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galaxy-dist commit e6e68c67dd97: Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288106620 14400 # Node ID e6e68c67dd9759154876546662f59ee280b78a34 # Parent 677bcc65f74f5a460277f089d0cdebf170f02831 Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported. Currently, there are limitations to this functionality; these will be fixed going forward. These limitations are: -history archives can be imported only via URL, not file; -histories must be shared in order for them to be importable via archive; -tags are not currently imported; -reproducibility is limited as parameters for imported jobs are not always recovered and set. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -79,7 +79,7 @@ class HistoryListGrid( grids.Grid ): def get_current_item( self, trans, **kwargs ): return trans.get_history() def apply_query_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False ) + return query.filter_by( user=trans.user, purged=False, importing=False ) class SharedHistoryListGrid( grids.Grid ): # Custom column types @@ -465,212 +465,40 @@ class HistoryController( BaseController, trans.sa_session.flush() return new_annotation - def import_archive( self, trans, archived_history=None, gzip=True ): - """ Import a history. """ + @web.expose + # TODO: Remove require_login when users are warned that, if they are not + # logged in, this will remove their current history. + @web.require_login( "use Galaxy histories" ) + def import_archive( self, trans, **kwargs ): + """ Import a history from a file archive. """ - def file_in_dir( file_path, a_dir ): - """ Returns true if file is in directory. """ - abs_file_path = os.path.abspath( file_path ) - return os.path.split( abs_file_path )[0] == a_dir + # Set archive source and type. + archive_file = kwargs.get( 'archive_file', None ) + archive_url = kwargs.get( 'archive_url', None ) + archive_source = None + if archive_file: + archive_source = archive_file + archive_type = 'file' + elif archive_url: + archive_source = archive_url + archive_type = 'url' - if archived_history is not None: - try: - history_archive_file = tarfile.open( archived_history.file.name ) - - # Unpack archive in temporary directory. - temp_output_dir = tempfile.mkdtemp() - history_archive_file.extractall( path=temp_output_dir ) - history_archive_file.close() - - # - # Create history. - # - history_attr_file_name = os.path.join( temp_output_dir, 'history_attrs.txt') - if not file_in_dir( history_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for history attributes file: %s" % history_attr_file_name ) - history_attr_in = open( history_attr_file_name, 'rb' ) - history_attr_str = '' - buffsize = 1048576 - try: - while True: - history_attr_str += history_attr_in.read( buffsize ) - if not history_attr_str or len( history_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - history_attr_in.close() - history_attrs = from_json_string( history_attr_str ) - - # Create history. - new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) - trans.sa_session.add( new_history ) - - new_history.hid_counter = history_attrs['hid_counter'] - new_history.genome_build = history_attrs['genome_build'] - trans.sa_session.flush() - - # Builds a tag string for a tag, value pair. - def get_tag_str( tag, value ): - if not value: - return tag - else: - return tag + ":" + value - - # Add annotation, tags. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), new_history, history_attrs[ 'annotation' ] ) - for tag, value in history_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) - - # - # Create datasets. - # - datasets_attrs_file_name = os.path.join( temp_output_dir, 'datasets_attrs.txt') - if not file_in_dir( datasets_attrs_file_name, temp_output_dir ): - raise Exception( "Invalid location for dataset attributes file: %s" % datasets_attrs_file_name ) - datasets_attr_in = open( datasets_attrs_file_name, 'rb' ) - datasets_attr_str = '' - buffsize = 1048576 - try: - while True: - datasets_attr_str += datasets_attr_in.read( buffsize ) - if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) - - # Create datasets. - for dataset_attrs in datasets_attrs: - metadata = dataset_attrs['metadata'] - - # Create dataset and HDA. - hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), - extension = dataset_attrs['extension'], - info = dataset_attrs['info'].encode( 'utf-8' ), - blurb = dataset_attrs['blurb'], - peek = dataset_attrs['peek'], - designation = dataset_attrs['designation'], - visible = dataset_attrs['visible'], - dbkey = metadata['dbkey'], - metadata = metadata, - history = new_history, - create_dataset = True, - sa_session = trans.sa_session ) - hda.state = hda.states.OK - trans.sa_session.add( hda ) - trans.sa_session.flush() - new_history.add_dataset( hda, genome_build = None ) - hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. - permissions = trans.app.security_agent.history_get_default_permissions( new_history ) - trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - trans.sa_session.flush() - - # Do security check and copy dataset data. - temp_dataset_file_name = os.path.join( temp_output_dir, dataset_attrs['file_name'] ) - if not file_in_dir( temp_dataset_file_name, os.path.join( temp_output_dir, "datasets" ) ): - raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) - shutil.move( temp_dataset_file_name, hda.file_name ) - - # Set tags, annotations. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), hda, dataset_attrs[ 'annotation' ] ) - for tag, value in dataset_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) - trans.sa_session.flush() - - # - # Create jobs. - # - - # Read jobs attributes. - jobs_attr_file_name = os.path.join( temp_output_dir, 'jobs_attrs.txt') - if not file_in_dir( jobs_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for jobs' attributes file: %s" % jobs_attr_file_name ) - jobs_attr_in = open( jobs_attr_file_name, 'rb' ) - jobs_attr_str = '' - buffsize = 1048576 - try: - while True: - jobs_attr_str += jobs_attr_in.read( buffsize ) - if not jobs_attr_str or len( jobs_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - jobs_attr_in.close() - - # Decode jobs attributes. - def as_hda( obj_dct ): - """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by - the encoded object. This only works because HDAs are created above. """ - if obj_dct.get( '__HistoryDatasetAssociation__', False ): - return trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=obj_dct['hid'] ).first() - return obj_dct - jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) - - # Create each job. - for job_attrs in jobs_attrs: - imported_job = model.Job() - imported_job.user = trans.user - imported_job.session = trans.get_galaxy_session().id - imported_job.history = new_history - imported_job.tool_id = job_attrs[ 'tool_id' ] - imported_job.tool_version = job_attrs[ 'tool_version' ] - imported_job.set_state( job_attrs[ 'state' ] ) - imported_job.imported = True - trans.sa_session.add( imported_job ) - trans.sa_session.flush() - - class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): - """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ - def default( self, obj ): - """ Encode an HDA, default encoding for everything else. """ - if isinstance( obj, model.HistoryDatasetAssociation ): - return obj.id - return simplejson.JSONEncoder.default( self, obj ) + # If no source to create archive from, show form to upload archive or specify URL. + if not archive_source: + return trans.show_form( + web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) \ + .add_input( "text", "Archived History URL", "archive_url", value="", error=None ) + # TODO: add support for importing via a file. + #.add_input( "file", "Archived History File", "archive_file", value=None, error=None ) + ) - # Set parameters. May be useful to look at metadata.py for creating parameters. - # TODO: there may be a better way to set parameters, e.g.: - # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): - # job.add_parameter( name, value ) - # to make this work, we'd need to flesh out the HDA objects. The code below is - # relatively similar. - for name, value in job_attrs[ 'params' ].items(): - # Transform parameter values when necessary. - if isinstance( value, model.HistoryDatasetAssociation ): - # HDA input: use hid to find input. - input_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=value.hid ).first() - value = input_hda.id - #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) - imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) - - # TODO: Connect jobs to input datasets. - - # Connect jobs to output datasets. - for output_hid in job_attrs[ 'output_datasets' ]: - #print "%s job has output dataset %i" % (imported_job.id, output_hid) - output_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=output_hid ).first() - if output_hda: - imported_job.add_output_dataset( output_hda.name, output_hda ) - trans.sa_session.flush() - - # Cleanup. - if os.path.exists( temp_output_dir ): - shutil.rmtree( temp_output_dir ) - - return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) - except Exception, e: - return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) - - return trans.show_form( - web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) - .add_input( "file", "Archived History File", "archived_history", value=None, error=None ) - ) - + # Run job to do import. + history_imp_tool = trans.app.toolbox.tools_by_id[ '__IMPORT_HISTORY__' ] + incoming = { '__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type } + history_imp_tool.execute( trans, incoming=incoming ) + return trans.show_message( "Importing history from '%s'. \ + This history will be visible when the import is complete" % archive_source ) + @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): """ Export a history to an archive. """ --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -608,6 +608,7 @@ class JobWrapper( object ): if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) + galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) except: log.exception( "Unable to cleanup job %d" % self.job_id ) --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -227,7 +227,13 @@ class JobExportHistoryArchive( object ): self.history_attrs_filename = history_attrs_filename self.datasets_attrs_filename = datasets_attrs_filename self.jobs_attrs_filename = jobs_attrs_filename - + +class JobImportHistoryArchive( object ): + def __init__( self, job=None, history=None, archive_dir=None ): + self.job = job + self.history = history + self.archive_dir=archive_dir + class Group( object ): def __init__( self, name = None ): self.name = name @@ -244,6 +250,7 @@ class History( object, UsesAnnotations ) self.name = name or "Unnamed history" self.deleted = False self.purged = False + self.importing = False self.genome_build = None self.published = False # Relationships --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -2,7 +2,7 @@ import os, shutil, logging, tempfile, si from galaxy import model from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.json import to_json_string +from galaxy.util.json import * from galaxy.web.base.controller import UsesHistory log = logging.getLogger(__name__) @@ -26,21 +26,252 @@ def load_history_imp_exp_tools( toolbox </outputs></tool> """ + + # Load export tool. tmp_name = tempfile.NamedTemporaryFile() tmp_name.write( tool_xml_text ) tmp_name.flush() history_exp_tool = toolbox.load_tool( tmp_name.name ) toolbox.tools_by_id[ history_exp_tool.id ] = history_exp_tool log.debug( "Loaded history export tool: %s", history_exp_tool.id ) + + # Load import tool. + tool_xml = os.path.join( os.getcwd(), "lib/galaxy/tools/imp_exp/imp_history_from_archive.xml" ) + history_imp_tool = toolbox.load_tool( tool_xml ) + toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool + log.debug( "Loaded history import tool: %s", history_imp_tool.id ) + +class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): + """ + Class provides support for performing jobs that import a history from + an archive. + """ + def __init__( self, job_id ): + self.job_id = job_id + + def cleanup_after_job( self, db_session ): + """ Set history, datasets, and jobs' attributes and clean up archive directory. """ + + # + # Helper methods. + # + + def file_in_dir( file_path, a_dir ): + """ Returns true if file is in directory. """ + abs_file_path = os.path.abspath( file_path ) + return os.path.split( abs_file_path )[0] == a_dir + + def read_file_contents( file_path ): + """ Read contents of a file. """ + fp = open( file_path, 'rb' ) + buffsize = 1048576 + file_contents = '' + try: + while True: + file_contents += fp.read( buffsize ) + if not file_contents or len( file_contents ) % buffsize != 0: + break + except OverflowError: + pass + fp.close() + return file_contents + + def get_tag_str( tag, value ): + """ Builds a tag string for a tag, value pair. """ + if not value: + return tag + else: + return tag + ":" + value + + # + # Import history. + # + + jiha = db_session.query( model.JobImportHistoryArchive ).filter_by( job_id=self.job_id ).first() + if jiha: + try: + archive_dir = jiha.archive_dir + user = jiha.job.user + + # + # Create history. + # + history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt') + history_attr_str = read_file_contents( history_attr_file_name ) + history_attrs = from_json_string( history_attr_str ) + + # Create history. + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \ + user=user ) + new_history.importing = True + new_history.hid_counter = history_attrs['hid_counter'] + new_history.genome_build = history_attrs['genome_build'] + db_session.add( new_history ) + jiha.history = new_history + db_session.flush() + + # Add annotation, tags. + if user: + self.add_item_annotation( db_session, user, new_history, history_attrs[ 'annotation' ] ) + """ + TODO: figure out to how add tags to item. + for tag, value in history_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) + """ + + # + # Create datasets. + # + datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt') + datasets_attr_str = read_file_contents( datasets_attrs_file_name ) + datasets_attrs = from_json_string( datasets_attr_str ) + + # Get counts of how often each dataset file is used; a file can + # be linked to multiple dataset objects (HDAs). + datasets_usage_counts = {} + for dataset_attrs in datasets_attrs: + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if ( temp_dataset_file_name not in datasets_usage_counts ): + datasets_usage_counts[ temp_dataset_file_name ] = 0 + datasets_usage_counts[ temp_dataset_file_name ] += 1 + + # Create datasets. + for dataset_attrs in datasets_attrs: + metadata = dataset_attrs['metadata'] + + # Create dataset and HDA. + hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), + extension = dataset_attrs['extension'], + info = dataset_attrs['info'].encode( 'utf-8' ), + blurb = dataset_attrs['blurb'], + peek = dataset_attrs['peek'], + designation = dataset_attrs['designation'], + visible = dataset_attrs['visible'], + dbkey = metadata['dbkey'], + metadata = metadata, + history = new_history, + create_dataset = True, + sa_session = db_session ) + hda.state = hda.states.OK + db_session.add( hda ) + db_session.flush() + new_history.add_dataset( hda, genome_build = None ) + hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. + # TODO: Is there a way to recover permissions? Is this needed? + #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) + #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + db_session.flush() + + # Do security check and move/copy dataset data. + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if not file_in_dir( temp_dataset_file_name, os.path.join( archive_dir, "datasets" ) ): + raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) + if datasets_usage_counts[ temp_dataset_file_name ] == 1: + shutil.move( temp_dataset_file_name, hda.file_name ) + else: + datasets_usage_counts[ temp_dataset_file_name ] -= 1 + shutil.copyfile( temp_dataset_file_name, hda.file_name ) + + # Set tags, annotations. + if user: + self.add_item_annotation( db_session, user, hda, dataset_attrs[ 'annotation' ] ) + # TODO: Set tags. + """ + for tag, value in dataset_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) + db_session.flush() + """ + + # + # Create jobs. + # + + # Read jobs attributes. + jobs_attr_file_name = os.path.join( archive_dir, 'jobs_attrs.txt') + jobs_attr_str = read_file_contents( jobs_attr_file_name ) + + # Decode jobs attributes. + def as_hda( obj_dct ): + """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by + the encoded object. This only works because HDAs are created above. """ + if obj_dct.get( '__HistoryDatasetAssociation__', False ): + return db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=obj_dct['hid'] ).first() + return obj_dct + jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) + + # Create each job. + for job_attrs in jobs_attrs: + imported_job = model.Job() + imported_job.user = user + # TODO: set session? + # imported_job.session = trans.get_galaxy_session().id + imported_job.history = new_history + imported_job.tool_id = job_attrs[ 'tool_id' ] + imported_job.tool_version = job_attrs[ 'tool_version' ] + imported_job.set_state( job_attrs[ 'state' ] ) + imported_job.imported = True + db_session.add( imported_job ) + db_session.flush() + + class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): + """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ + def default( self, obj ): + """ Encode an HDA, default encoding for everything else. """ + if isinstance( obj, model.HistoryDatasetAssociation ): + return obj.id + return simplejson.JSONEncoder.default( self, obj ) + + # Set parameters. May be useful to look at metadata.py for creating parameters. + # TODO: there may be a better way to set parameters, e.g.: + # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + # job.add_parameter( name, value ) + # to make this work, we'd need to flesh out the HDA objects. The code below is + # relatively similar. + for name, value in job_attrs[ 'params' ].items(): + # Transform parameter values when necessary. + if isinstance( value, model.HistoryDatasetAssociation ): + # HDA input: use hid to find input. + input_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=value.hid ).first() + value = input_hda.id + #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) + imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) + + # TODO: Connect jobs to input datasets. + + # Connect jobs to output datasets. + for output_hid in job_attrs[ 'output_datasets' ]: + #print "%s job has output dataset %i" % (imported_job.id, output_hid) + output_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=output_hid ).first() + if output_hda: + imported_job.add_output_dataset( output_hda.name, output_hda ) + + # Done importing. + new_history.importing = False + + db_session.flush() + + # Cleanup. + if os.path.exists( archive_dir ): + shutil.rmtree( archive_dir ) + except Exception, e: + jiha.job.stderr += "Error cleaning up history import job: %s" % e + db_session.flush() class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): - """ Class provides support for performing jobs that export a history to an archive. """ + """ + Class provides support for performing jobs that export a history to an + archive. + """ def __init__( self, job_id ): self.job_id = job_id # TODO: should use db_session rather than trans in this method. def setup_job( self, trans, jeha, include_hidden=False, include_deleted=False ): - # jeha = job_export_history_archive for the job. """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha object, and returns a command line for running the job. The command line --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1904,6 +1904,9 @@ class SetMetadataTool( Tool ): class ExportHistoryTool( Tool ): tool_type = 'export_history' + +class ImportHistoryTool( Tool ): + tool_type = 'import_history' # Populate tool_type to ToolClass mappings tool_types = {} --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -1,10 +1,56 @@ +import tempfile from __init__ import ToolAction from galaxy.util.odict import odict -from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper +from galaxy.tools.imp_exp import * import logging log = logging.getLogger( __name__ ) +class ImportHistoryToolAction( ToolAction ): + """Tool action used for importing a history to an archive. """ + + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True ): + # + # Create job. + # + job = trans.app.model.Job() + job.session_id = trans.get_galaxy_session().id + job.history_id = trans.history.id + job.tool_id = tool.id + job.user_id = trans.user.id + start_job_state = job.state #should be job.states.NEW + job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id are available + + # + # Setup job and job wrapper. + # + + # Add association for keeping track of job, history relationship. + archive_dir = tempfile.mkdtemp() + jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) + trans.sa_session.add( jiha ) + job_wrapper = JobImportHistoryArchiveWrapper( job ) + + # + # Add parameters to job_parameter table. + # + + # Set additional parameters. + incoming[ '__DEST_DIR__' ] = jiha.archive_dir + for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + job.add_parameter( name, value ) + + job.state = start_job_state #job inputs have been configured, restore initial job state + trans.sa_session.flush() + + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + + return job, odict() + class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ @@ -30,6 +76,7 @@ class ExportHistoryToolAction( ToolActio job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add( job ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml @@ -0,0 +1,10 @@ +<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history"> + <type class="ImportHistoryTool" module="galaxy.tools"/> + <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/> + <command interpreter="python">unpack_tar_gz_archive.py $__ARCHIVE_SOURCE__ $__DEST_DIR__ --$__ARCHIVE_TYPE__</command> + <inputs> + <param name="__ARCHIVE_SOURCE__" type="text"/> + <param name="__ARCHIVE_TYPE__" type="text"/> + <param name="__DEST_DIR__" type="text"/> + </inputs> +</tool> --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -53,10 +53,10 @@ galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } }, - ##"Other Actions": null, - ##"Import from File": function() { - ## galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; - ##} + "Other Actions": null, + "Import from File": function() { + galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; + } }); // Init tool options. --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -77,6 +77,7 @@ History.table = Table( "history", metada Column( "hid_counter", Integer, default=1 ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), + Column( "importing", Boolean, index=True, default=False ), Column( "genome_build", TrimmedString( 40 ) ), Column( "importable", Boolean, default=False ), Column( "slug", TEXT, index=True ), @@ -384,6 +385,13 @@ JobExportHistoryArchive.table = Table( " Column( "jobs_attrs_filename", TEXT ) ) +JobImportHistoryArchive.table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + PostJobAction.table = Table("post_job_action", metadata, Column("id", Integer, primary_key=True), Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), @@ -1220,6 +1228,9 @@ assign_mapper( context, JobExportHistory properties=dict( job = relation( Job ), history = relation( History ), dataset = relation( Dataset ) ) ) + +assign_mapper( context, JobImportHistoryArchive, JobImportHistoryArchive.table, + properties=dict( job = relation( Job ), history = relation( History ) ) ) assign_mapper( context, PostJobAction, PostJobAction.table, properties=dict(workflow_step = relation( WorkflowStep, backref='post_job_actions', primaryjoin=(WorkflowStep.table.c.id == PostJobAction.table.c.workflow_step_id)))) --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0060_history_archive_import.py @@ -0,0 +1,72 @@ +""" +Migration script to create column and table for importing histories from +file archives. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Columns to add. + +importing_col = Column( "importing", Boolean, index=True, default=False ) +ldda_parent_col = Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ) + +# Table to add. + +JobImportHistoryArchive_table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Add column to history table and initialize. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col.create( History_table ) + assert importing_col is History_table.c.importing + + # Initialize column to false. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE history SET importing=%s" % default_false ) + except Exception, e: + print str(e) + log.debug( "Adding column 'importing' to history table failed: %s" % str( e ) ) + + # Create job_import_history_archive table. + try: + JobImportHistoryArchive_table.create() + except Exception, e: + log.debug( "Creating job_import_history_archive table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop 'importing' column from history table. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col = History_table.c.importing + importing_col.drop() + except Exception, e: + log.debug( "Dropping column 'importing' from history table failed: %s" % ( str( e ) ) ) + + # Drop job_import_history_archive table. + try: + JobImportHistoryArchive_table.drop() + except Exception, e: + log.debug( "Dropping job_import_history_archive table failed: %s" % str( e ) ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" +Unpack a tar or tar.gz archive into a directory. + +usage: %prog archive_source dest_dir + --[url|file] source type, either a URL or a file. +""" + +import sys, optparse, tarfile, tempfile, urllib2, math + +# Set max size of archive/file that will be handled to be 100 GB. This is +# arbitrary and should be adjusted as needed. +MAX_SIZE = 100 * math.pow( 2, 30 ) + +def url_to_file( url, dest_file ): + """ + Transfer a file from a remote URL to a temporary file. + """ + try: + url_reader = urllib2.urlopen( url ) + CHUNK = 10 * 1024 # 10k + total = 0 + fp = open( dest_file, 'wb') + while True: + chunk = url_reader.read( CHUNK ) + if not chunk: + break + fp.write( chunk ) + total += CHUNK + if total > MAX_SIZE: + break + fp.close() + return dest_file + except Exception, e: + print "Exception getting file from URL: %s" % e, sys.stderr + return None + +def unpack_archive( archive_file, dest_dir ): + """ + Unpack a tar and/or gzipped archive into a destination directory. + """ + archive_fp = tarfile.open( archive_file, mode='r:gz' ) + archive_fp.extractall( path=dest_dir ) + archive_fp.close() + +if __name__ == "__main__": + # Parse command line. + parser = optparse.OptionParser() + parser.add_option( '-U', '--url', dest='is_url', action="store_true", help='Source is a URL.' ) + parser.add_option( '-F', '--file', dest='is_file', action="store_true", help='Source is a URL.' ) + (options, args) = parser.parse_args() + is_url = bool( options.is_url ) + is_file = bool( options.is_file ) + archive_source, dest_dir = args + + try: + # Get archive from URL. + if is_url: + archive_file = url_to_file( archive_source, tempfile.NamedTemporaryFile( dir=dest_dir ).name ) + elif is_file: + archive_file = archive_source + + # Unpack archive. + unpack_archive( archive_file, dest_dir ) + except Exception, e: + print "Error unpacking tar/gz archive: %s" % e, sys.stderr

1 0

galaxy-dist commit 314f8a5d3823: Complete functional test for cuffcompare.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288119881 14400 # Node ID 314f8a5d38237c3f1fafccb522ee45aebfa8464f # Parent 379d0701f198964fb964c3834cce7414cbc8f888 Complete functional test for cuffcompare. --- /dev/null +++ b/test-data/cuffcompare_out1.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out2.refmap @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code cuff_id_list +Xkr4 Xkr4 c CUFF.13|CUFF.13.1 --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -81,16 +81,15 @@ <param name="use_ref_annotation" value="Yes"/><param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="ignore_nonoverlapping_reference" value="Yes"/> - ## HACK: need to specify output name and it needs to work (right now it uses the final output file) - <output name="XXXX" file="cuffcompare_out6.tracking"/> -  + <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/><output name="input1_tmap" file="cuffcompare_out1.tmap"/><output name="input1_refmap" file="cuffcompare_out2.refmap"/><output name="input2_tmap" file="cuffcompare_out3.tmap"/><output name="input2_refmap" file="cuffcompare_out4.refmap"/> - <output name="transcripts_accuracy" file="cuffcompare_out7.txt"/> - --> + <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> + <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/></test></tests> --- /dev/null +++ b/test-data/cuffcompare_out4.refmap @@ -0,0 +1,1 @@ +ref_gene_id ref_id class_code cuff_id_list --- /dev/null +++ b/test-data/cuffcompare_out3.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out7.txt @@ -0,0 +1,50 @@ +# Cuffcompare v0.9.1 | Command line was: +#cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) + +#= Summary for dataset: cuffcompare_in1.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + +#= Summary for dataset: cuffcompare_in2.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + + Total union super-loci across all input datasets: 87 + (0 multi-transcript, ~1.1 transcripts per locus)

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galaxy-dist commit 262c91e3a2ea: Fix 'Select All' button in tool form due to a typo. Values next to checkboxes can now be clicked to check the corresponding box.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1288117861 14400 # Node ID 262c91e3a2ea7d11d65875ec2af42526c92b7123 # Parent bdcbd7ab6e7fe0a6ed869d8a682660c0cebb7658 Fix 'Select All' button in tool form due to a typo. Values next to checkboxes can now be clicked to check the corresponding box. --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -41,6 +41,7 @@ div.form-row-error{background:#FFCCCC;} div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;} div.form-row-input{float:left;width:300px;} div.form-row-input > input{max-width:300px;} +div.form-row-input label{font-weight:normal;display:inline;} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} select,input,textarea{font:inherit;font-size:115%;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -24,7 +24,7 @@ from galaxy.util.expressions import Expr file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); // create a new hidden field which stores the filename and has the original name of the file input var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type", "hidden", "value": file_value, "name": file_name } ); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); file.after(new_file_input); } }); @@ -36,14 +36,10 @@ from galaxy.util.expressions import Expr location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); } %endif -function checkUncheckAll( name, check ) -{ - if ( check == 0 ) - { +function checkUncheckAll( name, check ) { + if (!check) { $("input[name=" + name + "][type='checkbox']").attr('checked', false); - } - else - { + } else { $("input[name=" + name + "][type='checkbox']").attr('checked', true ); } } @@ -260,7 +256,7 @@ function checkUncheckAll( name, check ) ##inserts the Select All / Unselect All buttons for checkboxes $( function() { $("div.checkUncheckAllPlaceholder").each( function( i ) { - $( this )[0].innerHTML = '<a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', 1 );"><span>Select All</span></a><a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', 0 );"><span>Unselect All</span></a>'; + $( this )[0].innerHTML = '<a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', true );"><span>Select All</span></a><a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', false );"><span>Unselect All</span></a>'; }); }); --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -231,14 +231,14 @@ class SelectField(BaseField): rval.append ( '<div class="checkUncheckAllPlaceholder" checkbox_name="%s%s"></div>' % ( prefix, self.name ) ) #placeholder for the insertion of the Select All/Unselect All buttons for text, value, selected in self.options: style = "" + escaped_value = escape( str( value ), quote=True ) if len(self.options) > 2 and ctr % 2 == 1: style = " class=\"odd_row\"" + selected_text = "" if selected: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" checked%s>%s</div>' % \ - ( style, prefix, self.name, escape( str( value ), quote=True ), self.get_disabled_str( disabled ), text ) ) - else: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s"%s>%s</div>' % \ - ( style, prefix, self.name, escape( str( value ), quote=True ), self.get_disabled_str( disabled ), text ) ) + selected_text = "checked='checked'" + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s" %s%s><label for="%s">%s</label></div>' % \ + ( style, prefix, self.name, escaped_value, escaped_value, selected_text, self.get_disabled_str( disabled ), escaped_value, text ) ) ctr += 1 return "\n".join( rval ) def get_html_radio( self, prefix="", disabled=False ): --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -219,6 +219,11 @@ div.form-row-input > input { max-width: 300px; } +div.form-row-input label { + font-weight: normal; + display: inline; +} + div.form-row-error-message { width: 300px; float: left;

1 0

galaxy-dist commit aaacde471f03: When converting from GFF to BED, make all BED features with thick blocks.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288027566 14400 # Node ID aaacde471f036ea236155b9786e095382b391a9f # Parent 141e7055d2c633afee5262932adb1896ad0f937e When converting from GFF to BED, make all BED features with thick blocks. --- a/tools/filters/gff_to_bed_converter.py +++ b/tools/filters/gff_to_bed_converter.py @@ -41,8 +41,12 @@ def get_bed_line( chrom, name, strand, b # Bed format: chrom, chromStart, chromEnd, name, score, strand, \ # thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts # + # Render complete feature with thick blocks. There's no clear way to do this unless + # we analyze the block names, but making everything thick makes more sense than + # making everything thin. + # return "%s\t%i\t%i\t%s\t0\t%s\t%i\t%i\t0\t%i\t%s\t%s\n" % \ - ( chrom, t_start, t_end, name, strand, t_start, t_start, len( block_starts ), + ( chrom, t_start, t_end, name, strand, t_start, t_end, len( block_starts ), ",".join( block_sizes ), ",".join( block_starts ) ) def __main__():

1 0

galaxy-dist commit 141e7055d2c6: Update to Cufflinks tool suite: (a) better path joining; (b) update test data for cufflinks so that functional tests pass for v0.9.1; (c) add extensions to cuffcompare wrapper temporary inputs to fix #404.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288019385 14400 # Node ID 141e7055d2c633afee5262932adb1896ad0f937e # Parent 7114d0f8d487536853cf25cf30bb86636bf0b24c Update to Cufflinks tool suite: (a) better path joining; (b) update test data for cufflinks so that functional tests pass for v0.9.1; (c) add extensions to cuffcompare wrapper temporary inputs to fix #404. --- a/test-data/cufflinks_out3.expr +++ b/test-data/cufflinks_out3.expr @@ -1,2 +1,2 @@ -gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi -CUFF.1 6 test_chromosome 52 550 3.3557e+06 2.6976e+06 4.01381e+06 +gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi status +CUFF.1 3 test_chromosome 52 550 4.46429e+06 4.46006e+06 4.46851e+06 OK --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -42,13 +42,15 @@ def __main__(): # Add input files. - # Need to symlink inputs so that output files are written to temp directory. - input1_file_name = tmp_output_dir + "/input1" + # Need to symlink inputs so that output files are written to temp directory. + # Also need an extension for input file names so that cuffcompare produces + # output files properly. + input1_file_name = os.path.join( tmp_output_dir, "input1.gtf" ) os.symlink( options.input1, input1_file_name ) cmd += " %s" % input1_file_name two_inputs = ( options.input2 != None) if two_inputs: - input2_file_name = tmp_output_dir + "/input2" + input2_file_name = os.path.join( tmp_output_dir, "input2.gtf" ) os.symlink( options.input2, input2_file_name ) cmd += " %s" % input2_file_name @@ -78,7 +80,8 @@ def __main__(): raise Exception, stderr # check that there are results in the output file - if len( open( tmp_output_dir + "/cc_output", 'rb' ).read().strip() ) == 0: + cc_output_fname = os.path.join( tmp_output_dir, "cc_output") + if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffcompare. ' + str( e ) ) @@ -86,14 +89,14 @@ def __main__(): # Copy output files from tmp directory to specified files. try: try: - shutil.copyfile( tmp_output_dir + "/cc_output", options.transcripts_accuracy_output_file ) - shutil.copyfile( tmp_output_dir + "/input1.tmap", options.input1_tmap_output_file ) - shutil.copyfile( tmp_output_dir + "/input1.refmap", options.input1_refmap_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "cc_output" ), options.transcripts_accuracy_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "input1.tmap" ), options.input1_tmap_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "input1.refmap" ), options.input1_refmap_output_file ) if two_inputs: - shutil.copyfile( tmp_output_dir + "/cc_output.combined.gtf", options.transcripts_combined_output_file ) - shutil.copyfile( tmp_output_dir + "/cc_output.tracking", options.transcripts_tracking_output_file ) - shutil.copyfile( tmp_output_dir + "/input2.tmap", options.input2_tmap_output_file ) - shutil.copyfile( tmp_output_dir + "/input2.refmap", options.input2_refmap_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "cc_output.combined.gtf" ), options.transcripts_combined_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "cc_output.tracking" ), options.transcripts_tracking_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "input2.tmap" ), options.input2_tmap_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "input2.refmap" ), options.input2_refmap_output_file ) except Exception, e: stop_err( 'Error in cuffcompare:\n' + str( e ) ) finally: --- a/test-data/cufflinks_out1.gtf +++ b/test-data/cufflinks_out1.gtf @@ -1,4 +1,4 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "3355704.6979865772"; frac "1.000000"; conf_lo "2697596.861952"; conf_hi "4013812.534021"; cov "46.057047"; -test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "3355704.6979865772"; frac "1.000000"; conf_lo "2697596.861952"; conf_hi "4013812.534021"; cov "46.057047"; -test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "3355704.6979865772"; frac "1.000000"; conf_lo "2697596.861952"; conf_hi "4013812.534021"; cov "46.057047"; -test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "3355704.6979865772"; frac "1.000000"; conf_lo "2697596.861952"; conf_hi "4013812.534021"; cov "46.057047"; +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -98,7 +98,7 @@ def __main__(): raise Exception, stderr # check that there are results in the output file - if len( open( tmp_output_dir + "/isoforms.fpkm_tracking", 'rb' ).read().strip() ) == 0: + if len( open( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffdiff. ' + str( e ) ) @@ -107,17 +107,17 @@ def __main__(): # Copy output files from tmp directory to specified files. try: try: - shutil.copyfile( tmp_output_dir + "/isoforms.fpkm_tracking", options.isoforms_fpkm_tracking_output ) - shutil.copyfile( tmp_output_dir + "/genes.fpkm_tracking", options.genes_fpkm_tracking_output ) - shutil.copyfile( tmp_output_dir + "/cds.fpkm_tracking", options.cds_fpkm_tracking_output ) - shutil.copyfile( tmp_output_dir + "/tss_groups.fpkm_tracking", options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( tmp_output_dir + "/0_1_isoform_exp.diff", options.isoforms_exp_output ) - shutil.copyfile( tmp_output_dir + "/0_1_gene_exp.diff", options.genes_exp_output ) - shutil.copyfile( tmp_output_dir + "/0_1_tss_group_exp.diff", options.tss_groups_exp_output ) - shutil.copyfile( tmp_output_dir + "/0_1_splicing.diff", options.splicing_diff_output ) - shutil.copyfile( tmp_output_dir + "/0_1_cds.diff", options.cds_diff_output ) - shutil.copyfile( tmp_output_dir + "/0_1_cds_exp.diff", options.cds_diff_output ) - shutil.copyfile( tmp_output_dir + "/0_1_promoters.diff", options.promoters_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_isoform_exp.diff" ), options.isoforms_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_gene_exp.diff" ), options.genes_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_tss_group_exp.diff" ), options.tss_groups_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_splicing.diff" ), options.splicing_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds_exp.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "0_1_promoters.diff" ), options.promoters_diff_output ) except Exception, e: stop_err( 'Error in cuffdiff:\n' + str( e ) ) finally: --- a/test-data/cufflinks_out2.expr +++ b/test-data/cufflinks_out2.expr @@ -1,2 +1,2 @@ -trans_id bundle_id chr left right FPKM FMI frac FPKM_conf_lo FPKM_conf_hi coverage length -CUFF.1.1 6 test_chromosome 52 550 3.3557e+06 1 1 2.6976e+06 4.01381e+06 46.057 298 +trans_id bundle_id chr left right FPKM FMI frac FPKM_conf_lo FPKM_conf_hi coverage length effective_length status +CUFF.1.1 3 test_chromosome 52 550 4.46429e+06 1 1 4.46006e+06 4.46851e+06 61.2723 298 224 OK --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -91,7 +91,7 @@ def __main__(): raise Exception, stderr # check that there are results in the output file - if len( open( tmp_output_dir + "/transcripts.gtf", 'rb' ).read().strip() ) == 0: + if len( open( os.path.join( tmp_output_dir, "transcripts.gtf" ), 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cufflinks. ' + str( e ) ) @@ -99,9 +99,9 @@ def __main__(): # Copy output files from tmp directory to specified files. try: try: - shutil.copyfile( tmp_output_dir + "/transcripts.gtf", options.assembled_isoforms_output_file ) - shutil.copyfile( tmp_output_dir + "/transcripts.expr", options.transcripts_expression_output_file ) - shutil.copyfile( tmp_output_dir + "/genes.expr", options.genes_expression_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "transcripts.gtf" ), options.assembled_isoforms_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "transcripts.expr" ), options.transcripts_expression_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "genes.expr" ), options.genes_expression_output_file ) except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) finally:

1 0

galaxy-dist commit 5ee2200b2b6d: "Fix" zip uploads for Python < 2.6. The scare quotes are because in Python < 2.6 you can't read a zip member without loading the entire member into memory...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288037409 14400 # Node ID 5ee2200b2b6df5cbd31f21440124c7ae0bcbe10b # Parent aaacde471f036ea236155b9786e095382b391a9f "Fix" zip uploads for Python < 2.6. The scare quotes are because in Python < 2.6 you can't read a zip member without loading the entire member into memory... --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -270,22 +270,36 @@ def add_file( dataset, registry, json_fi stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' break fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - zipped_file = z.open( name ) - while 1: + if sys.version_info[:2] >= ( 2, 6 ): + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + else: + # python < 2.5 doesn't have a way to read members in chunks(!) try: - chunk = zipped_file.read( CHUNK_SIZE ) + outfile = open( uncompressed, 'wb' ) + outfile.write( z.read( name ) ) + outfile.close() + uncompressed_name = name + unzipped = True except IOError: os.close( fd ) os.remove( uncompressed ) file_err( 'Problem decompressing zipped data', dataset, json_file ) return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - zipped_file.close() - uncompressed_name = name - unzipped = True z.close() # Replace the zipped file with the decompressed file if uncompressed is not None:

1 0

galaxy-dist commit bb93b5da724b: Added a simple plugin for Nose that shows a diff-style output of failed tests,
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287806338 14400 # Node ID bb93b5da724b8f0420ed5cb2371075b08947d0db # Parent 6ce4e430b6a0d69e6397ca96a01350401ae05d20 Added a simple plugin for Nose that shows a diff-style output of failed tests, and added an error-only file to the Nose HTML plugin. This should make buildbot more useful. --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,8 @@ GeneTrack = 2.0.0_beta_1 lrucache = 0.2 Mako = 0.2.5 nose = 0.11.1 -NoseHTML = 0.3.1 +NoseHTML = 0.4 +NoseTestDiff = 0.1 Paste = 1.6 PasteDeploy = 1.3.3 PasteScript = 1.7.3 --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -12,6 +12,7 @@ from galaxy import eggs eggs.require( "nose" ) eggs.require( "NoseHTML" ) +eggs.require( "NoseTestDiff" ) eggs.require( "twill==0.9" ) eggs.require( "Paste" ) eggs.require( "PasteDeploy" )

1 0

galaxy-dist commit 30f83bcaf314: Only read the first 32K of stdout/stderr from jobs since that's all we're saving anyway. fileobj.read() is bad for the job runner when a tool prints 60GB of errors...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288037514 14400 # Node ID 30f83bcaf31451915ccf68c398a8e0ce0a3c80bb # Parent 5ee2200b2b6df5cbd31f21440124c7ae0bcbe10b Only read the first 32K of stdout/stderr from jobs since that's all we're saving anyway. fileobj.read() is bad for the job runner when a tool prints 60GB of errors... --- a/lib/galaxy/jobs/runners/sge.py +++ b/lib/galaxy/jobs/runners/sge.py @@ -312,8 +312,8 @@ class SGEJobRunner( object ): try: ofh = file(ofile, "r") efh = file(efile, "r") - stdout = ofh.read() - stderr = efh.read() + stdout = ofh.read( 32768 ) + stderr = efh.read( 32768 ) except: stdout = '' stderr = 'Job output not returned from cluster' --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -496,8 +496,8 @@ class PBSJobRunner( object ): try: ofh = file(ofile, "r") efh = file(efile, "r") - stdout = ofh.read() - stderr = efh.read() + stdout = ofh.read( 32768 ) + stderr = efh.read( 32768 ) except: stdout = '' stderr = 'Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.' --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -95,8 +95,8 @@ class LocalJobRunner( object ): if sleep_time < 8: # So we don't stat every second sleep_time *= 2 - stdout = proc.stdout.read() - stderr = proc.stderr.read() + stdout = proc.stdout.read( 32768 ) + stderr = proc.stderr.read( 32768 ) proc.wait() # reap log.debug('execution finished: %s' % command_line) except Exception, exc: --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -272,8 +272,8 @@ class DRMAAJobRunner( object ): try: ofh = file(ofile, "r") efh = file(efile, "r") - stdout = ofh.read() - stderr = efh.read() + stdout = ofh.read( 32768 ) + stderr = efh.read( 32768 ) except: stdout = '' stderr = 'Job output not returned from cluster'

1 0

galaxy-dist commit 9e27a8ad881d: trackster: Fix shared visualizations
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1288046966 14400 # Node ID 9e27a8ad881dc4451add6d518468a73dbc9028bc # Parent 30f83bcaf31451915ccf68c398a8e0ce0a3c80bb trackster: Fix shared visualizations - Add excanvas support for IE <9 to trackster, but performance is bad - Refactor unused/duplicate init code for trackster - Fix IE workflow bug with Input Datasets - Fix IE search button displaying twice --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -563,7 +563,7 @@ data.push( { name: '_', value: "true" } ); } }).each( function() { - form = this; + var form = this; $(this).find( "select[refresh_on_change='true']").change( function() { $(form).submit(); }); --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/st rand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_i d_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Clo se Overview</a>").addClass("overview-close").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_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();r eturn false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new Referenc eTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind ("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a. container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(!c.chrom){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.re set();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).re move()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left :a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Filter=functio n(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values" ,[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.f iltering_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(thi s.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending "){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}} ;b["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h= g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getCon text("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Tra ck.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrac k.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}}) ;var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs. min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)} })}},draw_tile:function(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb(" +h+","+h+","+h+")";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val() ;color=$("#track_"+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(C ACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this. inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(v<=MAX_FEATURE_DEPTH){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]= []}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(r,m,s,b,q,f,h,e){r.textAlign="center";var l=0,p=Math.round(m/2);for(cig_id in h){var k=h[cig_id],d="MIDNSHP"[k[0]],n=k[1];if(d==="H"||d==="S"){l-=n}var g=q+l,v=Math.floor(Math.max(0,(g-s)*m)),j=Math.floor(Math.max(0,(g+n-s)*m));switch(d){case"S":case"H":case"M":var o=f.slice(l,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&m>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+1,j-v,9);r.fillStyle=CONNECTOR_COLOR;for(var t=0,a=o.length;t<a;t++){if(g+t>=s&&g+t<=b){var u=Math.floor(Math.max(0,(g+t-s)*m));r.fillText(o[t],u+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+4,j-v,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(v+this.left_offset,e+5,j-v,1);break;case"D":r.fillStyle="red";r.fillRect(v+this.left_offset,e+4,j-v,3);break;case"P":case"I":break}l+=n}},dr aw_tile:function(ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fil lStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae= false}}}if(ae){S.addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];if(av[R]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] instanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],v,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],v,Y)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am ,ar,O,v,Y)}if(r!=="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==un defined&&!(d>ay||U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr ("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="Rea dTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createP attern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.t itle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addCla ss("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").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_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyC ode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id }:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("he ight",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math .min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chr om:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(!c.chrom){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.contai ner_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((t his.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_ window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a }if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class= 'track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.contr ol_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id" ,f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h) ;var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=tru e}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().le ngth>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu ,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.con tent_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,k=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var o=e.get(0).getContext("2d");if(p>PX_PER_CHAR){if(t his.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a );a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a =b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,w=p+"_"+s;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o. fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===und efined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b, b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chr om,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t =0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by_tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,m,s,b,q,f,h,e){r.textAlign="center";var l=0,p=Math.round(m/2);for(cig_id in h){var k=h[cig_id],d="MIDNSHP"[k[0]],n=k[1];if(d==="H"||d==="S"){l-=n}var g=q+l,v=Math.floor(Math.max(0,(g-s)*m)),j=Math.floor(Math.max(0,(g+n-s)*m));switch(d){case"S":case"H":case"M":var o=f.slice(l,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&m>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+1,j-v,9);r.fillStyle=CONNECTOR_COLOR;for(var t=0,a=o.length;t<a;t++){if(g+t>=s&&g+t<=b){var u=Math.floor(Math.max(0,(g+t-s)*m));r.fillText(o[t],u+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+4,j-v,3)}break;case"N": r.fillStyle=CONNECTOR_COLOR;r.fillRect(v+this.left_offset,e+5,j-v,1);break;case"D":r.fillStyle="red";r.fillRect(v+this.left_offset,e+4,j-v,3);break;case"P":case"I":break}l+=n}},draw_tile:function(ah,o,t,aw){var O=o*DENSITY*ah,am=(o+1)*DENSITY*ah,N=am-O;var ao=(!this.initial_canvas?"initial":O+"_"+am);var J=this.data_cache.get(ao);var e;if(J===undefined||(this.mode!=="Auto"&&J.dataset_type==="summary_tree")){this.data_queue[[O,am]]=true;this.get_data(O,am);return}var a=Math.ceil(N*aw),r=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,s=this.mode,A=25,af=(s==="Squish")||(s==="Dense")&&(s!=="Pack")||(s==="Auto"&&(J.extra_info==="no_detail")),X=this.left_offset,av,E,ax;var r=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(r)}r=$(r);if(J.dataset_type==="summary_tree"){E=this.summary_draw_height}else{if(s==="Dense"){E=A;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var B=(aw <0.0001?1/view.zoom_res:aw);E=this.incremental_slots(B,J.data,af,s)*ax+A;av=this.inc_slots[B]}}r.css({position:"absolute",top:0,left:(O-this.view.low)*aw-X});r.get(0).width=a+X;r.get(0).height=E;t.parent().css("height",Math.max(this.height_px,E)+"px");var K=r.get(0).getContext("2d");K.fillStyle=l;K.font=this.default_font;K.textAlign="right";this.container_div.find(".yaxislabel").remove();if(J.dataset_type=="summary_tree"){var Z=J.data,M=J.max,q=J.avg,b=Math.ceil(J.delta*aw);var p=$("<div />").addClass("yaxislabel").text(M);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,I=Z.length;aq<I;aq++){var ab=Math.floor((Z[aq][0]-O)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/M*this.summary_draw_height;K.fillStyle="black";K.fillRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&K.measureText(aa).width<b){K.fillStyle="#bbb";K.textAlign="center";K.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";t.appe nd(r);return r}if(J.message){r.css({border:"solid red","border-width":"2px 2px 2px 0px"});K.fillStyle="red";K.textAlign="left";K.fillText(J.message,100+X,ax)}var ae=false;if(J.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(J.data[0])){ae=false}}}if(ae){r.addClass(FILTERABLE_CLASS)}var au=J.data;var ap=0;for(var aq=0,I=au.length;aq<I;aq++){var T=au[aq],S=T[0],ar=T[1],ad=T[2],P=T[3];if(av[S]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=O){var ag=Math.floor(Math.max(0,(ar-O)*aw)),L=Math.ceil(Math.min(a,Math.max(0,(ad-O)*aw))),Y=(s==="Dense"?1:(1+av[S]))*ax;if(J.dataset_type==="bai"){var w=T[4];K.fillStyle=l;if(T[5] instanceof Array){var F=Math.floor(Math.max(0,(T[5][0]-O)*aw)),R=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-O)*aw))),D=Math.floor(Math.max(0,(T[6][0]-O)*aw)),z=Math.ceil(Math.min(a,Mat h.max(0,(T[6][1]-O)*aw)));if(T[5][1]>=O&&T[5][0]<=am){this.rect_or_text(K,aw,O,am,T[5][0],T[5][2],w,Y)}if(T[6][1]>=O&&T[6][0]<=am){this.rect_or_text(K,aw,O,am,T[6][0],T[6][2],w,Y)}if(D>R){K.fillStyle=CONNECTOR_COLOR;K.fillRect(R+X,Y+5,D-R,1)}}else{K.fillStyle=l;this.rect_or_text(K,aw,O,am,ar,P,w,Y)}if(s!=="Dense"&&!af&&ar>O){K.fillStyle=this.prefs.label_color;if(o===0&&ag-K.measureText(P).width<0){K.textAlign="left";K.fillText(S,L+2+X,Y+8)}else{K.textAlign="right";K.fillText(S,ag-2+X,Y+8)}K.fillStyle=l}}else{if(J.dataset_type==="interval_index"){if(af){K.fillStyle=l;K.fillRect(ag+X,Y+5,L-ag,1)}else{var H=T[4],W=T[5],ai=T[6],h=T[7];var G,ak,Q=null,ay=null;if(W&&ai){Q=Math.floor(Math.max(0,(W-O)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-O)*aw)))}if(s!=="Dense"&&P!==undefined&&ar>O){K.fillStyle=aj;if(o===0&&ag-K.measureText(P).width<0){K.textAlign="left";K.fillText(P,L+2+X,Y+8)}else{K.textAlign="right";K.fillText(P,ag-2+X,Y+8)}K.fillStyle=l}if(h){if(H){if(H=="+"){K.fillStyle= RIGHT_STRAND}else{if(H=="-"){K.fillStyle=LEFT_STRAND}}K.fillRect(ag+X,Y,L-ag,10);K.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var v=h[ao],d=Math.floor(Math.max(0,(v[0]-O)*aw)),U=Math.ceil(Math.min(a,Math.max((v[1]-O)*aw)));if(d>U){continue}G=5;ak=3;K.fillRect(d+X,Y+ak,U-d,G);if(Q!==undefined&&!(d>ay||U<Q)){G=9;ak=1;var al=Math.max(d,Q),C=Math.min(U,ay);K.fillRect(al+X,Y+ak,C-al,G)}}}else{G=9;ak=1;K.fillRect(ag+X,Y+ak,L-ag,G);if(T.strand){if(T.strand=="+"){K.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){K.fillStyle=LEFT_STRAND_INV}}K.fillRect(ag+X,Y,L-ag,10);K.fillStyle=l}}}}else{if(J.dataset_type==="vcf"){if(af){K.fillStyle=l;K.fillRect(ag+X,Y+5,L-ag,1)}else{var u=T[4],n=T[5],c=T[6];G=9;ak=1;K.fillRect(ag+X,Y,L-ag,G);if(s!=="Dense"&&P!==undefined&&ar>O){K.fillStyle=aj;if(o===0&&ag-K.measureText(P).width<0){K.textAlign="left";K.fillText(P,L+2+X,Y+8)}else{K.textAlign="right";K.fillText(P,ag-2+X,Y+8)}K.fillStyle=l}var m=u+" / "+n;if(ar>O&&K.measureText(m).width<(L-ag)){ K.fillStyle="white";K.textAlign="center";K.fillText(m,X+ag+(L-ag)/2,Y+8);K.fillStyle=l}}}}}ap++}}return r},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");i f(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -15,10 +15,15 @@ var DENSITY = 200, CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 30, CACHED_DATA = 5, - CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), - PX_PER_CHAR = CONTEXT.measureText("A").width, + DUMMY_CANVAS = document.createElement("canvas"), RIGHT_STRAND, LEFT_STRAND; +if (window.G_vmlCanvasManager) { + G_vmlCanvasManager.initElement(DUMMY_CANVAS); +} +CONTEXT = DUMMY_CANVAS.getContext("2d"); +PX_PER_CHAR = CONTEXT.measureText("A").width; + var right_img = new Image(); right_img.src = image_path + "/visualization/strand_right.png"; right_img.onload = function() { @@ -255,6 +260,12 @@ var View = function( container, title, v this.add_label_track( new LabelTrack( this, this.top_labeltrack ) ); this.add_label_track( new LabelTrack( this, this.nav_labeltrack ) ); + + $(window).bind("resize", function() { view.resize_window(); }); + $(document).bind("redraw", function() { view.redraw(); }); + + this.reset(); + $(window).trigger("resize"); }, update_location: function(low, high) { this.location_span.text( commatize(low) + ' - ' + commatize(high) ); @@ -348,22 +359,7 @@ var View = function( container, title, v track.container_div.fadeOut('slow', function() { $(this).remove(); }); delete this.tracks[this.tracks.indexOf(track)]; this.num_tracks -= 1; - },/* No longer needed as config is done inline, one track at a time - update_options: function() { - this.has_changes = true; - var sorted = $("ul#sortable-ul").sortable('toArray'); - for (var id_i in sorted) { - var id = sorted[id_i].split("_li")[0].split("track_")[1]; - this.viewport_container.append( $("#track_" + id) ); - } - - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; - if (track && track.update_options) { - track.update_options(track_id); - } - } - },*/ + }, reset: function() { this.low = this.max_low; this.high = this.max_high; @@ -391,8 +387,8 @@ var View = function( container, title, v this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview - var left_px = this.low / (this.max_high - this.max_low) * this.overview_viewport.width(); - var width_px = (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width(); + var left_px = ( this.low / (this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; + var width_px = ( (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; var min_width_px = 13; this.overview_box.css({ left: left_px, width: Math.max(min_width_px, width_px) }).show(); @@ -440,6 +436,11 @@ var View = function( container, title, v this.high = Math.round(cur_center + new_half); this.redraw(); }, + resize_window: function() { + this.viewport_container.height( this.container.height() - this.nav_container.height() - 45 ); + this.nav_container.width( this.container.width() ); + this.redraw(); + }, reset_overview: function() { this.overview_viewport.find("canvas").remove(); this.overview_viewport.height(this.default_overview_height); @@ -816,8 +817,8 @@ var TiledTrack = function() { if ( !(low > track.view.high || high < track.view.low) ) { tile_element = track.draw_tile( resolution, tile_index, parent_element, w_scale ); if (tile_element) { - // Store initial canvas in we need to use it for overview - if (!track.initial_canvas) { + // Store initial canvas in case we need to use it for overview + if (!track.initial_canvas && !window.G_vmlCanvasManager) { track.initial_canvas = $(tile_element).clone(); var src_ctx = tile_element.get(0).getContext("2d"); var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); @@ -905,7 +906,6 @@ var ReferenceTrack = function (view) { this.left_offset = 200; this.height_px = 12; this.container_div.addClass( "reference-track" ); - this.dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); this.data_queue = {}; this.data_cache = new Cache(CACHED_DATA); this.tile_cache = new Cache(CACHED_TILES_LINE); @@ -934,10 +934,14 @@ var ReferenceTrack = function (view) { draw_tile: function( resolution, tile_index, parent_element, w_scale ) { var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, - canvas = $("<canvas class='tile'></canvas>"), - ctx = canvas.get(0).getContext("2d"), key = resolution + "_" + tile_index; + var canvas = document.createElement("canvas"); + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); + + var ctx = canvas.get(0).getContext("2d"); + if (w_scale > PX_PER_CHAR) { if (this.data_cache.get(key) === undefined) { this.get_data( resolution, tile_index ); @@ -983,8 +987,6 @@ var LineTrack = function ( name, view, d this.data_cache = new Cache(CACHED_DATA); this.tile_cache = new Cache(CACHED_TILES_LINE); this.prefs = { 'color': 'black', 'min_value': undefined, 'max_value': undefined, 'mode': this.mode }; - if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } - if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { @@ -1056,9 +1058,12 @@ var LineTrack = function ( name, view, d var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, - canvas = $("<canvas class='tile'></canvas>"), key = resolution + "_" + tile_index; + var canvas = document.createElement("canvas"); + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); + if (this.data_cache.get(key) === undefined) { this.get_data( resolution, tile_index ); return; @@ -1204,9 +1209,6 @@ var FeatureTrack = function ( name, view this.left_offset = 200; this.prefs = { 'block_color': '#444', 'label_color': 'black', 'show_counts': true }; - if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; } - if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; } - if (prefs.show_counts !== undefined) { this.prefs.show_counts = prefs.show_counts; } }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -1249,7 +1251,6 @@ var FeatureTrack = function ( name, view var w_scale = this.inc_slots[level].w_scale, undone = [], highest_slot = 0, // To measure how big to draw canvas - dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"), max_low = this.view.max_low; var slotted = []; @@ -1284,7 +1285,7 @@ var FeatureTrack = function ( name, view f_end = Math.ceil( (feature_end - max_low) * w_scale ); if (feature_name !== undefined && !no_detail) { - var text_len = dummy_canvas.measureText(feature_name).width; + var text_len = CONTEXT.measureText(feature_name).width; if (f_start - text_len < 0) { f_end += text_len; } else { @@ -1395,7 +1396,7 @@ var FeatureTrack = function ( name, view } var width = Math.ceil( tile_span * w_scale ), - new_canvas = $("<canvas class='tile'></canvas>"), + canvas = $("<canvas class='tile'></canvas>"), label_color = this.prefs.label_color, block_color = this.prefs.block_color, mode = this.mode, @@ -1404,6 +1405,10 @@ var FeatureTrack = function ( name, view left_offset = this.left_offset, slots, required_height, y_scale; + var canvas = document.createElement("canvas"); + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); + if (result.dataset_type === "summary_tree") { required_height = this.summary_draw_height; } else if (mode === "Dense") { @@ -1417,16 +1422,16 @@ var FeatureTrack = function ( name, view slots = this.inc_slots[inc_scale]; } - new_canvas.css({ + canvas.css({ position: "absolute", top: 0, left: ( tile_low - this.view.low ) * w_scale - left_offset }); - new_canvas.get(0).width = width + left_offset; - new_canvas.get(0).height = required_height; + canvas.get(0).width = width + left_offset; + canvas.get(0).height = required_height; parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - var ctx = new_canvas.get(0).getContext("2d"); + var ctx = canvas.get(0).getContext("2d"); ctx.fillStyle = block_color; ctx.font = this.default_font; ctx.textAlign = "right"; @@ -1460,12 +1465,12 @@ var FeatureTrack = function ( name, view } } cur_mode = "Summary"; - parent_element.append( new_canvas ); - return new_canvas; + parent_element.append( canvas ); + return canvas; } if (result.message) { - new_canvas.css({ + canvas.css({ border: "solid red", "border-width": "2px 2px 2px 0px" }); @@ -1488,7 +1493,7 @@ var FeatureTrack = function ( name, view } } if ( filterable ) { - new_canvas.addClass(FILTERABLE_CLASS); + canvas.addClass(FILTERABLE_CLASS); } // Draw data points. @@ -1680,7 +1685,7 @@ var FeatureTrack = function ( name, view j++; } } - return new_canvas; + return canvas; }, gen_options: function(track_id) { var container = $("<div />").addClass("form-row"); --- a/templates/grid_common.mako +++ b/templates/grid_common.mako @@ -64,7 +64,7 @@ <span class="search-box"><% value = iff( column.filterable == "standard", column.label.lower(), "") %><input class="search-box-input" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="${value}" size="15"/> - <button class="submit-image" type="submit" title='Search'/> + <button class="submit-image" type="submit" title='Search'><span style="display: none;"></button></span></form> %else: --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -62,6 +62,11 @@ <%def name="javascripts()"> ${parent.javascripts()} + + + ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider" )} <script type="text/javascript"> @@ -103,22 +108,6 @@ } }); %endif - - $(document).bind( "redraw", function() { - view.redraw(); - }); - - // To adjust the size of the viewport to fit the fixed-height footer - var refresh = function() { - if (view !== undefined) { - view.viewport_container.height( $("#center").height() - $(".nav-container").height() - 40 ); - view.nav_container.width( $("#center").width() ); - view.redraw(); - } - }; - $(window).bind( "resize", function() { refresh(); } ); - $("#right-border").bind( "click dragend", function() { refresh(); } ); - $(window).trigger( "resize" ); // Execute initializer for EDITOR specific javascript function init() { @@ -227,47 +216,6 @@ error: function() { alert("Could not save visualization"); } }); }); - - function sidebar_box(track) { - if (!track.hidden) { - var track_id = track.track_id, - label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'), - title = $('<div class="historyItemTitle"></div>'), - icon_div = $('<div class="historyItemButtons"></div>'); - del_icon = $('<a href="#" class="icon-button delete" />'), - edit_icon = $('<a href="#" class="icon-button edit" />'), - body = $('<div class="historyItemBody"></div>'), - li = $('<li class="sortable"></li>').attr("id", "track_" + track_id + "_li"), - div = $('<div class="historyItemContainer historyItem"></div>'), - editable = $('<div style="display:none"></div>').attr("id", "track_" + track_id + "_editable"); - - edit_icon.bind("click", function() { - $("#track_" + track_id + "_editable").toggle(); - }); - del_icon.bind("click", function() { - $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id + "_li").remove(); }); - view.remove_track(track); - if (view.num_tracks === 0) { - $("#no-tracks").show(); - } - }); - icon_div.append(edit_icon).append(del_icon); - title.append(label).prepend(icon_div); - if (track.gen_options) { - editable.append(track.gen_options(track_id)).appendTo(body); - } - div.append(title).append(body).appendTo(li); - $("ul#sortable-ul").append(li); - } - }; - - // Populate sort/move ul - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; - sidebar_box(track); - } - - $(window).trigger("resize"); }; }); --- a/templates/visualization/display.mako +++ b/templates/visualization/display.mako @@ -3,23 +3,12 @@ <%def name="javascripts()"><% config = item_data %> ${parent.javascripts()} - ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster" )} - <script type="text/javascript"> - var view; - // To adjust the size of the viewport to fit the fixed-height footer - var refresh = function( e ) { - if (view !== undefined) { - view.viewport_container.height( $("#center").height() - $(".nav-container").height() - 40 ); - view.nav_container.width( $("#center").width() ); - view.redraw(); - } - }; - $(window).bind( "resize", function(e) { refresh(e); } ); - $("#right-border").bind( "click dragend", function(e) { refresh(e); } ); - $(window).trigger( "resize" ); - </script> +  + ${h.js( "jquery.event.drag", "jquery.autocomplete", "trackster" )} </%def><%def name="stylesheets()"> @@ -55,16 +44,21 @@ var data_url = "${h.url_for( controller='/tracks', action='data' )}", reference_url = "${h.url_for( controller='/tracks', action='reference' )}", chrom_url = "${h.url_for( controller='/tracks', action='chroms' )}", - view; - - var container_element = $("#${visualization.id}"); - view = new View( container_element, "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + view, + container_element = $("#${visualization.id}"); + + if (container_element.parents(".item-content").length > 0) { // Embedded viz + container_element.parents(".item-content").css( { "max-height": "none", "overflow": "visible" } ); + } else { // Viewing just one shared viz + container_element = $("#center"); + $("#right-border").live("click", function() { view.resize_window(); }); + } + view = new View( container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); %for track in config.get('tracks'): view.add_track( new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) ); %endfor - container_element.parents(".item-content").css( { "max-height": "none", "overflow": "visible" } ); </script></%def>

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galaxy-dist commit 7114d0f8d487: Fix for a bug I introduced in NoseHTML changes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287858470 14400 # Node ID 7114d0f8d487536853cf25cf30bb86636bf0b24c # Parent bb93b5da724b8f0420ed5cb2371075b08947d0db Fix for a bug I introduced in NoseHTML changes. --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ GeneTrack = 2.0.0_beta_1 lrucache = 0.2 Mako = 0.2.5 nose = 0.11.1 -NoseHTML = 0.4 +NoseHTML = 0.4.1 NoseTestDiff = 0.1 Paste = 1.6 PasteDeploy = 1.3.3

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