put empty name as placeholder. - if not name_col: payload.append( "" ) - payload.append( feature[strand_col] ) - - # Score (filter data) - if length >= 5 and filter_cols and filter_cols[0] == "Score": - try: - payload.append( float( feature[4] ) ) - except: - payload.append( feature[4] ) - - rval.append( payload ) - - return { 'data': rval, 'message': message } - - def write_data_to_file( self, regions, filename ): - raise Exception( "Unimplemented Function" ) - -class IntervalTabixDataProvider( TabixDataProvider, IntervalDataProvider ): - """ - Provides data from a BED file indexed via tabix. - """ - pass - - -# -# -- BED data providers -- -# - -class BedDataProvider( TracksDataProvider ): - """ - Processes BED data from native format to payload format. - - Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] - """ - - def get_iterator( self, chrom, start, end ): - raise Exception( "Unimplemented Method" ) - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Provides - """ - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>, - # <thick_end>, <blocks> ] - # - # First three entries are mandatory, others are optional. - # - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - rval = [] - message = None - for count, line in enumerate( iterator ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) - break - # TODO: can we use column metadata to fill out payload? - # TODO: use function to set payload data - - feature = line.split() - length = len(feature) - # Unique id is just a hash of the line - payload = [ hash(line), int(feature[1]), int(feature[2]) ] - - if no_detail: - rval.append( payload ) - continue - - # Name, strand, thick start, thick end. - if length >= 4: - payload.append(feature[3]) - if length >= 6: - payload.append(feature[5]) - if length >= 8: - payload.append(int(feature[6])) - payload.append(int(feature[7])) - - # Blocks. - if length >= 12: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip( block_sizes, block_starts ) - payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) - - # Score (filter data) - if length >= 5 and filter_cols and filter_cols[0] == "Score": - # If dataset doesn't have name/strand/thick start/thick end/blocks, - # add placeholders. There should be 8 entries if all attributes - # are present. - payload.extend( [ None for i in range( 8 - len( payload ) ) ] ) - - try: - payload.append( float( feature[4] ) ) - except: - payload.append( feature[4] ) - - rval.append( payload ) - - return { 'data': rval, 'message': message } - - def write_data_to_file( self, regions, filename ): - out = open( filename, "w" ) - - for region in regions: - # Write data in region. - chrom = region.chrom - start = region.start - end = region.end - iterator = self.get_iterator( chrom, start, end ) - for line in iterator: - out.write( "%s\n" % line ) - - out.close() - -class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): - """ - Provides data from a BED file indexed via tabix. - """ - pass - -class RawBedDataProvider( BedDataProvider ): - """ - Provide data from BED file. - - NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. - """ - - def get_iterator( self, chrom=None, start=None, end=None ): - # Read first line in order to match chrom naming format. - line = source.readline() - dataset_chrom = line.split()[0] - if not _chrom_naming_matches( chrom, dataset_chrom ): - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - # Undo read. - source.seek( 0 ) - - def line_filter_iter(): - for line in open( self.original_dataset.file_name ): - if line.startswith( "track" ) or line.startswith( "browser" ): - continue - feature = line.split() - feature_chrom = feature[0] - feature_start = int( feature[1] ) - feature_end = int( feature[2] ) - if ( chrom is not None and feature_chrom != chrom ) \ - or ( start is not None and feature_start > end ) \ - or ( end is not None and feature_end < start ): - continue - yield line - - return line_filter_iter() - -# -# -- VCF data providers -- -# - -class VcfDataProvider( TracksDataProvider ): - """ - Abstract class that processes VCF data from native format to payload format. - - Payload format: TODO - """ - - col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Returns a dict with the following attributes: - data - a list of variants with the format - [<guid>, <start>, <end>, <name>, cigar, seq] - - message - error/informative message - """ - rval = [] - message = None - - def get_mapping( ref, alt ): - """ - Returns ( offset, new_seq, cigar ) tuple that defines mapping of - alt to ref. Cigar format is an array of [ op_index, length ] pairs - where op_index is the 0-based index into the string "MIDNSHP=X" - """ - - cig_ops = "MIDNSHP=X" - - ref_len = len( ref ) - alt_len = len( alt ) - - # Substitutions? - if ref_len == alt_len: - return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ] - - # Deletions? - alt_in_ref_index = ref.find( alt ) - if alt_in_ref_index != -1: - return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ] - - # Insertions? - ref_in_alt_index = alt.find( ref ) - if ref_in_alt_index != -1: - return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] - - # Pack data. - for count, line in enumerate( iterator ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) - break - - feature = line.split() - start = int( feature[1] ) - 1 - ref = feature[3] - alts = feature[4] - - # HACK? alts == '.' --> monomorphism. - if alts == '.': - alts = ref - - # Pack variants. - for alt in alts.split(","): - offset, new_seq, cigar = get_mapping( ref, alt ) - start += offset - end = start + len( new_seq ) - - # Pack line. - payload = [ - hash( line ), - start, - end, - # ID: - feature[2], - cigar, - # TODO? VCF does not have strand, so default to positive. - "+", - new_seq, - None if feature[5] == '.' else float( feature[5] ) - ] - rval.append(payload) - - return { 'data': rval, 'message': message } - - def write_data_to_file( self, regions, filename ): - out = open( filename, "w" ) - - for region in regions: - # Write data in region. - chrom = region.chrom - start = region.start - end = region.end - iterator = self.get_iterator( chrom, start, end ) - for line in iterator: - out.write( "%s\n" % line ) - out.close() - -class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): - """ - Provides data from a VCF file indexed via tabix. - """ - pass - -class RawVcfDataProvider( VcfDataProvider ): - """ - Provide data from VCF file. - - NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. - """ - - def get_iterator( self, chrom, start, end ): - # Read first line in order to match chrom naming format. - line = source.readline() - dataset_chrom = line.split()[0] - if not _chrom_naming_matches( chrom, dataset_chrom ): - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - # Undo read. - source.seek( 0 ) - - def line_filter_iter(): - for line in open( self.original_dataset.file_name ): - if line.startswith("#"): - continue - variant = line.split() - variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ] - variant_start = int( variant_start ) - longest_alt = -1 - for alt in alts: - if len( alt ) > longest_alt: - longest_alt = len( alt ) - variant_end = variant_start + abs( len( ref ) - longest_alt ) - if variant_chrom != chrom or variant_start > end or variant_end < start: - continue - yield line - - return line_filter_iter() - -class SummaryTreeDataProvider( TracksDataProvider ): - """ - Summary tree data provider for the Galaxy track browser. - """ - - CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance - - def valid_chroms( self ): - st = summary_tree_from_file( self.converted_dataset.file_name ) - return st.chrom_blocks.keys() - - def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None ): - """ - Returns summary tree data for a given genomic region. - """ - filename = self.converted_dataset.file_name - st = self.CACHE[filename] - if st is None: - st = summary_tree_from_file( self.converted_dataset.file_name ) - self.CACHE[filename] = st - - # Look for chrom in tree using both naming conventions. - if chrom not in st.chrom_blocks: - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - if chrom not in st.chrom_blocks: - return None - - # Get or compute level. - if level: - level = int( level ) - elif resolution: - resolution = max( 1, ceil( float( resolution ) ) ) - level = ceil( log( resolution, st.block_size ) ) - 1 - level = int( max( level, 0 ) ) - else: - # Either level or resolution is required. - return None - - if level <= 1: - return "detail" - - # Use level to get results. - stats = st.chrom_stats[ chrom ] - results = st.query( chrom, int(start), int(end), level, detail_cutoff=detail_cutoff, draw_cutoff=draw_cutoff ) - if results == "detail" or results == "draw": - return results - else: - return results, stats[ level ][ "max" ], stats[ level ]["avg" ], stats[ level ][ "delta" ] - - def has_data( self, chrom ): - """ - Returns true if dataset has data for this chrom - """ - - # Get summary tree. - filename = self.converted_dataset.file_name - st = self.CACHE[filename] - if st is None: - st = summary_tree_from_file( self.converted_dataset.file_name ) - self.CACHE[filename] = st - - # Check for data. - return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None) - -class BamDataProvider( TracksDataProvider, FilterableMixin ): - """ - Provides access to intervals from a sorted indexed BAM file. Position data - is reported in 1-based, closed format, i.e. SAM/BAM format. - """ - - def get_filters( self ): - """ - Returns filters for dataset. - """ - # HACK: first 7 fields are for drawing, so start filter column index at 7. - filter_col = 7 - filters = [] - filters.append( { 'name': 'Mapping Quality', - 'type': 'number', - 'index': filter_col - } ) - return filters - - - def write_data_to_file( self, regions, filename ): - """ - Write reads in regions to file. - """ - - # Open current BAM file using index. - bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', \ - index_filename=self.converted_dataset.file_name ) - - # TODO: write headers as well? - new_bamfile = csamtools.Samfile( template=bamfile, filename=filename, mode='wb' ) - - for region in regions: - # Write data from region. - chrom = region.chrom - start = region.start - end = region.end - - try: - data = bamfile.fetch(start=start, end=end, reference=chrom) - except ValueError, e: - # Try alternative chrom naming. - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - try: - data = bamfile.fetch( start=start, end=end, reference=chrom ) - except ValueError: - return None - - # Write reads in region. - for i, read in enumerate( data ): - new_bamfile.write( read ) - - # Cleanup. - new_bamfile.close() - bamfile.close() - - def get_iterator( self, chrom, start, end ): - """ - Returns an iterator that provides data in the region chrom:start-end - """ - start, end = int(start), int(end) - orig_data_filename = self.original_dataset.file_name - index_filename = self.converted_dataset.file_name - - # Attempt to open the BAM file with index - bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) - try: - data = bamfile.fetch(start=start, end=end, reference=chrom) - except ValueError, e: - # Try alternative chrom naming. - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - try: - data = bamfile.fetch( start=start, end=end, reference=chrom ) - except ValueError: - return None - return data - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Returns a dict with the following attributes: - data - a list of reads with the format - [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] - where <read_1> has the format - [<start>, <end>, <cigar>, <strand>, <read_seq>] - and <read_2> has the format - [<start>, <end>, <cigar>, <strand>, <read_seq>] - Field 7 is empty so that mapq scores' location matches that in single-end reads. - For single-end reads, read has format: - [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>, <mapq_score>] - - NOTE: read end and sequence data are not valid for reads outside of - requested region and should not be used. - - max_low - lowest coordinate for the returned reads - max_high - highest coordinate for the returned reads - message - error/informative message - """ - # No iterator indicates no reads. - if iterator is None: - return { 'data': [], 'message': None } - - # Decode strand from read flag. - def decode_strand( read_flag, mask ): - strand_flag = ( read_flag & mask == 0 ) - if strand_flag: - return "+" - else: - return "-" - - # Encode reads as list of lists. - results = [] - paired_pending = {} - unmapped = 0 - message = None - for count, read in enumerate( iterator ): - if count < start_val: - continue - if ( count - start_val - unmapped ) >= max_vals: - message = self.error_max_vals % ( max_vals, "reads" ) - break - - # If not mapped, skip read. - is_mapped = ( read.flag & 0x0004 == 0 ) - if not is_mapped: - unmapped += 1 - continue - - qname = read.qname - seq = read.seq - strand = decode_strand( read.flag, 0x0010 ) - if read.cigar is not None: - read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length - else: - read_len = len(seq) # If no cigar, just use sequence length - - if read.is_proper_pair: - if qname in paired_pending: # one in dict is always first - pair = paired_pending[qname] - results.append( [ "%i_%s" % ( pair['start'], qname ), - pair['start'], - read.pos + read_len, - qname, - [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], - [ read.pos, read.pos + read_len, read.cigar, strand, seq ], - None, [ pair['mapq'], read.mapq ] - ] ) - del paired_pending[qname] - else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, - 'rlen': read_len, 'strand': strand, 'cigar': read.cigar, 'mapq': read.mapq } - else: - results.append( [ "%i_%s" % ( read.pos, qname ), - read.pos, read.pos + read_len, qname, - read.cigar, strand, read.seq, read.mapq ] ) - - # Take care of reads whose mates are out of range. - # TODO: count paired reads when adhering to max_vals? - for qname, read in paired_pending.iteritems(): - if read['mate_start'] < read['start']: - # Mate is before read. - read_start = read['mate_start'] - read_end = read['end'] - # Make read_1 start=end so that length is 0 b/c we don't know - # read length. - r1 = [ read['mate_start'], read['mate_start'] ] - r2 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] - else: - # Mate is after read. - read_start = read['start'] - # Make read_2 start=end so that length is 0 b/c we don't know - # read length. Hence, end of read is start of read_2. - read_end = read['mate_start'] - r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] - r2 = [ read['mate_start'], read['mate_start'] ] - - results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) - - # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data. - # bamfile.close() - - max_low, max_high = get_bounds( results, 1, 2 ) - - return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } - -class SamDataProvider( BamDataProvider ): - - def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): - """ Create SamDataProvider. """ - - # HACK: to use BamDataProvider, original dataset must be BAM and - # converted dataset must be BAI. Use BAI from BAM metadata. - if converted_dataset: - self.converted_dataset = converted_dataset.metadata.bam_index - self.original_dataset = converted_dataset - self.dependencies = dependencies - -class BBIDataProvider( TracksDataProvider ): - """ - BBI data provider for the Galaxy track browser. - """ - def valid_chroms( self ): - # No way to return this info as of now - return None - - def has_data( self, chrom ): - f, bbi = self._get_dataset() - all_dat = bbi.query(chrom, 0, 2147483647, 1) - f.close() - return all_dat is not None - - def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): - # Bigwig can be a standalone bigwig file, in which case we use - # original_dataset, or coming from wig->bigwig conversion in - # which we use converted_dataset - f, bbi = self._get_dataset() - - # If stats requested, compute overall summary data for the range - # start:endbut no reduced data. This is currently used by client - # to determine the default range. - if 'stats' in kwargs: - summary = bbi.summarize( chrom, start, end, 1 ) - f.close() - - min = 0 - max = 0 - mean = 0 - sd = 0 - if summary is not None: - # Does the summary contain any defined values? - valid_count = summary.valid_count[0] - if summary.valid_count > 0: - # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower - # bounds that contain ~95% of the data. - mean = summary.sum_data[0] / valid_count - var = summary.sum_squares[0] - mean - if valid_count > 1: - var /= valid_count - 1 - sd = numpy.sqrt( var ) - min = summary.min_val[0] - max = summary.max_val[0] - - return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) ) - - # Sample from region using approximately this many samples. - N = 1000 - - def summarize_region( bbi, chrom, start, end, num_points ): - ''' - Returns results from summarizing a region using num_points. - NOTE: num_points cannot be greater than end - start or BBI - will return None for all positions.s - ''' - result = [] - - # Get summary; this samples at intervals of length - # (end - start)/num_points -- i.e. drops any fractional component - # of interval length. - summary = bbi.summarize( chrom, start, end, num_points ) - if summary: - #mean = summary.sum_data / summary.valid_count - - ## Standard deviation by bin, not yet used - ## var = summary.sum_squares - mean - ## var /= minimum( valid_count - 1, 1 ) - ## sd = sqrt( var ) - - pos = start - step_size = (end - start) / num_points - - for i in range( num_points ): - result.append( (pos, float_nan( summary.sum_data[i] / summary.valid_count[i] ) ) ) - pos += step_size - - return result - - # Approach is different depending on region size. - if end - start < N: - # Get values for individual bases in region, including start and end. - # To do this, need to increase end to next base and request number of points. - num_points = end - start + 1 - end += 1 - else: - # - # The goal is to sample the region between start and end uniformly - # using ~N data points. The challenge is that the size of sampled - # intervals rarely is full bases, so sampling using N points will - # leave the end of the region unsampled due to remainders for each - # interval. To recitify this, a new N is calculated based on the - # step size that covers as much of the region as possible. - # - # However, this still leaves some of the region unsampled. This - # could be addressed by repeatedly sampling remainder using a - # smaller and smaller step_size, but that would require iteratively - # going to BBI, which could be time consuming. - # - - # Start with N samples. - num_points = N - step_size = ( end - start ) / num_points - # Add additional points to sample in the remainder not covered by - # the initial N samples. - remainder_start = start + step_size * num_points - additional_points = ( end - remainder_start ) / step_size - num_points += additional_points - - result = summarize_region( bbi, chrom, start, end, num_points ) - - # Cleanup and return. - f.close() - return { 'data': result } - -class BigBedDataProvider( BBIDataProvider ): - def _get_dataset( self ): - # Nothing converts to bigBed so we don't consider converted dataset - f = open( self.original_dataset.file_name ) - return f, BigBedFile(file=f) - -class BigWigDataProvider ( BBIDataProvider ): - """ - Provides data from BigWig files; position data is reported in 1-based - coordinate system, i.e. wiggle format. - """ - def _get_dataset( self ): - if self.converted_dataset is not None: - f = open( self.converted_dataset.file_name ) - else: - f = open( self.original_dataset.file_name ) - return f, BigWigFile(file=f) - -class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): - """ - Interval index files used only for GFF files. - """ - col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - - def write_data_to_file( self, regions, filename ): - source = open( self.original_dataset.file_name ) - index = Indexes( self.converted_dataset.file_name ) - out = open( filename, 'w' ) - - for region in regions: - # Write data from region. - chrom = region.chrom - start = region.start - end = region.end - for start, end, offset in index.find(chrom, start, end): - source.seek( offset ) - - reader = GFFReaderWrapper( source, fix_strand=True ) - feature = reader.next() - for interval in feature.intervals: - out.write( '\t'.join( interval.fields ) + '\n' ) - - out.close() - - def get_iterator( self, chrom, start, end ): - """ - Returns an array with values: (a) source file and (b) an iterator that - provides data in the region chrom:start-end - """ - start, end = int(start), int(end) - source = open( self.original_dataset.file_name ) - index = Indexes( self.converted_dataset.file_name ) - - if chrom not in index.indexes: - # Try alternative naming. - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - - return index.find(chrom, start, end) - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - results = [] - message = None - source = open( self.original_dataset.file_name ) - - # - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, - # <thick_end>, <blocks> ] - # - # First three entries are mandatory, others are optional. - # - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - for count, val in enumerate( iterator ): - start, end, offset = val[0], val[1], val[2] - if count < start_val: - continue - if count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) - break - source.seek( offset ) - # TODO: can we use column metadata to fill out payload? - - # GFF dataset. - reader = GFFReaderWrapper( source, fix_strand=True ) - feature = reader.next() - payload = package_gff_feature( feature, no_detail, filter_cols ) - payload.insert( 0, offset ) - - results.append( payload ) - - return { 'data': results, 'message': message } - -class RawGFFDataProvider( TracksDataProvider ): - """ - Provide data from GFF file that has not been indexed. - - NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. - """ - - def get_iterator( self, chrom, start, end ): - """ - Returns an iterator that provides data in the region chrom:start-end as well as - a file offset. - """ - source = open( self.original_dataset.file_name ) - - # Read first line in order to match chrom naming format. - line = source.readline() - dataset_chrom = line.split()[0] - if not _chrom_naming_matches( chrom, dataset_chrom ): - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - # Undo read. - source.seek( 0 ) - - def features_in_region_iter(): - offset = 0 - for feature in GFFReaderWrapper( source, fix_strand=True ): - # Only provide features that are in region. - feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) - if feature.chrom == chrom and feature_end > start and feature_start < end: - yield feature, offset - offset += feature.raw_size - - return features_in_region_iter() - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Process data from an iterator to a format that can be provided to client. - """ - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - results = [] - message = None - - for count, ( feature, offset ) in enumerate( iterator ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "reads" ) - break - - payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) - payload.insert( 0, offset ) - results.append( payload ) - - - return { 'data': results, 'message': message } - -class GtfTabixDataProvider( TabixDataProvider ): - """ - Returns data from GTF datasets that are indexed via tabix. - """ - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - # Loop through lines and group by transcript_id; each group is a feature. - - # TODO: extend this code or use code in gff_util to process GFF/3 as well - # and then create a generic GFFDataProvider that can be used with both - # raw and tabix datasets. - features = {} - for count, line in enumerate( iterator ): - line_attrs = parse_gff_attributes( line.split('\t')[8] ) - transcript_id = line_attrs[ 'transcript_id' ] - if transcript_id in features: - feature = features[ transcript_id ] - else: - feature = [] - features[ transcript_id ] = feature - feature.append( GFFInterval( None, line.split( '\t') ) ) - - # Process data. - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - results = [] - message = None - - for count, intervals in enumerate( features.values() ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "reads" ) - break - - feature = GFFFeature( None, intervals=intervals ) - payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) - payload.insert( 0, feature.intervals[ 0 ].attributes[ 'transcript_id' ] ) - results.append( payload ) - - return { 'data': results, 'message': message } - -# -# -- ENCODE Peak data providers. -# - -class ENCODEPeakDataProvider( TracksDataProvider ): - """ - Abstract class that processes ENCODEPeak data from native format to payload format. - - Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] - """ - - def get_iterator( self, chrom, start, end ): - raise "Unimplemented Method" - - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Provides - """ - - ## FIXMEs: - # (1) should be able to unify some of this code with BedDataProvider.process_data - # (2) are optional number of parameters supported? - - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>, - # <thick_end>, <blocks> ] - # - # First three entries are mandatory, others are optional. - # - no_detail = ( "no_detail" in kwargs ) - rval = [] - message = None - for count, line in enumerate( iterator ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) - break - - feature = line.split() - length = len( feature ) - - # Feature initialization. - payload = [ - # GUID is just a hash of the line - hash( line ), - # Add start, end. - int( feature[1] ), - int( feature[2] ) - ] - - if no_detail: - rval.append( payload ) - continue - - # Extend with additional data. - payload.extend( [ - # Add name, strand. - feature[3], - feature[5], - # Thick start, end are feature start, end for now. - int( feature[1] ), - int( feature[2] ), - # No blocks. - None, - # Filtering data: Score, signalValue, pValue, qValue. - float( feature[4] ), - float( feature[6] ), - float( feature[7] ), - float( feature[8] ) - ] ) - - rval.append( payload ) - - return { 'data': rval, 'message': message } - -class ENCODEPeakTabixDataProvider( TabixDataProvider, ENCODEPeakDataProvider ): - """ - Provides data from an ENCODEPeak dataset indexed via tabix. - """ - - def get_filters( self ): - """ - Returns filters for dataset. - """ - # HACK: first 8 fields are for drawing, so start filter column index at 9. - filter_col = 8 - filters = [] - filters.append( { 'name': 'Score', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c6' } ) - filter_col += 1 - filters.append( { 'name': 'Signal Value', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c7' } ) - filter_col += 1 - filters.append( { 'name': 'pValue', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c8' } ) - filter_col += 1 - filters.append( { 'name': 'qValue', - 'type': 'number', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c9' } ) - return filters - -# -# -- ChromatinInteraction data providers -- -# -class ChromatinInteractionsDataProvider( TracksDataProvider ): - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): - """ - Provides - """ - - rval = [] - message = None - for count, line in enumerate( iterator ): - if count < start_val: - continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "interactions" ) - break - - feature = line.split() - length = len( feature ) - - s1 = int( feature[1] ), - e1 = int( feature[2] ), - c = feature[3], - s2 = int( feature[4] ), - e2 = int( feature[5] ), - v = float( feature[6] ) - - # Feature initialization. - payload = [ - # GUID is just a hash of the line - hash( line ), - # Add start1, end1, chr2, start2, end2, value. - s1, e1, c, s2, e2, v - ] - - rval.append( payload ) - - return { 'data': rval, 'message': message } - - def get_default_max_vals( self ): - return 50000; - -class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): - def get_iterator( self, chrom, start, end ): - """ - """ - # Modify start as needed to get earlier interactions with start region. - start = max( 0, int( start) - 1000000 ) - def filter( iter ): - for line in iter: - feature = line.split() - s1 = int( feature[1] ), - e1 = int( feature[2] ), - c = feature[3] - s2 = int( feature[4] ), - e2 = int( feature[5] ), - if ( ( c == chrom ) and ( s1 < end and e1 > start ) and ( s2 < end and e2 > start ) ): - yield line - return filter( TabixDataProvider.get_iterator( self, chrom, start, end ) ) - -# -# -- Helper methods. -- -# - -# Mapping from dataset type name to a class that can fetch data from a file of that -# type. First key is converted dataset type; if result is another dict, second key -# is original dataset type. TODO: This needs to be more flexible. -dataset_type_name_to_data_provider = { - "tabix": { - Vcf: VcfTabixDataProvider, - Bed: BedTabixDataProvider, - Gtf: GtfTabixDataProvider, - ENCODEPeak: ENCODEPeakTabixDataProvider, - Interval: IntervalTabixDataProvider, - ChromatinInteractions: ChromatinInteractionsTabixDataProvider, - "default" : TabixDataProvider - }, - "interval_index": IntervalIndexDataProvider, - "bai": BamDataProvider, - "bam": SamDataProvider, - "summary_tree": SummaryTreeDataProvider, - "bigwig": BigWigDataProvider, - "bigbed": BigBedDataProvider -} - -def get_data_provider( name=None, original_dataset=None ): - """ - Returns data provider class by name and/or original dataset. - """ - data_provider = None - if name: - value = dataset_type_name_to_data_provider[ name ] - if isinstance( value, dict ): - # Get converter by dataset extension; if there is no data provider, - # get the default. - data_provider = value.get( original_dataset.datatype.__class__, value.get( "default" ) ) - else: - data_provider = value - elif original_dataset: - # Look up data provider from datatype's informaton. - try: - # Get data provider mapping and data provider for 'data'. If - # provider available, use it; otherwise use generic provider. - _ , data_provider_mapping = original_dataset.datatype.get_track_type() - if 'data_standalone' in data_provider_mapping: - data_provider_name = data_provider_mapping[ 'data_standalone' ] - else: - data_provider_name = data_provider_mapping[ 'data' ] - if data_provider_name: - data_provider = get_data_provider( name=data_provider_name, original_dataset=original_dataset ) - else: - data_provider = TracksDataProvider - except: - pass - return data_provider - -def package_gff_feature( feature, no_detail=False, filter_cols=[] ): - """ Package a GFF feature in an array for data providers. """ - feature = convert_gff_coords_to_bed( feature ) - - # No detail means only start, end. - if no_detail: - return [ feature.start, feature.end ] - - # Return full feature. - payload = [ feature.start, - feature.end, - feature.name(), - feature.strand, - # No notion of thick start, end in GFF, so make everything - # thick. - feature.start, - feature.end - ] - - # HACK: ignore interval with name 'transcript' from feature. - # Cufflinks puts this interval in each of its transcripts, - # and they mess up trackster by covering the feature's blocks. - # This interval will always be a feature's first interval, - # and the GFF's third column is its feature name. - feature_intervals = feature.intervals - if feature.intervals[0].fields[2] == 'transcript': - feature_intervals = feature.intervals[1:] - # Add blocks. - block_sizes = [ (interval.end - interval.start ) for interval in feature_intervals ] - block_starts = [ ( interval.start - feature.start ) for interval in feature_intervals ] - blocks = zip( block_sizes, block_starts ) - payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) - - # Add filter data to payload. - for col in filter_cols: - if col == "Score": - if feature.score == 'nan': - payload.append( feature.score ) - else: - try: - f = float( feature.score ) - payload.append( f ) - except: - payload.append( feature.score ) - elif col in feature.attributes: - if feature.attributes[col] == 'nan': - payload.append( feature.attributes[col] ) - else: - try: - f = float( feature.attributes[col] ) - payload.append( f ) - except: - payload.append( feature.attributes[col] ) - else: - # Dummy value. - payload.append( 0 ) - return payload diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ /dev/null @@ -1,111 +0,0 @@ -''' -Summary tree data structure for feature aggregation across large genomic regions. -''' - -import sys, os -import cPickle - -# TODO: What are the performance implications of setting min level to 1? Data -# structure size and/or query speed? It would be nice to have level 1 data -# so that client does not have to compute it. -MIN_LEVEL = 2 - -class SummaryTree: - def __init__( self, block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30 ): - self.chrom_blocks = {} - self.levels = levels - self.draw_cutoff = draw_cutoff - self.detail_cutoff = detail_cutoff - self.block_size = block_size - self.chrom_stats = {} - - def find_block( self, num, level ): - """ Returns block that num is in for level. """ - return ( num / self.block_size ** level ) - - def insert_range( self, chrom, start, end ): - """ Inserts a feature at chrom:start-end into the tree. """ - - # Get or set up chrom blocks. - if chrom in self.chrom_blocks: - blocks = self.chrom_blocks[ chrom ] - else: - blocks = self.chrom_blocks[ chrom ] = {} - self.chrom_stats[ chrom ] = {} - for level in range( MIN_LEVEL, self.levels + 1 ): - blocks[ level ] = {} - - # Insert feature into all matching blocks at all levels. - for level in range( MIN_LEVEL, self.levels + 1 ): - block_level = blocks[ level ] - starting_block = self.find_block( start, level ) - ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block + 1 ): - if block in block_level: - block_level[ block ] += 1 - else: - block_level[ block ] = 1 - - def finish( self ): - """ Compute stats for levels. """ - - for chrom, blocks in self.chrom_blocks.iteritems(): - for level in range( self.levels, MIN_LEVEL - 1, -1 ): - # Set level's stats. - max_val = max( blocks[ level ].values() ) - self.chrom_stats[ chrom ][ level ] = {} - self.chrom_stats[ chrom ][ level ][ "delta" ] = self.block_size ** level - self.chrom_stats[ chrom ][ level ][ "max" ] = max_val - self.chrom_stats[ chrom ][ level ][ "avg" ] = float( max_val ) / len( blocks[ level ] ) - - self.chrom_blocks[ chrom ] = dict( [ ( key, value ) for key, value in blocks.iteritems() ] ) - - def query( self, chrom, start, end, level, draw_cutoff=None, detail_cutoff=None ): - """ Queries tree for data. """ - - # Set cutoffs to self's attributes if not defined. - if draw_cutoff != 0: - draw_cutoff = self.draw_cutoff - if detail_cutoff != 0: - detail_cutoff = self.detail_cutoff - - # Get data. - if chrom in self.chrom_blocks: - stats = self.chrom_stats[ chrom ] - - # For backwards compatibility: - if "detail_level" in stats and level <= stats[ "detail_level" ]: - return "detail" - elif "draw_level" in stats and level <= stats[ "draw_level" ]: - return "draw" - - # If below draw, detail level, return string to denote this. - max = stats[ level ][ "max" ] - if max < detail_cutoff: - return "detail" - if max < draw_cutoff: - return "draw" - - # Return block data. - blocks = self.chrom_blocks[ chrom ] - results = [] - multiplier = self.block_size ** level - starting_block = self.find_block( start, level ) - ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block + 1 ): - val = 0 - if block in blocks[ level ]: - val = blocks[ level ][ block ] - results.append( ( block * multiplier, val ) ) - return results - - return None - - def write( self, filename ): - """ Writes tree to file. """ - self.finish() - cPickle.dump( self, open( filename, 'wb' ), 2 ) - -def summary_tree_from_file( filename ): - return cPickle.load( open( filename, "rb" ) ) - diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/visualization/tracks/visual_analytics.py --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ /dev/null @@ -1,80 +0,0 @@ -import urllib - -from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter -from galaxy.tools.parameters.dynamic_options import DynamicOptions - -class TracksterConfig: - """ Trackster configuration encapsulation. """ - - def __init__( self, actions ): - self.actions = actions - - @staticmethod - def parse( root ): - actions = [] - for action_elt in root.findall( "action" ): - actions.append( SetParamAction.parse( action_elt ) ) - return TracksterConfig( actions ) - -class SetParamAction: - """ Set parameter action. """ - - def __init__( self, name, output_name ): - self.name = name - self.output_name = output_name - - @staticmethod - def parse( elt ): - """ Parse action from element. """ - return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) - -def get_dataset_job( hda ): - # Get dataset's job. - job = None - for job_output_assoc in hda.creating_job_associations: - job = job_output_assoc.job - break - return job - -def get_tool_def( trans, hda ): - """ Returns definition of an interactive tool for an HDA. """ - - job = get_dataset_job( hda ) - # TODO: could use this assertion to provide more information. - # assert job is not None, 'Requested job has not been loaded.' - if not job: - return None - tool = trans.app.toolbox.get_tool( job.tool_id ) - # TODO: could use this assertion to provide more information. - # assert tool is not None, 'Requested tool has not been loaded.' - if not tool: - return None - - # Tool must have a Trackster configuration. - if not tool.trackster_conf: - return None - - # Get list of tool parameters that can be interactively modified. - tool_params = [] - tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) - tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) - for name, input in tool.inputs.items(): - if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter: - param_dict = { 'name' : name, 'label' : input.label, \ - 'value' : tool_param_values.get( name, input.value ), \ - 'type' : 'number', 'init_value' : input.value, - 'html' : urllib.quote( input.get_html() ) } - if input.min: - param_dict['min'] = input.min - if input.max: - param_dict['max'] = input.max - tool_params.append( param_dict ) - elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: - tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ - 'value' : tool_param_values.get( name, None ), \ - 'html' : urllib.quote( input.get_html() ) } ) - - # If tool has parameters that can be interactively modified, return tool. - if len( tool_params ) != 0: - return { 'name' : tool.name, 'params' : tool_params } - return None \ No newline at end of file diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -1,9 +1,9 @@ from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, messages, get_highest_priority_msg -from galaxy.visualization.tracks.visual_analytics import get_dataset_job +from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string -from galaxy.visualization.tracks.data_providers import * +from galaxy.visualization.genome.data_providers import * class ToolsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin ): """ diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -14,8 +14,8 @@ from galaxy.web.framework import simplejson from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField from galaxy.web.form_builder import WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field -from galaxy.visualization.tracks.data_providers import get_data_provider -from galaxy.visualization.tracks.visual_analytics import get_tool_def +from galaxy.visualization.genome.data_providers import get_data_provider +from galaxy.visualization.genome.visual_analytics import get_tool_def from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * diff -r 586506caaad452c533493e5db8f26a362fb61280 -r 6805c477d61601ad304577ad6603dab71b22df24 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -14,9 +14,9 @@ from galaxy.util.bunch import Bunch from galaxy.datatypes.interval import Gff, Bed from galaxy.model import NoConverterException, ConverterDependencyException -from galaxy.visualization.tracks.data_providers import * +from galaxy.visualization.genome.data_providers import * from galaxy.visualization.genomes import decode_dbkey, Genomes -from galaxy.visualization.tracks.visual_analytics import get_dataset_job +from galaxy.visualization.genome.visual_analytics import get_dataset_job class NameColumn( grids.TextColumn ): https://bitbucket.org/galaxy/galaxy-central/changeset/40f6d9738623/ changeset: 40f6d9738623 user: jgoecks date: 2012-09-14 18:35:20 summary: Begin process of migrating Phyloviz data provider to data provider framework. affected #: 2 files diff -r 6805c477d61601ad304577ad6603dab71b22df24 -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -1,13 +1,17 @@ from newickparser import Newick_Parser from nexusparser import Nexus_Parser from phyloxmlparser import Phyloxml_Parser +from galaxy.visualization.data_providers import BaseDataProvider -class Phyloviz_DataProvider(object): +# TODO: bring this class into line with BaseDataProvider by +# using BaseDataProvider.init() and providing original dataset +# and then reading from dataset rather than filepath. +class Phyloviz_DataProvider( BaseDataProvider ): - def __init__(self): + def __init__( self ): pass - def parseFile(self, filepath, fileExt): + def get_data( self, filepath, fileExt ): """returns [trees], meta Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus """ diff -r 6805c477d61601ad304577ad6603dab71b22df24 -r 40f6d9738623ee2b2c7ff1f5a82fe09c7628d766 lib/galaxy/web/controllers/phyloviz.py --- a/lib/galaxy/web/controllers/phyloviz.py +++ b/lib/galaxy/web/controllers/phyloviz.py @@ -84,7 +84,7 @@ else: try: pd = Phyloviz_DataProvider() - json, config = pd.parseFile(filepath, fileExt) + json, config = pd.get_data(filepath, fileExt) json = json[treeIndex] except Exception: pass 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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